title: hsa_ControlKBC12_RNASeq

city: Corvallis

first: David

middle: Anthony

last: Hendrix

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

description: RNA-Seq collected from human cerebral aneurysm tissue. RNA was harvested from patient samples using mirVana miRNA isolation kit, allowing total RNA to be isolated containing the miRNA population.

data_processing:
Reads were sequenced on the IonTorrent Proton
RNA quality and quantity were assessed by Fragment Analyzer (Advanced Analytical, Ames, IA) and Qubit (Invitrogen, Carlsbad, CA), respectively.
Reads were trimmed as part of the IonTorrent pipeline.
RNA-Seq fastq files were aligned to the iGenomes bowtie2 index for hg19 using TopHat v2.0.9, using the iGenomes gtf file for human ENSEMBL genes, and --no-novel-juncs and --no-coverage-search
Differential expression was measured with cuffdiff v2.2.1 with default parameters, and using the reference transcriptome GTF file from iGenome for hg19.
Genome_build: hg19
Supplementary_files_format_and_content: Computed with Cuffdiff v2.2.1 with default parameters, and using the reference transcriptome GTF file from iGenome.

source_name: human superficial temporal artery tissue

extract_protocol:
RNA-Seq collected from human cerebral aneurysm tissue. RNA was harvested from patient samples using mirVana miRNA isolation kit, allowing total RNA to be isolated containing the miRNA population
RNA was fragmented prior to adaptor ligation, reverse transcription was performed, and the resulting cDNA was purified and amplified.

tag: subject status

value: patients undergoing craniotomy for cerebral aneurysms

tag: subject/sample id


title: hsa_ControlKBC15_RNASeq

status: Public on Feb 24 2016

type: SRA

state: OR

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: human superficial temporal artery tissue


title: hsa_ControlKBC14_R2_RNASeq


title: hsa_ControlKBC8_RNASeq


title: hsa_ControlKBC11_RNASeq


title: hsa_ControlKBC13_RNASeq


title: hsa_ControlKBC16_RNASeq


title: hsa_ControlKBC7_R2_RNASeq


title: Het (Q92) 6 months Female Liver mRNA rep2 398901_71381_1_L3.D703

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl R.75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

organism: Mus musculus

source_name: Liver

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Liver

tag: genotype

value: Het (Q92) Knock-In

tag: age

value: 6 months

tag: Sex

value: Female

tag: housing condition

value: housed with Het (Q92) mice


title: hsa_ControlKBC3_RNASeq


title: hsa_ControlKBC14_R1_RNASeq


title: hsa_ControlKBC7_R1_RNASeq


title: hsa_ControlKBC10_RNASeq


title: hsa_BrainAneurysmKB3_RNASeq

source_name: human cerebral aneurysm tissue

value: human cerebral aneurysm tissue


title: hsa_BrainAneurysmKB20_RNASeq


title: hsa_BrainAneurysmKB7_RNASeq


title: hsa_BrainAneurysmKB5_RNASeq


title: hsa_BrainAneurysmKB6_RNASeq


title: Smad23_ChIP_Vector_TGFb_KSIC_c806

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake University

description:
ChIP DNA
ChIP-Seq

library_source: genomic

data_processing:
Sequencing data quality control: reads pairs in FASTQ format (50bp/50bp or 75bp/75bp) were quality assessed by FastQC v0.11.3 for sequencing integrity and completeness
Read mapping: RNA-Seq reads were mapped to mouse genome mm10 (GRCm38, Dec/2011) with STAR2.3.0e using standard settings for paired reads. In average 82% of raw reads were uniquely mapped. For ChIP-Seq, single-end (50bp) FASTQ reads were mapped to mouse genome  mm10 (GRCm38, Dec/2011) with Bowtie2 with default filtering criteria. Resulted SAM files were converted to BAM files though Samtools 0.1.19. BAM files were sorted and indexed with Samtools.
RNA-Seq read counting: Uniquely mapped reads were counted to each gene with HTSeq v0.5.4 with default settings.
RNA-Seq data normalization and differential expression analysis: Read counts were normalized by library size through the “DESeq2” package deposited in Bioconductor. Differential gene expression analysis between any two conditions was perform based on a model utilizing the negative binomial distribution.
ChIP-Seq data visualization: To visualize ChIP-Seq data, BAM files were converted to TDF file by IGV Tools 2.3.32 using the command “igvtools count -z 5 -w 25 -e 250”, specifying the coverage window size to be 25bp and average fragment size of 250bp.
Genome_build: mm10, GRCm38, Dec/2011
Supplementary_files_format_and_content: TDF files are contain whole-genome coverage data for eac ChIP-Seq sample. This file data can be loaded to IGV genome browser and visualize ChIP-Seq peak distribution.
Supplementary_files_format_and_content: Txt files contain raw read counts or normalized read counts of each gene in each sample from RNA-Seq experiments. Normalized read count table is derived by sequencing library size normalization.

molecule: genomic DNA

source_name: mouse pancreatic cancer cell line

growth_protocol: For Smad2/3, Klf5 and Sox4 ChIP-seq experiments, and all RNA-seq experiments, cells were grown in 2-dimensional culture in DMEM supplemented with 10% FBS, For Med1 ChIP-seq, cells were cultured as oncospheres in DMEM/F12 supplemented with B-27.

extract_protocol:
For RNA-Seq samples,  ~1 million cells were collected at the indicated time point and extracted with PrepEase RNA spin kit (Affymetrix). For ChIP-Seq sample preparation, PDA cells are treated  as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis.
For RNA-Seq library construction, total RNA purified from mES and mEB was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000. 500ng RNA with integrity number (RIN) > 9.5 from each sample was used for library construction with TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions.  For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Ribogreen and Agilent Bioanalyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.
Multiplexed sequencing libraries were ran on a Hiseq2500 platform and more than 40million raw paired-end reads were generated for each sample.

treatment_protocol: RNA-seq for Smad4 restored samples was performed in serum-starved cells treated with either 2.5 μM SB505124 (Sigma S4696) for 2h or 100 pM recombinant TGFβ1 (R&D Systems) for 90 minutes prior to RNA extraction. Smad2/3 ChIP-seq was performed after 90 minutes of treatment with 100 pM recombinant TGFβ1 (R&D Systems). For Sox4 dependent genes, Smad4-restored cells bearing a dox-inducible Sox4 shRNA were treated  +/- 1 μg/ml doxycline for 24h, then pre-treated with Akt inhibitor MK2206 (2.5 μM) for 1.5 hours, followed by either 2.5 μM SB505124 (Sigma S4696) or 100 pM recombinant TGFβ1 (R&D Systems) for 24h prior to RNA extraction.

tag: cell line

tag: genetic background

value: FVB

tag: antibody

tag: vendor

value: Cell Signaling

tag: catalog #

tag: lot#


title: Smad23_ChIP_Smad4RE_TGFb_KSIC_c806

description:
ChIP DNA
ChIP-Seq

value: KSIC_c806 + Smad4


title: Het (Q92) 6 months Female Liver mRNA rep3 398904_71457_1_L3.D706


title: Med1_ChIP_KSIC_c806

description:
ChIP DNA
ChIP-Seq

value: Bethyl


title: Sox4_ChIP_KSIC_c806

description:
ChIP DNA
ChIP-Seq

value: Diagenode


title: Vector_TGFb_rep2_KSIC_c806

description:
RNA
RNASeq_KSIC_c806_TGFb_response_Smad4Restore_count.table.txt
RNA-Seq


title: Vector_TGFb_rep1_KSIC_c806


title: Input_KSIC_c806

description:
Sonicated chromatin DNA
ChIP-Seq


title: Vector_SB505124_rep2_KSIC_c806


title: Vector_SB505124_rep1_KSIC_c806


title: hsa_BrainAneurysmKB8_RNASeq


title: Smad4RE_TGFb_rep2_KSIC_c806


title: PlusDox_TGFb_rep2_KSIC_c806_TetON_shSox4

description:
RNA
RNASeq_KSIC_c806_TetON_shSox4.normalized.count.table.txt
RNA-Seq


title: PlusDox_TGFb_rep1_KSIC_c806_TetON_shSox4


title: Smad4RE_TGFb_rep1_KSIC_c806


title: Smad4RE_SB505124_rep2_KSIC_c806


title: MinusDox_SB431542_rep2_KSIC_c806_TetON_shSox4


title: Smad4RE_SB505124_rep1_KSIC_c806


title: ASK10M475R 2

city: Jinan

first: Chunlei

last: JIAO

state: Shandong

address: 27 Shanda nan Road

department: School of Life Science

institute: Shandong University

data_processing:
Filtering raw data and quality control
Alignment/mapping of reads to reference using  BWA and Bowtie.
Screening of differentially expressed genes using DEGs

organism: Saccharomyces cerevisiae

growth_protocol: The cells were

extract_protocol:
Total RNA was extracted using UNIQ-10 Trizol RNA Purification Kit (Sangon Biotech, China)
mRNA was isolated and fragmented and cDNA was synthesized using the mRNA fragments as templates. The short fragments are connected with adapters, and suitable fragments are selected for the PCR amplification

tag: genotype/variation

tag: media

value: Sc-ura+20g/l Glucose


title: PlusDox_SB431542_rep1_KSIC_c806_TetON_shSox4


title: PlusDox_SB431542_rep2_KSIC_c806_TetON_shSox4


title: ASK10WT 2

source_name: ASK10 wild-type

value: ASK10 wild-type


title: ASK10WT 1


title: ask10Δ 1

source_name: ask10 del

value: ask10 del


title: ask10Δ 2


title: Klf5_ChIP_KSIC_c806

description:
ChIP DNA
ChIP-Seq

value: Abcam


title: Islet_B10.Rag-/-_#3

status: Public on Feb 23 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Sequenced reads were trimmed for quality (Q > 20, fastx toolkit), adaptor sequence (cutadapt), and filtered for low-quality sequence, low-complexity and illumina internal control phiX. Then mapped to the mouse GRCm38.73 whole genome (downloaded from ensembl) using tophat v2.0.8b with parameters --library-type fr-unstranded --min-intron-length 50 --max-intron-length 500000 --no-coverage-search --no-mixed --read-realign-edit-dist 3
The number of reads mapping to each Ensembl gene was counted with htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count; parameters: union and reverse stranded). Non-normalized counts used for a DESeq analysis.
Genome_build: GRCm38.73
Supplementary_files_format_and_content: htseq-count-table.txt contains non-normalized read counts assigned to genes.

source_name: isolated pancreatic islets

growth_protocol: Islets were suspended with 1mL Trizol (Invitrogen) and freezed in -20 degree immediately after isolation.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiangen) following the provided protocol.
RNA libraries were prepared for sequencing using Illumina Truseq Stranded mRNA library prep (versie 15031047_D)

treatment_protocol: Pancreata were digested by 0.8mg/mL collagenase NB 8 (Serva/Bio Connect) at 37 degree for 15 minutes. Digested pancreatic tissue were washed once with 20mL HBSS and re-suspend in 28% Dextron T70 solution. Islets were purified by Dextron T70 density gradient centrifugation (25.7%, 22.4%, 12.3%) and picked out under microscope. α-Amanitin(2μg/mL, Sigma) and Actinomycin D (5μg/mL, Sigma) were added to collagens NB 8 and HBSS solution used for isolation. Picked islets were washed once with 1mL HBSS.

tag: gender

value: male

value: 11 weeks

value: pancreatic islet

tag: haplotype

value: MHC k

value: Rag-/-

tag: phenotype

value: normoglycemia

tag: total islet number


title: Islet_NOD.Rag-/-_#2

tag: strain

tag: tissue


title: Islet_B10.Rag-/-_#1

tag: age


title: Islet_NOD.Rag-/-_#3


title: Islet_B10.Rag-/-.insHEL_#3


title: Islet_NOD.Rag-/-.insHEL_#3


title: Islet_B10.Rag-/-.insHEL_#2


title: MinusDox_TGFb_rep1_KSIC_c806_TetON_shSox4

tag: genotype


title: Islet_NOD.Rag-/-_#1


title: Islet_B10.Rag-/-.insHEL_#1


title: MinusDox_TGFb_rep2_KSIC_c806_TetON_shSox4


title: Islet_NOD.Rag-/-.insHEL_#2


title: Islet_NOD.Rag-/-.insHEL_#1


title: MinusDox_SB431542_rep1_KSIC_c806_TetON_shSox4


title: E24 cDNA sequencing library

city: Wuhan

first: Wankun

last: Deng

state: Not US or Canada

address: Huazhong University of Science and Technology, Wuhan, Hubei, P.R.C.

department: Life Science and Technology

description: Planted in 2000, and opened for tapping in 1995, on the s/2 d/4 system (half spiral tapped every four days) and with 1.5%-ethephon treatment one day before tapping at intervals of 15 days. Bark samples were collected from six trees by tapping at 24 h after 1.5%-ethephon application

data_processing:
De novo sequencing of the transcriptomes of C (bark without ethephon application), E8 (bark with 1.5%-ethephon treatment for 8 hours) and E24 (bark with 1.5%-ethephon treatment for 24 hours) rubber trees was conducted using Illumina HiSeq 2000.
Raw reads produced from sequencing machines were resorted to de novo assembly and gene annotation.

organism: Hevea brasiliensis

extract_protocol: Bark RNA was extracted and three cDNA libraries, C (bark without ethephon application), E8 (bark with 1.5%-ethephon treatment for 8 hours) and E24 (bark with 1.5%-ethephon treatment for 24 hours), were prepared using the mRNA-Seq 8 sample prep Kit (Illumina). . Poly(A) mRNA was first isolated from 20 μg of total RNA using magnetic beads containing poly-T molecules. Then, the purified samples were fragmented into small pieces using divalent cations at 94°C for 5 minutes and reverse transcribed into cDNAs with the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA). Then, end repair and adenylation of 3' ends were conducted and purified using the QIAquick PCR Purification Kit (QIAGEN). After that, Illumina paired end adapters were ligated to the resulting cDNA fragments. Finally, each cDNA library with an insert size of 200 bp was generated. After quality checking by an Agilent Technologies 2100 Bioanalyzer, the libraries were deep sequenced using Illumina HiSeqTM 2000 (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Trees of equal size in the same plot were selected and divided into three groups, each with six trees. Ethephon (2-chloroethane phosphonic acid; 1.5% v/v) was applied using a brush on the tapping panel. Bark samples were collected from two groups by tapping at 8 h and 24 h after ethephon application, respectively. Concurrently, bark was collected from a corresponding group of trees at 8 h after treatment in the same way with water only as control. The samples were immediately frozen in liquid nitrogen and shipped on dry ice to BGI Life Tech Co., Ltd (Shenzhen, China) for Illumina sequencing

tag: line

value: clone PR107

value: bark


title: C cDNA sequencing library

institute: Huazhong University of Science and Technology

description: Planted in 2000, and opened for tapping in 1995, on the s/2 d/4 system (half spiral tapped every four days) and with 1.5%-ethephon treatment one day before tapping at intervals of 15 days. Bark samples were collected from six trees by tapping at 8 h after application with water only as control

source_name: C (bark without ethephon application)


title: E8 cDNA sequencing library

description: Planted in 2000, and opened for tapping in 1995, on the s/2 d/4 system (half spiral tapped every four days) and with 1.5%-ethephon treatment one day before tapping at intervals of 15 days. Bark samples were collected from six trees by tapping at 8 h after 1.5%-ethephon application

source_name: E8 (bark with 1.5%-ethephon treatment for 8 hours)


title: myb-GFP_mcidas_input_9h_rep_1

city: La Jolla

first: Ian

middle: K

last: Quigley

state: CA

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

data_processing:
ChIPseq reads were aligned to X. laevis genome build v9.1 with bwa mem (PMID: 19451168)
Peaks were called against pooled input background with HOMER (PMID: 20513432). Replicates were pooled to generate peakfiles.
Genome_build: X. laevis build v9.1 (http://www.xenbase.org/)
Supplementary_files_format_and_content: Bed files of called peaks

organism: Xenopus laevis

source_name: epithelial progenitors (animal cap)

growth_protocol: Epithelial progenitors (animal caps) were  dissected from embryos at stage 10 were cultured in 0.5x MMR.

extract_protocol:
Embryos were fixed in 1% paraformaldehyde in PBS for 30 minutes at 22 degrees and fix was quenched with 0.125M glycine. ChIPseq was performed as described (PMID: 24934224) with the following antibodies: GFP (Invitrogen catalog no. A11122, lot no. 1296649), FLAG (Sigma, cat #F1804), H3K4me3 (Active Motif, cat #39159; lot #01609004), H3K27ac (Abcam, cat #ab4729, lot #GR71158-2), or rad21 (Abcam, cat #ab992).
Following sonication and immunoprecipitation of genomic fragments, we polished and adenylated ends (NEB End-It and A-tailing modules) and ligated Truseq v2 adapters (Illumina).

treatment_protocol: Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.

tag: ChIP

value: input

tag: harvest time/stage

value: 9h @ 22 deg after mid-11 (stage 18)

tag: injected mrna

value: myb-GFP, mcidas-HGR


title: ASK10M475R 1


title: Islet_B10.Rag-/-_#2


title: MYST5_ChIPseq1

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

data_processing:
Sequence reads were aligned to the Drosophila melanogaster genome (dm3) with Bowtie 0.12.8 using default settings.
log2(MYST5/Input) was calculated using in-house R scripting.
Genome_build: dm3
Supplementary_files_format_and_content: A bed file was generated for log2(MYST5/Input).

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown using standard growth procedures.

extract_protocol:
ChIP of MYST5 from Schneider cells (SL2, S2) was performed as described in Wu CH et al, Genes Dev 17: 1402 (2003).
ChIP samples from two independent MYST5 antibodies and input samples were prepared using the NEXTflex ChIP-Seq Kit.

tag: chipseq antibody

value: rabbit anti MYST5 (1)

tag: technique

value: Shearing technique:Bioruptor

tag: cell line


title: mac_repair2

city: ChongQing

first: Chi

last: Liu

address: TianShen road

institute: SouthWest university Of China

description: Sample 12

data_processing:
Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website (http://www.ensembl.org/index.html).
Reference genome library was built using the Bowtie2 v2.2.3 software, and clean data was aligned to the library using the TopHat v2.0.12 software.
Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software.
Genes with P value<0.05 and |log2 ratio|≥1 were identified as differentially expressed genes using the DESeq (v1.16.0) software.
These data were then subject to GO (gene ontology, http://geneontology.org/) analyses and aligned to KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) database to build pathway maps.
Genome_build: zv9
Supplementary_files_format_and_content: [rpkm.txt] tab-delimited text file includes RPKMs for each Sample
Supplementary_files_format_and_content: [Table s1.xls] foldChange between lesion stages in each cell type

organism: Danio rerio

source_name: mac-repair

extract_protocol:
Focused photoconversions of endothelial end cells or macrophages at three lesion stages (uninjured control, macrophage arrival, and macrophage traction) were achieved by irradiating Tg(flk1:DenNTR; coro1a:eGFP) or Tg(coro1a:Kaeda; flk1:eGFP) transgenic larvae with a 405-nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells (repairing macrophages or endothelial end cells) in twenty animals were photoconverted. After photoconversion, zebrafish heads were dissected, collected, and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then, the supernatant was removed and the cell pellet was resuspended in PBS, followed by cell sorting by flow cytometry (Moflo XDP, Beckman).
cDNA libraries were generated from these sorted cells using the Smart-seq2 protocol.
RNA sequencing was performed using the PE100 strategy (HiSeq 2500, Illumina)

value: ABGO

tag: fluorescence

value: Kaeda(red)

tag: lesion stage

value: macrophage traction

value: brain

tag: cell type

value: Macrophage


title: MYST5_ChIPseq2

value: rabbit anti MYST5 (2)


title: rad21_input_3h_rep_1

value: 3h @ 22 deg after mid-11 (stage 18)


title: myb-GFP_input_9h_rep_1

value: myb-GFP


title: foxj1-FLAG_input_9h_rep_1


title: mac_ab2

description: Sample 10

source_name: mac-ab

value: macrophage arrival


title: mac_con2

description: Sample 11

source_name: mac-con

value: uninjured control


title: histone_input_9h_rep_2


title: EC_con2

description: Sample 8

source_name: EC-con

value: Endothelial cell


title: histone_input_9h_rep_1


title: EC_repair2

description: Sample 9

source_name: EC-repair


title: foxj1-FLAG_rfx2_MO_9h_rep_1

value: foxj1-FLAG, rfx2 morpholino


title: EC_ab1

description: Sample 7

source_name: EC-ab


title: Ec_ab2

description: Sample 6


title: Input


title: foxj1-FLAG_9h_rep_1


title: mac-con1

description: Sample 4


title: mac-ab1

description: Sample 3


title: myb-GFP_mcidas_9h_rep_1


title: mac-repair1

description: Sample 5


title: wt_H3K27ac_ChIPseq_9h_rep_1_and_2


title: EC-repair1

description: Sample 2


title: wt_rad21_3h_rep1

value: 3h @ 22 deg after mid-11 (stage 13)


title: myb-GFP_9h_rep_1

value: 9h @ 22 deg after mid-11 (stage 18)


title: EC-con1

description: Sample 1


title: wt_H3K27ac_ChIPseq_3h_rep_1


title: H3 WT Control (SC H3)

status: Public on Feb 22 2016

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Demultiplexing: data were demultiplexed from the raw reads using Illumina's BCL2Fastq version 2.15.
Alignment: demultiplexed data were aligned to UCSC reference genome build hg19 downloaded from iGenomes. Alignments were generated with Bowtie 2.2.4, allowing for one distinct alignment and one mismatch per seed region (-N1 -K1). All other default parameters were used.
Track creation: reads were counted to 100-bp fixed bins using featureCounts from the Subreads package version 1.4.6-p2. Normalized TPTM was used. Input was subtracted from γH2A.X, while all H3K4me3 tracks had H3 divided to account for the extensive histone loss seen in senescence.
Genome_build: hg19
Supplementary_files_format_and_content: BigWigs: bigWig files represent the distribution of H3K4me3 and gH2A.x genome-wide in 100bp contiguous, non-overlapping bins, weighted per 10 million aligned reads, and adjusted for local sonication efficiency biases by dividing by H3 or subtracting input (also weighted per 10 million aligned reads), respectively. The file H3K4me3-H3.MLL1_KD_OIS-SC_OIS.bw is the subtraction of the OIS scramble control from the OIS MLL1 knockdown track.

source_name: IMR90 Lung Fibroblasts

growth_protocol: IMR90 cells (obtained from Coriell Institute for Medical Research) were grown in DMEM without phenol with 10% FBS and 1% penicillin/streptomycin at 3% oxygen. The cells were generated by retrovirally infecting normal IMR90 fibroblasts with pLNCX-ER:Ras.

extract_protocol:
Cells in 10-cm2 dishes were fixed in 1% formaldehyde for 5 min, and fixation was quenched with addition of glycine to 125 mM for an additional 5 min. Cells were harvested by scraping from plates and were washed twice in 1× PBS before storage at −80°C. ChIP was performed as previously described (Shah et al. 2013) except that extracts were sonicated nine times for 5 min each round (30 sec of sonication with intermediate incubation of 30 sec per round) using a Bioruptor (Diagenode). All ChIPs were performed using 500 µg of extract and 2 µg of antibody per sample. Thirty microliters of Protein G Dynabeads (Invitrogen, 100.02D) was used per ChIP.
ChIP DNA was used to make sequencing libraries using NEBNext (New England Biolabs). Libraries were quantified (Kapa Biosystems), and sequencing was performed on either Hi-Seq or NextSeq platforms (50-bp, single-end reads) (Illumina).

treatment_protocol: Senescence was induced with 4-OHT (Sigma-Aldrich). For the viral transfections, IMR90 fibroblasts were infected with virus (scrambled control (SC) or MLL1 KD shRNA) at 60% confluency on 10-cm2 plates for 24 h in the presence of polybrene. Forty-eight hours following infections, cells underwent selection with puromycin to obtain completely puromycin-resistant cell populations. Senescent cells were maintained in dishes for 10 d to ensure growth termination. Senescence was determined by monitoring CDKN2A/P16 up-regulation and down-regulation of cyclin genes and by SA-β-gal (Chemicon International).

tag: genotype/variation

value: WT

tag: treatment

tag: antibody

value: Abcam, ab1791


title: H3 Mll1 KD OIS (MLL1 KD OIS H3)

value: MLL1 KD

value: 4-OHT induced H-Ras V12


title: H3 WT OIS (SC OIS H3)


title: wt_H3K4me3_ChIPseq_9h_rep_1_and_2


title: H3K4me3 WT OIS (SC OIS H3K4me3)

value: Abcam, ab8580


title: Input WT Control (SC Input)

value: Input


title: Input MLL1 KD OIS (MLL1 KD OIS Input)


title: gH2A.x MLL1 KD OIS (MLL1 KD  OIS gH2A.x)

value: Abcam, ab2893


title: H3K4me3 MLL1 KD OIS (MLL1 KD  OIS H3K4me3)


title: H3K4me3 WT Control (SC H3K4me3)


title: gH2A.x WT Control (SC gH2A.x)


title: RNA MLL1 KD Control

data_processing:
Alignment: data were aligned using RNA STAR version 2.3.0e under default settings, Homo sapiens ENSEMBL release 75.
Expression quantitation: Cufflinks version 2.2.1 was used to map aligned tags to exons and gene features (-G parameter) and tabulate expression scores. All tRNA, rRNA, and mtRNA transcripts, downloaded from the University of California at Santa Cruz (UCSC) goldenPath database, were masked from the counting procedure. The ENSEMBL Homo sapiens release GRCh37.75 was used as the feature table. All other Cufflinks settings were the default parameters.
Track creation: aligned tags were binned in 100bp contiguous, non-overlapping bins and were multiplied by a per-10-million aligned tag adjustment coefficient (reads were counted to 100-bp fixed bins using featureCounts from the Subreads package version 1.4.6-p2).
Genome_build: human ENSEMBL release 75
Supplementary_files_format_and_content: BigWigs: bigWig files represent the accumulation of aligned RNA-seq tags in 100bp bins genome-wide, adjusted per 10 million aligned tags.

molecule: polyA RNA

growth_protocol: IMR90 cells (obtained from Coriell Institute for Medical Research) were grown in DMEM without phenol with 10% FBS and 1% penicillin/streptomycin at 3% oxygen. The cells were generated by retrovirally infecting normal IMR90 fibroblasts with pLNCX-ER:Ras. For the viral transfections, IMR90 fibroblasts were infected with virus (either scrambled control (SC) or MLL1 KD shRNA (MLL1 KD)  at 60% confluency on 10-cm2 plates for 24 h in the presence of polybrene. Forty-eight hours following infections, cells underwent selection with puromycin to obtain completely puromycin-resistant cell populations.

extract_protocol:
RNA was extracted from whole cells using RNeasy kit (Qiagen catalog no. 74014) following the manufacturer's instructions.
Following Poly-A selection, the RNA-seq libraries for the WT (SC), WT OIS (SC OIS), and MLL1 knockdown (Control and OIS) cells were made using a ScriptSeq version 2 RNA-seq library preparation kit from Epicentre (now Illumina).

treatment_protocol: Senescence was induced with 4-OHT (Sigma-Aldrich). Senescent cells were maintained in dishes for 10 d to ensure growth termination. Senescence was determined by monitoring CDKN2A/P16 up-regulation and down-regulation of cyclin genes and by SA-β-gal (Chemicon International).


title: gH2A.x WT OIS (SC OIS gH2A.x)


title: RNA WT OIS


title: RNA WT Control


title: RNA MLL1 KD OIS


title: WT-2

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …

organism: Fusarium graminearum

source_name: Fungi culture

growth_protocol: Each fungal strain was grown in complete medium (CM)  for 24 hour

extract_protocol: Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

value: wild-type strain Z-3639


title: fhs1-2

value: fhs1 deletion mutant


title: WT-3


title: Anther_A2AS_Control_MACE

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

description: OTHER (MACE) Massive Analysis of cDNA ends

data_processing:
FastQC preprocessing
Filtering for sequences shorter than 14bp
MACE reads were aligned using SSAHA2 via the pipeline CRACPipe; kmer 14, skip 1
Data were weighted concerning equal hits and filtered for mapping with a max. of 1 insertion, deletion or mismatches
Genome_build: ITAG2.3
Supplementary_files_format_and_content: comma separated files (csv) representing the Transcript per million (TPM) for the mRNAs.

organism: Solanum lycopersicum

growth_protocol: Wild type and A2AS tomato plants (cv Moneymaker) were grown in a glasshouse under a 16/8h day/night cycle (24-20°C). Young leaves and anthers from different developmental stages were collected from 8-week old plants for transcroptome analysis.

extract_protocol:
Total RNA was extracted using the NucleoSpin® RNA isolation kit (Macherey and Nagel) following the manufacturer’s instructions.
The mRNA was enriched by binding the poly-A-tail at the 3'-end and the last 500 bp were sequenced so that each transcript is represented by one read in the library

treatment_protocol: Eight-week-old wild type and A2AS tomato plants (Solanum lycopersicum cv Moneymaker) grown in a glasshouse under a 16/8h day/night cycle (24-20oC) were transferred to a growth chamber (120 μmol m-2 sec-1 light intensity) and exposed to heat stress conditions for 1 hour at 39oC and then allowed to recover at 24oC for 1.5 h.

value: Anther

tag: stress

value: Control

tag: cultivar

value: Moneymaker


title: fhs1-1


title: Anther_WT_Heatstress_MACE

tag: tissue

value: Heat stress

value: Wild type


title: Anther_A2AS_Heatstress_MACE


title: WT-1


title: Input WT OIS (SC OIS Input)


title: Leaf_A2AS_Heatstress_MACE

value: Leaf


title: Leaf_A2AS_Control_MACE


title: H202 treated 3_RNAseq

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

data_processing:
Sequence quality was assessed using Fastqc QC (v0.5; http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Tophat/Bowtie (v2.0.9; Trapnell C, Pachter L, Salzberg SL 2009) was used to align and distribute Fastq sequence files to the zebrafish genome (Zv9 version 73)
For each sample, transcript abundance (i.e. as read counts per million (CPM)) and differential expression were estimated and queried using Cufflinks/diff (v2.1.1; Trapnell C. et al 2010, http://cufflinks.cbcb.umd.edu/manual.html), where transcripts with an unadjusted p-value < 0.05 was considered statistically significant
Isoforms were appraised and annotated using both tophat/cufflinks/cuffdiff, RSEM and R/edgeR
Genome_build: Intronic and exonic reads were based on collected UCSC, RefSeq refgenes, and Ensembl transcripts (Zv9 version 73) which were downloaded from the UCSC browser (www.ucsc.edu).
Supplementary_files_format_and_content: MS Excel worksheet, logFC, CPM, gene name, Ensembl ID, description

source_name: whole larvae_H2O2

growth_protocol: 28 degree celcius

extract_protocol:
Trizol/Chloroform,  mRNA enriched by biotin-tagged poly dT oligonucleotides and streptavidin-coated magnetic beads
To generate the library, the ends of the fragmented cDNA were converted into phosphorylated blunt ends. An ‘A’ base was added to the 3' ends and Illumina®-specific adaptors were ligated to the cDNA fragments. Using magnetic bead technology, the ligated fragments were size-selected and a final PCR was performed to enrich the adapter-modified cDNA fragments using primers annealing to the adaptors. The sequencing library was validated using an Agilent Technologies 2100 Bioanalyzer to characterize cDNA fragment sizes.

treatment_protocol: 3mM hydrogen peroxide added to water

tag: strain

value: Nacre

tag: age

value: whole larvae


title: H202 treated 2_RNAseq


title: Untreated 3_RNAseq

source_name: whole larvae_untreated


title: Leaf_WT_Control_MACE


title: Leaf_WT_Heatstress_MACE


title: Untreated 2_RNAseq


title: H202 treated 1_RNAseq


title: Untreated 1_RNAseq


title: fhs1-3


title: PolII

city: Chicago

first: Noboru

middle: Jo

last: Sakabe

state: IL

address: 920 E 58th st

department: Human Genetics

institute: University of Chicago

description: PolII

data_processing:
Basecalls performed with Illumina bcl2fastq2-v2.17.1.14 by the Functional Genomics Facility at the University of Chicago
Reads were aligned to hg19 with bowtie2-2.2.3
Reads with MAPQ < 10 were filtered out
HOMER was used to call peaks using FDR < 0.001 and the region and histone settings. H3K27me3 peaks were called with FDR < 0.005 and -size 500
Genome_build: hg19
Supplementary_files_format_and_content: bed files were parsed from HOMER's output and contain peaks called

source_name: iPSC-derived cardiomyocytes

growth_protocol: iPSC-derived cardiomyocytes were generated as in Burridge et al (2014):  Lymphoblastoid cell line (LCL)-derived iPSCs (passage 20-30) were grown in Essential 8 media (Invitrogen) to 80-90% confluency and then treated with a GSK-3 inhibitor (CHIR99021, Tocris) for 24 hours.  48 hours later, the cells were treated with a Wnt antagonist (Wnt-C59, Tocris) for 48 hours and then maintained in general heart media (RPMI supplemented with B27-minus Insulin, Invitrogen).  On day 15 of the differentiation, cardiomyocytes were selected using media supplemented with lactate and then 4 days later the cells were harvested.  Aliquots of 5 million cells were immediately crosslinked in 1% formaldehyde for 10 minutes following the protocol provided by Rao et al. (2014).  An additional 1-2 million cells were used in flow cytometry to assess purity using both TNNT2 (Troponin T) and TNNI3 (Troponin I) antibodies.  Cells used in Hi-C were > 80% positive for both markers.

extract_protocol:
Histone-DNA or PolII-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions provided with the TrueSeq ChIP Sample Preparation Kit (Catalog #: IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. Coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: iPSC-derived cardiomyocytes

tag: passages

tag: iPSc source

value: individual ID:YRI-NA18852

value: PolII-(H-224) (Santa Cruz) cat# sc-9001x-lot12412


title: H3K4me1 ChIP-seq

description: H3K4me1 ChIP-seq

value: Millipore cat#07-436 lot#2684917


title: chromatin input

description: chromatin input


title: H3K27ac ChIP-seq

description: H3K27ac ChIP-seq

value: Abcam – cat# Ab4729


title: H3K4me3 ChIP-seq

description: H3K4me3 ChIP-seq

value: Active motif - cat# 39159 - lot# 01609004


title: Atpao5-2_1_T_Spm_MACE

data_processing:
Library strategy: MACE
FastQC preprocessing
Filtering for sequences shorter than 14bp
MACE reads were aligned using SSAHA2 via the pipeline CRACPipe; kmer 14, skip 1
Data were weighted concerning equal hits and filtered for mapping with a max. of 1 insertion, deletion or mismatches
Genome_build: TAIR10
Supplementary_files_format_and_content: Text files representing the Transcript per million (TPM) for the mRNAs.

organism: Arabidopsis thaliana

source_name: Atpao5-2, 5µM thermospermine

growth_protocol: Wild type (Col-0) and Atpao5-2 mutant plants were grown on half strength MS agar media or on half strength MS agar media containing 5 uM T-Spm, respectively for 18 days at 22°C with a 14 h light/10 h dark photocycle. Whole aerial parts of plants where harvested for transcriptome analysis.

extract_protocol:
Total RNA was extracted using the using Qiagen RNeasy Plant Mini-kit following the manufacturer’s instructions.
The mRNA was enriched by binding the poly-A-tail at the 3'-end and the last 500 bp were sequenced so that each transcript is represented by one read in the library

value: knock-out mutant (Atpao5-2)

value: Aerial part


title: Input WT OIS 2

value: WT

value: 4-OHT induced H-Ras V12

tag: ChIP

value: Input


title: Atpao5-2_2_T_Spm_MACE

treatment_protocol: Wild type (Col-0) and Atpao5-2 mutant plants were grown on half strength MS agar media or on half strength MS agar media containing 5 uM T-Spm, respectively for 18 days at 22°C with a 14 h light/10 h dark photocycle.


title: H3K27me3 ChIP-seq

description: H3K27me3 ChIP-seq

value: Millipore cat# 07449


title: Input WT Control 2


title: Anther_WT_Control_MACE

value: Anther

value: Control

value: Moneymaker


title: Atpao5-2_2_Control_MACE

source_name: Atpao5-2, Control


title: Atpao5-2_1_Control_MACE


title: gH2A.x WT Control 2

value: Abcam, ab2893


title: gH2A.x WT OIS 2


title: WT2_Control_MACE

source_name: Wild type, Control

value: Wild type


title: WT1_T_Spm_MACE

source_name: Wild type, 5µM thermospermine


title: ko RRBS

city: Södertälje

first: Joëlle

last: Rüegg

address: Forskargatan 20

country: Sweden

institute: Karolinska Institutet/Swetox

description: Pool of three batches of genomic DNA

data_processing:
Basecalls using CASAVA version 1.4
alignement to  mm9 genome assembly using Genomatix Mapper (version 3.4.1) using bisulfite mode, fast seed search, allowing point mutations and a minimum alignment quality of 92%
covered CpGs (at least 4 reads) grouped based on detected methylation levels: unmethylated: methylation level <= 20%; low methylated: 20% < methylation level <= 50%; high methylated: 50% < methylation level <= 80%; fully methylated: 80% < methylation level <= 100%
CpGs were considered differentially methylated if CpGs switched from unmethylated to fully methylated level (or vice versa) between wt and ko.
Genome_build: mm9
Supplementary_files_format_and_content: txt files containing CpGs covered in both cell types, DMPs only methylated in wt or ko

source_name: embryonic fibroblasts

growth_protocol: MEFs were kept in high glucose DMEM supplemented with 10% FCS, 1 mM L-glutamine, 1 mM sodium pyruvate, and 1x non-essential amino acids

extract_protocol: Genomic DNA was isolated using the QIAamp DNA mini kit (Qiagen). Three batches of genomic DNA of each cell type were pooled, and 1 mg was digested with 20 U MspI overnight. The reaction was stopped by addition of 1 ml 0.5 M EDTA and purified using MinElute gel extraction kit (Qiagen). Subsequently, DNA fragments were end-repaired and A-tailed by incubation with 5 U Klenow fragment (New England Biolabs Inc.) and 0.5 mM dATP and 0.05 mM dGTP and dCTP at 30°C for 20 min followed by 20 min at 37°C. After purification using the MinElute gel extraction kit, methylated Illumina standard adapters were ligated to the fragments overnight at 16°C using 400 U T4 ligase (New England Biolabs Inc.). The fragments were then separated on a 3% Nusieve 3:1 agarose 0.5x TBE gel and 160-340 bp fragments were excised and purified using the MinElute gel extraction kit. The purified DNA was subjected to two rounds of bisulfite conversion using the EZ DNA Methylation kit (Zymo Research). Subsequently, the final library was prepared by 19 cycles of PCR amplification and purification using the MinElute gel extraction kit.

tag: genotype


title: SIL-ALL-input

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

data_processing:
FastQC (V 0.10.1) was used to check the data quality. To obatin the peaks,  the first 3 bases of the reads were trimmed based on the FastQC results
Samples were aligned to hg19 using bowtie aligner (Version 1.1.1), with default parameters. Only uniquely aligned reads were kept.
Peaks were called used MACS (V1.4.2) with default parameters with p-values < 1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files were generated by MACS in BED format.

source_name: SIL-ALL

growth_protocol: Human leukemia cell lines were maintained in IMDM supplemented with 10% FBS

extract_protocol: Library preapred according to Illumina's instructions

value: leukemia cell line SIL-ALL

tag: chip antibody

value: input


title: SIL-ALL-KDM2B

tag: cell line

value: anti-KDM2B (Millipore, catalog# 09-864)


title: WEHI-control, stimulated, AGM3_2

first: Changchun

last: Xiao

state: California

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

description:
R143_AGM3_2
Processed data file: R137_R143_Xiao_gene_counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.
Reads were quality trimmed and adapter trimmed (GATCGGAAGAGCACACGTCTG) using cutadapt part of python program.
Alignment to mm10 genome with TopHat v2.0.13 and Bowtie2.
Reads counted using Partek Genomics Suite v6.15.0730.
The Bioconductor package, edgeR and GLM method for changed transcript discovery.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Raw Count data for each known transcript for mm10 and each sample.

source_name: WEHI-control, anti-IgM stimulated

growth_protocol: In DMEM media supplemented with 10% FBS, 2 mmol/l L-glutamine and Pen/Strep, and 50 uM 2-mercaptoethanol.

extract_protocol:
RNA was extracted using Trizol reagent.
One ug of total RNA for each sample was prepared by polyA selection using oligodT beads followed by the NEB Ultra Directional RNA library prep kit following manufacturer's instructions.

treatment_protocol: WEHI-control and WEHI-miR-148a were stimulated with anti-IgM at a final concentration of 2 ug/ml for 14 h.

value: WEHI-control

value: B lymphocytes, immature

value: anti-IgM stimulation


title: HPB-ALL-input

source_name: HPB-ALL

value: leukemia cell line HPB-ALL


title: JURKAT-KDM2B

source_name: JURKAT

value: leukemia cell line JURKAT


title: HPB-ALL-KDM2B


title: WEHI-control, non-stimulated, AGM1_2

description:
R143_AGM1_2
Processed data file: R137_R143_Xiao_gene_counts.txt

source_name: WEHI-control, non-stimulated


title: WEHI-miR-148a, stimulated, AGM4_2

description:
R143_AGM4_2
Processed data file: R137_R143_Xiao_gene_counts.txt

source_name: WEHI-miR-148a, anti-IgM stimulated


title: WEHI-miR-148a, stimulated, AGM4

description:
R137L5_AGM4
Processed data file: R137_R143_Xiao_gene_counts.txt


title: SUP-B15-input

value: leukemia cell line SUP-B15


title: SUP-B15-KDM2B


title: REH-input

source_name: REH

value: leukemia cell line REH


title: WEHI-miR-148a, non-stimulated, AGM2

description:
R137L5_AGM2
Processed data file: R137_R143_Xiao_gene_counts.txt

source_name: WEHI-miR-148a, non-stimulated


title: WEHI-control, stimulated, AGM3

description:
R137L5_AGM3
Processed data file: R137_R143_Xiao_gene_counts.txt


title: WEHI-control, non-stimulated, AGM1

description:
R137L5_AGM1
Processed data file: R137_R143_Xiao_gene_counts.txt


title: REH-KDM2B


title: WT2_T_Spm_MACE

value: Aerial part


title: K562-KDM2B

value: leukemia cell line K562


title: HG

city: Athens

first: Lance

last: Wells

state: Georgia

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

data_processing:
Quality control checks on raw sequence data from each sample was performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were mapped to the reference human genome hg19/GRCh37 using TopHat v1.4 with two mismatches allowed and other default parameters. The alignment metrics of the mapped reads was estimated using SAMtools . Aligned reads were then imported onto the commercial data analysis platform, Avadis NGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped as patient and control identifiers and quantification of transcript abundance was done on this final read list using Trimmed Means of M-values (TMM) as the normalization method. Differential expression of genes was calculated on the basis of fold change (using default cut-off ≥ ±2.0) observed between defined conditions, and the p-value of the differentially expressed gene list was estimated by z-score calculations with Benjamini Hochberg False discovery rate (FDR) correction of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: txt file contains normalized expressions for each sample

source_name: Min6 cell line

growth_protocol: Min6 cells were cultured in complete DMEM containing L-glutamine and 4.5mM glucose media and passaged when 70% confluent.

extract_protocol:
Total RNA was extracted using the Rneasy Plus Minikit (Qiagen) as outlined by manufacturer.
RNA samples with a RNA integrity Number (RIN) value of at least 9.5 or higher was used for further processing. From each 3 samples, 500ng RNA was used for PolyA mRNA library prep using NEBNext PolyA magnetic Isolation module New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer's protocol. Samples were individually barcoded with unique in-house genomics service lab (GSL) primers and amplified through 10 cycles of PCR using KAPA HiFi HotStart Ready Mix (Kapa Biosystems, Inc., Woburn, MA, USA). The quality of the libraries were assessed by Qubit® 2.0 Fluorometer , and the concentration of the libraries was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer, respectively. Accurate quantification of the prepared mRNA libraries for downstream sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA, USA). Each library was then diluted to a final concentration of 12.5nM and pooled equimolar prior to clustering. Cluster generation was carried out on a cBot v1.4.36.0 using the Truseq Paired-end (PE) Cluster Kit v3.0 (Illumina, Inc., San Diego, CA, USA). Paired End (PE) sequencing was performed using a 200 cycle TruSeq SBS HS v3 kit on an Illumina HiSeq2000, running HiSeq Control Software (HCS) v1.5.15.1 (Illumina, Inc., San Diego, CA, USA). Image analysis and base calling was performed using the standard Illumina Pipeline consisting of Real time Analysis (RTA) version v1.13. Raw reads were demultiplexed using a bcl2fastq conversion software v1.8.3 (Illumina, Inc., San Diego, CA, USA) with default settings.

treatment_protocol: Cells were incubated in described conditions for 6 hrs, washed w/ 1X PBS, incubated in complete DMEM containing L-glutamine and 0.5mM glucose plus inhibitors (where applicable) before being reintroduced into described treatment conditions for 1 hr.

value: Mouse insulinoma 6 derived line

value: high glucose


title: methanol 2%-adapted 3

city: Hørsholm

first: Pier-Luc

last: Tremblay

address: Kogle Alle 6

department: The Novo-Nordisk Foundation Center for Biosustainability

country: Denmark

institute: Technical University of Denmark

data_processing:
Quality-scored basecalling was performed with the Illumina MiSeq Control software.
Alignment, data normalization, and transcript abundance quantification was done with Rockhopper version 2.0.2.
Genome_build: ASXP00000000.1
Supplementary_files_format_and_content: tab-delimited text file including gene, annotation, raw count for each replicate, normalized count for each replicate, RPKM, expression, p-value, and q-value.

organism: Sporomusa ovata DSM 2662

source_name: Bacterial culture

growth_protocol: S. ovata wild type and methanol-adapted strain were grown autotrophically to mid-log in 311 minimal medium under an atmosphere (1.7 atm) of H2/CO2  (80:20). Both strains were grown in triplicate in a 100 ml volume.

extract_protocol:
Total RNA was extracted from S. ovata cells with the TRIzol Max Bacterial RNA Isolation Kit from Life Technologies. Extracted total RNA was further purified with QIAGEN Rneasy minikit with on-column Dnase digestion. rRNA was depleted with the Ribo-Zero- rRNA Removal Kits from Epicentre.
The library was constructed with the Illumina TruSeq RNA sample preparation kit.

value: methanol-adapted

tag: number of transfer (methanol 2%)

tag: growth medium

tag: growth phase

value: mid-log


title: LG+GNS

tag: cell type

value: LG+GlcNAcstatin


title: methanol 2%-adapted 1


title: methanol 2%-adapted 2


title: WT1_Control_MACE

tag: genotype/variation

value: Wild type


title: LG

tag: treatment

value: Low glucose


title: wt RRBS

description: Pool of three batches of genomic DNA

value: wildtype


title: KO-Rep2

data_processing:
FastQC (V 0.10.1) was used to check the data quality. The first 10 bases and last 20 bases were trimmed based on FastQC results.
Tophat (V 2.0.12) was used for the alignment with default parameters.
Cuffdiff from Cufflinks (V 2.2.1) was used to call the differentially expressed genes, with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The DEGs file was generated using cuffdiff. It followed the standard gene_exp.diff format of cuffdiff outputs.

source_name: HSPCs

growth_protocol: HSPCs were sorted fy flow cytometry and cultured for 24 hours . Total RNA was isolated with a QIAGEN Rnase kit.

extract_protocol:
Qiagen Rnase kit
Illumina

value: HSPCs

value: KO


title: WEHI-miR-148a, non-stimulated, AGM2_2

description:
R143_AGM2_2
Processed data file: R137_R143_Xiao_gene_counts.txt

value: B lymphocytes, immature


title: DND41-KDM2B

value: leukemia cell line DND41

value: anti-KDM2B (Millipore, catalog# 09-864)


title: wild type 3

value: wild type


title: KO-Rep1


title: input control

city: Duarte

first: Dustin

middle: E

last: Schones

address: 1500 E Duarte Rd.

institute: City of Hope

description: Input control library for MCF7 cells

data_processing:
Reads passing quality filtering were aligned to the hg19 build of the human genome with bowtie2 (Langmead and Saslzberg 2012).
Peak finding was performed with MACS (Zhang et al., Genome Bio 2009) with a p-value threshold of 1e-5. Only peaks identified in both replicates were considered for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing coordinates of peaks

source_name: MCF7 cells

growth_protocol: MCF7 BCa cells from the American Type Culture Collection were cultured in DMEM (Mediatech, Inc.) supplemented with 10% FBS (Gemini Bio-products).  The MCF7/shRx1RUNTdox and MCF7/shRx13’UTRdox sublines were created by transducing MCF7 cells with pSLIK-based lentiviruses engineered as previously described (Baniwal et al. 2010) to conditionally express shRNAs that target either the RUNT domain or the 3’UTR of RUNX1, respectively. Transduced cells were selected with 2 mg/ml Neomycin (Gemini Bio-products).

extract_protocol: Libraries were prepared according to Illumina protocols for DNA samples

treatment_protocol: G1/S cell cycle synchronization was achieved by double-thymidine block. Cells were incubated for 16 h in media containing 2 mM thymidine (Sigma-Aldrich), released for 8-12 h in DMEM containing 10% FBS, and then incubated again in 2 mM thymidine for 16-18 h. For G2/M synchronization, cells were released from the double-thymidine block for 4 hours prior to treatment with 100 nM nocodazole (Sigma-Aldrich) for 14h. Percentage of cells in the various phases of the cell cycle were quantitated by propidium iodide staining and flow cytometry using BD LSRII flow cytometer (BD Biosciences) and the Modfit LT SynchWizard Tool (Verity Software House).


title: RUNX1 ChIP-seq replicate 2

description: ChIP-seq library for RUNX1 in MCF7 cells

tag: antibody vendor/catalog#

value: ab23980, Abcam


title: wild type 1


title: wild type 2


title: RUNX1 ChIP-seq replicate 1


title: WT-Rep2

value: WT


title: WT-Rep1


title: 2xSCS70

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Data were analyzed by the MAP-RSeq pipeline developed by the Mayo Clinic Bioinformatics Core (Kalari et al., BMC Bioinformatics 2014;15:224).
RSeQC software was used for estimating the distance between paired-end reads, evaluating the sequencing depth for alternate splicing analysis, determining the rate of duplicate reads, evaluating coverage of reads across genes, and more.
Paired-end reads were aligned by TopHat 2.0.6 against the mm10 genome build using the bowtie1 aligner option.
Gene counts were generated using HTseq software and gene annotation files were obtained from Illumina.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include gene counts with corresponding RPKM values.

source_name: Cells derived from H-2Kb-tsA58 gastric tunica muscularis

growth_protocol: Cell line was cultured in NeuroCult® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) at 39.5°C and without interferon-gamma.

extract_protocol:
Qiagen miRNeasy
Illumina TruSeq mRNA Sample Preparation Kit v2.

value: interstitial cells of Cajal (ICC) progenitor cell line


title: 2xSCS2F10

source_name: Cells derived from C57BL/6J gastric tunica muscularis

growth_protocol: Cell line was cultured in NeuroCult® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) plus 5% cell-free chick embryo extract (CEE; Accurate Chemical) at 37°C.


title: Hdac3ctrl

status: Public on Feb 21 2016

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (genes.fpkm tracking)

source_name: control optic nerve

extract_protocol:
Optic nerves were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent. Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed

value: Postnatal day 12

tag: geneotype/variation

value: Hdac3f/+; Olig1-cre


title: Hdac3cKO

source_name: Hdac3cKO optic nerve

value: Hdac3f/f; Olig1-cre


title: K562-input

value: leukemia cell line K562

value: input


title: p300_OPC

data_processing:
ChIP-seq reads were aligned to the rn4 genome assembly
peaks were called using MACS version 1.4.0 with default settings.
peaks were further filtered using following criteria to define a more stringent protein-DNA interactome: 1) the p-value cutoff was set to <10-9; 2) an enrichment of 5 fold; 3) tag number > 20
Genome_build: All sequencing data were mapped to November 2004 rat genome assembly (Baylor 3.4/rn4)
Supplementary_files_format_and_content: bed files

organism: Rattus norvegicus

source_name: Oligodendrocyte

growth_protocol: Primary rat OPCs were isolated from cortices of pups at P2 using a differential detachment procedure as previously described (Y. Chen, V. Balasubramaniyan, J. Peng, E.C. Hurlock, M. Tallquist, J. Li, Q.R. Lu Isolation and culture of rat and mouse oligodendrocyte precursor cells Nat. Protoc., 2 (2007), pp. 1044–1051).

extract_protocol:
ChIP assays were performed as previously described with minor modifications (Q. Weng, Y. Chen, H. Wang, X. Xu, B. Yang, Q. He, W. Shou, Y. Chen, Y. Higashi, V. van den Berghe, et al. Dual-mode modulation of Smad signaling by Smad-interacting protein Sip1 is required for myelination in the central nervous system Neuron, 73 (2012), pp. 713–728).
The ChIP-seq libraries were prepared using 5500 SOLiD Fragment Library Core Kit (PN 4464412) as recommended by the manufacturer.

treatment_protocol: Isolated rat OPCs were collected or grown in the OPC Growth Medium (Sato medium supplemented mitogens 10 ng/ml PDGF-AA and 20 ng/ml bFGF), and differentiated in Oligodendrocyte Differentiation Medium (Sato medium supplemented with 15 nM thyroid hormone T3 and 10 ng/ml ciliary neurotrophic factor).

value: Oligodentrocyte precursor cells

tag: strain background

value: Sprague Dawley

value: p300 (Santa Cruz sc-585)


title: Hdac3_OPC

value: Hdac3 (Abcam ab7030)


title: pSer5 PolII_Pax5R AIDR SD#10_ChIPseq

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

description: Illumina NextSeq 500 (Gallus gallus)

data_processing:
The 76 bp reads obtained after the sequencing run were trimmed (5bp from 5' and 20 bp from 3') to get 50 bp reads for alignment.
The reads were aligned to the galGal4 genome assembly or to the GFP constract. Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 2 -m1 -l 50
Genome_build: galGal4
Supplementary_files_format_and_content: wig files were generated using MACS (version 1.4.2) with parameter --space 100, and then normalized to RPM. Scores in the wig files represent the averaged RPM over overlapping 100bp window

organism: Gallus gallus

source_name: DT40 cells

extract_protocol:
cells were crosslinked with 1% HCHO, quenched with 0.125 M glycine, washed and resuspended in RIPA buffer (10 mM Tris pH 7.4, 1 mM EDTA, 1% tritonX-100, 0.1% sodium deoxycholate, 0.1% SDS) containing 0.8 M NaCl and sonicated using a water bath sonicator (Diagenode) to obtain DNA of ≈ 100–250 bp.
libraries were prepared and sequenced following standard Illumina protocols

value: B cell

value: Bcl6-/- Pax5R

tag: strain

value: pSer5 PolII

value: rabbit polyclonal

tag: antibody vendor name

value: Abcam

tag: antibody vendor id

tag: Sex

tag: control

value: Input


title: pSer5 PolII_WT AIDO/E SD_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)

tag: genotype

value: WT

tag: age


title: Spt5_Pax5R AIDR SD#10_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)

tag: chip antibody

value: Santa Cruz


title: Spt5_Bcl6R AIDR SD#10_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)

value: Bcl6-/- Pax5R Bcl6R


title: Spt5_WT AIDO/E SD_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)


title: pSer5 PolII_Bcl6R AIDR SD#10_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)


title: PolII_WT AIDO/E SD_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)

value: PolII


title: PolII_Bcl6R AIDR SD#10_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)


title: PolII_Pax5R AIDR SD#10_ChIPseq

description: Illumina NextSeq 500 (Gallus gallus)


title: dMSN_1 (RNA-seq)

status: Public on Feb 20 2016

city: New York

first: Shifra

middle: Liba

last: Klein

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell

description: Replicate 1

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Alignment: DNA samples were aligned to the mm9 genome using Bismark software as part of an in-house pipeline (PMID 22737091).  RNA fragments were mapped to the mosue genome using TopHat version 2.0.2 (http://tophat.cbcb.umd.edu) with bowtie version 1.0.0 against mm9 and annotated with NCBIM37 coding transcripts
DNA methylation analysis was performed using MethylKit software (PMID 23034086). RNA samples were counted using Htseq-count -m -intersection-strict and analysis was performed using tagwise dispersion and default parameters in edgeR (PMCID: PMC2796818).
Genome_build: mm9
Supplementary_files_format_and_content: DNA files are in the wig format. RNA files are the raw counts per gene as processed by Htseq-count.

source_name: Dorsal Medial Spiny Neurons

extract_protocol:
Following sacrifice animal brains were frozen, cryosectioned and microdissected. DNA was collected using Qiagen DNeasy Blood and tissue extraction kit (cat# 69582). RNA was harvested using Qiagen RNeasy mini kit (cat# 74106). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Male

tag: tissue

value: brain

value: Dorsal Medial Spiny Neurons


title: HP (RNA-seq)

description: Replicate 1

source_name: Hippocampal Precursors

value: Hippocampal Precursors


title: yMSN (RNA-seq)

description: Replicate 1

source_name: Young Medial Spiny Neurons

value: Young Medial Spiny Neurons


title: vMSN (eRRBS)

description:
eRRBS
Replicate 1

source_name: Vental Medial Spiny Neurons

value: Vental Medial Spiny Neurons


title: GC_Dnmt3a_CrePos_2 (eRRBS)

description:
eRRBS
Replicate 2

source_name: Granule Cells of the Dentate Gyrus

value: 129S4/SvJae x C57BL/6 x Sv129 x B6/CBA

value: Granule Cells of the Dentate Gyrus


title: GC_Dnmt3a_CreNeg_1 (eRRBS)

description:
eRRBS
Replicate 1


title: dMSN_2 (RNA-seq)

description: Replicate 2


title: Hdac3_d3

value: Differentiating oligodendrocytes

value: Sprague Dawley

value: Hdac3 (Abcam ab7030)


title: GC_Dnmt3a_CrePos_1 (eRRBS)

description:
eRRBS
Replicate 1


title: GC (eRRBS)

description:
eRRBS
Replicate 1


title: CA1 (eRRBS)

description:
eRRBS
Replicate 1

source_name: Pyrimidal cells of the CA1

value: Pyrimidal cells of the CA1


title: yCA (RNA-seq)

description: Replicate 1

source_name: Young Hippocampal CA Pyrimidal Neurons

value: Young Hippocampal CA Pyrimidal Neurons


title: p300_d3

value: p300 (Santa Cruz sc-585)


title: yCA (eRRBS)

description:
eRRBS
Replicate 1

value: WT


title: yMSN (eRRBS)

description:
eRRBS
Replicate 1


title: CA3 (eRRBS)

description:
eRRBS
Replicate 1

source_name: Pyrimidal cells of the CA3

value: Pyrimidal cells of the CA3


title: yGC (eRRBS)

description:
eRRBS
Replicate 1

source_name: Young Hippocampal Granule Cells

value: Young Hippocampal Granule Cells


title: HP (eRRBS)

description:
eRRBS
Replicate 1

value: Male


title: SP (eRRBS)

description:
eRRBS
Replicate 1

source_name: Striatal Precursors

value: brain

value: Striatal Precursors


title: OIM-d2 rep#1 DNase-seq

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
RTA 1.12.42 was used for Basecalling and Casava 1.8.2 ws used for demultiplexing.
Alignment was performed by Bowtie2 software with the hg19 reference genome.
Areas of enrichment were identified using DNase2Hotspots software(http://sorceforge.net/proujects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.

source_name: hFOB

growth_protocol: see additional columns of the SAMPLES section

extract_protocol: Cells were washed, resuspended in Trypsin and nuclei prepared in hypotonic buffer as per protocol

treatment_protocol: Cells were plated for experiments at the same time and shifted to respective temperature after 24 hours. Cells were harvested after 1 or 2 days.

tag: cell line

value: hFOB

value: Fetal bone immortalized using ts SV40 pUCSVtsA58 vector

value: untreated, grow at 39oC in OIM

tag: concentration

value: OIM media:100nM Dexamethasone, 100µM Ascorbic Acid, and 100µM β-GlyceroPhosphate, βGP

tag: time

tag: replicate

value: replicate 1

tag: growth proptocol

value: Cultured in DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin + OIM media components


title: SP (RNA-seq)

description: Replicate 1

tag: genotype/variation

tag: cell type


title: OIM-d1 rep#1 DNase-seq

description: hs_RC_OIM_24_RC_GH1032x2xGH1033_FDR0.csv

tag: treatment


title: B39-d2 rep#1 DNase-seq

value: untreated, grow at 39oC in BM

value: Basal Media

value: BM, basal madia:DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: B39-d1 rep#2 DNase-seq

value: replicate 2


title: Oim-d2 rep#2 DNase-seq


title: OIM-d1 rep#2 DNase-seq


title: B34 rep#2 DNase-seq

description: hs_RC_B34_NA_RC_GH1029x2xGH1030_FDR0.csv

value: untreated, grow at 34oC in BM


title: Untreated leaf sequencing sample (control)

city: Nanjing

first: Songtao

last: Jiu

state: Jiangsu

address: Weigang 1

department: College of Horticulture

institute: Nanjing Agricultural University

description:
Mixed 'Summer Black' grapevine young leaves (2 weeks old), large leaves (5 weeks old), and old leaves (9 week old) in randomly-selected plants.
'Summer Black' is an elite table grapevine cultivar native to Japan and currently one of the most economically popular cultivars in Chinese viticulture.
Small RNA Solexa sequencing.

data_processing:
HCS1.5 + RTA1.13.48 + BclConverter-1.9.0-11-03-08 HCS is 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 transferred 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.
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome with parameter -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap
If there is miRNA information of the species in miRBase, we use NCBI BLAST software analysis the known miRNA, the main parameter is -p blastn -F F -e 0.01, the other parameter is default. If there is no miRNA information of the species in miRBase, we use software developed by BGI tag2miRNA with default parameter.
Map to GenBank database, Rfam database to identify all small RNA contain rRNA, sRNA, snRNA, tRNA with Blast software with parameter -p blastn -F F -e 0.01
We use software OVERLAP developed by BGI (unpublished) to align small RNA tags to exons and introns of mRNA to find the degraded fragments of mRNA in the small RNA tags.
We developed a prediction software Mireap to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated small RNA tags which could be mapped to genome. Mireap can be accessed from the following link: http://sourceforge.net/projects/mireap/
We use plant targets prediction pipeline for identify 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. 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.
Genome_build: Genoscope 12X Vitis vinifera reference genome (http://www.genoscope.cns.fr/spip/Vitis-vinifera-e.html) was used for mapping.
Supplementary_files_format_and_content: .txt: Tab-delimited text files include raw counts.

organism: Vitis labrusca x Vitis vinifera

source_name: leaves, water treated

extract_protocol:
The modified CTAB method.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cultivar

value: Summer Black

value: leaf

value: mix of 2wks, 5wks, 9wks

value: water


title: B39-d2 rep#2 DNase-seq


title: B34 rep#1 DNase-seq


title: B39-d1 rep#1 DNase-seq


title: Cu-treated leaf sequencing sample

source_name: leaves, copper treated

value: copper


title: GC_Dnmt3a_CreNeg_2 (eRRBS)

description:
eRRBS
Replicate 2

value: Male

tag: strain

value: 129S4/SvJae x C57BL/6 x Sv129 x B6/CBA

value: brain

value: Granule Cells of the Dentate Gyrus


title: dMSN (eRRBS)

description:
eRRBS
Replicate 1

value: WT

value: Dorsal Medial Spiny Neurons


title: AtoC_EB

status: Public on Feb 19 2016

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

data_processing:
Base calling: HiSeq Control Software 2.0.12.0, RTA 1.17.21.3, CASAVA-1.8.2
Alignment: Bowtie-0.12.9, samtools-0.1.18
Peak calling: SeqMonk software (Braham Bionformatics Institute)
Peak refinement and annotation: SeqMonK output were processed by Java and Perl programs (in house written, decribed in the paper) to refine the peaks annotation and eliminate background
Genome_build: Waddlia chondrophila NC_014225
Supplementary_files_format_and_content: the xls files reporting peaks annotations and abundance were generated by Java and Perl programs (described in the paper) and consist of two sheet the ANNO and the NO-ANNO sheet. The ANNO probes sheets are organized in columns as follows:  column 1: gene name to which the peak is associated is reported in the reference genome used for the reads alignment  column 2 : probe start   column 3 : probe end  column 4 : COG categories to which the gene associated to the corresponding peak belongs to  column 5 : PubMed Identification number of the protein encoded by the gene associated to the peak  column 6 : Length of the protein  column 7 : The gene strand of the gene associated to the peak (0 plus strand, 1 reverse strand)  column 8 : Gene start  column 9 : Gene end  column10: Probe distance, the distance of the probe from ORF start  column 11 : It is reported here the abundance of reads per probe expressed as the percentage of total reads number  column 12: N possible association, it is reported here the number of possible association that the probe associated to the gene reported in the first column can have (i.e.: two genes that are divergent but shares the same peak)  column 13 : Name of the gene that can be associated to this probe and the distance of the probe from the gene start)  The NO-ANNO probes files contain all those probes that made the cut off, (are recognized as peaks) but they cannot be associated to any genes. File organization is the same as before except that only information about the probe location and reads abundance are reported.

organism: Waddlia chondrophila

source_name: Waddlia chondrophila cells

growth_protocol: Waddlia chondrophila strain ATCC VR-1470 was co-cultivated at 32°C with Acanthamoeba castellani strain ATCC 30010 in 75 cm2 flask containing 30 ml of peptone-yeast-extract-glucose broth. After 7 days of culture, the suspension was filtered on 5 µm filter to eliminate trophozoites and cysts and to isolate bacteria in the filtrate. The filtrate was then diluted at the appropriate dilution in DMEM in order to proceed to Vero cells infection. One day before the infection, 5x105 Vero cells were seeded per well in 24-well plates. A 1/2000 dilution of W. chondrophila was used to infect Vero cells. This corresponded to an MOI of 2-3, as estimated by qPCR. This infectious dose led to 50% of infected cells with 2-3 bacteria, as determined by confocal microscopy. The Vero cells with the bacterial suspension were centrifuged at 1790g for 10 minutes at room temperature and then incubated for 15 minutes at 37°C with a 5% CO2 atmosphere. To remove non-internalized bacteria in order to obtain a synchronous infection, cells were washed with the DMEM medium. Then, infected cells were incubated for different time periods.

extract_protocol:
Lysates were clarified from sonicated host cells and transcription factors DNA complexes were isolated with ChIP antibody
DNA libraries were prepared by FASTERIS SA (Geneva, CH) using standard Illumina protocls

treatment_protocol: Vero cells were infected in 25 cm2 flask as described above (10 flasks per ChIP-seq for late time points, 40 flasks for early time point). At different time post-infection, infected cells were transferred in falcons and cross-linked in presence of 1% of formaldehyde and 10 μM of sodium phosphate (pH 7.6) during 10 min at RT followed by 30 min on ice. Cells were washed twice in phosphate buffer saline, resuspended in TES  buffer (10 mM TRIS-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT and incubated during 10 min at 37°C. Cells were pelleted and resuspended in a Ready-Lyse lysozyme solution (Epicentre, Madison, WI), according to the manufacturer's instructions. The lysates were sonicated on ice by 10 cycles of 20 sec to shear DNA and obtain fragments of lengh ranging from 300 to 700 bp. Samples were centrifuged at 14 000 rpm 2 min and the supernatants were take off and diluted to 1 mL in ChIP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, containing protease inhibitors (Roche, Rotkreuz, Switzerland)). The diluted supernatants were pre-cleared with 150 μl of protein-A agarose (for rabbit polyclonal antibodies) protein-G agarose (for mouse polyclonal antibodies) (Roche, Rotkreuz, Switzerland). The pre-cleared supernatants were incubated overnight at 4° with 2 μL of specific polyclonal rabbit/mouse antibodies. The immuno-complexes were captured after incubation with Protein-A/G agarose pre-saturated with BSA during 2h at 4°C and washed once with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), then once with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), once with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The complexes were eluted twice with 250 µl of elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and incubated overnight at 65°C with 300mM NaCl to reverse the crosslinks. The samples were then treated with 2 µg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 µg of glycogen as carrier and finally resuspended in 100 µl of water.

value: Elementary bodies

value: policlonal-anti-AtoC, Mice


title: DnaA3_24h

value: reticuate bodies

value: policlonal-Anti-DnaA3, Mice


title: DnaA1_72h

value: Reticulate and elementary bodies

value: policlonal-Anti-DnaA1, Mice


title: Euo_72h

value: policlonal-anti-Euo, Rabbit


title: Wcw_1223_56h

value: Reticulate bodies

value: policlonal-anti-Wcw1223, Mice


title: NrdR_EB

value: policlonal-anti-NrdR, Rabbit


title: PhoB_EB

value: policlonal-anti-PhoB, Rabbit


title: ParB_EB

value: policlonal-anti-ParB, Rabbit


title: Wcw_1671_EB

value: policlonal-anti-Wcw1671, Rabbit


title: HrcA_72h

value: policlonal-anti-HrcA, Rabbit


title: Bcell_Cebpa18h_ChIPseq_Pu1

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

data_processing:
reads were mapped using STAR (parameters: -outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.1 -alignIntronMax 1 -alignEndsType EndToEnd).
Duplicates reads were removed using picard
For quantitative analysis, reads were counted on genes exon using the Rpackage Rsubread (1.16.1)(parameters: GTF.featureType="exon", GTF.attrType="gene_id", isPairedEnd=T, nthreads=12, strandSpecific=0)
bigwig tracks were made using DeepTools BamCompare to subtract the input from the ChIP (parameters: -scaleFactorsMethod SES -ratio subtract -normalizeUsingRPKM -fragmentLength 200 -binSize 1)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, track of fragment signal (elongated to 200b)

growth_protocol: ESCs (E14TG2) were cultured on gelatinized plates in N2B27 media (50 %DMEM/F12, 50% Neurobasal medium, N2 (500X), B27 (1000X)) supplemented with small-molecule inhibitors PD (1 μM, PD0325901), CHIR (3 μM, CHIR99021) and LIF. CD19+ pre-B cells were obtained from bone marrow with monoclonal antibody to CD19 (BD Pharmingen) using MACS sorting (Miltenyi Biotech). The purity of the sorted cell fractions was confirmed by FACS using an LSR2 machine (BD). After isolation, B cells were grown in RPMI medium supplemented with 10% FBS and 10ng/ml IL-7 (Peprotech). All medium contain 100 X L-glutamine, 100X penicillin/streptomycin, 100X nonessential amino acids, 1000X β-mercaptoethanol. All reagents are from Life Technologies unless otherwise specified. Lin- c-Kit+ Sca-1- CD16+/CD32+ CD34+ GMP cells were isolated by FACS sorting using a BD INFLUX sorting machine and culture in STEMSPAN medium (Stemcell technologies) supplemented with 100ng/ml SCF, 50ng/ml IL3, 50ng/ml Flt3L and 50ng/ml mTPO (all from Peprotech). The antibodies used from GMPs isolation were from BD Biosciences.

extract_protocol:
ChIP was performed as described in Jakobsen et al, BMC genomics, 16, 46 (2015)
Amplification of 2 ng ChIP DNA was essentially performed as described by the manufacturer (NEB, cat#E6240S), with the use of precast 2% SYBR agarose gels (Invitrogen, cat#G5218-02) and excision of band size 175–400 bp. Key modifications consisted of a 30 minute ligation step, 30 minute gel solubilization at 37°C of excised gel fragments, and a prolonged, double run-through elution step (each three minutes) with preheated (55°C) elution buffer for all column purifications (Qiagen, cats#28104,28704,28004) to ensure robust recovery.

treatment_protocol: For the reprogramming experiments B cells were exposed for 18h to 100nM of -Estradiol (E2) in gelatinized plates seeded with a feeder layer of the MEFs in RPMI medium. After E2 washout, the cultures were switched to serum-free N2B27 medium supplemented with 2μg/ml of doxycycline, IL-4 10ng/ml, IL-7 10ng/ml and IL-15 2ng/ml. B cells were seeded at a density of 500 cells/cm2 in 12 well plates.

value: B cell

tag: target

value: ChIP Pu1

tag: antibody

value: sc-352, Santa Cruz


title: Bcell_UT_ChIPseq_Brd4

source_name: Bcell

value: ChIP Brd4

value: Bethyl Laboratories, A301-985A)


title: Bcell_Cebpa18h_ChIPseq_Brd4


title: Bcell_Cebpa18h_OSKM1d_ChIPseq_K27ac

treatment_protocol: For the reprogramming experiments B cells were exposed for 18h to 100nM of β-Estradiol (E2) in gelatinized plates seeded with a feeder layer of the MEFs in RPMI medium. After E2 washout, the cultures were switched to serum-free N2B27 medium supplemented with 2μg/ml of doxycycline, IL-4 10ng/ml, IL-7 10ng/ml and IL-15 2ng/ml. B cells were seeded at a density of 500 cells/cm2 in 12 well plates.

value: bone marrow

value: ChIP H3K27ac

value: Abcam, ab4729


title: Bcell_Cebpa18h_OSKM2d_ChIPseq_K27ac


title: Bcell_Cebpa18h_ChIPseq_Cebpa

value: ChIP Cebpa

value: Santa Cruz, SC-61


title: Bcell_Cebpa18h_OSKM2d_ChIPseq_Klf4

value: ChIP Klf4


title: Bcell_Cebpa18h_ChIPseq_K27ac


title: Bcell_ChIPseq_K27ac


title: Bcell_ChIPseq_Cebpa


title: Bcell_Cebpa18h_ChIPseq_Klf4


title: Bcell_ChIPseq_Klf4


title: Bcell_Cebpa18h_OSKM1d_ChIPseq_Klf4


title: Mbnl2KOCorticalNeuronsNeurite1

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

institute: University of Colorado Anschutz Medical Campus

description: Mbnl2 KO cortical neurons neurite Rep1

data_processing:
Reads were aligned to the mm9 genome using either Tophat version 2.0.12 or STAR 2.0.4d
Expression values were calculated using Cufflinks version 2.1.1
Alternative isoform abundances were calculated using MISO
Genome_build: mm9 supplemented with alternative isoforms identified in Merkin et al (Science) 2012

source_name: Mbnl2 KO E18.5 cortical neurons neurite

extract_protocol:
Cells were fractionated using porous membranes into soma and neurite fractions.
For all N2A and CAD samples, libraries were prepared using the standard "dUTP" strand-specific method.  For cortical neuron samples, libraries were prepared using the Clontech Low Input Kit.

value: E18.5 cortical neurons

tag: compartment

value: neurite

tag: genotype

value: Mbnl2 KO


title: Mbnl2KOCorticalNeuronsNeurite2

description: Mbnl2 KO cortical neurons neurite Rep2


title: Mbnl2KOCorticalNeuronsSoma1

description: Mbnl2 KO cortical neurons soma Rep1

source_name: Mbnl2 KO E18.5 cortical neurons soma

value: soma


title: Mbnl1KOCorticalNeuronsNeurite1

description: Mbnl1 KO cortical neurons neurite Rep1

source_name: Mbnl1 KO E18.5 cortical neurons neurite

value: Mbnl1 KO


title: Mbnl1KOCorticalNeuronsSoma2

description: Mbnl1 KO cortical neurons soma Rep2

source_name: Mbnl1 KO E18.5 cortical neurons soma


title: Mbnl1KOCorticalNeuronsNeurite2

description: Mbnl1 KO cortical neurons neurite Rep2


title: Mbnl1KOCorticalNeuronsSoma1

description: Mbnl1 KO cortical neurons soma Rep1


title: WTCorticalNeuronsSoma1

description: WT cortical neurons soma Rep1

source_name: WT E18.5 cortical neurons soma

value: wild type


title: Bcell_UT_ChIPseq_Pu1

value: B cell


title: WTCorticalNeuronsSoma2

description: WT cortical neurons soma Rep2


title: Mbnl2KOCorticalNeuronsSoma2

description: Mbnl2 KO cortical neurons soma Rep2


title: 17-day-old mutant rep. 2

city: Blacksburg

first: Delasa

last: Aghamirzaie

state: VA

address: 101L Price Hall, Virginia Tech

department: GBCB

institute: virginia Tech

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to hard-masked Arabidopsis TAIR10 genome using Tophat2
Transcript assembly was done using StringTie
Assembled transcripts from all samples were merged using Cuffmerge to generate a reference transcriptome GTF file
StringTie-B was used to prepare read coverage tables from aligned reads
Raw count abundance values were normalized to the library size and transcript sizes to obtain Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values.
Genome_build: TAIR10
Supplementary_files_format_and_content: Final FPKM values and raw counts are provided as Expression.txt

source_name: developing embryos

growth_protocol: Normal growth in Farfard superfine germinating mix (Sun Gro Horticulture, Vancouver, British Columbia, Canada) in 2-inch pots. Irrigation was done with deionized water every 3 – 4 days until the plants were 3 – 4 weeks old.  After that, the plants received Miracle Gro All-Purpose Plant Food (1 tsp per 2 gallons) with every watering. Controlled environment at ~115 E, 20/18 oC day/night, 65% humidity, and a 16-hour photoperiod

extract_protocol:
RNA was extracted from frozen embryos using phenol/chloroform and LiCl precipitation and purified by using the Qiagen RNeasy Plant Mini kit.  RNA quality and integrity analysis was performed by the Virginia Bioinformatics Institute (Virginia Tech, Blacksburg, VA).
Reverse transcription of mRNA, library preparation, and paired-end RNA-Seq generating 75-bp reads, including removing low quality reads and adapter sequence trimming, was performed by Beckman Coulter Genomics (Danvers, MA) using established protocols.

treatment_protocol: Seeds and embryos from siliques of defined stages were dissected at low temperatures to slow down any metabolic processes. This was achieved by performing these dissections on wet glass-fiber filters placed on Petri dishes completely filled with frozen water and ensuring that temperatures were maintained between -5 and 5 oC by frequent measurements with an infrared thermometer. We found that these temperatures are the lowest that can be used without freezing the seeds, which would cause cell damage that would be problematic for the subsequent embryo washing steps. Depending on the developmental stage of the embryos, embryo dissection from a single silique (40–60 seeds) took between 10 and 25 minutes.  Wild type and val1 mutant embryos were dissected under dissecting microscopes in parallel by two personnel. Embryos were rinsed off from the glass-fiber filter into ice-cold mass spectrometry-grade water, briefly centrifuged at 4 oC prior to an additional wash to remove any remaining endosperm, snap-frozen in liquid nitrogen, and stored at -80 oC until RNA extraction was performed.

tag: developmental stage

value: val1 mutant


title: 17-day-old mutant rep. 1


title: 17-day-old mutant rep. 3


title: 15-day-old mutant rep. 3


title: 15-day-old mutant rep. 2


title: 13-day-old mutant rep. 2


title: 13-day-old mutant rep. 1


title: 12-day-old mutant rep. 1


title: 12-day-old mutant rep. 3


title: 10-day-old mutant rep. 2


title: 12-day-old mutant rep. 2


title: 10-day-old mutant rep. 3


title: 10-day-old mutant rep. 1


title: 8-day-old mutant rep. 3


title: WTCorticalNeuronsNeurite2

description: WT cortical neurons neurite Rep2

source_name: WT E18.5 cortical neurons neurite


title: 8-day-old mutant rep. 1


title: 7-day-old mutant rep. 3


title: 7-day-old mutant rep. 2


title: 7-day-old mutant rep. 1


title: 8-day-old mutant rep. 2


title: 17-day-old wild type rep. 1


title: 17-day-old wild type rep. 2


title: 15-day-old wild type rep. 1


title: 15-day-old wild type rep. 2


title: 13-day-old mutant rep. 3


title: 13-day-old wild type rep. 2


title: 12-day-old wild type rep. 3


title: WTCorticalNeuronsNeurite1

description: WT cortical neurons neurite Rep1


title: 15-day-old mutant rep. 1


title: 13-day-old wild type rep. 1


title: 12-day-old wild type rep. 1


title: 10-day-old wild type rep. 2


title: 10-day-old wild type rep. 1


title: 8-day-old wild type rep. 3


title: 7-day-old wild type rep. 2


title: 8-day-old wild type rep. 2


title: 8-day-old wild type rep. 1


title: 7-day-old wild type rep. 1


title: 7-day-old wild type rep. 3


title: MCF7+E2 6h AGO HITS-CLIP (Nested, Protected)

first: Peter

last: Kabos

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

description: RNA from Argonaute IP

data_processing:
Raw reads were processed with cutadapt (https://code.google.com/p/cutadapt/) to remove 3’ adaptor sequences and 3’ bases with QUAL < 10.
Trimmed reads were aligned to the genome using GSNAP (http://research-pub.gene.com/gmap/).
Peaks were called on alignments with MAPQ >10 using piranha (http://smithlabresearch.org/software/piranha/).
Overlapping peaks were merged and all peaks were resized to a uniform 200bp centered on the summit of each peak using peaktools (https://github.com/jayhesselberth/peaktools).
Genome_build: hg19

source_name: breast carcinoma

growth_protocol: MCF-7 were maintained in MEM supplemented with 5% fetal bovine serum (FBS).

extract_protocol:
Extraction was performed as in Balakrishnan I, et al. Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. Stem Cells Dayt Ohio. 2013.
Library construction was performed as in Balakrishnan I, et al. Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. Stem Cells Dayt Ohio. 2013. with the following modifications: First, a nested reverse transcription primer (5’-CCGCTGGAAGTGACTGA-3’) was used in place of the DP3 primer for all samples. Second, for the "Nested, Protected" samples, phosphorothioate bonds were added between the final four bases of the reverse PCR primer to prevent cleavage by exonuclease activity of the polymerase (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCCCGCTGGAAGTGACTGA*C*A*C-3’, “*” indicate phosphorothioate bonds). The second PCR was performed with index primers compatible with the new first-stage primers (5’-CAAGCAGAAGACGGCATACGAGATCGGT NNNNNN GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3’).

treatment_protocol: MCF-7 were grown in estrogen-free conditions (phenol red-free MEM supplemented with 5% Dextran coated charcoal (DCC) stripped FBS) for 48 hours, at which time they were treated with 10nM 17β-estradiol (E2) for 0, 6 or 24 hours prior to crosslinking.

value: 10nM 17β-estradiol for 6 hours

value: Argonaute IP


title: MCF7+E2 0h AGO HITS-CLIP (Nested, Protected)

description: RNA from Argonaute IP


title: MCF7+E2 24h AGO HITS-CLIP (Nested, Protected)

description: RNA from Argonaute IP

value: 10nM 17β-estradiol for 24 hours


title: 13-day-old wild type rep. 3


title: MCF7+E2 6h AGO HITS-CLIP (Nested)

description: RNA from Argonaute IP


title: 15-day-old wild type rep. 3


title: MCF7+E2 0h AGO HITS-CLIP (Nested)

description: RNA from Argonaute IP


title: MCF7+E2 24h AGO HITS-CLIP (Nested)

description: RNA from Argonaute IP


title: JHU_UM_04

city: Baltimore

first: Srikanth

middle: Srinivas

last: Manda

state: Maryland

address: 733 N Broadway

department: School of Medicine

institute: Johns Hopkins University

data_processing:
The RNA libraries were sequenced on Illumina HiSeq 2000 Platform
The qualities of all sequences in fastq format were assessed using FASTQC . The adaptors and low quality bases were trimmed from the sequence using Trimmomatic. Reads with a phred quality (Q > 20) were used for further alignment and assembly.
Quality trimmed raw reads from all 15 samples were aligned to the human reference genome sequence (GRCh38.79 assembly) separately using HISAT (v 0.1.4) with Gencode V22 junctions as a guided reference annotation.
The aligned reads for each sample were assembled into transcripts using Stringtie (v1.3.3). The transcripts abundance was estimated as Fragments Per Kilobases of exon per Million fragments mapped (FPKM)
Separate GTF files for each sample were generated
Genome_build: GRCh38.79
Supplementary_files_format_and_content: GTF files

source_name: Monocyte Cells

extract_protocol:
CD14-Positive monocytes cells were isolated from PBMC by negative selection method using Miltenyi Monocyte Isolation kit II (Miltenyi biotec).
Total RNA was extracted from monocytes cells using the RNesasy mini kit (QIAGEN)
Messenger RNA isolation and sequencing libraries preparation was performed using TruSeq RNA Sample preparation Kit and SuperScript II Reverse Transcriptase.

value: Primary Monocyte Cells

tag: age

value: Healthy individuals


title: JHU_UM_02


title: JHU_UM_01