title: ESC_chr4_134502243

description: 4C PCR product

value: TTTGAAGCCTTCCTGTGATC


title: ESC_chr4_119659293

status: Public on Oct 29 2015

type: SRA

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 4C PCR product

library_source: genomic

data_processing:
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII or NlaIII sites (fragment ends) depending on the first restriction enzyme used, using custom perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse mm9.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated from the 4C mapping procedure using custom perl scripts. Scores represent the number of reads mapping to a DpnII restriction fragment end.

molecule: genomic DNA

organism: Mus musculus

source_name: E14 ESC

growth_protocol: E14Tg2A (E14) ES cells (IB10 cells) were cultured in BRL-conditioned Dulbecco’s Modified Eagle Medium (DMEM with High Glucose, GlutaMAX™, Pyruvate; Life technologies) supplemented with 10% fetal calf serum (FCS), non-essential amino acids (NEAA) (Life technologies), 1000 U/ml leukemia inhibitory factor (LIF) and 2-mercaptoethanol. NPCs were derived from E14 ESCs as described in Peric-Hupkes et al. (2010) and were cultured on gelatin (0.1%) coated plates in DMEM/F12 medium (GIBCO-BRL) with addition of N2-supplement (life technologies), human basic FGF (20ng/ml; peprotech), murine EGF (20ng/ml; peprotech) and penicillin-streptomycin (P/S) (50U/ml - 50ug/ml) (Life technologies). Fetal livers (FL) were isolated from e14.5 embryos by dissection. Single cell suspensions for FL were obtained by filtration through a cell strainer (BD biosciences).

extract_protocol: The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics), remain unchanged. Cells are cross linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS, nuclei are isolated, after which chromatin is digested with DpnII or NlaIII and subsequently ligated. After reversal of the cross links the DNA is purified and treated with the second restriction enzyme treatment (Csp6I or NlaIII, respectively). After a second re-ligation step the sample is purified and a 4C PCR is performed.

treatment_protocol: cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

tag: cell type

value: E14 ESC

tag: barcode

value: ATGTCAGGTGGCTCAGCATG

tag: bait


title: ESC_chr4_46382734

description: 4C PCR product

value: AGGCTGCCGTGTGTCAGATC


title: ESC_chr3_51219225

description: 4C PCR product

value: GAGTTGGCTTCTAATTCATG


title: ESC_chr4_119634899

description: 4C PCR product

value: TTCTGGCTCAGGAGAGCATG


title: ESC_chr3_36081587

description: 4C PCR product

value: CCTCTATGAGAAAGAACATG


title: ESC_chr4_116861947

description: 4C PCR product

value: TCTTCCTAAATGTTGGCATG


title: ESC_chr3_35873314

description: 4C PCR product

value: TCACGTGCAGAAAGGCGATC


title: ESC_chr3_34647410

description: 4C PCR product

value: AGTGTCAAAGTAGAACCATG


title: ESC_chr3_34658794

description: 4C PCR product

value: AAATAAATTGGGCCCACATG


title: ESC_chr3_35472989

description: 4C PCR product

value: AGTGGCCTCTAACCTCGATC


title: ESC_chr3_34580073

description: 4C PCR product

value: AGGATGGTTGTGCACCCATG


title: ESC_chr3_34670292

description: 4C PCR product

value: GGTCAGGGAGGAAGCTCATG


title: ESC_chr3_34548270

description: 4C PCR product

value: GCTCTACAGTCAGCTACATG


title: ESC_chr3_33855757

description: 4C PCR product

value: AAAGACCAAGTAATTGCATG


title: ESC_chr3_146658343

description: 4C PCR product

value: ACACGAACCTGTGGCATG


title: ESC_chr3_34533736

description: 4C PCR product

value: AGCAGTAGCAGGAGGCCATG


title: ESC_chr3_113822502

description: 4C PCR product

value: E14 ESC

value: TTTATTTAAAGGCACTGATC


title: ESC_chr3_33691481

description: 4C PCR product

value: TCATAGCCTGCCAAGATC


title: ESC_chr3_80776364

description: 4C PCR product

value: GATGAAACATTTAATAGATC


title: ESC_chr3_113810999

description: 4C PCR product

value: TTGCAAGTGTAATATAGATC


title: ESC_chr2_59584273

description: 4C PCR product

value: CTGAGGAGGTTGCAGTGATC


title: ESC_chr2_59360368

description: 4C PCR product

value: AGCGTTAGCCAACATGGATC


title: ESC_chr2_59279353

description: 4C PCR product

value: GACAACAGGTGTCTGGGATC


title: ESC_chr2_58517745

description: 4C PCR product

value: AGGCTATGCCACGATGCATG


title: ESC_chr2_58311565

description: 4C PCR product

value: AATTTAAAACAGCCCCGATC


title: ESC_chr2_57242178

description: 4C PCR product

value: AGTTCAAAAACATCCTGATC


title: ESC_chr2_56970173

description: 4C PCR product

value: GGCCCCCTACTGACAAGATC


title: ESC_chr2_58533577

description: 4C PCR product

value: ATCGTCTAGATGGAGAGATC


title: ESC_chr2_56293545

description: 4C PCR product

value: GCAGATGGAATGCTAACATG


title: ESC_chr2_55694518

description: 4C PCR product

value: CTTCCTAAATCTGTCTGATC


title: ESC_chr2_53972192

description: 4C PCR product

value: ACTGAACTGCTCATTTGATC


title: ESC_chr2_54942278

description: 4C PCR product

value: TTTGGCTCCCAACTATGATC


title: ESC_chr2_116946594

description: 4C PCR product

value: E14 ESC

value: TTGTTATGCTGCCCACGATC


title: ESC_chr2_151854960

description: 4C PCR product

value: GTGCAGACAACGGAGATC


title: ESC_chr2_53939033

description: 4C PCR product

value: ACTCCAGAAGATACAGGATC


title: ESC_chr1_74033465

description: 4C PCR product

value: ACGTGAGAGAGATACTCATG


title: ESC_chr1_74009781

description: 4C PCR product

value: TGTAGGAAGCCTGTGGGATC


title: ESC_chr1_71219536

description: 4C PCR product

value: TCTCAGGGACTGAAGACATG


title: ESC_chr1_71235263

description: 4C PCR product

value: CTGTGAAGGACCATATGATC


title: ESC_chr1_163342008

description: 4C PCR product

value: CTGCTCAGAGACATTCCATG


title: ESC_chr1_71255030

description: 4C PCR product

value: AGAAGCTCACTGGGGGCATG


title: ESC_chr1_66737732

description: 4C PCR product

value: TCAATCCTTTGAGCTTGATC


title: ESC_chr1_186013204

description: 4C PCR product

value: GATGCTAAGGTATATAGATC


title: ESC_chr1_163313640

description: 4C PCR product

value: CATACCACTCAGTCCTCATG


title: ESC_chr19_5850247

description: 4C PCR product

value: AAGCCCTACTCAAGAACATG


title: ESC_chr1_186019971

description: 4C PCR product

value: TTTGGATGGGGCTGGATC


title: ESC_chr1_134134795

description: 4C PCR product

value: TAAAAATGTGTGTGCGCATG


title: ESC_chr19_22958563

description: 4C PCR product

value: CCGCCCAAATTTCTGATC


title: ESC_chr1_163330215

description: 4C PCR product

value: E14 ESC

value: ATAGCAAATCATCCAACATG


title: ESC_chr19_5750697

description: 4C PCR product

value: TAGAATCCTAGGCAGGCATG


title: ESC_chr19_22970173

description: 4C PCR product

value: CTCAAGTTCGTGTTGGGATC


title: ESC_chr2_55961628

description: 4C PCR product

value: CTCTGTAGCTGGGAAGGATC


title: NPC_chr9_75446737

description: 4C PCR product

source_name: NPC

value: NPC

value: CATCTTCGGAGCTCCAGATC


title: ESC_chr19_10983266

description: 4C PCR product

value: CACTCAGTGGTAGGCAGATC


title: ESC_chr18_67090059

description: 4C PCR product

value: CACACAACTTAGCGCTGATC


title: ESC_chr18_68634563

description: 4C PCR product

value: CTTCTTAAGAGGAGCTGATC


title: ESC_chr18_66751774

description: 4C PCR product

value: AGTGGTGTCTACTTGGGATC


title: ESC_chr19_10341018

description: 4C PCR product

value: TGAAGGCCCTGTTGGATC


title: ESC_chr18_66123148

description: 4C PCR product

value: AGATGAATGCAGAAACCATG


title: ESC_chr18_65650559

description: 4C PCR product

value: CCCTCTTCCCAAGATGGATC


title: ESC_chr18_66084401

description: 4C PCR product

value: TTCTCTTGTCCTAGGTGATC


title: ESC_chr18_64638642

description: 4C PCR product

value: GTCAATCTTGAACAAAGATC


title: ESC_chr18_64627519

description: 4C PCR product

value: TTTAGTAGATGCACTTGATC


title: ESC_chr18_64616255

description: 4C PCR product

value: E14 ESC

value: ATTTGAAAGTCTTTGGGATC


title: ESC_chr18_64910288

description: 4C PCR product

value: TACAAAATCCAGTGGAGATC


title: ESC_chr18_63811083

description: 4C PCR product

value: AAGAGATGGAGATTATGATC


title: ESC_chr18_61682530

description: 4C PCR product

value: TCTTAAGCATTCCTTCCATG


title: ESC_chr18_61650211

description: 4C PCR product

value: TTTTTCAGCAACTTCAGATC


title: ESC_chr18_63651530

description: 4C PCR product

value: GGGACTCAGCTCTATTCATG


title: ESC_chr18_60946694

description: 4C PCR product

value: TGTGTTCATAGTCATGGATC


title: ESC_chr19_10993768

description: 4C PCR product

value: GGTAGGTGACGGGTTAGATC


title: ESC_chr18_60622875

description: 4C PCR product

value: AAGTGTAACCTTGCCTCATG


title: ESC_chr18_60871192

description: 4C PCR product

value: GGTGCTCTGTGAAAGAGATC


title: ESC_chr18_61019948

description: 4C PCR product

value: CTGCAGCGGCAATTCTGATC


title: ESC_chr18_60316140

description: 4C PCR product

value: CAGAGACATGACGAAGGATC


title: ESC_chr18_59235870

description: 4C PCR product

value: GCTACCCCTCAGTTTAGATC


title: ESC_chr18_60285071

description: 4C PCR product

value: CGCGATATCATTTCTTCATG


title: ESC_chr18_59351688

description: 4C PCR product

value: GTCACCGTAACAAGTGCATG


title: ESC_chr18_60337611

description: 4C PCR product

value: GGTCACTCCTCCCTAGCATG


title: ESC_chr18_58857120

description: 4C PCR product

value: E14 ESC

value: AAAACACTCCTTCTCCCATG


title: ESC_chr18_58138077

description: 4C PCR product

value: TTACTATGTATATGGCGATC


title: ESC_chr18_56522429

description: 4C PCR product

value: CCAATTCCCTTCACAGGATC


title: ESC_chr18_59187534

description: 4C PCR product

value: TCATTTCCCCTTCCACGATC


title: ESC_chr18_59311638

description: 4C PCR product

value: CTGGGGATAAAAACTAGATC


title: ESC_chr18_37499833

description: 4C PCR product

value: AAGTAGTTGCTGCTGTGATC


title: ESC_chr18_58629367

description: 4C PCR product

value: GCATTCTTCTGTGAACCATG


title: ESC_chr18_58669133

description: 4C PCR product

value: GCACAAGGGTAAGTTTCATG


title: ESC_chr18_57488404

description: 4C PCR product

value: AGTGACTTTATGACTGGATC


title: ESC_chr18_37377876

description: 4C PCR product

value: GTATTGTAAAGTGGTCGATC


title: ESC_chr18_37121212

description: 4C PCR product

value: TCTGATTAGCGTGTCAGATC


title: ESC_chr18_37126634

description: 4C PCR product

value: CTGTGCATCTCAGGATGATC


title: ESC_chr18_37377867

description: 4C PCR product


title: ESC_chr18_12394357

description: 4C PCR product

value: GCTAAGTAAATGTGTGCATG


title: ESC_chr18_37098808

description: 4C PCR product

value: CTGTCTACCAGAGAGTGATC


title: ESC_chr17_50430446

description: 4C PCR product

value: AGTTGAAATGCATCCATG


title: ESC_chr17_50768048

description: 4C PCR product

value: AACAGTGCAGCTTGGAGATC


title: ESC_chr17_50328697

description: 4C PCR product

value: E14 ESC

value: AAAAGAATCTGGCACAGATC


title: ESC_chr16_91322719

description: 4C PCR product

value: GGATGCTAACAGGGTGGATC


title: ESC_chr18_57559968

description: 4C PCR product

value: TTCCTCTCACAAACCAGATC


title: ESC_chr17_50089370

description: 4C PCR product

value: CTTATTGCACAGTTATGATC


title: ESC_chr16_91314856

description: 4C PCR product

value: TTCTGGGATACTGCCAGATC


title: ESC_chr16_91224690

description: 4C PCR product

value: AAGCTGAGAAACTGGATC


title: ESC_chr18_57923652

description: 4C PCR product

value: AGAAGAAATGTTGCAAGATC


title: ESC_chr16_90197456

description: 4C PCR product

value: CAGCACTTTGCTTCTACATG


title: ESC_chr15_89028294

description: 4C PCR product

value: ACAATGGTAACTCTCTCATG


title: ESC_chr18_37454455

description: 4C PCR product

value: TTCTGGAAGAAAGGCTGATC


title: ESC_chr17_50376256

description: 4C PCR product

value: CCCTAGGGTTCTGCCATG


title: ESC_chr16_91046624

description: 4C PCR product

value: AGAGGCCAATGGTGTGGATC


title: ESC_chr15_8577349

description: 4C PCR product

value: GAGAAACTGGAAGTCTCATG


title: ESC_chr16_91022464

description: 4C PCR product

value: TGAGGACGTTCTTACTGATC


title: ESC_chr14_77370919

description: 4C PCR product

value: ATGTTTTCTCTGAGAGCATG


title: ESC_chr15_8564527

description: 4C PCR product

value: AACACTTAGCCCATAACATG


title: ESC_chr16_91298758

description: 4C PCR product

value: E14 ESC

value: TAAGGAATTCAGCCCAGATC


title: ESC_chr18_37164843

description: 4C PCR product

value: CAGCAGAAGAAAATCAGATC


title: ESC_chr14_77361458

description: 4C PCR product

value: AATGTAGGAGGAAACTCATG


title: ESC_chr11_77487588

description: 4C PCR product

value: AATCCCCGTAACCATACATG


title: ESC_chr12_30412470

description: 4C PCR product

value: CCTTCAAGGTCACCAGGATC


title: ESC_chr12_74319439

description: 4C PCR product

value: CTGCAAACTGCTGTCACATG


title: ESC_chr11_32224410

description: 4C PCR product

value: GTGGGTTGTAAGGACATG


title: ESC_chr11_32149201

description: 4C PCR product

value: TGGAAAATTAGGTGGGCATG


title: ESC_chr11_32041144

description: 4C PCR product

value: ACAGAGCCCTAGGGTAGATC


title: ESC_chr11_103194723

description: 4C PCR product

value: GAAGAGCTTCAGGGCACC


title: ESC_chr11_31537749

description: 4C PCR product

value: AGCGTTCCCATTACGATC


title: ESC_chr11_32609632

description: 4C PCR product

value: GGGAGATATATAAGGGGATC


title: ESC_chr11_102864574

description: 4C PCR product

value: ACTTCCCATGTGTCTTGATC


title: ESC_chr11_102854422

description: 4C PCR product

value: CACTCACTCAAGCCTGGATC


title: ESC_chr11_102755095

description: 4C PCR product

value: CCAGACTGTCACTGCATG


title: ESC_chr11_102552165

description: 4C PCR product

value: AACTGCAGCTTGGTGGGATC


title: ESC_chr11_102282204

description: 4C PCR product

value: E14 ESC

value: GTTGCCTGTAAGTTGTGATC


title: ESC_chr11_102160656

description: 4C PCR product

value: CATCTATGACCTTGTCATG


title: ESC_chr11_102273033

description: 4C PCR product

value: CTCCCACAGTGGGTGATC


title: ESC_chr11_102348013

description: 4C PCR product

value: CTACAACCTCCTAGCACATG


title: ESC_chr11_32138087

description: 4C PCR product

value: TAGGTCTTGACTGGGATC


title: ESC_chr10_57473250

description: 4C PCR product

value: CCTTGTCCCTCACTTACATG


title: ESC_chr10_57568589

description: 4C PCR product

value: GCCCTAGAAAAAATTTCATG


title: ESC_chr10_69781902

description: 4C PCR product

value: AGTGATTTCTCCTCATCATG


title: ESC_chr11_102263652

description: 4C PCR product

value: GGACACCCAGATTACAGATC


title: ESC_chr11_102295886

description: 4C PCR product

value: CTCCAAGCACTGGGCTGATC


title: ESC_chr10_57454886

description: 4C PCR product

value: ATTACTAAGCTAAGGACATG


title: ESC_chr10_79132358

description: 4C PCR product

value: TCCTAAAGGTGCTGGAGATC


title: ESC_chr10_57463988

description: 4C PCR product

value: AATTGAGACTTATTTGGATC


title: ESC_chr10_57142766

description: 4C PCR product

value: AATTTGGTCCTTTTGTGATC


title: ESC_chr10_57190786

description: 4C PCR product

value: GTGTCGGAGGGGCTATGATC


title: ESC_chr10_57515889

description: 4C PCR product

value: AGAAGGAGAGTCACATGATC


title: MLM-P9A

city: Baltimore

first: S. Amer

last: Riazuddin

state: Maryland

address: 600 N. Wolfe St

country: USA

institute: Johns Hopkins University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.8 used for basecalling and de-indexing.
The analysis included preprocessing of FASTQ file format sequencing reads by removing the adapter sequences using SeqPrep (https://github.com/jstjohn/SeqPrep).
The preprocessed sequencing reads were aligned against the Mus musculus (GRCm38/mm10) transcriptome using default parameters
Subsequently, duplicates reads caused by PCR amplification were removed using the rmdup option of SAMtools (version 0.1.18)
The expression data were normalized by calculating the reads per kilobase per million mapped reads (RPKM) values for each gene (Mortazavi et al., Nat Methods, 2008)
Small RNA sequencing reads were aligned against the Mus musculus (GRCm38/mm10) reference genome with the mapper module of miRDeep2 that uses Bowtie (version 0.12.8)
Reported microRNAs were identified by miRDeep2 through reported miRNA hairpins and mature miRNA sequences downloaded from the miRBase (Release 20) database
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files include RPKM and RPM values for mRNA and microRNA data, respectively.

molecule: total RNA

source_name: P9_ocular lens_miRNA-seq

extract_protocol:
To obtain the lenses, mice were first anesthetized by isoflurane and subsequently euthanized through cervical dislocation. The lenses were isolated using forceps under a microscope. Two biological replicates, each consisting of 8-9 pups, were used for each developmental stage. Lenses were dissolved immediately in the Trizol reagent (Invitrogen; Carlsbad, CA) and total RNA was extracted.
Illumina TruSeq RNA Sample Preparation Kit v2 and TruSeq Small RNA Sample Prep Kit was used to prepare mRNA and small RNA sequencing libraries

tag: strain

tag: developmental stage

value: Postnatal day 9

tag: tissue

value: Ocular Lens


title: MLM-P3B

source_name: P3_ocular lens_miRNA-seq

value: Postnatal day 3


title: MLM-P3A


title: MLM-P6A

source_name: P6_ocular lens_miRNA-seq

value: Postnatal day 6


title: MLM-P9B


title: MLM-P0A

source_name: P0_ocular lens_miRNA-seq

value: Postnatal day 0


title: MLM-P0B


title: ESC_chr10_79639380

description: 4C PCR product

value: E14 ESC

value: TCAGCAGGTGAAGCCACATG


title: MLM-E18B

source_name: E18_ocular lens_miRNA-seq

value: Embryonic day 18


title: MLM-E18A


title: ESC_chr13_72906854

description: 4C PCR product

value: CTGCAGCTGCAGCTGATC


title: ESC_chr10_57168814

description: 4C PCR product

value: GACGGCCATATCTAGGGATC


title: MLM-E15A

source_name: E15_ocular lens_miRNA-seq

value: Embryonic day 15


title: MLM-E15B


title: MLT-P9A

source_name: P9_ocular lens_RNA-seq


title: MLT-P6B

source_name: P6_ocular lens_RNA-seq


title: MLT-P3A

source_name: P3_ocular lens_RNA-seq


title: MLT-P0B

source_name: P0_ocular lens_RNA-seq


title: MLT-P9B


title: MLT-P3B


title: MLT-P6A


title: MLT-E15B

source_name: E15_ocular lens_RNA-seq


title: mES GRO-seq DMSO

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: nascent RNA

data_processing:
Reads were trimmed at the 3’ end at the sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC using cutadapt –m 18.  Trimmed reads were aligned with bowtie with parameters –p 20 –n 2 –S –k 1 –m 1 –best and these reads were discarded in favor of those that had polyA tails.  PolyA tails for unmapped reads were trimmed using prinseq –trim_tail_right 1. PolyA-trimmed reads were aligned using bowtie –n 2 –S –k 1 –m 1 –best to retain reads that could be uniquely mapped.  WIG files were made using MACS -w -S --space=50 --shiftsize=40 --nomodel
Library strategy: GRO-Seq
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the read count in 50bp bins and were created uing MACS 1.4 with parameters -w -S --space=50 --nomodel --shiftsize=40
Supplementary_files_format_and_content: BigWig files represent coverage per nucleotide and were created using bedtools and wigToBigWig

source_name: Embryonic stem cells

growth_protocol: BirA cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media

extract_protocol:
RNAs containing BrdU-labeled were purified using agarose beads (Santa Cruz Biotech).  Purified RNA was reverse trancribed into cDNA, circularized and amplified.
Nuclei were isolated from lysed cells and re-suspended.  BrdU-labeled nucleotides were allowed to be incorporated into nascent RNA.

value: Embryonic stem cells

tag: genotype/variation

value: BirA


title: mES GRO-seq ActD

description: nascent RNA


title: MLM-P6B


title: MLT-E15A


title: mES Control CLIP-Seq

data_processing:
Library strategy: CLIP-Seq
Cutadapt was used to trim the sequence TGGAATTCTCGGGTGCCAAGG off of the 3’ end of CLIP-Seq reads with parameter –m 18.  First, bowtie was used to map trimmed reads to the mm9 mouse genome with parameters –best –strata –m1 –n 2 -5 5 –p 50 –S.  Bowtie2  was used to map those reads bowtie failed to map (accounting for deletions caused by UV crosslinking) with parameters -5 5 –sensitive –p 50.  The resulting bowtie and bowtie2 mappings were combined and used for downstream analysis.
Multiple reads were collapsed to one if they had the same chromosome, start, end, and first four nucleotides (barcode) to account for PCR duplicates.  RepeatMasker regions for mm9 were downloaded from the UCSC Genome Browser and subsetted for rRNA repeats.  Reads contacting these regions were discarded.  Remaining reads were separated into + and – strand reads using samtools view.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the denity of strand-separated mapped reads in 50bp bins using MACS with parameters –w –S –space=50 –nomodel –shiftsize=40 –keep-dup=1.

growth_protocol: Bio-YY1 and BirA -expressing murine embryonic stem cells (mESCs) and control mESCs expressing only biotin ligase BirA were grown on irradiated murine embryonic fibroblasts (MEFs). Cells were grown on 0.2% gelatinized (Sigma, G1890) tissue culture plates in ESC media; DMEMKO (Invitrogen, 10829-018) supplemented with 15% fetal bovine serum (Sigma, F4135-500), 1000 U/mL LIF (ESGRO, ESG1106), 100 μM nonessential amino acids (Invitrogen, 11140-050), 2 mM L-glutamine (Invitrogen, 25030-081), 100 U/mL penicillin, 100 μg/mL streptomycin (Invitrogen, 15140-122), and 8 nL/mL of 2-mercaptoethanol (Sigma, M7522).

extract_protocol:
RNA was UV crosslinked to protein using 254nm light, nuclei were purfied and lysed
RNA crosslinked with BioYY1 protein was purified using streptavidin beads (Dynabeads MyOne T1 magnetic beads, Life Technologies 65601) and reverse transcribed into cDNA.


title: mES YY1 CLIP-Seq

data_processing:
Library strategy: CLIP-Seq
Cutadapt was used to trim the sequence TGGAATTCTCGGGTGCCAAGG off of the 3’ end of CLIP-Seq reads with parameter –m 18.  First, bowtie was used to map trimmed reads to the mm9 mouse genome with parameters –best –strata –m1 –n 2 -5 5 –p 50 –S.  Bowtie2  was used to map those reads bowtie failed to map (accounting for deletions caused by UV crosslinking) with parameters -5 5 –sensitive –p 50.  The resulting bowtie and bowtie2 mappings were combined and used for downstream analysis.
Multiple reads were collapsed to one if they had the same chromosome, start, end, and first four nucleotides (barcode) to account for PCR duplicates.  RepeatMasker regions for mm9 were downloaded from the UCSC Genome Browser and subsetted for rRNA repeats.  Reads contacting these regions were discarded.  Remaining reads were separated into + and – strand reads using samtools view.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the denity of strand-separated mapped reads in 50bp bins using MACS with parameters –w –S –space=50 –nomodel –shiftsize=40 –keep-dup=1.
BED files represent the mm9 genomic coordinates of high signal of CLIP-Seq reads and were identified using MACS with strand-separated reads.  Reported peaks are required to have at least one bowtie2-mapped read, which represents a UV crosslinking-induced deletion.

value: BirA BioYY1


title: MLT-E18A

source_name: E18_ocular lens_RNA-seq


title: mES GRO-seq

description: nascent RNA

data_processing:
Reads were filtered for ribosomal RNAs using SortmeRNA with the eukaryote rRNA databases.  Filtered reads were then trimmed at their 3′ ends to remove residual sequencing adaptor sequences, and trimmed reads over 24bp were aligned using Bowtie.  Reads having a Phred score quality under 33 or aligning to more than 10 locations in the genome were discarded, and only the best mapping location was retained for each read.  A high number of reads mapping to chr17:39979942-39985774 + strand region encoding a 45S rRNA precursor not entirely contained in the eukaryote rRNA database were additionally removed.  Reads aligning to the + or - strand of the genome were respectively separated into Watson and Crick strand read containing files and wiggle tracks were generated for each file using bedtools.  Wig format wiggle files were converted into BigWig format with wigToBigWig.
Library strategy: GRO-Seq
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the read count in 50bp bins and were created uing MACS 1.4 with parameters -w -S --space=50 --nomodel --shiftsize=40
Supplementary_files_format_and_content: BigWig files represent coverage per nucleotide and were created using bedtools and wigToBigWig

growth_protocol: V6.5 mESCs were grown on irradiated murine embryonic fibroblasts

extract_protocol:
RNAs containing BrdU-labeled were purified using agarose beads (Santa Cruz Biotech).  Purified RNA was reverse trancribed into cDNA and amplified.
Nuclei were isolated from lysed cells and re-suspended.  BrdU-labeled nucleotides were allowed to be incorporated into nascent RNA.


title: Sample 14049: WTSolInn

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

data_processing:
Basecalls performed with CASAVA version 1.8.2
Sequences were trimmed to remove PCR primers, adapter sequences and low-quality base calls (score <20) with TRIM_GALORE version 0.2.1
Reads (50b single-end) were aligned to the Mus musculus reference genome using BOWTIE2 2.0.0.7 and known transcript levels were quantified with TOPHAT v2.0.3 (parameters --max-multihits 5 --b2-very-sensitive --no-coverage-search)
CUFFDIFF v2.0.2 was used to determine which known transcripts are differentially expressed between the various conditions, with an FDR of 5%, fold change greater than 1.5 and abundance greater than 5 FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files with FPKM, ExternalScaledFrags and RawFrags values for each Sample extracted from CUFFDIFF output

molecule: polyA RNA

source_name: Soleus muscle, Innervated, WT

extract_protocol:
RNA was isolated from innervated and 3 day denervated Wt soleus muscle and denervated Dach2-/-/Hdac9-/- soleus muscle using Direct-zol RNA MiniPrep Kit (Zymo Research) and was treated with DNase (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Innervated

tag: age

value: Adult

value: muscle

tag: genotype

value: wild-type


title: Sample 14051: Dach2-/-/Hdac9-/-SolDen

source_name: Soleus muscle, Denervated; Dach2-/-/Hdac9-/-

treatment_protocol: Denervated for 3 days


title: UJ02

city: New York

first: Jianbo

last: Sun

state: NY

department: Microbiology and Immunology

institute: Columbia University

description: UJ01 and UJ02 were from same cell culture

data_processing:
55 TO 60 MILLION 2x100 BP PAIRED END RAW PASSING FILTERS READS SEQUENCED ON ILLUMINA HISEQ 2000 V3 INSTRUMENT
map reads onto reference genome mm9
estimate normalized expression level (FPKM) of known genes and transcripts
tophat-1.3.2 for mapping, cufflinks-2.1.1 for transcriptome construction and normalization.
Genome_build: mm9
Supplementary_files_format_and_content: gene FPKM other than splice isoform, FPKM-conf_lo or FPKM_conf_hi.
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1,2] with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2,3] with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
[1] reference: Trapnell C et al 2009 Bioinformatics
[2] reference: Trapnell C et al 2010 Nature Biotech
[3] reference: Anders S et al 2010 Genome Biology

source_name: B10- cells from mouse splenic B cell

growth_protocol: all cells were cultured in RPMI1640 medium plus anti-Cd40 antibody for 48h and LPS+PMA+Ionomycin for the last 5h

extract_protocol:
total RNA was extracted with Trizol, rRNA was depleted with the Ribo-Zero rRNA removal kit (Epicentre)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: B cells

tag: subsets

value: B10- cells (Cd1d-Cd5-Cd19hiIl10-)

tag: culture

value: Cd40 antibody incubation for 48h followed by LPS+PMA+Ionomycin for 5h


title: UJ01

source_name: B10+ cells from mouse splenic B cell

value: B10+ cells (Cd1dhiCd5+Cd19hiIl10+)


title: Sample 14043: WTSolInn


title: Sample 14044: WTSolDen

source_name: Soleus muscle, Denervated, WT


title: Villi_WT

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

description: total RNA extracted with Rneasy Plus Micro Kit Qiagen processed for mRNA library preparation

data_processing:
Sequencing data is aligned to mouse (mm9) genome in a reference guided manner by tophat.
Differentially expressed genes were identified using DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reporting genes with mean read count, fold change and p-value.

source_name: Villi

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001 )

treatment_protocol: The mice were treated with 3 injection of Tamoxifen and sacrified at 6 days post injection. The small intestine of the mice were isolated and the Villi were purified.

value: Rosa26-CreERT2 Cdkn2a-/-

value: small intestine

value: Villi


title: Villi_RingKO

value: Rosa26-CreERT2 Cdkn2a-/- Ring1a-/- Ring1bf/f


title: ISC_Tcf4_WT

description:
The small intestine ISC of the mice were isolated
Immuno-precipitation of chromatin using a specific antibody against Tcf4 (Cell signaling C48H11, catalog 2569S and lot2).

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie allowing to retain only reads with unique alignment.
Peaks: Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locus of of enriched regions for target of interest

source_name: ISC

extract_protocol:
The villi were isolated from the small intestine while  the Lgr5-GFP+ ISCs were sorted from the isolated crypts
Villi cells or ISCs were cross-linked with 1% formaldehyde and chromatin sonicated. Chromatin was precipitated with specific antibody, which was further purified using magnetic protein A coupled beads, and recovered DNA was used for high-throughput sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: ISC

tag: chip antibody

value: Tcf4 (C48H11) (Cell signaling, catalog# 2569S, lot# 2)


title: Villi_Input

description:
The small intestine villis of the mice were isolated
Input.

value: none (input)


title: Villi_Ring1b

description:
The small intestine villis of the mice were isolated
Immuno-precipitation of chromatin using a specific antibody against Ring1b (Home made).

value: Ring1b (Home made)


title: MLT-E18B

value: Embryonic day 18

value: Ocular Lens


title: ISC_Tcf4_RingKO

value: Lgr5Gfp-CreERT2 Ring1a-/- Ring1bf/f


title: ISC_Bactenin

data_processing:
Sequencing data is aligned to mouse (mm9) genome in a reference guided manner by tophat.
Differentially expressed genes were identified using DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: list of genes with mean read count, fold change and p-value.

source_name: Intestine Stem Cells

extract_protocol:
The mice were treated with 3 injection of Tamoxifen and sacrified at 6 days post injection. The small intestine crypts of the mice were isolated and the Lgr5-GFP+ ISCs were sorted.
total RNA extracted with Rneasy Plus Micro Kit Qiagen processed for mRNA library preparation
Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001 )

tag: background strain

value: WT


title: MLT-P0A

value: Postnatal day 0


title: UJ03

description: UJ03 and UJ04 were from same cell culture

value: spleen

value: B cells


title: ISC_Bactenin_Ring KO

value: Ring KO


title: UJ04

value: B10- cells (Cd1d-Cd5-Cd19hiIl10-)

value: Cd40 antibody incubation for 48h followed by LPS+PMA+Ionomycin for 5h


title: ISC_WT_rep1

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 (RS-122-2001)

treatment_protocol:
The mice were treated with 3 injection of Tamoxifen and sacrified at 6 days post injection. The small intestine crypts of the mice were isolated and the Lgr5-GFP+ ISCs were sorted.
total RNA extracted with Rneasy Plus Micro Kit Qiagen processed for mRNA library preparation

value: Intestine Stem Cells


title: Sample 14050: WTSolDen

value: Adult

value: muscle

value: wild-type


title: ISC_WT_rep2


title: Crypt_Tcf4_WT

description: Immuno-precipitation of chromatin using a specific antibody against Tcf4 (Cell signaling C48H11, catalog 2569S and lot2).

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie allowing to retain only reads with unique alignment.
Peaks: Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locus of enriched regions for target of interest

source_name: Crypt

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol:
The small intestine crypts of the mice were isolated
The small intestine crypts of the mice were isolated and, in the ISCs samples, the Lgr5-GFP+ ISCs were sorted
Crypt cells or ISCs were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using magnetic protein A coupled beads, and recovered DNA was used for high-throughput sequencing.

value: R26-CreERT2 Cdkn2a-/-

value: anti-Tcf4 (Cell signaling, catalog 2569S and lot2)

value: Crypt cells


title: ISC_RingKO_rep2


title: ISC_RingKO_rep1


title: Crypt_Tcf4_RingKO

value: R26-CreERT2 Cdkn2a-/- Ring1a-/- Ring1bf/f


title: ISC_Input

description: Input.

source_name: IntestineStemCells

treatment_protocol:
The small intestine crypts of the mice were isolated and the Lgr5-GFP+ ISCs were sorted
The small intestine crypts of the mice were isolated and, in the ISCs samples, the Lgr5-GFP+ ISCs were sorted
Crypt cells or ISCs were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using magnetic protein A coupled beads, and recovered DNA was used for high-throughput sequencing.

value: input


title: Sample 14045: Dach2-/-/Hdac9-/-SolDen


title: ISC_H2AK119Ubq

description: Immuno-precipitation of chromatin using a specific antibody against H2AK119 ubiquitination (Cell signaling D27C4, catalog 8240S and lot2).

value: anti-H2AK119 (Cell signaling, catalog 8240S and lot2)


title: Crypt_Ring1b

description: Immuno-precipitation of chromatin using a specific antibody against Ring1b (Home made).

value: WT

value: anti-Ring1b (Home made)


title: Crypt_Input

description: Input.


title: Villi_H2AK119Ubq

description:
The small intestine villis of the mice were isolated
Immuno-precipitation of chromatin using a specific antibody against H2AK119 ubiquitination (Cell signaling D27C4, catalog 8240S and lot2).

value: small intestine

value: Villi

value: Ubiquityl-Histone H2A (Lys119) (D27C4) (Cell signaling, catalog# 8240S, lot# 2)


title: Crypt_H2AK119Ubq


title: Sox2_targeted_wt_1

description: 4C PCR product

source_name: E14 ESC

value: E14 ESC

value: TCAAAATGGATGCAAGAAGATC


title: Sox2_targeted_inv_2

description: 4C PCR product

value: GAAAAATGGATGCAAGAAGATC


title: Sox2_targeted_wt_2

description: 4C PCR product


title: Sox2_targeted_del_2

description: 4C PCR product

value: AAAATGGATGCAAGAAGATC


title: Sox2_targeted_inv_3

description: 4C PCR product

value: CTAAAATGGATGCAAGAAGATC


title: Sox2_contacted_wt_2

description: 4C PCR product

value: TCGAGGGTAATTTTAGCCGATC


title: Sox2_targeted_del_1

description: 4C PCR product

value: AGAAAATGGATGCAAGAAGATC


title: Sox2_contacted_inv_3

description: 4C PCR product

value: CTGAGGGTAATTTTAGCCGATC


title: Sox2_contacted_inv_2

description: 4C PCR product

value: GAGAGGGTAATTTTAGCCGATC


title: Sox2_contacted_del_2

description: 4C PCR product

value: GAGGGTAATTTTAGCCGATC


title: Sox2_contacted_del_1

description: 4C PCR product

value: AGGAGGGTAATTTTAGCCGATC


title: ISC_Ring1b

description: Immuno-precipitation of chromatin using a specific antibody against Ring1b  (Home made).

value: Intestine Stem Cells


title: Malt1_targeted_wt_1

description: 4C PCR product

value: TCCCCTCTTCCCAAGATGGATC


title: Malt1_targeted_inv_2

description: 4C PCR product

value: GACCCTCTTCCCAAGATGGATC


title: Malt1_targeted_wt_2

description: 4C PCR product

value: CTCCCTCTTCCCAAGATGGATC


title: Malt1_targeted_del_2

description: 4C PCR product

value: CCCTCTTCCCAAGATGGATC


title: Malt1_contacted_wt_2

description: 4C PCR product

value: CTTCACTCCAGCCCACCAGATC


title: Malt1_contacted_inv_2

description: 4C PCR product

value: E14 ESC

value: GATCACTCCAGCCCACCAGATC


title: Sox2_contacted_inv_1

description: 4C PCR product


title: Malt1_targeted_inv_1

description: 4C PCR product

value: AGCCCTCTTCCCAAGATGGATC


title: Sox2_targeted_inv_1

description: 4C PCR product


title: Sox2_contacted_wt_1

description: 4C PCR product

value: CGAGGGTAATTTTAGCCGATC


title: Malt1_contacted_del_2

description: 4C PCR product

value: TCACTCCAGCCCACCAGATC


title: Fbn2_contacted_wt_1

description: 4C PCR product

value: AGCTTGTCTTCATCTTCTGATC


title: Fbn2_targeted_del_2

description: 4C PCR product

value: TTACTATGTATATGGCGATC


title: Fbn2_targeted_wt_2

description: 4C PCR product

value: TCTTACTATGTATATGGCGATC


title: Fbn2_contacted_wt_2

description: 4C PCR product

value: TCCTTGTCTTCATCTTCTGATC


title: Fbn2_targeted_inv_1

description: 4C PCR product

value: AGTTACTATGTATATGGCGATC


title: Fbn2_targeted_del_1

description: 4C PCR product


title: Malt1_contacted_del_1

description: 4C PCR product

value: AGTCACTCCAGCCCACCAGATC


title: Fbn2_targeted_wt_3

description: 4C PCR product

value: TCCTTACTATGTATATGGCGATC


title: Fbn2_targeted_inv_2

description: 4C PCR product

value: GATTACTATGTATATGGCGATC


title: Fbn2_targeted_wt_1

description: 4C PCR product


title: Malt1_targeted_del_1

description: 4C PCR product


title: Fbn2_contacted_del_2

description: 4C PCR product

value: CTTGTCTTCATCTTCTGATC


title: Malt1_contacted_wt_1

description: 4C PCR product


title: Fbn2_contacted_del_1

description: 4C PCR product


title: Fbn2_contacted_inv_2

description: 4C PCR product

value: GACTTGTCTTCATCTTCTGATC


title: large leaf - 7 weeks

city: Nanjing

first: Tariq

last: Pervaiz

state: Jaingsu

address: wei Gang

department: Horticulture

country: China

institute: Nanjing Agricultural University

data_processing:
HCS1.5 + RTA1.13.48 + BclConverter-1.9.0-11-03-08 HCS - HiSeq Sequencing Control Software - RTA is Real-time analysis software - the sequencing profiles were performed basecalling, and turned into binary file bcl, then the bcl file was tranferred into the readable sequence file by the BclConverter-1.9.0-11-03-08 software,  the quality value of the fasta produced by this version is phred+64.
We use software developed by BGI (unpublished) to deal with the data from HiSeq sequencing  adaptor sequence, or low-quality sequence
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed. After raw reads are filtered into clean reads which will be aligned to the reference sequences withSOAPaligner. QC of alignment is performed to determine if resequencing is needed.
The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis. If alignment result passes QC, we will proceed with downstream analysis including gene expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation and SNP detection.
We use plant targets prediction pipeline for indentify target prediction are based on those suggested by Allen et al. (microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005, 121:207-221) - Supplemental document S1 and by Schwab et al. (Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 2005, 8: 517 - 527)
GO enrichment analysis is used on predicted target gene candidates of novel miRNAs . It will provide all GO terms significantly enriched in the predicted target gene candidates of novel miRNAs compared to the reference gene background, as well as the genes corresponding to certain biological function. The result could reveal the functions significantly related with predicted target gene candidates of novel miRNAs. This method firstly maps all target gene candidates to GO terms in the database (http://www.geneontology.org/), calculating gene numbers for each term, then using hypergeometric test to find significantly enriched GO terms in target gene candidates comparing to the reference gene background.We use the Bonferroni Correction for the p-value to obtain a corrected p-value. GO terms with corrected p-value <= 0.05 are defined as significantly enriched in target gene candidates.
KEGG pathway analysis is also used for the target gene candidates. In organisms, genes usually interact with each other to play different roles in certain biological function. The analysis based on pathways could facilitate the understanding of biological functions of genes. KEGG is the major public pathway-related database[8]. KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways in target gene candidates comparing with the whole reference gene background. The calculating formula is the same as that in GO analysis. Here N is the number of all genes with KEGG annotation, n is the number of target gene candidates in N, M is the number of all genes annotated to a certain pathway, and m is the number of target gene candidates in M. Genes with FDR<=0.05 are considered as significantly enriched in target gene candidates

organism: Vitis vinifera

source_name: large leaf

extract_protocol:
The modified CTAB method
RNA libraries were prepared for sequencing using standard Illumina protocols
Ultra™ RNA Library Prep Kit for Illumina (NEB, USA)

value: 7 weeks

tag: cultivar

value: Summer Black

value: leaf


title: mature leaf - 10 weeks

source_name: mature leaf

value: 10 weeks


title: Malt1_contacted_inv_1

description: 4C PCR product

value: E14 ESC


title: Fbn2_contacted_inv_1

description: 4C PCR product


title: Capture Hi-C Sample4

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: Hi-C ditag

data_processing:
Base calling with standard Illumina software
Mapping and filtering with HiCUP v0.5.3 (using Bowtie 1.1.0)
Genome_build: mm9
Supplementary_files_format_and_content: The processed files were generated with HiCUP (v0.5.3), homepage:
http://www.bioinformatics.babraham.ac.uk/projects/hicup
In the tab-delimited output file, each line represents a Hi-C di-tag and comprises 7 columns (index ID; chromsome read 1; position read 1; strand read 1; chromsome read 2, position read 2; strand read 2)

extract_protocol:
Cells were fixed in 2% formaldehyde for 10 min, and the reaction was quenched by the addition of ice-cold glycine (0.125 M final concentration). After centrifugation (400xg, 10 min), cells were washed with PBS, spun down (400xg, 10 min), the supernatant was removed, and the cell pellet was flash-frozen in liquid nitrogen and stored at -80˚C. Cell pellets were incubated in 50 ml ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal CA-630, protease inhibitor cocktail (Roche)) for 30 min on ice, followed by a centrifugation to pellet cell nuclei (650xg, 5 min). Nuclei were resuspended in 1.25x NEBuffer 2, SDS was added (0.3% final concentration), and nuclei were incubated at 37˚C and 950 rpm (shaking) for one hour. Triton X-100 was added to a final concentration 1.7%, and nuclei were incubated at 37˚C and 950 rpm (shaking) for one hour. After digestion with HindIII (NEB; 1500 units per 5 million cells) overnight at 37˚C and 950rpm (shaking), restriction sites were filled in with Klenow (NEB) using biotin-14-dATP (Life Technologies), dCTP, dGTP and dTTP (all at a final concentration of 30 µM) for 60 min at 37˚C. After addition of SDS (1.42% final concentration) and incubation at 65˚C and 950rpm (shaking) for 25 min, ligation was performed for four hours at 16˚C (50 units T4 DNA ligase (Life Technologies) per 5 million cells starting material) in a total volume of 8.2 ml ligation buffer (50 mM Tris-HCl, 10 mM MgCl2, 1mM ATP, 10 mM DTT, 100 ug/ml BSA, 0.9% Triton X-100). The reversal of crosslinks (65˚C overnight in the presence of Proteinase K), was followed by RNase A treatment and two sequential phenol chloroform extractions of DNA.
The concentration DNA was determined using Quant-iT Pico Green (Life Technologies), and 40 µg of Hi-C library DNA were subjected to removal of biotin (T4 DNA polymerase (NEB), 4 hours at 20˚C) from non-ligated fragment ends, followed by DNA purification (Qiagen PCR purification kit) and sonication (Covaris E220). Sonicated DNA was end-repaired (T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB)), and a double size selection using AMPure XP beads (ratio SPRI beads solution volume to sample volume to 0.6:1, then 0.9:1) was performed, before dATP-addition with Klenow exo- (NEB). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Life Technologies) in binding buffer (5 mM Tris pH8, 0.5 mM EDTA, 1 M NaCl) for 30 min at room temperature, followed by two washes in binding buffer, and one wash in ligation buffer (NEB). PE adapters (Illumina) were ligated onto Hi-C ligation products bound to streptavidin beads for 2 hours at room temperature (T4 DNA ligase NEB, in ligation buffer, slowly rotating). After washes in wash buffer (5 mM Tris, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) and binding buffer, the DNA-bound beads were resuspended in a final volume of 30 µl NEBuffer 2. Bead-bound Hi-C DNA was amplified with 6 to 8 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). The concentration and size distribution of Hi-C library DNA after PCR amplification was determined by Bioanalyzer profiles (Agilent Technologies).  Bait capture system design for Promoter Capture Hi-C A list of transcripts was obtained from the Ensembl BioMart system, detailing the positions and assigned biotype for all transcripts in their gene build. The list was filtered to keep only transcripts with a biotype of protein-coding, non-coding (lincRNA), antisense, snRNA, miRNA or snoRNA. A genomic restriction map was then created to generate a list of all HindIII fragments in the genome, and this was subsequently filtered against the transcript list to keep only restriction fragments which contained the transcriptional start position for one or more transcripts. For each restriction fragment containing a transcription start site, two 120 bp capture probes were designed, one to each end of the fragment. Because of the size selection step following sonication, the probes had to fall entirely within a region no more than 500 bp from the end of the fragment. Each probe was required to have no more than 3 consecutive bases masked by repeatmasker, and they had to have a GC content of 25 to 65% to match the efficient capture range of the SureSelect target enrichment system (Agilent Technologies). Where multiple probes passed these criteria, the probe nearest the end of the restriction fragment was chosen.

value: Embryonic stem cells


title: Capture Hi-C Sample5

description: Hi-C ditag


title: medium size leaf - 5 weeks

source_name: medium size leaf

value: 5 weeks


title: young leaf - 2 weeks

source_name: young leaf

value: 2 weeks


title: mucin treatment, replicate B

status: Public on Oct 28 2015

city: Davis

first: Danielle

middle: G

last: Lemay

state: CA

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

description: MUC-B

data_processing:
Reads were demultiplexed and imported into CLC-Bio Genomics Workbench Version 5.0
Reads were trimmed setting at 2 the maximum of ambiguous base pairs, and deleted if their quality scores were below 0.5.
Edited reads were aligned to fasta files generated at IMG from the genome sequences (reference) of B. longum subsp. infantis ATCC 15697.
Alignment allowed a maximum of 2 mismatches, and a maximum of 10 matches to other reads. Other settings were considered as default.
The CLC-BIO tools retrieved information regarding the gene length, total and unique gene reads aligning to a specific locus tag, and automatically calculated the RPKM value (Reads Per Kilobase per Million mapped reads) and total read counts.
Genome_build: draft genome sequence of Bifidobacterium bifidum SC555 genome available at https://img.jgi.doe.gov, GOLD Project ID: Gi17163
Supplementary_files_format_and_content: tab-delimited text files contain abundance measurements as RPKM and counts

organism: Bifidobacterium bifidum

source_name: bacterial isolate_mucin

growth_protocol: B. bifidum SC555 was grown in mMRS supplemented with either 2% lactose, 2% HMO, 2% LNT, 2% LNnT, 2% 2’FL, 2% 3FL, 2% 6’SL, or 1% MUC in a microplate reader, and cultures were taken at mid-exponential phase OD 0.5-0.6. In the case of HMO, the samples were collected at multiple different points in the growth curve, approximately OD600nm = 0.25, 0.5, 0.7, 0,9 and 1.1. Samples were immediately pelleted at 12000 x g for 1 min and stored in RNA later Ambion.

extract_protocol:
One ml of each sample stored in RNAlater, with OD above 0.6, was used in the procedure. Samples were centrifuged at 10,000 x g for 2 min on a bench centrifuge to collect the cell pellet. Pellet was washed twice with PBS buffer to remove RNAlater, and centrifuged at 10,000 x g. Pellets were later resuspended in 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), previously prepared and filter-sterilized in TE buffer (10 mM Tris, 1mM EDTA, pH 7.2). Samples were incubated at 37˚C for 10 min. Pre-lysed cells were centrifuged at 8000 x g for 1 min, and the Ambion RNAqeous kit (LifeTechnologies) was used to extract total RNA following manufacturer instructions and eluting the RNA in 50 μl of EB buffer. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour. RNA was stored at -80C at this point, but previously quantified in Qubit using the Qubit High Sensitivity RNA Assay Kit (Life Technologies). One μl of RNA was the minimum used in next steps. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip. RNA (1-2 µl) was first denatured at 65-70 ºC for 2 min before the run. Samples were further processed only if their RIN (RNA Integrity Number), was above 7.Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit, Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. mRNA was later converted to cDNA. For first strand cDNA conversion, the Superscript II Reverse Transcriptase was used (Invitrogen), following manufacturer protocol. Reaction also contained Random Primers (3 μg/μl, Invitrogen). We used 11 μl of rRNA depleted RNA, 1 μl of 10 mM dNTPs and 1 μl of random primers. After this, second cDNA strand was synthesized using the NEB NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA) following manufacturer instructions. Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. Final elution was done in two rounds of 15 μl in EB buffer.  At this point cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and diluted to a volume of 100 μl with EB buffer, for fragmentation in a Bioruptor (Diagenode). Eight cycles of 15 s on and 90 s off were used for each sample. Fragmented cDNA was quantified with Qubit High Sensitivity DNA kit. DNA was also analyzed in a Bioanalyzer with the Agilent High Sensitivity DNA kit. An average fragment length of 300-500 bp was desired for next steps.
Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles.
Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads).

tag: isolate

tag: cultured with

value: mucin

tag: collection time point

value: mid-exponential phase OD 0.5-0.6


title: 6’sialyllactose treatment, replicate A

source_name: bacterial isolate_6’sialyllactose


title: 6’sialyllactose treatment, replicate B


title: 3-fucosyllactose treatment, replicate B

source_name: bacterial isolate_3-fucosyllactose


title: 2’fucosyllactose treatment, replicate A

source_name: bacterial isolate_2’fucosyllactose


title: lacto-N-neotetraose treatment, replicate B

description: LNnT-B

source_name: bacterial isolate_lacto-N-neotetraose

value: lacto-N-neotetraose


title: lacto-N-neotetraose treatment, replicate A

description: LNnT-A


title: 3-fucosyllactose treatment, replicate A


title: pooled HMO, late time point, replicate B

description: HMOlate-B

source_name: bacterial isolate_pooled HMO

value: pooled human milk oligosaccharides (HMO)

value: late-exponential phase OD 0.9-1.1


title: lacto-N-tetraose treatment, replicate B

description: LNT-B

source_name: bacterial isolate_lacto-N-tetraose

value: lacto-N-tetraose


title: Capture Hi-C Sample3

description: Hi-C ditag

source_name: Foetal liver cells

tag: cell type


title: pooled HMO, late time point, replicate A

description: HMOlate-A


title: pooled HMO, early time point, replicate A

description: HMOearly-A

value: early-exponential phase OD 0.25


title: lactose treatment, replicate A

description: LAC-A

source_name: bacterial isolate_lactose

value: lactose


title: pooled HMO, mid time point, replicate A

description: HMOmid-A

value: mid-exponential phase OD 0.5-0.7


title: pooled HMO, mid time point, replicate B

description: HMOmid-B


title: 2’fucosyllactose treatment, replicate B


title: lacto-N-tetraose treatment, replicate A

description: LNT-A


title: lactose treatment, replicate B

description: LAC-B


title: 6’sialyllactose treatment, replicate A

data_processing:
Reads were demultiplexed and imported into CLC-Bio Genomics Workbench Version 5.0
Reads were trimmed setting at 2 the maximum of ambiguous base pairs, and deleted if their quality scores were below 0.5.
Edited reads were aligned to fasta files generated at IMG from the genome sequences (reference) of B. longum subsp. infantis ATCC 15697.
Alignment allowed a maximum of 2 mismatches, and a maximum of 10 matches to other reads. Other settings were considered as default.
The CLC-BIO tools retrieved information regarding the gene length, total and unique gene reads aligning to a specific locus tag, and automatically calculated the RPKM value (Reads Per Kilobase per Million mapped reads) and total read counts.
Genome_build: B. longum subsp. infantis ATCC 15697
Supplementary_files_format_and_content: tab-delimited text files contain abundance measurements as RPKM and counts

organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

source_name: bacterial isolate

growth_protocol: B. longum subsp. infantis ATCC 15697 was grown in mMRS supplemented with either 2% lactose, 2% HMO, 2% LNT, 2% LNnT, 2% 2’FL, 2% 3FL, 2% 6’SL in a microplate reader, and cultures were taken at mid-exponential phase OD 0.5-0.6. In the case of HMO, the samples were collected at four different points in the growth curve, approximately OD600nm = 0.25, 0.5, 0.7, 0,9 and 1.1. Samples were immediately pelleted at 12000 x g for 1 min and stored in RNA later Ambion.

tag: treatment

value: 6’sialyllactose treatment

tag: replicate

value: A


title: 3-fucosyllactose treatment, replicate A

value: 3-fucosyllactose treatment


title: 2’fucosyllactose treatment, replicate B

value: 2’fucosyllactose treatment

value: B


title: 3-fucosyllactose treatment, replicate B


title: 6’sialyllactose treatment, replicate B


title: 2’fucosyllactose treatment, replicate A


title: mucin treatment, replicate A

description: MUC-A


title: ESC_chr11_102762586

description: 4C PCR product

value: E14 ESC

tag: barcode

value: CAAGCCACTGCGTCCATG

tag: bait


title: lacto-N-tetraose treatment, replicate B

value: lacto-N-tetraose treatment


value: lacto-N-neotetraose treatment


value: pooled HMO, late time point


title: pooled HMO, early time point, replicate B

description: HMOearly-B


value: pooled HMO, early time point


title: lactose treatment, replicate B

value: lactose treatment


title: lactose treatment, replicate A


title: pooled HMO, mid time point, replicate A

value: pooled HMO, mid time point


title: 44ab1

city: MD

first: Jianhua

last: Zhu

address: 2102 Plant Sciences Building  College Park

institute: University of Maryland

data_processing:
RNA-seq raw reads were respectively trimmed using Trimmomatic v0.32 (Bolger et al. 2014, Bioinformatics, 30(15), pp2114-2120) and PRINSEQ v0.20.4 (Schmieder and Edwards 2011, Bioinformatics, 27(6), pp863-864). Trimmomatic was used to remove the potential Illumina adapter contamination and conduct reads trimming and clipping the low quality bases. PRINSEQ was subsequently employed to mainly remove low-complexity reads.
The remained reads were then aligned to Arabidopsis thaliana (A. thaliana) genome sequence and the reference annotated genes (TAIR10) using TopHat v2.0.13 program (Kim et al. 2013, Genome Biol, 14(4), R36) with customized parameters specially for our RNA-seq libraries from plant A. thaliana (--read-edit-dist 3 --read-realign-edit-dist 0 --b2-very-sensitive -r 150 --mate-std-dev 200 -a 6 -i 8 -I 10000 --min-segment-intron 8 --max-segment-intron 10000 --microexon-search).
According to RNA-seq mapped reads and the reference annotated transcripts, transcriptomes were reconstructed respectively for each sample by Cufflinks v2.2.1 (Trapnell et al. 2013, Nat Biotechnol, 31(1), pp46-53). Given variable efficiency of mRNA enrichments and rRNA depletion kits in samples, these transcripts were masked in transcriptome constructions to improve the overall robustness of transcript abundance estimates. To obtain a high confidence of transcriptomes, the novel constructed transcript was filtered out when the abundance was lower than 20% (default is 10%) of the most abundant isoform for each gene. Then all of the constructed transcriptomes were merged with the reference annotated transcripts using Cuffmerge (Trapnell et al. 2013, Nat Biotechnol, 31(1), pp46-53) to yield comprehensive re-annotated gene transcripts including known and novel annotated transcripts in our RNA-seq samples.
Significantly differentially expressed genes were predicted by Cuffdiff (Trapnell et al. 2013, Nat Biotechnol, 31(1), pp46-53) between the controls and tested samples, using absolute Log2 (fold-change) > 1 and multiple test q-value < 0.05.
We adopted juncBASE v0.6 (Brooks et al. 2011, Genome Res, 21(2), pp193-202) to identify AS events within genes for our samples. A series of python scripts from juncBASE were employed to identify exon-exon junctions, exon-intron junctions and AS events, qualify the events and give significantly differentially splicing events between samples. Moreover, a module from CASH (Comprehensive alternative splicing hunting, the renewed version of ASD, alternative splicing detector (Zhou et al. 2014, Nucleic Acids Res, 42(6), pp4019-4030)) was used to rescue 19 to 50 differential intron retention events.
Genome_build: TAIR10
Supplementary_files_format_and_content: The files (WTckVS44ck-differential_genes.txt, WTabVS44ab-differential_genes.txt, and WTckVSWTab-differential_genes.txt) indicate differential genes between conditions produced from Cufflinks and were modified manually. In the current version, they include geneID, locus, FPKM (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) of the gene for the sample, log2 (fold chang) from sample 2 compared to sample 1, and statistially Pvalue and qvalue between the two conditions. Whereas the files (WTckVS44ck-AS_genes.txt, WTabVS44ab-AS_genes.txt, and WTckVSWTab-AS_genes.txt) indicate alternative splicing genes produced from juncBASE and they include geneID, splicing loci, PSI (Percent Spliced In) values, statistially pvalues and etc.

organism: Arabidopsis thaliana

source_name: rbm25-1 ABA_1

growth_protocol: After 4-day stratification at 4°C, seeds of the Arabidopsis (ecotype Col-0) plants were surface-sterilized and planted on 1x MS medium agar plates supplemented with 2% sucrose. Germinated seedlings were allowed to grow for two weeks in a growth chamber at 21 ± 1°C  with a long-day photoperiod (16 h light/8 h dark; 120 μmol m-2 s-1) .

extract_protocol:
Total RNA was isolated with the Universal Plant Total RNA Extraction Kit (Cat#RP3302, BioTeke) and treated with TURBO DNA-free™ Kit (Cat#AM1907, Ambion) to remove any genomic DNA contaminants.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings were sprayed with 0.1 mM ABA solution and allowed to grow for an additional 6 hours under light.

value: 0.1 mM ABA, 6 hours

value: 2 weeks


title: 44ab2

source_name: rbm25-1 ABA_2


title: 44ck1

value: No treatment


title: 44ck2


title: 44ck3


title: 44ab3

source_name: rbm25-1 ABA_3


title: WTck3

source_name: WT ck_3

value: wild type


title: WTab1

source_name: WT ABA_1


title: lacto-N-tetraose treatment, replicate A


title: WTck1

source_name: WT ck_1


title: WTck2

source_name: WT ck_2


title: SE_8+TEX

city: Irvine

first: Lei

last: Li

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (via READemption)
Read mapping using segemehl (vi READemption)
Coverage calculation and normalisation (via READemption)
Genome_build: NC_009725.1
Supplementary_files_format_and_content: wiggle

organism: Bacillus velezensis FZB42

source_name: bacterial cells

growth_protocol: B. amyloliquefaciens FZB42 was grown in 1CM media supplemented with maize root exudates (RE), or soil extract (SE), or both (RS) and sampled from different growth stage (#3 and #8).

extract_protocol:
The bacterial cells were quick-frozen in liquid nitrogen before total RNA preparation. RNAs were isolated with Trizol® agent and glass beading on FastPrep®-24 system.
Libraries for Illumina sequencing (HiSeq) of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis.

value: TEX treament

tag: medium supplements

value: soil extract (SE)

tag: growth stage

value: middle stationary phase (#8)


title: SE_3+TEX

value: early stationary phase (#3)


title: SE_8-TEX

value: no TEX treament


title: SE_3-TEX


title: RS_8+TEX

value: maize root exudates (RE) and soil extract (SE)


title: pooled HMO, mid time point, replicate B

value: B


title: RS_3+TEX


title: RS_8-TEX


title: RS_3-TEX


title: RE_3-TEX

value: maize root exudates (RE)


title: 1CM_3+TEX

value: No supplement


title: WTab3

source_name: WT ABA_3

tag: age


title: 1CM_3-TEX


title: WTab2

source_name: WT ABA_2

tag: genotype


title: Mbd3

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Paired end reads were collapsed and adapter sequences were removed from fastq files. Reads were mapped to the mouse mm9 genome using Bowtie2 and only uniquely mapped reads with zero, one, or two mismatches were used for further analysis. The read size distribution was determined for each library and reads were separated into nucleosome sized fragments (135-165), subnucleosome sized fragments (100-130) and factor binding fragments (less than 80). To calculate occupancy around sites, aligned reads were processed in HOMER by using the "annotatePeaks" command with 20bp bins  2000 bp upstream and downstream of the reference sequence. Reads were normalized to the average genome-wide coverage.
These libraries are resequenced to provide deeper sequencing coverage from the Mbd3 KD MNase-Seq found in GSE57170
Other MNase-Seq samples (GFP KD and Smarca4 KD) are from GSE57170
Genome_build: mm9

source_name: murine embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol:
ES cells were crosslinked with formaldehyde (Sigma) to a final concentration of 1%, incubated at room temperature for 10 min and quenched with glycine to a final concentration of 125 mM. Cells were washed with ice cold PBS and pelleted. Cell pellets were resuspended in lysis buffer (10 mM Tris [pH 7.5], 10 mM NaCl, 2 mM MgCl2, 0.5% NP-40, 1 mM CaCl2) with protease inhibitors (Roche) and incubated for 15 min at 4°C. Permeabilized cells were treated with ~10 Units/106 cells of micrococcal nuclease (Roche) for 5 min at 37°C. Reactions were stopped with the addition of EDTA. Control samples with no MNase addition were treated similarly. Samples were incubated for 4 hr at 4°C with rotation with RNaseA/T1 (Ambion) then incubated overnight at 65°C with 0.01% SDS and proteinase K (Ambion). DNA was extracted with PCI using phase-lock tubes, ethanol precipitated, and resuspended in 30 μL TE.
Samples were treated with CIP, end-repaired, A-tailed, and adaptor-ligated as described (Illumina). Between each step, DNA was cleaned with PCI extraction and ethanol precipitation. After adaptor ligation, DNA was selected and purified with Agencourt Ampure beads and then PCR amplified with KAPA HiFi polymerase using 16 cycles of PCR.

treatment_protocol: One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection

tag: genotype/variation

value: Mbd3 KD

tag: cell line

value: embryonic stem cells


title: Leaf_rep2

city: Yangling

first: Yizhen

last: Wan

address: Taicheng Road

institute: Northwest Agriculture and Forestry University

description: total RNA

data_processing:
Reads sets were mapped to the Arabidopsis genome (TAIR10) using TopHat2 with a parameter of ‘-b2-fast’ .
The potential PCR duplicates were removed by the parameter ‘rmdup’ rooted in SAMtools
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split -trackline -trackopts name="\"read coverage\"".

source_name: Rosette leaves at flowering

growth_protocol: The plants were grown in the greenhouse under a photoperiod of 16 h light/8 h dark at 22-24 °C.

extract_protocol:
Modified CTAB buffer
Library for mRNA-seq was generated using mRNA sequencing kit (Illumina Inc., San Diego, CA)

treatment_protocol: When the plants were at the blooming period (five weeks after seed germination), the plant materials of the flowers, rosette leaves and roots were separately collected, treated with liquid nitrogen and stored at -80 °C until use.

tag: tissue

value: Leaf at flowering

tag: sample type

value: total RNA-Seq

tag: rip type

value: as Input for RIP


title: Root_rep2

description: total RNA

source_name: Total roots at flowering

value: Root at flowering


title: L1

description: mRNA

value: mRNA-Seq


title: 8946-H3K4me3_ChIP

first: Mark

middle: Yat-fung

last: Chiang

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

data_processing:
The reads were mapped to mm10 assembly using Bowtie (version 0.12.7) to generate uniquely mapped alignments.
FastQC (version 0.10.0) (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and cross-correlation test were applied to evaluate the data quality.
MACS (version 2.0.10) and SICER (version 1.1) were used to identify peaks or enriched segments for transcription factors and histone modifications, respectively.
Blacklisted genomic regions were filtered before the analysis of each peak or segment set.
The peaks or segments were annotated for their locations regarding to nearby genes using Homer (version 4.2).
Genome_build: mm10
Supplementary_files_format_and_content: peak files in .bed and .txt format. Txt format includes output from MACS or SICER.

source_name: 8946: H3K4me3 Chromatin IP

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Crosslinking was performed with either 1%  formaldehyde alone (histone mark samples) or 2 mM DSG and 1% formaldehyde ( Zmiz1/ICN1/Rbpj samples). Nuclear were sonicated and protein-DNA complexes were isolated with antibody.
The sequencing library was prepared using the Illumina Hi-Seq library preparation kit.

treatment_protocol: 8946 cells were retrovirally transduced with epitope tagged Zmiz1-IRES-NGFR and activated Notch1-IRES-GFP constructs and sorted for GFP+/NGFR+ cells.

value: 8946 cells - Flag-Zmiz1/ L1601PDP

tag: disease

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte

tag: antibody

value: H3K4me3 (Millipore, 07-473)


title: 8946-Input-1

source_name: 8946: Input


title: 8946-H3K27ac_ChIP

source_name: 8946: H3K27ac Chromatin IP

value: H3K27ac (Abcam, ab4729)


title: 8946-H3K4me1_ChIP

source_name: 8946: H3K4me1 Chromatin IP

value: H3K4me1 (Abcam, ab8895)


title: R1

description: mRNA


title: R07

description: total RNA

value: RIP of total RNA


title: 8946-Input-2

value: 8946 cells - HA-Zmiz1/ DEGFDLNRDP


title: 8946-ICN1-2_ChIP

source_name: 8946: ICN1 Chromatin IP

value: ICN1 (Cell Signaling Technology, 4147s)


title: 8946-Rbpj_ChIP

source_name: 8946: Rbpj Chromatin IP

value: Rbpj (Cell Signaling Technology, 5313)


title: RE_3+TEX

value: TEX treament

value: maize root exudates (RE)

value: early stationary phase (#3)


title: F23

description: total RNA

source_name: Inflorescence

value: Flower


title: F1

description: mRNA


title: Root_rep1

description: total RNA

value: total RNA-Seq

value: as Input for RIP


title: 8946-ICN1-1_ChIP


title: 8946-Zmiz1-2_ChIP

source_name: 8946: HA-Zmiz1 Chromatin IP

value: HA (Abcam, ab9110)


title: Flower_rep1

description: total RNA


title: Leaf_rep1

description: total RNA

value: Leaf at flowering


title: zhwRoot8CK

description: mRNA

value: Root at flowering

value: mRNA-Seq


title: 8946-Zmiz1-1_ChIP

source_name: 8946: Flag-Zmiz1 Chromatin IP

value: 8946 cells - Flag-Zmiz1/ L1601PDP

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte

value: Flag (F1804, Sigma)


title: Flower_rep2

description: total RNA


title: LE03

description: total RNA

value: RIP of total RNA


title: zhwF15_input

description: mRNA


title: zhwLD24

description: mRNA


title: 8946 - Notch1+Zmiz1 - 2

data_processing:
FastQC version 0.10.0 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (UCSC mm10) (http://genome.ucsc.edu/) using TopHat (version 2.0.9) and Bowtie (version 2.1.0.0). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation and differential expression analysis, using UCSC mm10.fa as the reference genome sequence and UCSC mm10.gtf as the reference transcriptome annotation. Thsi analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5. Genes and isoforms were annotated with NCBI Entrez GeneIDs, text description, and Gene Ontology (GO) (http://david.abcc.ncifcrf.gov/) terms using NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Fpkm data

source_name: RNA

extract_protocol:
Whole RNA was extracted from 5 million cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
Sequencing libraries were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002)

treatment_protocol: 8946 cells were retrovirally co-transduced with empty MigR1 vector or L1601P-IRES-GFP and empty NGFR vector or Zmiz1-IRES-NGFR and sorted for GFP+/NGFR+ cells.


title: 8946-H3K27me3_ChIP

source_name: 8946: H3K27me3 Chromatin IP

value: H3K27me3 (Millipore #07-449)


title: zhwRoot8

description: total RNA


title: zhwF15

description: total RNA


title: 8946 - Notch1+Zmiz1 - 1


title: 8946 - Notch1 - 2


title: zhwA01

description: total RNA


title: 8946 - Notch1 - 3


title: 8946 - Zmiz1 - 3


title: 8946 - Zmiz1 - 2


title: 8946 - Notch1+Zmiz1 - 3


title: 8946 - Zmiz1 - 1


title: 8946 - Notch1 - 1


title: mRNA18_Mxn3, Mid log phase, Xylan carbon source

city: Urbana

first: Christopher

middle: John

last: Fields

state: IL

address: 1206 W. Gregory Dr.

department: Carver Biotechnology Center

institute: University of Illinois Urbana-Champaign

data_processing:
Illumina Casava1.8 software used for basecalling.
Quality filtering and adapter trimming were performed with Trimmomatic v0.30 using Illumina TruSeq3 adapter sequences for adapter clipping.
The B. xylanisolvens XB1A genome (GenBank accession NC_021017.1) was indexed using novoindex v1.0, and reads aligned with novoalign v. 3.00.05 (http://www.novocraft.com) against the indexed genome. For downstream gene expression analysis only the aligned R1 reads were used; these were extracted from the paired-end alignment file using samtools v0.1.19 using the bitwise flag for the first read for a read pair.  Read counts were
Gene counts were determined for the aligned data using featureCounts v. 1.4.3-p1 and the NCBI GFF3 feature file  (obtained from the NCBI FTP site Dec. 2013).
Differential gene expression was performed using R 3.0.0 using edgeR/limma. Samples were assessed for potential outliers based on counts using normalized counts (RPKM) that would affect downstream analyses. From this analysis we determined that samples mRNA1, 2, 3, 7 and 10 were problematic and thus removed them from the analysis. Counts per million (CPM) mapped reads were calculated per gene; genes with more 1 CPM in three or more samples were retained in the final edgeR analysis.  Samples were normalized using edgeR’s TMM normalization. A simple generalized linear model was generated using the aforementioned filtered data from all remaining samples, and simple contrasts based on carbon source and growth stage were used to determine genes differentially expressed under the conditions shown.
Genome_build: B. xylanisolvens XB1A genome (GenBank accession NC_021017.1)
Supplementary_files_format_and_content: tab-delimited text, gene counts

organism: Bacteroides xylanisolvens

source_name: Xylan_mid-log phase_whole cell

growth_protocol: B. xylanisolvens XB1AT (DSM 18836T) was grown anaerobically at 37°C in a complex medium containing clarified rumen fluid [33] and 5g/L of of polysaccharide (citrus peel pectin from Fluka, France; apple pectin from Sigma-Aldrich, France;  oat-spelt xylan from Serva, France; washed twice in distilled water and autoclaved to remove free sugars) or sugars (glucose or xylose). The media were prepared, dispensed and inoculated by using strictly anaerobic techniques in Balch tubes. A 2.5% (v/v) inoculum of culture pre-adapted on each substrate was used for inoculation. Bacterial growth was followed by optical density of the culture at 600 nm (OD600nm) recorded directly in Balch tubes using a Jenway 6320D spectrophotometer. Three independent cultures were performed for each substrate condition for subsequent transcriptomic analyses

extract_protocol:
Total RNAs were isolated from cultures harvested at mid- and late-log phase using a modified guanidinium–phenol–chloroform procedure previously described for rumen fluid. Briefly, bacterial cultures (4 tubes x 8 ml) were centrifuged for 15 min at 3,000 g at 4 °C. The pellets were resuspended in 9 ml of a RNA-E solution containing solution D [39], water saturated phenol, sodium acetate 0.2 M pH 4.0 and 2-mercaptoethanol (1:1:0.1:0.007). Cells were then disrupted by bead beating for 1 min with 0.1 g zirconia beads (0.1 mm) followed by a 2-min incubation at 60 °C. These two steps were then repeated once. After addition of 3.75 ml of chloroform, the samples were briefly mixed, incubated for 15 min on ice and centrifuged (12,000 g, 20 min, 10 °C). The RNAs contained in the aqueous supernatants (approximately 6 ml) were precipitated with 0.25 volume isopropanol and washed with 1 volume 75% cold ethanol in DEPC-treated water. Total RNAs were solubilized in 100 µl of DEPC-treated water. Genomic DNA was removed using the Turbo DNA-Free DNAse (Ambion, France) for 30 min at 37°C. RNAs were quantified using a ND-2000 NanoDrop spectrophotometer (Nanodrop Technologies, France).
Enriched fractions of mRNAs were prepared using the MicrobExpress™ Bacterial mRNA Purification kit (Ambion, France). The high RNA quality and the reduction in 16S and 23S rRNA in enriched fractions of mRNAs were confirmed using an Agilent 2100 Bioanalyser (Agilent technologies, France).  cDNA libraries were prepared with 100ng of mRNA-enriched fractions following the protocols of the Illumina TruSeq Stranded RNA-seq Sample Preparation Kit. The final libraries had an average fragment size of ∼250 bp and were quantified by qPCR before being sequenced with an Illumina HiSeq 2000 instrument on a single lane in paired end reads

tag: strain

value: XB1AT; DSM 18836T

tag: carbon source

value: Xylan

tag: growth phase

value: mid-log phase


title: 3CIP

city: Durham

first: Jeff

last: Blackinton

state: NC

address: 207 Research Dr Rm 412

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Tophat2
htseq-count
edgeR
Genome_build: hg19
Supplementary_files_format_and_content: excel spreadsheet with RPM means and SD at each time point

organism: Homo sapiens

source_name: Jurkat T cells

growth_protocol: grown in RPMI1640

extract_protocol:
Trizol extraction, separation of 4sU labeled mRNA using biotin-HPDP followed by strepatividin magnetic bead pulldown
Epicentre ScriptSeq kit following RiboZero depletion

treatment_protocol: plated at 10^6 cells/ml and treated with 0.5 μg/ml PMA and 2 μg/ml PHA

tag: treatment

value: 3 hours

value: 4sU-labeled RNA

value: Jurkat


title: 2CIP

value: 2 hours


title: 4BIP

value: 4 hours


title: 8946 - control - 2

tag: cell type


title: 4CIP


title: 8946 - control - 1


title: 3AIP


title: 2BIP


title: mRNA16_Mxn1, Mid log phase, Xylan carbon source


title: mRNA17_Mxn2, Mid log phase, Xylan carbon source


title: imecs_ha_chip.wig

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Reads were aligned to the human genome (hg19) with BOWTIE v0.12.8 using  standard-options
Peaks were called and wig-files were produced with MACS-1.4.2
All further analysis were performed in R or Bedtools
Genome_build: hg19
Supplementary_files_format_and_content: MACS output files in bed format are provided.

source_name: wig

extract_protocol:
Cells were crosslinked with 1% formaldehyde at 37°C for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments at nucleosomal size. Chromatin bound to target proteins (HA-tag) was precipitated by incubation with Protein A dynabeads beads overnight. After several washings chromatin was eluted with 1 % SDS and  crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction and enrichments were checked by qPCR.
Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired,  A-tailed  and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles.

tag: generation of cells

value: primary breast epithelial cells

value: HA (Abcam ab 9110)

tag: construct

value: pRRL-MYC-HA


title: mRNA21_Mcp3, Mid log phase, Citrus Pectin carbon source

source_name: Citrus Pectin_mid-log phase_whole cell

value: Citrus Pectin


title: 2AIP


title: imecs_input.wig


title: mRNA20_Mcp2, Mid log phase, Citrus Pectin carbon source


title: 1CIP

value: 1 hour


title: 4AIP


title: mRNA19_Mcp1, Mid log phase, Citrus Pectin carbon source


title: mRNA24_MG3, Mid log phase, Glucose carbon source

source_name: Glucose_mid-log phase_whole cell

value: Glucose


title: rep2_imecs_vector_dox

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Reads were aligned to the human genome (hg19) with BOWTIE v0.12.8 using  standard-options
Differential expression and statistical inference was done using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: The txt-file contains a table showing the differential expression (as log FoldChange) of ensemble annotated genes (ensemble gene ids, in rows) between samples (=experimental conditions) and the calculated p-value and adjusted p-value for each FoldChange.

source_name: IMEC cell line

growth_protocol: IMEC cell lines were grown in DMEM/F-12 with appropriate supplements. HMLE cells were kept in MEGM medium.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion 48 h after transfection. Poly-A RNA was isolated from total RNA using the NEBNext Poly(A)mRNA Magnetic Isolation Module (E7490).
Libraries for the RNA-seq samples were constructed using the NEBNext Library Prep Kit (6100) following the instruction manual. Briefly, poly-A RNA was fragmented to generate 200 nucleotides long fragments. First and second strand cDNA synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBNext adaptors. The cDNA was size selected using agarose gels and amplified by PCR. For the resulting RNA-seq libraries, amplicon sizes and quantities were determined using the Biorad Experion system. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacture’s instructions.

treatment_protocol: Cell were infected with the indicated doxycycline-inducible constructs and treated with Dox or EtOH as solvent control. HMLE cells were additionally sorted according to CD44 & Cd24 surface markers.

tag: facs sorting

value: Unsorted

tag: infected construct

value: pInducer21 empty

tag: etoh/dox treatment

value: Dox

tag: replicates


title: 3BIP

tag: cell line


title: rep2_imecs_myc_dox


title: 1AIP


title: UBIP

value: Unactivated


title: mRNA22_MG1, Mid log phase, Glucose carbon source

value: XB1AT; DSM 18836T


title: rep1_imecs_vector_dox


title: mRNA23_MG2, Mid log phase, Glucose carbon source

value: mid-log phase


title: UAIP


title: rep1_imecs_myc_dox


title: UCIP


title: mRNA15, Late log phase, Xylose carbon source

source_name: Xylose_late-log phase_whole cell

value: Xylose

value: late-log phase


title: 4CT

value: total RNA

value: Jurkat


title: rep2_cd44low_dox

description: cd44high_dox_vs_etoh.txt and cd44high_etoh_vs_cd44low_etoh.txt

source_name: Sorted HMLE cell line


title: rep2_cd44low_etoh

value: EtOH


title: 4AT

value: 4 hours


title: rep2_cd44high_etoh


title: 4BT


title: rep2_cd44high_dox


title: mRNA13, Late log phase, Xylose carbon source


title: mRNA3, Late log phase, Xylan carbon source

source_name: Xylan_late-log phase_whole cell

value: Xylan


title: patient3_metastasis

city: Dublin

first: Leonie

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

data_processing:
Using default parameters, TopHat v1.4.1 was used to align the reads from our patient samples to the hg19 genome.
The reads were quantified into gene counts by using HT‐Seq v0.5.3 ("htseq-count -q --mode=intersection-nonempty --stranded=no").
Genome_build: hg19
Supplementary_files_format_and_content: The all_counts file contains the gene abundance measurements from using HT-seq v0.5.3.

source_name: Liver Metastasis Tumour

extract_protocol:
RNA isolation was performed with High Pure FFPE RNA Micro Kit (Roche) and subjected to duplex specific thermostable nuclease (DSN) treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following ethical approval, formalin fixed paraffin embedded (FFPE) tumour samples were macrodissected to select regions with >70% tumour cells. Insufficient RNA was obtained from the nodal sample of patient 1 for sequencing. All other patient samples were RNA-sequenced.

tag: tissue

value: metastasis tumour

tag: disease state

value: Post-treatment metastasis


title: rep1_cd44low_etoh


title: mRNA2, Late log phase, Xylan carbon source


title: 3BT

value: 3 hours

tag: sample type


title: mRNA1, Late log phase, Xylan carbon source


title: patient2_metastasis


title: 3AT


title: patient1_metastasis


title: mRNA12, Late log phase, Glucose carbon source

source_name: Glucose_late-log phase_whole cell

value: Glucose


title: rep1_cd44low_dox


title: patient3_nodal

source_name: Adjacent Nodal Tumour

value: nodal tumour

value: Untreated


title: rep1_cd44high_dox

value: Dox


title: 2CT

value: 2 hours


title: mRNA10, Late log phase, Glucose carbon source

value: XB1AT; DSM 18836T


title: mRNA14, Late log phase, Xylose carbon source


title: rep1_cd44high_etoh


title: mRNA11, Late log phase, Glucose carbon source


title: 2AT


title: patient2_nodal


title: mRNA6, Late log phase, Citrus Pectin carbon source

source_name: Citrus Pectin_late-log phase_whole cell

value: Citrus Pectin


title: mRNA5, Late log phase, Citrus Pectin carbon source


title: patient3_primary

source_name: Primary Breast Tumour

value: primary tumour


title: 1CT

value: 1 hour


title: patient2_primary


title: 3CT

value: total RNA


title: 1AT

value: Jurkat


title: UCT

value: Unactivated


title: patient1_primary


title: mRNA9, Late log phase, Apple Pectin carbon source

source_name: Apple Pectin_late-log phase_whole cell

value: Apple Pectin

value: late-log phase


title: UBT


title: mRNA8, Late log phase, Apple Pectin carbon source


title: UAT


title: mRNA7, Late log phase, Apple Pectin carbon source


title: 2BT


title: Exp016-3_H3K27me3_30u_Ad_BC12_Pfeiffer_GSK126

status: Public on Oct 27 2015

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description:
Mint-ChIP
This sample is missing processed data because the data was not processed beyond alignment (bam). The number of reads was simply used to generate figures for the manuscript.

data_processing:
Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.

source_name: Pfeiffer

growth_protocol: K562 cells and mouse YAC-1 cells were cultured in RPMI with 10% FCS, penicillin-streptomycin and L-glutamine. Pfeiffer, SKM-1 and Toledo were cultured in RPMI with 20% FCS, penicillin-streptomycin, L-glutamine and β-mercaptoethanol (3.5 µl in 1000 ml).

extract_protocol:
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Mint-ChIP: In vitro transcription, reverse transcription, PCR (see manuscript).

treatment_protocol: K562 cells were treated for 48 hours with C646 (25 µM), 48 hours with GSK126 (2 µM), or 96 hours with KDM5-C70 (5 µM). Pfeiffer, SKM-1 and Toledo were treated for 72 hours with GSK126 (1 µM).

tag: experiment

tag: histone modification

tag: mnase units


title: Exp016-3_H3K27me3_30u_Ad_BC11_Pfeiffer_GSK126


title: mRNA4, Late log phase, Citrus Pectin carbon source

tag: strain

tag: carbon source


title: Exp016-3_H3K27me3_30u_Ad_BC10_Pfeiffer_DMSO

tag: treatment

value: DMSO


title: 10A-P2

city: guangzhou

first: fei meng

last: zheng

state: guangdong

address: dongfeng East Road No. 651,yuexiu District

institute: Sun Yat-sen university cancer center

data_processing:
RTA(Real Time Analysis) 1.12 software used for basecalling.
The following reads(ie. tags) will be filtered:  tags with only adaptor; tags with unknown base
map the clean tags to reference(hg19) by using pattern matching with no more than 1 mismatch
The TPM(Transcripts per million) of each gene was computed with the following formula: TPM=the tag copy number * 1M /the total tags copy number
Genome_build: hg19
Supplementary_files_format_and_content: The content of each column in gene expression files:column 1, ID of gene; column 2,raw expression of gene(ie. The tag number of all tags in this gene); column 3, TPM(Transcripts per million) of gene; column 4,Gene Symbol; column 5, the mapped tag sequence;  column 6, The Nth "CATG" site from 3'end of gene; column 7, the tag copy number; column 8, TPM of tag; The remaining columns refer to column 6-8, if there are more columns.

source_name: MCF-10A cells

growth_protocol: MCF-10A cells overexpressed AURKA or the empty vector were cultured in the standard medium for MCF-10A as recommended by ATCC.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies) according to the manufacturer's protocol.
Extract 6 µg total RNA, use Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize the first and second-strand cDNA.The bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library.

tag: cell type

value: Epithelial cell

tag: overexpression

value: Breast


title: Exp016-3_H3K27me3_30u_Ad_BC09_Pfeiffer_DMSO


title: Exp016-3_H3K27me3_30u_Ad_BC07_Toledo_GSK126

source_name: Toledo


title: Exp016-3_H3K27me3_30u_Ad_BC06_Toledo_DMSO


title: Exp016-3_H3K27me3_30u_Ad_BC05_Toledo_DMSO


title: 10A-A2 AURKA

value: AURKA


title: Exp016-3_H3K27me3_30u_Ad_BC04_SKM1_GSK126


title: Exp016-3_H3K27me3_30u_Ad_BC02_SKM1_DMSO


title: Exp016-3_H3K27me3_30u_Ad_BC03_SKM1_GSK126


title: Exp016-3_H3K27me3_30u_Ad_BC01_SKM1_DMSO


title: Exp016-3_H3K27me3_150u_Ad_BC12_SKM1_DMSO


title: Exp016-3_H3K27me3_150u_Ad_BC09_SKM1_GSK126


title: Exp016-3_H3K27me3_150u_Ad_BC08_Toledo_DMSO


title: Exp016-3_H3K27me3_150u_Ad_BC10_SKM1_GSK126


title: Exp016-3_H3K27me3_150u_Ad_BC06_Toledo_GSK126


title: Exp016-3_H3K27me3_150u_Ad_BC07_Toledo_DMSO


title: Exp016-3_H3K27me3_150u_Ad_BC04_Pfeiffer_DMSO


title: Exp016-3_H3K27ac_30u_Ad_BC10_Pfeiffer_DMSO


title: Exp016-3_H3K27ac_30u_Ad_BC11_Pfeiffer_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC08_Toledo_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC12_Pfeiffer_GSK126


title: Exp016-3_H3K27me3_150u_Ad_BC02_Pfeiffer_GSK126


title: Exp016-3_H3K27me3_150u_Ad_BC01_Pfeiffer_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC09_Pfeiffer_DMSO


title: Exp016-3_H3K27ac_30u_Ad_BC07_Toledo_GSK126


title: Exp016-3_H3K27me3_30u_Ad_BC08_Toledo_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC05_Toledo_DMSO


title: Exp016-3_H3K27ac_30u_Ad_BC04_SKM1_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC03_SKM1_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC06_Toledo_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC09_SKM1_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC01_SKM1_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC08_Toledo_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC05_Toledo_GSK126


title: Exp016-3_H3K27ac_150u_Ad_BC12_SKM1_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC07_Toledo_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC06_Toledo_GSK126


title: Exp016-3_H3K27ac_150u_Ad_BC10_SKM1_GSK126


title: Exp016-3_H3K27ac_30u_Ad_BC02_SKM1_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC04_Pfeiffer_DMSO


title: Exp016-3_H3K27me3_150u_Ad_BC05_Toledo_GSK126


title: Exp016-3_H3K27ac_150u_Ad_BC03_Pfeiffer_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC11_SKM1_DMSO


title: Exp016-3_H3_30u_Ad_BC11_Pfeiffer_GSK126


title: Exp016-3_H3K27me3_150u_Ad_BC11_SKM1_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC01_Pfeiffer_GSK126


title: Exp016-3_H3_30u_Ad_BC12_Pfeiffer_GSK126


title: Exp016-3_H3_30u_Ad_BC09_Pfeiffer_DMSO


title: Exp016-3_H3_30u_Ad_BC07_Toledo_GSK126


title: Exp016-3_H3_30u_Ad_BC10_Pfeiffer_DMSO


title: Exp016-3_H3_30u_Ad_BC06_Toledo_DMSO


title: Exp016-3_H3_30u_Ad_BC08_Toledo_GSK126


title: Exp016-3_H3_30u_Ad_BC05_Toledo_DMSO


title: Exp016-3_H3_150u_Ad_BC11_SKM1_DMSO


title: Exp016-3_H3_150u_Ad_BC07_Toledo_DMSO


title: Exp016-3_H3K27ac_150u_Ad_BC02_Pfeiffer_GSK126


title: Exp016-3_H3_30u_Ad_BC02_SKM1_DMSO


title: Exp016-3_H3_150u_Ad_BC04_Pfeiffer_DMSO


title: Exp016-3_H3_150u_Ad_BC06_Toledo_GSK126


title: Exp016-3_H3_150u_Ad_BC02_Pfeiffer_GSK126


title: Exp016-3_H3_150u_Ad_BC05_Toledo_GSK126


title: Exp016-3_H3_150u_Ad_BC12_SKM1_DMSO


title: Exp016-3_H3_30u_Ad_BC01_SKM1_DMSO


title: Exp016-3_H3_150u_Ad_BC08_Toledo_DMSO


title: Exp016-3_H3K27me3_150u_Ad_BC03_Pfeiffer_DMSO


title: Exp016-3_H3_150u_Ad_BC10_SKM1_GSK126


title: Exp016-3_H3_150u_Ad_BC03_Pfeiffer_DMSO


title: Exp016-3_H3_150u_Ad_BC01_Pfeiffer_GSK126


title: Exp015-2_H3K4me3_80000c_Ad_BC07_30u

description: Mint-ChIP

tag: cell number


title: Exp016-3_H3_30u_Ad_BC04_SKM1_GSK126


title: Exp016-3_H3_30u_Ad_BC03_SKM1_GSK126


title: Exp016-3_H3_150u_Ad_BC09_SKM1_GSK126


title: Exp015-2_H3K4me3_500c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K4me3_500c_Ad_BC01_300u

description: Mint-ChIP


title: 8946 - control - 3

source_name: RNA

tag: disease

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte


title: Exp015-2_H3K4me3_80000c_Ad_BC05_150u

description: Mint-ChIP


title: Exp015-2_H3K4me3_500c_Ad_BC05_150u

description: Mint-ChIP


title: Exp015-2_H3K4me3_5000c_Ad_BC08_15u

description: Mint-ChIP


title: Exp015-2_H3K4me3_80000c_Ad_BC01_300u

description: Mint-ChIP


title: Exp015-2_H3K4me3_500c_Ad_BC07_30u

description: Mint-ChIP


title: Exp015-2_H3K4me3_80000c_Ad_BC08_15u

description: Mint-ChIP


title: Exp015-2_H3K4me3_5000c_Ad_BC07_30u

description: Mint-ChIP


title: Exp015-2_H3K4me3_5000c_Ad_BC01_300u

description: Mint-ChIP


title: Exp015-2_H3K4me3_1000c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K4me3_1000c_Ad_BC05_150u

description: Mint-ChIP