title: faireseq_cr0.5_control

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description:
processed data file: Cr0.5VsCtrl_peaks.bed
Puga-Jerry-8

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat for RNA-Seq samples and bwa for FAIRE-Seq samples
For RNA-Seq samples, number of reads was calculated for each Entrez gene. Differential expression analysis was performed using Deseq.
For FAIRE-Seq samples, peaks were identified using MACS.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns for RNA-Seq samples. Bed files for FAIRE-Seq data.

growth_protocol: Hepa-1c1c7 (Hepa-1) mouse hepatoma cells from the American Tissue Culture Collection were maintained in α-minimum essential media (α-MEM, Gibco) with 5%(v/v) fetal bovine serum (Sigma) and 1% (v/v) antibiotic-antimycotic (Gibco) in a 5% CO2 humidified atmosphere  at 37° C.

extract_protocol:
mRNA was extracted by TirReagent. Cell debris were removed by micro-centrifugation and free DNA was extracted from the collected supernatant by phenol/chloroform extraction. Under these conditions, DNA not crosslinked to proteins remains in the aqueous phase while the DNA crosslinked to proteins remains in the phenol phase.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells exposed acutely with high concentration Cr(VI) were treated with a final concentration of 25 µM CrK2O4 in their growth medium for 90 minutes.  The medium of cells chronically exposed to low concentration Cr(VI) was supplemented with 0.5 μM CrK2O4 every 24 hours and the cells were grown for a total of 20 passages, approximately equivalent to 50 cell divisions.  Control cells were passaged for the same number of passages in the absence of chromium.

value: Hepa-1c1c7 (Hepa-1)

value: mouse hepatoma cells

value: control


title: EC_Cont2_RNA

status: Public on Apr 10 2014

type: SRA

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: processed data file: EC_Cont_RNA.txt

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software was used for basecalling.
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads.
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1)
Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

molecule: total RNA

organism: Escherichia coli

source_name: Untreated E. coli cells

growth_protocol: Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim.

extract_protocol:
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation.
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis.

tag: strain

tag: genotype/variation

value: wild type

tag: treated with

value: none (untreated control)

tag: molecule subtype

value: total RNA, rRNA depleted


title: Snyder_EFL-1_GFP_L1 ChIP Rep3

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.

library_source: genomic

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: EFL-1_GFP_L1 ChIP Rep.3

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: YL418(official name :YL418 genotype :unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR genotype :unc-119 (+)] outcross :0 mutagen :None tags :GFP::3xFlag description :The EFL-1::GFP fusion protein is driven by the ges-1 promoter and expressed in the instestine. made_by :Michelle Kudron (Valerie Reinke's lab) )

tag: developmental stage

value: fed L1

tag: genotype

tag: Sex

value: Hermaphrodite


title: faireseq_cr25_control

country: USA

description:
processed data file: Cr25VsCtrl_peaks.bed
s_5

organism: Mus musculus

tag: cell line

tag: cell type


title: EC_Trim2_DNA

description: processed data file: EC_Trim_DNA.txt

source_name: Trimethoprim-treated E. coli cells

extract_protocol:
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega).
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: the DNA samples were treated with ultrasound (3-5 pulses of 30 sec at 4°C). After end-repair, TruSeq sequencing adapters were ligated to the DNA fragments. Finally, the DNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase (9-11 cycles, depending on the sample). Aliquots of the PCR amplified libraries were examined by capillary electrophoresis.

value: 0.5 μg/ml trimethoprim


title: EC_Cont1_RNA

description: processed data file: EC_Cont_RNA.txt


title: Snyder_EFL-1_GFP_L1 ChIP Rep2

source_name: EFL-1_GFP_L1 ChIP Rep.2

value: unc-119(ed3) III; vrIs65[pGES-1::EFL-1::GFP FLAG:EFL-1 3'-UTR


title: EC_Cont2_DNA

description: processed data file: EC_Cont_DNA.txt


title: rnaseq_control_2

description:
processed data file: countTable.txt
PJ-8


title: faireseq_cr25_treatment

description:
processed data file: Cr25VsCtrl_peaks.bed
s_7

value: Cr25 (25 µM CrK2O4)


title: Snyder_EFL-1_GFP_L1 Input Rep3

description: input DNA

source_name: EFL-1_GFP_L1 Input Rep.3


title: Tumor_tissue

city: Wenzhou

first: ZhaoYun

last: Li

state: Zhejiang province

address: Chashan Higher Education Park

department: School of Laboratory Medicine and Life Science

country: China

institute: Wenzhou Medical University

data_processing:
Adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats were discarded followed the procedures as described in a previous study (Li et al., 2010).
Small RNA sequencing reads were aligned against 2,578 mature miRNA sequences from miRBase build 20 using bowtie.
Expression values are quantified by aggregating reads into counts and differential expression analysis is performed based on normalized deep-sequencing counts RPM values (NOISeq). In this study, we chose q = 0.8 for NOISeq to screen significant genes and log2FC as supplementary threshold.
Genome_build: human miRBase build 20
Supplementary_files_format_and_content: tab-delimited text files including RPM values for each sample.

organism: Homo sapiens

source_name: breast cancer tumor tissue

extract_protocol:
Total RNA was isolated for each of tissue and serum samples and treated with Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent) with RIN number >7.0.
Approximately 1 ug of total pooled RNA were used to prepare small RNA library according to protocol of TruSeq™ Small RNA Sample Prep Kits (Illumina).

tag: disease status

value: breast cancer

value: tissue


title: rnaseq_Cr25_1

description:
processed data file: countTable.txt
PJ-3


title: rnaseq_Cr25_2

description:
processed data file: countTable.txt
PJ-7


title: Normal_serum

source_name: serum from healthy woman control

value: Normal

value: serum


title: rnaseq_control_1

description:
processed data file: countTable.txt
PJ-4


title: Normal_tissue

source_name: breast cancer serum


title: EC_Trim1_DNA

description: processed data file: EC_Trim_DNA.txt


title: EC_Cont1_DNA

description: processed data file: EC_Cont_DNA.txt


title: Snyder_EFL-1_GFP_L1 Input Rep2 extraction3_seq3

description: input DNA

source_name: EFL-1_GFP_L1 Input Rep.2 extraction4_seq4


title: DICER ChIP

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
The stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to human genome (UCSC HG19) using BOWTIE software (V0.12.7).
The uniquely mapped reads were used for peak detection by MACS v1.4 (Model-based Analysis of ChIP-Seq) software. Statistically significant ChIP-enriched regions (peaks) were identified by comparison to a Poisson background model (Cut-off p-value=10-5).
MACS called peaks were filtered, and only those with score > 100 were retained for further analysis (file Dicer_peaks.bed)
genome build hg19
supplementary files format and content: IP_HG19_bowtie_alignment.sam.gz aligned reads SAM format; Dicer_peaks.bed MACS-called and filtered peaks.

source_name: HEK 293 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
10 ng of the DNA sample was used for Illumina/Solexa sequencing in the following steps: 1) DNA samples were blunt-ended with T4 DNA polymerase and Klenow polymerase; 2) a dA base was added to the 3' end of each strand by Klenow (exo minus) polymerase; 3) Illumina's genomic adapters were ligated to the DNA fragments; 4) PCR amplification was performed to enrich ligated fragments; 5) Enriched product of ~300-400bp was cut out from gel and purified with QIAquick Gel Extraction Kit. The completed libraries were quantified by Agilent 2100 Bioanalyzer. The libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cell, amplified in situ. The libraries were then sequenced on the Genome Analyzer IIx following the SBS Sequencing 36 Cycle Kit v5 protocol.

value: HEK 293

tag: dicer status

value: wt

tag: chip antibody

value: Dicer


title: Input.EE18

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing:
ChIP-seq reads were aligned to the WS220/CE10 assembly of the C. elegans genome using bowtie version 0.12.7 (Langmead B et al, Genome Biology, 2009) with a -m 2 and otherwise default settings.
Read pileup signal tracks were generated in wig format with MACS 1.4 (Zhang et al, Genome Biology, 2008). Duplicate reads were removed, step size for wig file was set to 25bp.
Genome_build: WS220/CE10
Supplementary_files_format_and_content: wig format for genome browser display, read pileup in 25bp steps

source_name: early embryos Input DNA seq

growth_protocol: Worm_embryo_growth_and_harvest_vSS5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5  and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 14 times in ice water bath followed by 1 minute pause at the highest setting. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 m filter units (cat. UFC30HV0S) at 13,000 rpm, 4C for 1 minute to remove lipids.  Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/. Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Qiagen kit. For a detailed protocol see http://www.modencode.org/.
Solexa_Library_Prep_vKI3 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel.

tag: tissue

value: whole embryo

tag: Stage

value: early embryos

value: none (input)

tag: chip antibody supplier

tag: chip antibody catalog#


title: Tumor_serum

source_name: breast cancer tumor serum


title: Input.EE8.1B


title: Prostate_VA-PC-92-67

status: Public on Apr 11 2014

city: Atlanta

first: Carlos

last: Moreno

state: Georgia

address: 615 Michael St

department: Department of Pathology & Laboratory Medicine

institute: Emory University

data_processing:
filtered in FASTQC, not trimmed, and mapped with a maximum of 2bp mismatch to hg19.
Quality control : FastQC, RNA-SEQc
Mapping : Tophat 2.0.8, Bowtie 2.1.0
FPKM : Cufflinks
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM - tab delimited

source_name: formalin-fixed, paraffin-embedded (FFPE) prostatectomy sample

growth_protocol: FFPE - Formalin fixed Parrafin embedded tissue blocks

extract_protocol:
RNA extraction Omega XP -FFPE from two 1mm cores
Modified TruSeq RNA Sample preparation with Ambion Ribominus step and no poly-A selection

tag: collection site

value: Atlanta VA Medical Center

tag: cgsr id

tag: external id

value: prostate

tag: months to bcr

tag: months total f/u

tag: bcr

tag: prepsa

tag: race

value: W

tag: pstage

tag: gleason score

tag: tgleason

tag: sms

value: Positive

tag: no of uniquely mapped reads

tag: no. of total reads

tag: % mapped


title: H4K16ac.MP07329.EE8.1B

source_name: early embryos H4K16ac ChIP seq

tag: tissue

tag: strain

tag: Stage

tag: chip antibody

tag: chip antibody supplier

value: Millipore


title: faireseq_cr0.5_treatment

description:
processed data file: Cr0.5VsCtrl_peaks.bed
Puga-Jerry-12

tag: cell line

value: Hepa-1c1c7 (Hepa-1)

tag: cell type

value: mouse hepatoma cells

tag: treated with


title: H4K16ac.MP07329.EE18

tag: chip antibody catalog#


title: Input, rep1

city: Cambridge

first: Przemyslaw

middle: Aleksander

last: Stempor

state: United Kingdom

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

description: Input sample for H4K16ac ChIP-seq, rep1.

data_processing:
ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using BWA (Li and Durbin, 2010) with default settings.
Data were normalized using BEADS algorithm (Cheung et al., 2011).
Signals were exported to bigWig tracks at 1bp resolution.
Genome_build: WS220
Supplementary_files_format_and_content: Normalized bigWig track files were generated using BEADS pipeline in R; Scores represent BEADS normalized values (linear fold enrichment relative to input).

source_name: L3 larvae, input

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage, they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection, DIC pictures are taken and about 100 worms are assayed by DAPI staining to assess the stage.

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (normally 500ug-1mg extract with 2-3ug antibody). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) two times with 57 ul volume each, at 65°C. Samples are treated with RNase, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. The protocol uses the Illumina TruSeq DNA Sample Prep Kit. Prepared samples are sequenced using Illumina GAII or HiSeq 2000 at the High-Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

tag: strain/background

tag: genotype/variation

value: wild-type

value: whole body

tag: developmental stage

tag: Sex

value: mixed male and hermaphrodite

tag: chip antibody lot#


title: H4K16ac ChIP-seq, rep2

source_name: L3 larvae, H4K16ac ChIP


title: Input, rep2

description: Input sample for H4K16ac ChIP-seq, rep2.


title: NE MTT

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

country: Germany

institute: MDC-Berlin

description: Tumor sample obtained from a patient undergoing surgery at the Department of Surgical Gastroenterology, Rigshospitalet.

data_processing:
Ts at the begining of reads were trimmed from sequenced reads
Trimmed reads were mapped to the genome (hg19) with HeliSphere software using a seed length of 18nt and allowing only one mismatch in the seed region.
Only uniquely mapped reads with a minimum length of 21nt and a minimum score of 4 where further analyzed.
Reads arising from internal priming events were further discarded.
To identify polyA sites, read starts that were than 24nt apart were iteratively clustered. Cleavage sites were defined as the median position of the cleavage sites in the cluster.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files of mapped reads
Supplementary_files_format_and_content: Bed files of polyA site clusters. The score represents the number of reads in each cluster.

source_name: Illeum

extract_protocol: Immediately after tumor resection, tumor tissue samples from the surgical specimens were placed in RNAlater® for overnight incubation. Samples were subsequently stored at 80°C until RNA was extracted using TRIzol.

value: Illeum

tag: tumor type

value: Small intestinal neuroendocrine tumor

tag: donor age

tag: gender

value: Male

tag: synaptofysin staining

tag: chromogranin staining

tag: serotonin staining

tag: cd117 staining

tag: ppp staining

tag: vip staining

tag: ghrelin staining

tag: cka staining

value: NA.


title: H4K16ac ChIP-seq, rep1

tag: tissue

tag: chip antibody

tag: chip antibody supplier

tag: chip antibody catalog#


title: 60.24hr.U266.NMP.C

status: Public on Apr 09 2014

city: Melbourne

first: Geoffrey

middle: Mark

last: Matthews

state: Victoria

address: St Andrews Place

department: Cancer Therapeutics

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were quality checked by FastQC and trimmed if necessary for low base quality or adaptor, and then mapped to the human reference genome (GRCh37) using Tophat2 v.2.0.8b with maximum number of multiple hits set to 1 and using the option to map first to the reference transcriptome (Ensembl v.69).
Counts per gene were obtained using HTSeq v.0.5.3p9 with mode intersection-nonempty and normalised using limma-voom v3.14.4 was used to normalise.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include voom normalised log2 values for each Sample

source_name: Multiple myeloma

growth_protocol: JJN3 cells cultured in Dulbecco's Modified Eagle's Medium : Iscove's MDM (1 : 1) + 20% fetal bovine serum (FBS) + Pen/Strep; U266 cells cultured in RPMI medium + 10% FBS + Pen/Strep.

extract_protocol:
Qiagen RNA extraction as per kit instructions.
RNA libraries were prepared for sequencing using the Illumina TruSeq v2 kit and standard Illumina protocol.

treatment_protocol: For panobinostat and NMP single agent treatments cells were treated for 4h or 24h prior to harvest; For 5-Azacytidine treatment, cells were pretreated with 5-Azycytidine for 24h then harvested after a further 4h and 24h; For combination treatments, cells were pre-treated with 5-Azacytidine for 24h then treated with panobinostat and harvested after 4h and 24h.

tag: tissue source

value: peripheral blood

tag: cell line

tag: treatment

value: NMP

tag: timepoint


title: NE CT1

tag: tumor type

tag: donor age

tag: gender

value: Female


title: 56.24hr.U266.Control.C

value: Control


title: 57.24hr.U266.LBH.589.C


title: 58.24hr.U266.5.AZA.C


title: 59.24hr.U266.Combo.C

value: Combo


title: 51.24hr.JJN3.Control.C

value: bone marrow


title: 53.24hr.JJN3.5.AZA.C


title: 55.24hr.JJN3.NMP.C


title: 49.4hr.U266.Combo.C


title: 48.4hr.U266.5.AZA.C


title: 46.4hr.U266.Control.C


title: 54.24hr.JJN3.Combo.C


title: 52.24hr.JJN3.LBH.589.C


title: 47.4hr.U266.LBH.589.C


title: 50.4hr.U266.NMP.C


title: 45.4hr.JJN3.NMP.C


title: 44.4hr.JJN3.Combo.C


title: NE 2TC

tag: synaptofysin staining

tag: chromogranin staining

tag: serotonin staining


title: 43.4hr.JJN3.5.AZA.C


title: PIT

description: Sample purchased from BioChain (Hayward, CA, USA)

source_name: Pituitary

extract_protocol: Isolated by modified guanidine thiocyanate technique and stored in RNA storage buffer

value: Pituitary

value: Normal tissue

tag: cd117 staining

tag: ppp staining

tag: vip staining


title: 41.4hr.JJN3.Control..C


title: 42.4hr.JJN3.LBH.589.C


title: 40.24hr.U266.NMP.B


title: 38.24hr.U266.5.AZA.B


title: 37.24hr.U266.LBH.589.B


title: 33.24hr.JJN3.5.AZA.B


title: 28.4hr.U266.5.AZA.B


title: 27.4hr.U266.LBH.589.B


title: 32.24hr.JJN3.LBH.589.B


title: 31.24hr.JJN3.Control.B


title: 36.24hr.U266.Control.B


title: 30.4hr.U266.NMP.B


title: 19.24hr.U266.Combo


title: 21.4hr.JJN3.Control.B


title: 24.4hr.JJN3.Combo.B


title: 34.24hr.JJN3.Combo.B


title: 29.4hr.U266.Combo.B


title: 23.4hr.JJN3.5.AZA.B


title: 16.24hr.U266.Control


title: 17.24hr.U266.LBH.589


title: 22.4hr.JJN3.LBH.589.B


title: 14.24hr.JJN3.Combo


title: 39.24hr.U266.Combo.B


title: 25.4hr.JJN3.NMP.B


title: 13.24hr.JJN3.5.AZA


title: 10.4hr.U266.NMP


title: 12.24hr.JJN3.LBH.589


title: 26.4hr.U266.Control.B


title: 11.24hr.JJN3.Control


title: 35.24hr.JJN3.NMP.B


title: 20.24hr.U266.NMP


title: 7.4hr.U266.LBH.589


title: 8.4hr.U266.5.AZA


title: 9.4hr.U266.Combo


title: 5.4hr.JJN3.NMP


title: 2.4hr.JJN3.LBH.589


title: 1.4hr.JJN3.Control


title: 3.4hr.JJN3.5.AZA


title: S14

city: Seattle

first: Ruth

last: Kohen

state: WA

address: 1959 Pacific Ave NE

department: Psychiatry and Behavioral Sciences

institute: University of Washington

description: LCM harvest + two rounds of aRNA amplification

data_processing:
Transcripts were mapped and counted using the Applied Biosystems software BioScope 1.2.1. Transcripts were mapped using the UCSC RefGene annotations and the BioScope default seed- and extend approach for mapping. Reads were mapped to the whole genome file, supplemented by a transcript annotation file allowing reads to align across known splice junctions with no gap penalty.
Repeat and ambiguously mapped sequences were removed from the counts files using a UCSC RepeatMasker file. Only reads with a mapping quality of 10 or larger were used.
The BEDTools bamToBed program was used to generate files of read locations. Only reads mapping to the opposite strand were counted.
Genes expressing with greater than zero counts in four or more of our subjects (i.e. more than 5% of subjects) were excluded; for multiple transcripts at a given genomic location, e.g. due to the presence of splice variants, only one transcript with the highest number of counts was retained.
Two alternate normalization methods, length normalization scaling, and noise reduction scaling, were used in parallel and their results compared.
Genome_build: hg19
Supplementary_files_format_and_content: RawCounts, Raw counts per subject and mapped transcript, output of data processing step 3.
Supplementary_files_format_and_content: CleanedRawCounts, Processed version of RawCounts file with genes expressing close to background and duplicate transcripts removed, output of data processing step 4.
Supplementary_files_format_and_content: LengthNormalizationScaledCounts, Normalized and scaled counts, output of data processing step 5.
Supplementary_files_format_and_content: NoiseReductionScaledCounts, Normalized and scaled counts, output of data processing step 5.

source_name: postmortem hippocampus DG granule cells

extract_protocol:
Slide-mounted coronal cryostat sections from mid-hippocampus were stained and dehydrated using the Arcturus HistoGene LCM frozen section staining kit (Life Technologies, NY), and following the manufacturer’s instructions. From each subject, triplicate samples of about 2,000 DG granule cells each were harvested by laser capture microdissection, using an Arcturus AutoPix LCM system and CapSure Macro LCM caps (Molecular Devices, CA). Triplicates were processed separately during cell harvest, RNA extraction, and aRNA amplification in order to reduce experimental noise introduced during these stages of the experiment. Harvested cells were removed from the caps and RNA extracted using PicoPure RNA isolation kits (Life Technologies, NY). RNA was then linearly amplified over two rounds of aRNA amplification, using MessageAmp II aRNA amplification kits (Life Technologies, NY), and following the manufacturer’s protocol. The quality and concentration of aRNA was checked by spectrophotometry. Equimolar amounts of triplicate aRNA samples for each of the 79 subjects were then pooled for the preparation of sequencing libraries.
Sequencing libraries were prepared using Applied Biosystem's Total RNA Sequencing Kit, following the directions for Whole Transcriptome Libraries, and analyzed with an Applied Biosystems SOLiD 4 high-throughput sequencer (Life Technologies, NY).

tag: age at death

value: M

tag: diagnosis

value: schizophrenia


title: 4.4hr.JJN3.Combo


title: S16

value: F


title: S15


title: S9


title: S11


title: S10


title: S8


title: S5


title: S4


title: S6


title: S7


title: S1


title: D17

value: depression


title: S3


title: S2


title: 18.24hr.U266.5.AZA


title: D16


title: 6.4hr.U266.Control


title: D15


title: S17


title: S13


title: D13


title: D14


title: S12


title: 15.24hr.JJN3.NMP


title: D12


title: D10


title: D11


title: D9


title: D7


title: D8


title: D6


title: D4


title: D5


title: D1


title: C27

value: control


title: C29


title: D3


title: D2


title: C26


title: C22


title: C24


title: C23


title: C20


title: C28


title: C18


title: C12


title: C19


title: C13


title: C21


title: C16


title: C11


title: C14


title: C10


title: C17


title: C8


title: C9


title: C25


title: C5


title: C15


title: C2


title: B16

value: bipolar


title: C4


title: B15


title: C3


title: B12


title: B11


title: B13


title: B10


title: B7


title: B9


title: Wild type DP thymocytes replicate 2

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
Reads aligned to mm9 using Tophat2
All UCSC known genes quantified and tested for differential expression using Cuffdiff2 (MTC alpha cutoff 0.05)
Cuffdiff2 data imported into cummeRbund v1.99.3 for analysis
Replicate FPKM values summarized by condition
Table of differential results exported via diffTable
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited table of gene-level attributes, summarized expression values, and differential expression results.

source_name: Wild type DP thymocytes

extract_protocol:
CD4+ CD8+ DP thymocytes were isolated by cell sorting to a purity of more than 95%. RNA from cells was extracted using either Trizol (Invitrogen) or with the RNeasy mini kit (QIAGEN) according to the manufactures instructions.
Libraries were generated for sequencing using the TruSeq RNA sample preparation kit (Illumina) according to the manufactures instructions.

tag: strain

tag: genotype/variation

value: Wild type

tag: cell type

value: CD4+/CD8+ sorted thymocytes


title: Wild type DP thymocytes replicate 3


title: B5


title: B6


title: mir181a1/b1 Knockout DP thymocytes replicate 3

source_name: mir181a1/b1 Knockout DP thymocytes

value: mir181a1/b1 Knockout


title: C7


title: B8


title: Wild type DP thymocytes replicate 1


title: B4


title: B1


title: C6


title: mir181a1/b1 Knockout DP thymocytes replicate 1


title: B3


title: B2


title: B14


title: MJB147_RR_red-bisulphite_ESC_mouse_R4

status: Public on Apr 08 2014

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

description: reduced representation (MspI treatment) of reduced bisulphite treatment for mouse ESC, replicate 4

data_processing:
fastq file processed using trim_galore (version 0.2.6) and aligned using bismark (version  0.10.0).
Modifications at each site were then counted using the command mpileup from samtools (version  0.1.18).
The previous steps have been wrapped in the program bsExpress (http://code.google.com/p/oxbs-sequencing-qc/wiki/bsExpressDoc).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are in BedGraph Track Format (http://genome.ucsc.edu/goldenPath/help/bedgraph.html), extended with additional columns. Columns are tab-separated and they are, respectively: chromosome, start, end, modification percentage, modification count, total count, strand.

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells, derived in-house from Black6/Castaneous mice, were cultured on gelatine-coated plates in a DMEM-KO medium (Invitrogen) supplemented with 10% FCS, 100 µM non-essential amino acids, 2 mM glutamine, 1 mM sodium pyruvate, 50 µg/ml penicillin/streptomycin (all GIBCO), 100 µM 2-mercaptoethanol (Sigma), 1000 U/ml mouse Leukemia Inhibitory Factor (Chemicon) and 2i (MEK inhibitor PD0325901 (Axon) and GSK-3 inhibitor CT99021 (Axon)).

extract_protocol:
Cells were resuspended in lysis buffer (100 mM Tris, pH 5.5, 5 mM EDTA, 200 mM NaCl, 0.2% SDS), supplemented with 400 µg/ml proteinase K (Invitrogen) and 200 µg/ml RNase A (Qiagen), and were incubated at 55°C overnight. DNA was extracted using phenol-chloroform and Phase Lock Gel Light tubes (5 Prime), was precipitated in 70% ethanol and resuspended in pure water.
Samples of genomic DNA (12 x 1 µg) were digested with MspI (1 µL) in a digestion (30 µL total volume) overnight at 37 °C. To terminate the digestions, EDTA (3 µL, 0.5 M) was added. The DNA was subsequently worked up using the GeneJET PCR kit and eluted in EB (60 µL). The internal control DNA (1 µL, 0.6 ng/µL) was then added to all samples. All twelve MspI digested samples were subjected to an Illumina library preparation with the Illumina TruSeq kit using a 1/10 dilution of adapters. For the last AMPureXP purification from the TruSeq protocol the DNA was left to dry for 30 mins and eluted in water.

treatment_protocol: no treatment applied

value: MspI

tag: bisulphite treatment

value: reduced bisulphite


title: MJB146_RR_red-bisulphite_ESC_mouse_R3

description: reduced representation (MspI treatment) of reduced bisulphite treatment for mouse ESC, replicate 3


title: MJB145_RR_red-bisulphite_ESC_mouse_R2

description: reduced representation (MspI treatment) of reduced bisulphite treatment for mouse ESC, replicate 2


title: MJB144_RR_red-bisulphite_ESC_mouse_R1

description: reduced representation (MspI treatment) of reduced bisulphite treatment for mouse ESC, replicate 1


title: MJB140_RR_ox-bisulphite_ESC_mouse_R1

description: reduced representation (MspI treatment) of oxidative bisulphite treatment for mouse ESC, replicate 1

value: oxidative bisulphite


title: MJB139_RR_bisulphite_ESC_mouse_R4

description: reduced representation (MspI treatment) of bisulphite treatment for mouse ESC, replicate 4

value: bisulphite


title: MJB143_RR_ox-bisulphite_ESC_mouse_R4

description: reduced representation (MspI treatment) of oxidative bisulphite treatment for mouse ESC, replicate 4


title: MJB141_RR_ox-bisulphite_ESC_mouse_R2

description: reduced representation (MspI treatment) of oxidative bisulphite treatment for mouse ESC, replicate 2


title: MJB142_RR_ox-bisulphite_ESC_mouse_R3

description: reduced representation (MspI treatment) of oxidative bisulphite treatment for mouse ESC, replicate 3


title: mir181a1/b1 Knockout DP thymocytes replicate 2


title: MJB136_RR_bisulphite_ESC_mouse_R1

description: reduced representation (MspI treatment) of bisulphite treatment for mouse ESC, replicate 1


title: MJB138_RR_bisulphite_ESC_mouse_R3

description: reduced representation (MspI treatment) of bisulphite treatment for mouse ESC, replicate 3


title: MJB137_RR_bisulphite_ESC_mouse_R2

description: reduced representation (MspI treatment) of bisulphite treatment for mouse ESC, replicate 2


title: Mouse Ts65Dn

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

description:
14.5 days old mouse embryos
processed data file: final_mouse_QN_file.txt

data_processing:
Basecalling performed with CASAVA version 1.8
Mapping using GEM, default parameters
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: final_mouse_QN_file.txt: text file, chromosome, start, end, gene symbol, rpkm values, rpkm values after quantile normalization, log2 fold change (TsT1/TsN1)
Supplementary_files_format_and_content: final_QN_4rep_file.sorted.txt: text file, chromosome, start, end, gene type, gene symbol, rpkm values, rpkm values after quantile normalization, log2 fold change
Supplementary_files_format_and_content: final_unr_QN_file.txt: text file, chromosome, start, end, ensembl gene ID, gene symbol, rpkm values, rpkm values after quantile normalization, log2 fold change
Supplementary_files_format_and_content: Expression_iPS_cells.txt: text file, chromosome, start, end, strand, ensembl gene ID, gene symbol, rpkm values

extract_protocol:
Illumina mRNA-Seq Sample Preparation kit
Total RNA was collected using the TRIzol® reagent (Life Technologies) following the manufacturer’s instructions.

tag: disease/status

tag: tissue

value: Mouse embryonic fibroblasts (MEFs)


title: Mouse WT

value: wild type


title: adult AT2, biological replicate 1, single cells, transcriptome 37

city: Stanford CA

first: Barbara

last: Treutlein

address: 318 Campus Drive

department: Bioengineering

institute: Stanford University

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: distal lung epithelium

growth_protocol: Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols. Timed-pregnant C57BL/6J females (JAX) were used for all embryonic time points reported with gestation age verified by crown-rump length prior to use.  For adult mice, a transgenic-labeling approach was employed. Mice were bred to be homozygous for a knock-in allele into Sftpc encoding for a reverse tetracycline transactivator (SftpC-Cre-ERT2-rtTA) and heterozygous for an inserted transgene, which drives the expression of a GFP tagged human histone 1 in a tetracycline-dependent manner (tetO-HIST1H2BJ/GFP).

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells. In addition, one "no cell control" was prepared using reagents without any cell input in a PCR tube.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: To obtain AT2 cells from the adult lung, an adult mouse whose genome contained a tetracycline-responsive, nuclear reporter only transcribed in cells transcribing Sftpc (Sftpc-Cre-ERT2-rtta-/- tetO-HIST1H2BJ-GFP+/-) was injected with 2 mg of doxycycline (Sigma) and used 3 days afterwards. Pregnant and non-pregnant adult mice were euthanized by CO2 administration. For embryonic samples (E14.5, 16.5, and 18.5), embryonic lungs were isolated and either a single embryonic lung was used or 5-7 sibling lungs were pooled. For the adult experiment, the pulmonary vasculature was cleared and lungs were gently inflated with digestion buffer prior to isolation and mincing of the lung. All tissue was digested at 37C for 45 min using Elastase and DNase I, triturated and subsequently filtered using 100µm and 40µm strainers to obrtain a single cell suspension. Embryonic lung epithelial cells were purified by magnetic-assisted cell sorting using CD45 depletion followed by EpCAM enrichment. Transgenically labeled adult AT2 cells were purified by fluorescence-assisted cell sorting.

value: lung

tag: age

value: post natal day 107

tag: genotype


title: adult AT2, biological replicate 1, single cells, transcriptome 38


title: adult AT2, biological replicate 1, single cells, transcriptome 41


title: adult AT2, biological replicate 1, single cells, transcriptome 40


title: C1

tag: gender

value: M


title: adult AT2, biological replicate 1, single cells, transcriptome 34


title: adult AT2, biological replicate 1, single cells, transcriptome 45


title: adult AT2, biological replicate 1, single cells, transcriptome 46


title: adult AT2, biological replicate 1, single cells, transcriptome 36


title: adult AT2, biological replicate 1, single cells, transcriptome 44


title: adult AT2, biological replicate 1, single cells, transcriptome 43


title: adult AT2, biological replicate 1, single cells, transcriptome 39


title: adult AT2, biological replicate 1, single cells, transcriptome 42


title: adult AT2, biological replicate 1, single cells, transcriptome 35


title: adult AT2, biological replicate 1, single cells, transcriptome 33


title: adult AT2, biological replicate 1, single cells, transcriptome 30


title: adult AT2, biological replicate 1, single cells, transcriptome 32


title: adult AT2, biological replicate 1, single cells, transcriptome 28


title: adult AT2, biological replicate 1, single cells, transcriptome 27


title: adult AT2, biological replicate 1, single cells, transcriptome 25


title: adult AT2, biological replicate 1, single cells, transcriptome 23


title: adult AT2, biological replicate 1, single cells, transcriptome 24


title: adult AT2, biological replicate 1, single cells, transcriptome 22


title: adult AT2, biological replicate 1, single cells, transcriptome 20


title: adult AT2, biological replicate 1, single cells, transcriptome 29


title: adult AT2, biological replicate 1, single cells, transcriptome 31


title: adult AT2, biological replicate 1, single cells, transcriptome 21


title: adult AT2, biological replicate 1, single cells, transcriptome 18


title: adult AT2, biological replicate 1, single cells, transcriptome 19


title: adult AT2, biological replicate 1, single cells, transcriptome 17


title: adult AT2, biological replicate 1, single cells, transcriptome 16


title: adult AT2, biological replicate 1, single cells, transcriptome 26


title: adult AT2, biological replicate 1, single cells, transcriptome 5


title: adult AT2, biological replicate 1, single cells, transcriptome 8


title: adult AT2, biological replicate 1, single cells, transcriptome 12


title: adult AT2, biological replicate 1, single cells, transcriptome 4


title: adult AT2, biological replicate 1, single cells, transcriptome 13


title: adult AT2, biological replicate 1, single cells, transcriptome 9


title: adult AT2, biological replicate 1, single cells, transcriptome 7


title: adult AT2, biological replicate 1, single cells, transcriptome 6


title: adult AT2, biological replicate 1, single cells, transcriptome 14


title: adult AT2, biological replicate 1, single cells, transcriptome 10


title: adult AT2, biological replicate 1, single cells, transcriptome 15


title: adult AT2, biological replicate 1, single cells, transcriptome 3


title: adult AT2, biological replicate 1, single cells, transcriptome 11


title: adult AT2, biological replicate 1, single cells, transcriptome 2


title: E14.5, biological replicate 1, single cells, transcriptome 44

value: Embryonic day 14.5


title: E14.5, biological replicate 1, single cells, transcriptome 42


title: E14.5, biological replicate 1, single cells, transcriptome 37


title: E14.5, biological replicate 1, single cells, transcriptome 38


title: E14.5, biological replicate 1, single cells, transcriptome 41


title: E14.5, biological replicate 1, single cells, transcriptome 36


title: E14.5, biological replicate 1, single cells, transcriptome 40


title: E14.5, biological replicate 1, single cells, transcriptome 39


title: E14.5, biological replicate 1, single cells, transcriptome 35


title: E14.5, biological replicate 1, single cells, transcriptome 34


title: E14.5, biological replicate 1, single cells, transcriptome 33


title: E14.5, biological replicate 1, single cells, transcriptome 32


title: adult AT2, biological replicate 1, single cells, transcriptome 1


title: E14.5, biological replicate 1, single cells, transcriptome 30


title: E14.5, biological replicate 1, single cells, transcriptome 45


title: E14.5, biological replicate 1, single cells, transcriptome 29


title: E14.5, biological replicate 1, single cells, transcriptome 28


title: E14.5, biological replicate 1, single cells, transcriptome 25


title: E14.5, biological replicate 1, single cells, transcriptome 19


title: E14.5, biological replicate 1, single cells, transcriptome 26


title: E14.5, biological replicate 1, single cells, transcriptome 24


title: E14.5, biological replicate 1, single cells, transcriptome 21


title: E14.5, biological replicate 1, single cells, transcriptome 22


title: E14.5, biological replicate 1, single cells, transcriptome 31


title: E14.5, biological replicate 1, single cells, transcriptome 43


title: E14.5, biological replicate 1, single cells, transcriptome 23


title: E14.5, biological replicate 1, single cells, transcriptome 15


title: E14.5, biological replicate 1, single cells, transcriptome 14


title: E14.5, biological replicate 1, single cells, transcriptome 10


title: E14.5, biological replicate 1, single cells, transcriptome 13


title: E14.5, biological replicate 1, single cells, transcriptome 20


title: E14.5, biological replicate 1, single cells, transcriptome 11


title: E14.5, biological replicate 1, single cells, transcriptome 12


title: E14.5, biological replicate 1, single cells, transcriptome 16


title: E14.5, biological replicate 1, single cells, transcriptome 7


title: E14.5, biological replicate 1, single cells, transcriptome 8


title: E14.5, biological replicate 1, single cells, transcriptome 6


title: E14.5, biological replicate 1, single cells, transcriptome 5


title: E14.5, biological replicate 1, single cells, transcriptome 27


title: E14.5, biological replicate 1, single cells, transcriptome 18


title: E14.5, biological replicate 1, single cells, transcriptome 4


title: E14.5, biological replicate 1, single cells, transcriptome 17


title: E14.5, biological replicate 1, single cells, transcriptome 2


title: E14.5, biological replicate 1, single cells, transcriptome 3


title: E14.5, biological replicate 1, single cells, transcriptome 1


title: E18.5, biological replicate 3, 200 cell bulk control, transcriptome 1

value: Embryonic day 18.5


title: E14.5, biological replicate 1, single cells, transcriptome 9


title: E18.5, biological replicate 3, single cells, transcriptome 26


title: E18.5, biological replicate 3, single cells, transcriptome 17


title: E18.5, biological replicate 3, single cells, transcriptome 21


title: E18.5, biological replicate 3, single cells, transcriptome 19


title: E18.5, biological replicate 3, single cells, transcriptome 24


title: E18.5, biological replicate 3, single cells, transcriptome 23


title: E18.5, biological replicate 3, single cells, transcriptome 22


title: E18.5, biological replicate 3, single cells, transcriptome 15


title: E18.5, biological replicate 3, single cells, transcriptome 14


title: E18.5, biological replicate 3, single cells, transcriptome 12


title: E18.5, biological replicate 3, single cells, transcriptome 20


title: E18.5, biological replicate 3, single cells, transcriptome 25


title: E18.5, biological replicate 3, single cells, transcriptome 16


title: E18.5, biological replicate 3, single cells, transcriptome 10


title: E18.5, biological replicate 3, single cells, transcriptome 9


title: E18.5, biological replicate 3, single cells, transcriptome 8


title: E18.5, biological replicate 3, single cells, transcriptome 7


title: E18.5, biological replicate 3, single cells, transcriptome 6


title: E18.5, biological replicate 3, single cells, transcriptome 5


title: E18.5, biological replicate 3, single cells, transcriptome 4


title: E18.5, biological replicate 3, single cells, transcriptome 3


title: E18.5, biological replicate 3, single cells, transcriptome 2


title: E18.5, biological replicate 3, single cells, transcriptome 18


title: E18.5, biological replicate 3, single cells, transcriptome 1


title: E18.5, biological replicate 2, single cells, transcriptome 34


title: E18.5, biological replicate 3, single cells, transcriptome 13


title: E18.5, biological replicate 2, single cells, transcriptome 31


title: E18.5, biological replicate 3, single cells, transcriptome 11


title: E18.5, biological replicate 2, single cells, transcriptome 28


title: E18.5, biological replicate 2, single cells, transcriptome 25


title: E18.5, biological replicate 2, single cells, transcriptome 27


title: E18.5, biological replicate 2, single cells, transcriptome 24


title: E18.5, biological replicate 2, single cells, transcriptome 23


title: E18.5, biological replicate 2, single cells, transcriptome 29


title: E18.5, biological replicate 2, single cells, transcriptome 19


title: E18.5, biological replicate 2, single cells, transcriptome 21


title: E18.5, biological replicate 2, single cells, transcriptome 20


title: E18.5, biological replicate 2, single cells, transcriptome 22


title: E18.5, biological replicate 2, single cells, transcriptome 30


title: E18.5, biological replicate 2, single cells, transcriptome 26


title: E18.5, biological replicate 2, single cells, transcriptome 18


title: E18.5, biological replicate 2, single cells, transcriptome 16


title: E18.5, biological replicate 2, single cells, transcriptome 17


title: E18.5, biological replicate 2, single cells, transcriptome 15


title: E18.5, biological replicate 2, single cells, transcriptome 13


title: E18.5, biological replicate 2, single cells, transcriptome 14


title: E18.5, biological replicate 2, single cells, transcriptome 12


title: E18.5, biological replicate 2, single cells, transcriptome 33


title: E18.5, biological replicate 2, single cells, transcriptome 10


title: E18.5, biological replicate 2, single cells, transcriptome 11


title: E18.5, biological replicate 2, single cells, transcriptome 32


title: E18.5, biological replicate 2, single cells, transcriptome 7


title: E18.5, biological replicate 2, single cells, transcriptome 9


title: E18.5, biological replicate 2, single cells, transcriptome 8


title: E18.5, biological replicate 2, single cells, transcriptome 6


title: E18.5, biological replicate 2, single cells, transcriptome 5


title: E18.5, biological replicate 2, single cells, transcriptome 4


title: E18.5, biological replicate 2, single cells, transcriptome 1


title: E18.5, biological replicate 2, single cells, transcriptome 3


title: E18.5, biological replicate 2, single cells, transcriptome 2


title: E18.5, biological replicate 1, no cell control, transcriptome 1


title: E18.5, biological replicate 1, single cells, transcriptome 20


title: E18.5, biological replicate 1, single cells, transcriptome 17


title: E18.5, biological replicate 1, single cells, transcriptome 19


title: E18.5, biological replicate 1, single cells, transcriptome 14


title: E18.5, biological replicate 1, single cells, transcriptome 12


title: E18.5, biological replicate 1, single cells, transcriptome 16


title: E18.5, biological replicate 1, single cells, transcriptome 11


title: E18.5, biological replicate 1, single cells, transcriptome 18


title: E18.5, biological replicate 1, single cells, transcriptome 9


title: E18.5, biological replicate 1, single cells, transcriptome 10


title: E18.5, biological replicate 1, single cells, transcriptome 8


title: E18.5, biological replicate 1, single cells, transcriptome 7


title: E18.5, biological replicate 1, single cells, transcriptome 3


title: E18.5, biological replicate 1, single cells, transcriptome 4


title: E18.5, biological replicate 1, single cells, transcriptome 5


title: E18.5, biological replicate 1, single cells, transcriptome 6


title: WT_HLH1_FCL_(20130920_1_2_12)

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release WS220 (Feb 2011) of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random. 2. We extracted properly paired reads mapped only to C. elegans (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: crosslinked ChIPed chromatin

extract_protocol:
N2 wildtype adults were formaldehyde crosslinked (FCL). Chromatin was fragmented and solubilized by sonication, and HLH-1 was pulled-down with anti-FLAG antibody.
MNase_ChIP_Seq_protocol.rtf

value: adults

value: WT

tag: antibody

value: anti-FLAG


title: EAP1-null_input

city: San Diego

first: Yun

last: Zhu

address: 9300 Gilman Dr

department: Chemistry Departmant

institute: UCSD

data_processing:
All sequences were mapped to C.elegans genome assembly (WS220) by BOWTIE package (Langmead B,2009) allowing for zero mismatches and removing monoclonal reads (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, 2009)
Genome_build: WS220
Supplementary_files_format_and_content: BED

source_name: whole young adult worm lysates

growth_protocol: Worms were maintained at 16 degrees until the appropriate generation and then switched to 25 degrees at birth. They were snap frozen at the young adult stage

extract_protocol:
Chromatin preparation was performed as described in (Stock et al., 2007) with some modifications. Strains were maintained at 16°C until the appropriate generation and then shifted to 25°C after birth. 50 µl packed young adult worms were subjected to five freeze/thaw cycles in liquid N2, and fixed in 1% formaldehyde in PBS (10 min, RT). During fixation, worms were dounced 100 times in a glass homogenizer. Fixation was stopped by addition of Glycine to 0.125M (5 min, RT). Worms were washed in cold PBS, before “swelling” buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl and 0.1% NP-40) was added to lyse the cells (10 min, 4°C). After resuspension in “sonication” buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and 0.1% SDS), nuclei were sonicated using a Misonix 3000 (Amplitude 60; 25 cycles; 15s ‘on’, 45s ‘off’; 4°C). The resulting material was centrifuged twice (10 min, 4°C) at 14,000 rpm. Swelling and sonication buffers were supplemented with 5 mM NaF, 1 mM PMSF, and protease inhibitor cocktail (Roche).
ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6000) and the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads. ChIP-seq libraries were generated from two biological repeats for G0 and G20, a single repeat for G10, and four Input samples.

tag: developmental stage

value: young adult

value: input


title: E18.5, biological replicate 1, single cells, transcriptome 2


title: spr-5_G20_input_rep1

tag: generation


title: E18.5, biological replicate 1, 200 cell bulk control, transcriptome 1


title: E18.5, biological replicate 1, single cells, transcriptome 1


title: EAP1-null

value: EAP-1 antibody


title: spr-5_G10_input


title: E18.5, biological replicate 1, single cells, transcriptome 13


title: WT_input_rep2


title: spr-5_G20_rep2_#2


title: WT_input_rep1


title: spr-5_G20_input_rep2


title: spr-5_G10


title: E18.5, biological replicate 1, single cells, transcriptome 15


title: E16.5, biological replicate 1, single cells, transcriptome 26

value: Embryonic day 16.5


title: E16.5, biological replicate 1, single cells, transcriptome 27


title: WT_rep2_#1


title: WT_rep2_#2


title: E16.5, biological replicate 1, single cells, transcriptome 24


title: knl2_input_(20120223_2)

description:
soluble chromatin
age:embryos, strain:N2, mutant:WT, RNAi:knl2

data_processing:
1. We used Novoalign (2.07.00 - Aug 5 2010) to map paired-end 25bp reads to release WS220 (Feb 2011) of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads mapped only to C. elegans (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.
Genome_build: WS220
Supplementary_files_format_and_content: bam, wig, and bed

source_name: soluble chromatin

extract_protocol:
KNL-2 depleted (knl-2(RNAi),knl2) embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction. KNL-2 was depleted by RNAi by feeding N2 worms on bacteria expressing dsRNA, so the depletion is entirely post-transcriptional.
see MNase_ChIP_Seq_protocol

value: embryo

tag: genetic background

tag: knockdown


title: knl2_CenH3_(20120223_3)

description:
ChIPed chromatin
age:embryos, backgroun strain:N2, mutant:WT, RNAi:knl2, antibody:anti-cenH3

source_name: ChIPed chromatin

extract_protocol:
KNL-2 depleted (knl-2(RNAi),knl2) embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction followed by ChIP with anti-cenH3 (CENP-A, HCP-3) antibody. KNL-2 was depleted by RNAi by feeding N2 worms on bacteria expressing dsRNA, so the depletion is entirely post-transcriptional.
see MNase_ChIP_Seq_protocol

tag: chip antibody


title: E16.5, biological replicate 1, single cells, transcriptome 23


title: E16.5, biological replicate 1, single cells, transcriptome 22


title: WT_pellet_2min_(20111011_2)

description:
insoluble chromatin
age:embryos, strain:N2, mutant:WT

source_name: insoluble chromatin

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction, insoluble chromatin was retained.
see MNase_ChIP_Seq_protocol


title: WT_input_FCL_(20120817_3_12)

description:
crosslinked chromatin
age:embryos, strain:N2, mutant:WT

source_name: crosslinked chromatin

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was formaldehyde crosslinked (FCL) and solubilized by sonication.
see MNase_ChIP_Seq_protocol


title: WT_pellet_10min_(20110914_7)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 10 minutes and soluble chromatin was purified by needle extraction, insoluble chromatin was retained.
see MNase_ChIP_Seq_protocol


title: WT_input_5min_(20110706_3)

description:
soluble chromatin
age:embryos, strain:N2, mutant:WT

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 5 minutes and soluble chromatin was purified by needle extraction.
see MNase_ChIP_Seq_protocol


title: E16.5, biological replicate 1, single cells, transcriptome 18


title: WT_input_2min_rep1_(20110706_2)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction.
see MNase_ChIP_Seq_protocol


title: WT_input_2min_rep2_(20111011_1)


title: E16.5, biological replicate 1, single cells, transcriptome 17


title: WT_input_1min_(20110706_1)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 1 minute and soluble chromatin was purified by needle extraction.
see MNase_ChIP_Seq_protocol


title: WT_rep1


title: WT_input_10min_(20110706_4)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 10 minutes and soluble chromatin was purified by needle extraction.
see MNase_ChIP_Seq_protocol


title: E16.5, biological replicate 1, single cells, transcriptome 19


title: E16.5, biological replicate 1, single cells, transcriptome 25


title: WT_HCP4_FCL_(20120817_3_4)

description:
crosslinked ChIPed chromatin
age:embryos, strain:N2, mutant:WT, antibody:anti-CENP-C

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was formaldehyde crosslinked (FCL) and solubilized by sonication followed by ChIP with anti-CENP-C (HCP-4) antibody.
see MNase_ChIP_Seq_protocol

value: CENP-C


title: WT_CenH3_2min_rep2_(20111011_3)

description:
ChIPed chromatin
age:embryos, strain:N2, mutant:WT, antibody:anti-cenH3

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction followed by ChIP with anti-cenH3 (CENP-A, HCP-3) antibody.
see MNase_ChIP_Seq_protocol


title: knl2_pellet_(20120223_8)

description:
insoluble chromatin
age:embryos, strain:N2, mutant:WT, RNAi:knl2

extract_protocol:
KNL-2 depleted (knl-2(RNAi),knl2) embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction, insoluble chromatin was retained. KNL-2 was depleted by RNAi by feeding N2 worms on bacteria expressing dsRNA, so the depletion is entirely post-transcriptional.
see MNase_ChIP_Seq_protocol


title: E16.5, biological replicate 1, single cells, transcriptome 21


title: E16.5, biological replicate 1, single cells, transcriptome 16


title: E16.5, biological replicate 1, single cells, transcriptome 14


title: E16.5, biological replicate 1, single cells, transcriptome 13


title: E16.5, biological replicate 1, single cells, transcriptome 12


title: WT_CenH3_5min_(20110706_7)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 5 minutes and soluble chromatin was purified by needle extraction followed by ChIP with anti-cenH3 (CENP-A, HCP-3) antibody.
see MNase_ChIP_Seq_protocol


title: spr-5_G20_rep1


title: E16.5, biological replicate 1, single cells, transcriptome 11


title: E16.5, biological replicate 1, single cells, transcriptome 20


title: WT_CenH3_1min_(20110706_5)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 1 minute and soluble chromatin was purified by needle extraction followed by ChIP with anti-cenH3 (CENP-A, HCP-3) antibody.
see MNase_ChIP_Seq_protocol


title: E16.5, biological replicate 1, single cells, transcriptome 10

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells. In addition, one "no cell control" was prepared using reagents without any cell input in a PCR tube.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.


title: WT_CenH3_2min_rep1_(20110706_6)


title: E16.5, biological replicate 1, single cells, transcriptome 8


title: E16.5, biological replicate 1, single cells, transcriptome 9


title: WT_CenH3_10min_(20110706_8)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 10 minutes and soluble chromatin was purified by needle extraction followed by ChIP with anti-cenH3 (CENP-A, HCP-3) antibody.
see MNase_ChIP_Seq_protocol


title: spr-5_G20_rep2_#1

extract_protocol:
Chromatin preparation was performed as described in (Stock et al., 2007) with some modifications. Strains were maintained at 16°C until the appropriate generation and then shifted to 25°C after birth. 50 µl packed young adult worms were subjected to five freeze/thaw cycles in liquid N2, and fixed in 1% formaldehyde in PBS (10 min, RT). During fixation, worms were dounced 100 times in a glass homogenizer. Fixation was stopped by addition of Glycine to 0.125M (5 min, RT). Worms were washed in cold PBS, before “swelling” buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl and 0.1% NP-40) was added to lyse the cells (10 min, 4°C). After resuspension in “sonication” buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and 0.1% SDS), nuclei were sonicated using a Misonix 3000 (Amplitude 60; 25 cycles; 15s ‘on’, 45s ‘off’; 4°C). The resulting material was centrifuged twice (10 min, 4°C) at 14,000 rpm. Swelling and sonication buffers were supplemented with 5 mM NaF, 1 mM PMSF, and protease inhibitor cocktail (Roche).
ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6000) and the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads. ChIP-seq libraries were generated from two biological repeats for G0 and G20, a single repeat for G10, and four Input samples.


title: E16.5, biological replicate 1, single cells, transcriptome 7


title: E16.5, biological replicate 1, single cells, transcriptome 4


title: E16.5, biological replicate 1, single cells, transcriptome 2


title: E16.5, biological replicate 1, single cells, transcriptome 3


title: E16.5, biological replicate 1, single cells, transcriptome 5


title: E16.5, biological replicate 1, single cells, transcriptome 1


title: T2N iPS cells

description: processed data file: Expression_iPS_cells.txt

source_name: twin 2_euploid_iPSCs

extract_protocol:
Illumina mRNA-Seq Sample Preparation kit
Total RNA was collected using the TRIzol® reagent (Life Technologies) following the manufacturer’s instructions.

value: Euploid

value: Induced pluripotent stem cells


title: T2N H3K4me3 ChIP

data_processing:
Basecalling performed with CASAVA version 1.8
Mapping with BWA, default parameters
Peak calling by HOMER
Genome_build: hg19
Supplementary_files_format_and_content: H3K4me3_2Ain1B.txt: text file, peak coordinates T2N, normalized tag count of peaks in T2N, peak coordinates T1DS, normalized tag count of peaks in T1DS

source_name: twin 2_euploid_fetal primary fibroblasts_ChIP

extract_protocol:
Histone-DNA complexes were isolated with H3K4me3 antibody (Abcam ab8580)
ChIP-Seq DNA Sample Prep Kit from Illumina

tag: disease

value: Fetal primary fibroblasts

value: H3K4me3 antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: T1DS H3K4me3 ChIP

source_name: twin 1_T21_fetal primary fibroblasts_ChIP

value: Trisomy 21


title: Normal twin MZ2

description: processed data file: final_QN_4rep_file.sorted.txt

source_name: normal twin Cord fibroblasts

value: Cord fibroblasts


title: T2N RRBS

data_processing:
Basecalling performed with CASAVA version 1.7
Mapping using Bismark aligner (-n 3 -l 20 -I 20)
MethylKit R package was used to calculate methylation percentages per each CpG
Genome_build: hg19
Supplementary_files_format_and_content: methT21_N.txt: genomic position of each CpG, methylation percentage in T1DS, methylation percentage in T2N

source_name: twin 2_euploid_fetal primary fibroblasts

extract_protocol:
DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit.
RRBS protocol: genomic DNA digested with MspI restriction enzyme, end repair, A-tailing,adapter ligation, size selection, bisulfite conversion, PCR amplification

value: Eupoid


title: T2N DNaseI Rep2

description: Sample 4

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Illumina chastity filtered reads were aligned to the Human GRCh37/hg19 reference with bowtie version 0.12.7 with the following parameter equivalents: bowtie -p <nodes> -n 2 -m 1 --best --phred33-quals
Read densities where obtained by generating a sliding window (+/-75bp) across the genome at 20bp step, using the bedmap utility from the BEDOPS suite: https://github.com/bedops/bedops
Density bigWigfiles were generated with bedGraphToBigWig (UCSC)
FDR 1% Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration for 36mer mappability
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format

source_name: twin 2_euploid_fetal primary fibroblasts_DNaseI

extract_protocol:
Refer to the Nuclei isolation section of John et.al. Current Protocols in Molecular Biology PMID: 23821440
Illumina TruSeq v2


title: Normal twin MZ1


title: ILTV_RNASeq_Inoculated_2

city: College Park

first: Jose

middle: Adrian

last: Carrillo

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

data_processing:
Sequencing using Illumina HiSeq 2000
Alignment to the galGal3 genome reference were obtained with Bowtie, trimming the first 15 5' nucleotides, resulting in reads of 35 bases
Aligned bam files were transformed to bed files, using the bamtobed function in bedtools
Normalized reads counts was obtained using GenomicRanges and DESeq
The final list of genes with their respective fold change, log2 fold change , p-value and adjusted p value was obtained using DESeq
Genome_build: Gallus_gallus-2.1 (galGal3)
Supplementary_files_format_and_content: Count_Normalized.txt is a matrix where each row represents a gene. The first column shows gene names, the other columns are normalized counts for each sample. Columns labeled KZ59-10 and KZ59-11 correspond to inoculated, and KZ59-9 to control
Supplementary_files_format_and_content: GenesTable.txt is a matrix with columns for gene id, baseMean across samples, baseMeanA corresponds to inoculated and baseMeanB to control, fold changes between conditions, log2fold change between conditions, the p-value and the adjusted p-value for each gene.

organism: Gallus gallus

source_name: Tracheal scraps

extract_protocol:
mRNA was extracted directly from tracheal samples using the Oligotex Direct mRNA Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. First strand cDNA was generated using the SuperScript II Reverse Transcriptase Kit (Invitrogen, Carlsbad, CA, USA) with random hexamers (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions in a final volume of 40µl. Second strand cDNA was synthesized using DNA polymerase I (NEB, Ipswich, MA, USA) supplemented with 30nmol dNTPs and 2U RNase H (Invitrogen, Carlsbad, CA, USA), incubated at 25° C for 2.5 hours, then purified with QIAquick PCR purification kit (Qiagen, Valencia, CA, USA).
Libraries were constructed using Multiplexing Sample Preparation Oligonucleotide Kit (Illumina, San Diego, CA, USA) following the manufacturer's instructions. Briefly, the double stranded cDNA (dscDNA) was sonicated to approximately 200-500bp using a Bioruptor sonicator (Diagenode, Denville, NJ, USA) in a final volume of 50µl for 40 minutes. The resulting fragments were repaired using End repair module (NEB, Ipswich, MA, USA) and 3′A was added by Klenow Fragment (NEB, Ipswich, MA, USA).  The Solexa adaptors (Illumina, San Diego, CA, USA) were then ligated to the dscDNA fragments by T4 DNA ligase (NEB, Ipswich, MA, USA). PCR with 18 cycles was performed using the adaptor primers and index primers. PCR products with a length of 200-500bp were isolated by QIAquick Gel purification kit (Qiagen, Valencia, CA, USA). Clustering and sequencing then was performed on the Hi-Seq 2000 (Illumina, San Diego, CA, USA) following the manufacturers protocols.

treatment_protocol: Ten, 15-day-old SPF white leghorn chickens were obtained (Charles River, Wilmington, Massachusetts, USA) and divided into two groups of 5 birds each.  At 21 days of age, one group of 5 birds was inoculated with sterile vaccine diluent without addition of the lyophilized Trachivax® vaccine (50 μL per nostril, 50 μL per eye; 200μL total) and placed in a separate animal room as a control group.  The vaccine was then prepared according to the manufacturer's recommendation for the eye drop administration method.  The second group of birds was then inoculated with Trachivax® vaccine (50 μL per nostril, 50 μL per eye; 200μL total at a concentration of 3.3 x 103 pfu) and were housed as a group in an animal isolator.  All animal experiments and procedures were performed under Institutional Animal Care and Use Committee (IACUC) guidelines and approval

tag: sample collection time

value: Six days post inoculation (6 dpi)

tag: breed

value: Leghorn


title: ILTV_RNASeq_Control


title: ILTV_RNASeq_Inoculated_1


title: T1DS DNaseI Rep2

description: Sample 2

source_name: twin 1_T21_fetal primary fibroblasts_DNaseI


title: T1DS DNaseI Rep1

description: Sample 1


title: T2N DNaseI Rep1

description: Sample 3


title: RD19-NI+TEX

city: Saint Paul lez Durance

first: Arjan

last: de Groot

address: CEA Cadarache

department: BIAM-SBVME

country: France

institute: CEA

description:
Sample 3
processed data file: geneTSScount_RD19+TEX.txt
processed data file: orphanTSScount_RD19+TEX.txt
barcode: ATCACG

data_processing:
In a first step, the RNA-Seq data quality was assessed by including option like reads trimming or merging/split paired-end reads.
In a second step, reads were mapped onto the D. deserti VCD115 genome sequence (GenBank accession numbers CP001114, CP001115, CP001116 and CP001117 for the chromosome and plasmids P1, P2 and P3, respectively) using the SSAHA2 package (Ning et al, 2001) that combines the SSAHA searching algorithm (sequence information is encoded in a perfect hash function) aiming at identifying regions of high similarity, and the cross-match sequence alignment program (Ewing et al, 1998), which aligns these regions using a banded Smith-Waterman-Gotoh algorithm. An alignment score equal to at least half of the read is required for a hit to be retained.
To lower false positives discovery rate, the SAMtools (v.0.1.8) were then used to extract reliable alignments from SAM formatted files.
The number of reads matching each genomic object harbored by the reference genome was subsequently computed with the Bioconductor-GenomicFeatures package.
The Bioconductor-DESeq package with default parameters was used to analyze raw counts data and test for differential expression between conditions.
Genome_build: Deinococcus deserti VCD115
Supplementary_files_format_and_content: Tab-delimited text file include raw number of reads mapped to individual genes for RD19-NI and RD19-IR experiments.
Supplementary_files_format_and_content: Tab-delimited text file include differential expression analysis from RD19 IR compared to RD19 NI.
Supplementary_files_format_and_content: Tab-delimited text file include reads first positions counts at gene TSSs for RD19-NI+TEX and RD19-IR+TEX experiments.
Supplementary_files_format_and_content: Tab-delimited text file include reads first positions counts at orphan TSSs for RD19-NI+TEX and RD19-IR+TEX experiments.

organism: Deinococcus deserti

source_name: upper sand layers of the Sahara

growth_protocol: D. deserti strain RD19 is a spontaneous streptomycin resistant derivative of the wild-type strain VCD115. It is routinely grown at 30°C with aeration in tenfold diluted tryptic soy broth supplemented with trace elements

extract_protocol:
RNAprotect-treated cells were centrifuged and cell pellets stored at -80°C. Cell pellets were pretreated with lysozyme and proteinase K. Total RNAs were isolated using the mirVana RNA isolation kit (Ambion) including DNase treatment.
From each RNA preparation (i.e. non-irradiated and irradiated cells), two cDNA syntheses were carried out, one with and one without Terminator exonuclease (TEX, Epicentre) treatment. cf SAMPLES
RNA was incubated with TEX (Terminator exonuclease (TEX, Epicentre)), which specifically degrades RNA species that carry a 5' mono-phosphate (5'P). The exonuclease resistant RNA (primary transcripts with 5'PPP) was poly(A)-tailed using poly(A) polymerase and treated with TAP (tobacco acid pyrophosphatase), which degrades 5'PPP to 5'P. Then an RNA adapter was ligated to the 5'P of the “de-capped” RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 30 ng/μl using a high fidelity DNA polymerase. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina, with the 3’-sequencing adapter containing a barcode specific for each library. The +TEX cDNA samples were pooled at approximately equimolar amounts and the cDNA pool was used for sequencing without further treatment. The pools were sequenced on a Illumina HiSeq 2000 machine (read length: 100 bp).

treatment_protocol: For RNAseq, a 100 ml culture of RD19 was grown to exponential phase (OD600 0.5), and then divided in two. One part (45 ml) was exposed to 1 kGy gamma irradiation at room temperature (23 Gy/min, 60Co source; CEA/Cadarache, France), and then recovered for 30 min. The other part (45 ml) was not irradiated but otherwise treated in the same manner. After recovery, 15 ml of each culture was added to RNAprotect Bacteria Reagent (Qiagen) to stabilize RNA, following the instructions of the manufacturer.

tag: strain

tag: genotype/variation

value: wild-type

tag: treatment

value: non-irradiated, TEX-treated


title: RD19-IR+TEX

description:
Sample 4
processed data file: geneTSScount_RD19+TEX.txt
processed data file: orphanTSScount_RD19+TEX.txt
barcode: CGATGT

value: irradiated, TEX-treated


title: RD19-NI

description:
Sample 1
processed data file: readCountGenes_RD19.txt
processed data file: differentialExpressionGenes_RD19.txt
barcode: TTAGGC

extract_protocol:
RNAprotect-treated cells were centrifuged and cell pellets stored at -80°C. Cell pellets were pretreated with lysozyme and proteinase K. Total RNAs were isolated using the mirVana RNA isolation kit (Ambion) including DNase treatment.
From each RNA preparation (i.e. non-irradiated and irradiated cells), two cDNA syntheses were carried out, one with and one without Terminator exonuclease (TEX, Epicentre) treatment. cf SAMPLES
RNA was directly poly(A)-tailed using poly(A) polymerase, followed by TAP treatment. An RNA adapter was then ligated to the 5'P of the total RNA samples. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV H- reverse transcriptase. The resulting cDNAs were PCR-amplified to about 60-90 ng/μl using a high fidelity DNA polymerase. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina, with the 3’-sequencing adapter containing a barcode specific for each library. For Illumina sequencing, the samples were pooled at approximately equimolar amounts and size fractionated in the range between 250 – 500 bp on Agarose Gel. The pools were sequenced on a Illumina HiSeq 2000 machine (read length: 100 bp).

value: non-irradiated


title: WT_input_FCL_rep2_(20130920_1_2_6)

extract_protocol:
N2 wildtype embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was formaldehyde crosslinked (FCL) and solubilized by sonication. Replicate 2.
MNase_ChIP_Seq_protocol.rtf

tag: age

value: embryos

value: WT


title: ddm1F6 AGO1-IP rep3

status: Public on Apr 07 2014

city: Columbus

first: Richard

middle: Keith

last: Slotkin

address: 318 West 12th Ave.

institute: The Ohio State University

description: Sample 6

data_processing:
library strategy: small RNA-seq
Illumina Casava1.7 software was used for basecalling.
Sequenced reads de-multiplexed and were trimmed for adaptor sequence
Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, then mapped to the genome using bowtie with parameters -v 0 to align only perfectly genome-matching reads
tRNA and rRNA-matching reads were removed
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced

organism: Arabidopsis thaliana

source_name: ddm1F6 AGO1-IP

growth_protocol: Plants were grown on soil in 18 hour long days at 23C. All plants were grown side-by-side.

extract_protocol:
RNA was extracted from the IP using Trizol reagent
Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Total soluble protein was immunoprecipitated overnight with the AGO1 antibody and washed four times.

tag: ecotype background

tag: tissue

value: unopened flower buds

tag: ip antibody

value: AGO1 polyclonal

tag: ip antibody vendor

value: Agriseria

tag: ip antibody cat. #

tag: molecule subtype

value: Immunoprecipitated small RNA


title: E16.5, biological replicate 1, single cells, transcriptome 6

source_name: distal lung epithelium

value: lung

value: Embryonic day 16.5

tag: genotype

value: wild type


title: ddm1F6 AGO1-IP rep1

description: Sample 4


title: WT Col AGO1-IP rep2

description: Sample 2

source_name: WT Col AGO1-IP


title: WT Col AGO1-IP rep1

description: Sample 1


title: Uhrf1 fl/fl Tconv

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: His-tagged MBD1

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
MeDIP-seq reads were aligned to mm9 genome using bowtie2 (version 2.1.0) with default parameters.
Mapped reads were normalized with total mapped reads and bin size (50bp) with cutoff threshold 1 reads / bin for Tconv and 2 reads / bin for Treg.
Genome_build: mm9
Supplementary_files_format_and_content: WIG format having normalized read counts (per million reads per kilobase)

source_name: Uhrf1 fl/fl Tconv

growth_protocol: Sorted

extract_protocol:
Genomic DNA was isolated using QIAGEN All-prep kit
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina.  Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.

value: Uhrf1 cKO

tag: cell type

value: Non-Treg

tag: cell population


title: T1DS RRBS

source_name: twin 1_T21_fetal primary fibroblasts

tag: disease

value: Trisomy 21

value: Fetal primary fibroblasts


title: T1DS iPS cells

source_name: twin 1_T21_iPSCs

tag: disease/status

value: Induced pluripotent stem cells (iPSCs)


title: WT Col AGO1-IP rep3

description: Sample 3


title: Uhrf1 fl/fl Treg

description: His-tagged MBD1

source_name: Uhrf1 fl/fl Treg

value: Treg


title: Uhrf1 +/+ Tconv

description: His-tagged MBD1

source_name: Uhrf1 +/+ Tconv

value: Wild type


title: Chlamydomonas reinhardtii CC-1690 (21gr) phosphate deprivation

status: Public on Apr 05 2014

city: Stanford

first: Arthur

last: Grossman

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institute for Science

data_processing:
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length.
Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html)
Supplementary_files_format_and_content: Processed files correpond to average expression estimates per experiment in units of RPKMs.

organism: Chlamydomonas reinhardtii

source_name: phosphate deprived

growth_protocol: cells were grown in continuous light of 70 µmol/m2*sec at 25°C, under constant agitation (200 rpm)

extract_protocol:
Isolation of total RNA using a phenol-chloroform procedure, cDNA synthesis, and qRT-PCR was performed by standard methods as previously described (Schloss, J. A., C. D. Silflow and J. L. Rosenbaum (1984) mRNA abundance changes during flagellar regeneration in Chlamydomonas reinhardtii. Mol. Cell. Biol. 4: 424–434; Moseley, J.L., Gonzalez-Ballester, D., Pootakham, W., Bailey, S., and Grossman, A.R. (2009) Genetic Interactions Between Regulators of Chlamydomonas Phosphorus and Sulfur Deprivation Responses. Genetics. 181. 889-905).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells inoculated into TAP or TA medium with no additional Pi at a chlorophyll density of 2.5 mg/mL and grown for 24h

tag: media

value: TA (without phosphate)

tag: light

value: 70 umol/m2*sec


title: Uhrf1 +/+ Treg

description: His-tagged MBD1

source_name: Uhrf1 +/+ Treg

tag: strain


title: pgWAT_2

status: Public on Apr 04 2014

city: Boston

first: Jonathan

middle: Z

last: Long

state: MA

address: 3 Blackfan Circle, Rm 11115

institute: Dana-Farber Cancer Institute

description:
Translating RNA from UCP1-positive cells
2 weeks cold exposure

data_processing:
Tophat/Cufflinks used for data processing
Genome_build: mm9
Supplementary_files_format_and_content: GTF with FPKM

source_name: Adipose tissue

extract_protocol:
Immunoprecipitation antibody was Abcam #ab290, rabbit anti-GFP. Translating RNAs were harvested from freshly dissected tissues.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: UCP1-TRAP mice were bred at 30 degC and weaned into room temperature at 3 weeks. At 4 weeks, UCP1-TRAP females were placed into 4 degC. After an additional 2 weeks, tissues were harvested and translating RNAs from UCP1-positive cells were immunoprecipitated.

value: C57B/6 UCP1-TRAP

value: Perigonadal WAT

value: 6 week

tag: gender

value: female


title: iWAT_3

value: Inguinal WAT


title: BAT_2

value: Interscapular BAT


title: pgWAT_1


title: BAT_3


title: RD19-IR

description:
Sample 2
processed data file: readCountGenes_RD19.txt
processed data file: differentialExpressionGenes_RD19.txt
barcode: TGACCA

tag: genotype/variation

value: wild-type

tag: treatment

value: irradiated


title: iWAT_1

tag: age


title: 48h input mRNA run 3

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

data_processing:
Base calling was performed using CASAVA-1.8.2.
The Illumina TruSeq adaptor sequence was then trimmed from raw reads by aligning its sequence, requiring 100% match of the first five base-pairs and a minimum alignment score of 60 (Matches:5, Mismatches:-4, Gap opening:-7, Gap extension:-7). Trimmed reads were then depleted of rRNA, tRNA, snRNA, snoRNA, and misc_RNA from Ensembl and RepeatMasker annotations using strand-specific alignment performed with Bowtie2 v2.1.0 with default parameters.
Filtered reads were aligned strand-specific to the Zebrafish Zv9 genome assembly using Tophat v2.0.8 with default parameters and the exon-junction coordinates from Ensembl r70.
Using the spliced version of each transcript (ensembl r73, Pauli et al lincRNAs, Ulitsky et al lincRNAs) we defined all ORFs as stop codon to most distal in-frame AUG codon without an intervening stop. Read coverage and counts were calculated using 28 & 29nt reads. For position-related calculation of ORFScore and Frame1 coverage, we counted reads only with the +12 position within the interior of the ORF (defined as the region excluding the reads aligning to the start and stop(-1) codons). RPKM values were calculated using input mRNA per transcript, normalizing WITHIN but not between transcript sets (total reads mapping to ensembl r73 or either lincRNA set). ORFScore and coverage values were calculated as outlined in Bazzini et al, 2013. Sequencing data were combined for each timepoint.
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: allinfo_final_ORFs.txt :: orfID=unique ID of ORF; geneID; transcriptID; startLoc & stopLoc=1-based transcript coordinates of ORF; txCDSStart&txCDSEnd=start and end of annotated CDS; Source=transcript source; orfFrame=ORFScore; orfRate=# of reads in ORF; covF1Prop=proportion of in-frame positions with aligning read(s); tx_Input_RPKM=RPKM of transcript from input mRNA

molecule: polyA RNA

organism: Danio rerio

source_name: Whole embryos

growth_protocol: Embryos are incubated at 28C

extract_protocol:
For ribosome profiling, 50 wild type embryos for each condition were collected at a given stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction (ARTseq Ribosome Profiling Kit, RPHMR12126, Epicentre). For nuclease treatment, 3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28-29nt fragments were gel purified as previously described in (Bazzini et al., 2012) and cloned according to the manufacturers protocol (ARTseq Ribosome Profiling Kit, RPHMR12126, Epicentre). For RNA input, total RNA was isolated from 400 ul of the 800 ul of clarified extract before ART- seq Nuclease treatment. Poly-A selection was done according to manufacturer guide- lines (Dynabeads mRNA Purification Kit, Cat no.610.06), and RNA fragmented using the Artseq Ribosome Profiling Kit Mammalian protocol.
Both RPF and RNA input fragments were cloned according to the Artseq Ribosome Profiling Kit, Mammalian. The final PCR was carried out with an initial 15 second denaturation at 98 °C, followed by 9-12 cycles of 15 seconds at 98 °C, 5 seconds at 55 °C and extension at 72 °C for 10 s. Reactions were separated on a non-denaturing 8% polyacrylamide TBE gel and DNA fragments of the correct size were extracted and sequenced.

value: TUAB

tag: Stage

tag: separation

value: column


title: ddm1F6 AGO1-IP rep2

department: Molecular Genetics

description: Sample 5

tag: ecotype background

tag: tissue

value: unopened flower buds

tag: ip antibody

value: AGO1 polyclonal

tag: ip antibody vendor

value: Agriseria

value: Immunoprecipitated small RNA


title: iWAT_2


title: 5h input mRNA run 3


title: 2h RPFs run 1


title: 2h RPFs run 3


title: 2h RPFs run 2


title: 48h RPFs run 2


title: 24h RPFs run 2


title: Chlamydomonas reinhardtii CC-1690 (21gr) phosphate replete

source_name: phosphate replete

value: TA + 1.1 mM phosphate (TAP)


title: 24h input mRNA run 2


title: 12h RPFs run 3


title: 12h input mRNA run 2


title: 2h input mRNA run 2


title: 48h input mRNA run 2


title: BAT_1