title: MM1S_MED1_JQ1_5nM_JL_ChipSeq

description: Chromatin IP against MM1S_MED1_JQ1_5nM_JL

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
08282012_C1260ACXX_4.AGTTCC.wig.gz: hg18

treatment_protocol: 5nM JQ1 for 6h


title: U87_POL2_DMSO_ChipSeq

status: Public on Jul 26 2013

type: SRA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against U87_POL2_DMSO

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01312013_D1TBRACXX_5.TTAGGC.wig.gz: hg18

molecule: genomic DNA

organism: Homo sapiens

source_name: Glioblastoma

growth_protocol: The base medium for this cell line is ATCC-formulated Eagle's Minimum Essential Medium (Catalog No. 30-2003)+ 1% GMAX and 10% FBS

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: 0.05% DMSO for 6 hours

tag: chip antibody

value: RNA Pol II (Rpb1 N-terminus)

tag: antibody catalog number

value: Santa Cruz SC-899

tag: cell type

tag: duration

tag: drug

value: DMSO


title: MM1S_CDK9_JQ1_5000nM_JL_ChipSeq

description: Chromatin IP against MM1S_CDK9_JQ1_5000nM_JL

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
08282012_C1260ACXX_7.GAGTGG.wig.gz: hg18

source_name: Multiple myeloma

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

treatment_protocol: 5000nM JQ1 for 6h

value: Santa Cruz SC-484

tag: concentration


title: U87_BRD4_JQ1_ChipSeq

description: Chromatin IP against U87_BRD4_JQ1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01312013_D1TBRACXX_5.CGATGT.wig.gz: hg18

treatment_protocol: 500nM JQ1 for 6 hours

value: Bethyl A301-985A


title: Whole cell extract from pre-MBT embryos (replicate 1)

status: Public on Jul 25 2013

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Base calls were performed using the default settings of CASAVA
Reads were aligned to the UCSC dm3 genome using Bowtie 0.12.8, allowing only unique alignments with up to 2 mismatches
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED file containing aligned reads after extending to estimated insert size of the library (fragment size of paired-end samples was determined by read pair alignments)

organism: Drosophila melanogaster

source_name: Staged embryos

growth_protocol: D. melanogaster embryos were collected and aged on yeasted apple juice plates at 25 °C and 60 % humidity.

extract_protocol: Each ChIPs were performed as previously described (Zeitlinger 2007) using 200ul embryos for pre-MBT embryos and 50ul for older embryos. Libraries were prepared from the immunoprecipitated DNAs using the Paired-End DNA Sample Preparation Kit (Illumina: PE-102-1001) but with a modified protocol. To remove adapter dimers, biotin-labeled dATP (Invitrogen: 19524-016) was added in the A-tailing reaction after end-repair. After ligation to the PE adaptor, the samples were incubated with streptavidin beads (Invitrogen: 650-01) in 500ul binding buffer at room temperature for 15min. DNA bound to the beads was then washed twice with 800ul binding buffer with0.05% Tween 20, twice with NEB buffer 2 and resuspended in 31ul NEB buffer 2. The PCR reaction was then performed according to the Illumina protocol.

tag: Stage

value: pre-MBT 01to02h AEL

tag: genotype

value: Oregon-R

tag: ChIP


title: U87_POL2_JQ1_ChipSeq

description: Chromatin IP against U87_POL2_JQ1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01312013_D1TBRACXX_6.TGACCA.wig.gz: hg18


title: ChIP-seq TBP in pre-MBT embryos (replicate 1)

value: TBP

tag: antibody vendor/catalog

value: rabbit poly-antibody against dTBP


title: ChIP-seq TBP in pre-MBT embryos (replicate 2)


title: ChIP-seq Pol II in pre-MBT embryos (replicate 3)

value: Pol II

value: Covance 8WG16 (MMS-126R)


title: ChIP-seq Pol II in pre-MBT embryos (replicate 2)


title: ChIP-seq Pol II in pre-MBT embryos (replicate 1)


title: ChIP-seq Pol II in pre-MBT embryos (replicate 4)


title: ChIP-seq H3K4me3 in pre-MBT embryos (replicate 2)

value: Cell Signaling Technology 9751S


title: ChIP-seq H3K4me3 in pre-MBT embryos (replicate 1)


title: ChIP-seq Pol II in post-MBT embryos (replicate 1)

value: post-MBT 02to04h AEL


title: ChIP-seq H3K27me3 in post-MBT embryos (replicate 1)

value: Active Motif 39155


title: ChIP-seq TBP in post-MBT embryos (replicate 1)


title: HH_MM.1S_RNAPII_5nM_JQ1_ChipSeq

description: Chromatin IP against HH_MM.1S_RNAPII_5nM_JQ1

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
05242012_D0WUYACXX_4.ACTTGA.wig.gz: hg18

treatment_protocol: 5nM JQ1 treatment for 6hr

value: Plasma cell

tag: duration of treatment

value: 6 hr


title: ChIP-seq Pol II in MBT embryos (replicate 3)

value: MBT 02to03h AEL


title: Whole cell extract from post-MBT embryos (replicate 1)


title: Whole cell extract from MBT embryos (replicate 1)


title: ChIP-seq Pol II in MBT embryos (replicate 2)


title: ChIP-seq Pol II in MBT embryos (replicate 1)


title: ChIP-seq TBP in MBT embryos (replicate 1)


title: ChIP-seq H3K4me3 in MBT embryos (replicate 2)


title: ChIP-seq H3K27me3 in MBT embryos (replicate 1)


title: ChIP-seq H3K4me3 in MBT embryos (replicate 1)


title: U87_BRD4_DMSO_ChipSeq

description: Chromatin IP against U87_BRD4_DMSO

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 and mm8
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome Build:
01312013_D1TBRACXX_5.ATCACG.wig.gz: hg18


title: ChIP-seq H3Ac in MBT embryos (replicate 1)

value: Millipore 07-360


title: ChIP-seq H3Ac in MBT embryos (replicate 2)


title: ChIP-seq H3K27me3 in 6-8h embryos (replicate 1)

value: 06to08h AEL


title: ChIP-seq TBP in MBT embryos (replicate 2)


title: 28298_BKSO_M_KN

city: Seoul

first: HYEONGMIN

last: KIM

address: Seoul National Univ., Daehak-dong, Gwanak-gu,

department: College of Agriculture Sciences

country: South Korea

institute: Seoul National University

description: mRNA-Sequencing

library_source: transcriptomic

data_processing:
Quality of RNA-seq reads from all of the adipose tissues were checked using FastQC.
Reads passed the quality control were mapped to Bovine Taurus genome (bosTau6) from UCSC using Tophat2 (v2.0.2).
The reads were counted using HTseq (v0.5.3p3).
Genome_build: bosTau6
Supplementary_files_format_and_content: tab-delimited text files include raw counts of genes (abundance measurements) for each sample.

molecule: total RNA

organism: Bos taurus

source_name: intramuscular fat tissue

extract_protocol: Total RNA was isolated using GeneAll Hybrid-RTM Kit (Cat# 305-101) from each tissues. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.

tag: breed

value: Hanwoo/coreanae

tag: gender

value: male

tag: age

value: 30 months

tag: feeding barn

value: Hanwoo Experimental Station in National Institute of Animal Science

tag: tissue

value: intramuscular fat tissue


title: 28298_BKSO_M_PH

description: mRNA-Sequencing

source_name: subcutaneous fat tissue

value: subcutaneous fat tissue


title: Mnase-seq in MBT staged embryos

data_processing:
Base calls were performed using the default settings of CASAVA
Reads were aligned to the UCSC dm3 genome using Bowtie 0.12.8, allowing only unique alignments with up to 2 mismatches
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED file containing aligned reads (read pairs merged into a single fragment)

extract_protocol: 50ul sorted 2-3h embryos were homogenized as previously described (Zeitlinger 2007) and digested based on a previously published protocol (Mavrich 2008). Briefly, homogenized chromatin in 4.5 ml NPS buffer was aliquoted into 9 microfuge tubes and digested with an MNase (Worthington: LS004798) gradient of 20U, 10U, 5U, 5/2U, 5/4U, 5/8U, 5/16, to 5/32U, and one negative control for 30 min at 37°C. Digestion was stopped by adding 20ul 0.5M EDTA to each tube and kept on ice for 10min. After treating with RNase and proteinase K, reverse crosslinking was performed at 60°C for 6h, and the DNA was cleaned up as previously described (Zeitlinger 2007). The ethanol-precipitated DNA was resuspended with 10ul ddH2O and run on a 1.7% agarose gel. Mono-nucleosome size DNA was extracted from the line with two clear bands, and prepared for paired-end sequencing.

value: Oregon-R


title: 28298_BKSO_M_BB

description: mRNA-Sequencing

source_name: omental fat tissue

value: omental fat tissue


title: 28298_BKSO_M_KY

description: mRNA-Sequencing

source_name: muscle

value: muscle


title: 28261_KSO_M_BB

description: mRNA-Sequencing

tag: gender type

value: castrated male


title: 28261_KSO_M_KN

description: mRNA-Sequencing


title: 28261_KSO_M_KY

description: mRNA-Sequencing


title: 28046_F_KN

description: mRNA-Sequencing

value: female


title: 28046_F_PH

description: mRNA-Sequencing


title: 28261_KSO_M_PH

description: mRNA-Sequencing


title: 27258_BKSO_M_KN

description: mRNA-Sequencing


title: 27258_BKSO_M_KY

description: mRNA-Sequencing


title: 27258_BKSO_M_BB

description: mRNA-Sequencing


title: 28271_KSO_M_KY

description: mRNA-Sequencing


title: 28271_KSO_M_KN

description: mRNA-Sequencing


title: 28271_KSO_M_PH

description: mRNA-Sequencing


title: 28271_KSO_M_BB

description: mRNA-Sequencing


title: 27258_BKSO_M_PH

description: mRNA-Sequencing


title: 28057_F_KY

description: mRNA-Sequencing


title: 28057_F_KN

description: mRNA-Sequencing


title: 28300_BKSO_M_KY

description: mRNA-Sequencing


title: 28300_BKSO_M_PH

description: mRNA-Sequencing


title: 28300_BKSO_M_BB

description: mRNA-Sequencing


title: 28300_BKSO_M_KN

description: mRNA-Sequencing


title: 28057_F_BB

description: mRNA-Sequencing


title: 28046_F_BB

description: mRNA-Sequencing


title: 28260_KSO_M_KY

description: mRNA-Sequencing


title: 28260_KSO_M_KN

description: mRNA-Sequencing


title: 28049_F_BB

description: mRNA-Sequencing


title: 28049_F_KN

description: mRNA-Sequencing


title: 28260_KSO_M_BB

description: mRNA-Sequencing


title: 28260_KSO_M_PH

description: mRNA-Sequencing


title: 28049_F_KY

description: mRNA-Sequencing


title: BR1.3

city: Leuven

first: Pierre

last: Lau

address: 49 Herestraat

country: Belgium

institute: KUL-VIB

description: Sample 6

data_processing:
Trimming of adaptor with Flicker v3.0
quality read filtering and contaminant removal
Manual removal of reads with N
Reads longer than 15 nucleotides were mapped to the hg19 build genome using the short-read aligner Bowtie2 (version 2.0.2) and allowing one mismatch
Reads were processed with HTSeq-counts (version 0.5.3p9)
Normalized expression was determined with DESeq (version 1.6.1) after discarding miRNAs with less than 30 counts over the 12 samples
Genome_build: hg19
Supplementary_files_format_and_content: count data

source_name: early stage_prefrontal cortex

extract_protocol:
Total RNA were obtained by TRIzol homogeneization of prefrontal cortex tissues and purification on miRVana columns
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA Sample Preparation Kit (Part# RS-200-0012).

tag: alzheimer's disease stage

value: early stage (control)

value: brain

tag: region

value: prefrontal cortex

tag: molecule subtype

value: microRNA


title: BR5.7

description: Sample 7

source_name: late stage_prefrontal cortex

value: late stage


title: BR6.5

description: Sample 11


title: BR6.4

description: Sample 10


title: BR6.7

description: Sample 12


title: BR0.5

description: Sample 3


title: BR6.3

description: Sample 9


title: BR1.2

description: Sample 5


title: BR0.7

description: Sample 4


title: BR0.4

description: Sample 2


title: BR0.2

description: Sample 1


title: BR6.2

description: Sample 8


title: IL1RN CRISPRs, Rep 2

city: Durham

first: Timothy

middle: E

last: Reddy

state: NC

address: 2347 CIEMAS, 101 Science Drive

department: Department of Biostatistics & Bioinformatics

institute: Duke University

description:
IL1RN.Rep2
PolyA RNA

data_processing:
Base-calling was performed on instrument using CASAVA software.
Reads were aligned to known RefSeq transcripts from hg19 using Bowtie version 0.12.9, reporting only the best alignment by using the --best option.
Read counts were normalized and differential expression was called using Deseq (v. 1.10.1) by using a chi-squared test to compare fits to a model that contained donor and count (i.e. count ~ donor + condition) to a model that only contained donor information (i.e. count ~ donor).
P-values were converted to a False Discovery Rate using the method of Benjamini and Hochberg (1995).
Genome_build: RefSeq transcripts from genome build GRCh37
Supplementary_files_format_and_content: GSE47114_All_counts.tab: Tab-delimited matrix; Raw (not normalized) counts of the number of reads aligned to each RefSeq transcript.

source_name: HEK293T cells transiently transfected with Cas9 and IL1RN guide RNA expressing plasmids

growth_protocol: HEK293T cells were grown in DMEM with 10% fetal bovine serum and 1% Penicillin/Streptomycin in 6-well cell culture plates.

extract_protocol:
Total RNA was extracted using Qiagen Mini RNA prep kits. PolyA+ RNA was subsequently purified using oligo-dT beads (Invitrogen).
First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000.

treatment_protocol: For IL1RN-CRISPRs and HBG-CRISPRs, each well was transfected with 3 ug of Cas9-expressing plasmid, 250 ng (each) of four different guide RNA-expression PCDNA vectors, and 10 uL of lipofectamine in a total volume of 500 uL. For control experiments, 4 ug of empty PCDNA vector was transfected instead. RNA was harvested after three days.

tag: cell line

tag: guide rna

tag: replicate


title: HBG CRISPRs, Rep 2

description:
HBG.Rep2
PolyA RNA

source_name: HEK293T cells transiently transfected with Cas9 and HBG1/2 guide RNA expressing plasmids


title: Control treated, Rep 2

description:
Ctl.Rep2
PolyA RNA

source_name: HEK293T cells transiently transfected with empty guide-RNA expressing vector

value: Control


title: Control treated, Rep 1

description:
Ctl.Rep1
PolyA RNA


title: 28049_F_PH

description: mRNA-Sequencing

value: Hanwoo/coreanae


title: IL1RN CRISPRs, Rep 1

description:
IL1RN.Rep1
PolyA RNA


title: HBG CRISPRs, Rep 1

description:
HBG.Rep1
PolyA RNA


title: HBG CRISPRs, Rep 3

description:
HBG.Rep3
PolyA RNA


title: Ras_rep1_RNAseq

status: Public on Jul 24 2013

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Basecalls performed using CASAVA version 1.7
sequence reads mapped to reference genome hg19 using Tophat (Trapnell et al., 2009). Quantification of gene expression was done using Cufflinks (Trapnell et al., 2010) and annotations from Ensembl release 57. For each transcript the resulting FPKM were converted into raw read counts and these counts were added for each gene locus. Data normalization was performed as described by Anders et al. (Anders and Huber, 2010) and implemented in the DESeq Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Ensembl release 57 human gene id, RPKM values for each Sample.

growth_protocol: Culturing of human diploid WI38 fibroblasts (ATCC) was performed at physiological oxygen concentration of 3% as previously described (Bischof et al., 2006)

extract_protocol:
Total RNA was prepared using RNeasy RNA isolation kit (Quiagen) 5 days post-infection
libraries were prepared using mRNA-seq sample prep kit (#RS-100-0801, Illumina Inc.) following the manufacturer's protocol with some modifications. Briefly, mRNA was purified from 2 µg of total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 95°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers and SuperScript II reverse transcriptase (# 18064-014, Invitrogen). This was followed by second strand cDNA synthesis using Polymerase I and RNase H. The double stranded cDNA fragments were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were separated by 2% agarose gel electrophoresis and ~200-250bp fragments were excised and purified using QIAquick Gel Extraction Kit (Qiagen) and then enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 13 cycles; 5 min at 72°C). After PCR amplification, surplus PCR primers were removed by purification using Agencourt AMPure XP beads (#A63881, Beckman). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 6pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Genome Analyzer IIx as single-end 54 base reads following Illumina’s instructions.

treatment_protocol: Infection by retroviral-mediated gene transfer with either pBABE-puro-H-RasG12V or empty vector were performed as previously described (Bischof et al., 2006)

tag: cell type

value: primary fibroblasts

tag: status

value: Senescent

tag: genotype/variation

value: infected with pBABE-puro-H-RasG12V


title: Proliferatives_rep2_RNAseq

value: Proliferative

value: infected with pBABE-puro-empty


title: prolif_PIASy_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.7 or 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using the Illumina Genome Analyzer Pipeline or Bowtie aligner.
Peaks were called using the Model-based Analysis of ChIP-Seq (MACS 1.3.7) algorithm (http://liulab.dfci.harvard.edu/MACS/). Results were visualized using the UCSC Genome Browser (http://genome.ucsc.edu). Global clustering analysis and quantitative comparisons were performed using seqMINER [(34) (http://bips.ustrasbg. fr/seqminer/].
Wig files: For all samples, aligned sequences were extended to 200bp downstream (with respect to read strand) and allocated into 25bp bins.
Genome_build: hg19
Supplementary_files_format_and_content: bed (macs peaks)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen). Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 8pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Genome Analyzer IIx as single-end 36 base reads following Illumina’s instructions.

tag: chip antibodies

value: PIASy (non-commercial)


title: Ras_rep3_RNAseq


title: Proliferatives_rep3_RNAseq


title: Proliferatives_rep1_RNAseq


title: ras_PIASy_ChIPSeq

value: Ras induced senescent


title: ras_H3K4me3_ChIPSeq


title: ras_H3K9me3_ChIPSeq


title: 28057_F_PH

description: mRNA-Sequencing

value: 30 months

value: Hanwoo Experimental Station in National Institute of Animal Science

value: subcutaneous fat tissue


title: ras_H3K27me3_ChIPSeq


title: ras_PolII_ChIPSeq

value: anti-PolII (sc-9001)


title: ras_SUMO1_rep1_ChIPSeq

value: SUMO1 (non-commercial)


title: ras_SUMO2_ChIPSeq

value: SUMO2 (non-commercial)


title: untagged_4hrs_RAP_RapExpt_Input

city: New York

first: David

last: Allis

state: NY

address: 1230 York Ave Box 78

department: Laboratory of Chromatin Biology and Epigenetics

institute: The Rockefeller University

data_processing:
ChIP-seq reads were aligned at 51bp to the SacCer2 genome assembly using Bowtie: only unique reads with no more than 2 mismatches were kept
Aligned BAM files were converted to Wig files using IGVtools
Genome_build: sacCer2

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae untagged strain

growth_protocol: Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.4)

extract_protocol:
Samples were crosslinked by adding formaldehyde (final conc 1%) at room temp for 20 minutes, and then quenched with glycine (final conc 125 mM).  ChIPs were performed as described (Aparicio et al. 2005 Curr Protoc Mol Biol). Briefly cells were lysed using glass beads, and chromatin was sheared to 150-500 bp. Chromatin was isolated and used for ChIP with the anti-Myc 9E10 antibody (Millipore #05-419) according to standard procedures.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Preparation Kit (cat # FC-121-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 21 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: An aliquot of each yeast culture was taken for the 0 hour (T0) ChIP/Input samples. Each culture was then divided into two separate cultures: one of these was treated with rapamycin dissolved in DMSO (final rapamycin concentration 50 nM), while the other cultures was treated with DMSO as a control. Samples were taken 0.5 and 4 hours after treatment for ChIP/Inputs.

tag: yeast strain

tag: treatment

value: rapamycin

tag: hours treatment

tag: antibody

value: no antibody


title: ras_input_DNA

value: none (input)


title: prolif_H3K9me3_ChIPSeq


title: prolif_H3K27me3_ChIPSeq


title: untagged_4hrs_DMSO_RapExpt_Input

value: DMSO


title: Ras_rep2_RNAseq

value: primary fibroblasts


title: prolif_H3K4me3_ChIPSeq


title: untagged_0hrs_beforetreatment_RapExpt_Input

value: untreated (0 hour time-point)


title: untagged_0.5hrs_RAP_RapExpt_Input


title: ECM5_4hrs_RAP_RapExpt_Input

source_name: S. cerevisiae Ecm5-13Myc strain


title: prolif_SUMO1_rep1_ChIPSeq


title: prolif_PolII_ChIPSeq


title: prolif_SUMO2_ChIPSeq


title: prolif_Ubc9_ChIPSeq

value: (BD transduction)


title: prolif_input_DNA

value: Proliferative


title: ECM5_0.5hrs_RAP_RapExpt_Input


title: ECM5_0.5hrs_DMSO_RapExpt_Input


title: s_8_raw_MeDIP_17_1XH

city: New Orleans

first: Chuan

last: Qiu

state: LA

address: 1440 Canal St.

department: Department of Biostatistics and Bioinformatics

institute: Tulane University School of Public Health & Tropical Medicine

data_processing:
Images analysis and base-calling were performed using Solexa pipeline V1.6 (OFF-LINE BASE CALLER V1.6 SOFTWARE)
MeDIP-seq reads (pass solexa CHASTITY quality filter) were aligned to human genome (UCSC HG19) using NOVOALIGN (V2.05)
Methylation signals were calculated and normalized by using MEDIPS package (version 1.2).
Genome_build: UCSC HG19
Supplementary_files_format_and_content: text files include 1kb sliding window methylation signal

source_name: Peripheral Blood Monocytes

extract_protocol: For MeDIP, Genomic DNA was sonicated to ~100-500bp with a Bioruptor sonicator (Diagenode). 1 μg of sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol. After agarose size-selection to remove unligated adapters, the adaptor-ligated DNA was used for immunoprecipitation using a mouse monoclonal anti-5-methylcytosine antibody (Diagenode). For this, DNA was heat-denatured at 94°C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μL primary antibody overnight at 4°C with rocking agitation in 400 μL immunoprecipitation buffer (0.5% BSA in PBS). To recover the immunoimmuniprecipated DNA fragments, 200 μL of magnetic beads were added and incubated for an additional 2 hours at 4°C with agitation. After immunoprecipitation, a total of five immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific mouse IgG immunoprecipitation was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/mL proteinase K for 2 hours at 65°C and then allowed to cool down to room temperature. MeDIP and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μL EB (Qiagen). 14 cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (200-300 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Agilent DNA Bioanalyzer 2100. An aliquot of each library was diluted in EB to 5 ng/μL and 1 μL was used in real-time PCR reactions to confirm the enrichment for methylated region.

tag: race

value: Caucasion

tag: gender

value: female

value: Peripheral Blood Monocytes


title: s_4_raw_MeDIP_16_1XC


title: s_5_raw_MeDIP_18_1ZP


title: ECM5_0hrs_beforetreatment_RapExpt_Input


title: SNT2_4hrs_RAP_RapExpt_Input

source_name: S. cerevisiae Snt2-13Myc strain


title: s_3_raw_MeDIP_14_1VJ


title: s_8_raw_MeDIP_15_1YW


title: SNT2_4hrs_DMSO_RapExpt_Input


title: SNT2_0.5hrs_RAP_RapExpt_Input


title: s_7_raw_MeDIP_12_1ZN


title: s_7_raw_MeDIP_13_204


title: ras_Ubc9_ChIPSeq

value: Ras induced senescent

value: infected with pBABE-puro-H-RasG12V


title: SNT2_0.5hrs_DMSO_RapExpt_Input


title: SNT2_0hrs_beforetreatment_RapExpt_Input


title: s_2_raw_MeDIP_10_1XB


title: untagged_0.5hrs_DMSO_RapExpt_Input


title: untagged_0.5hrs_DMSO_RapExpt_ChIP

value: anti-Myc (9E10 monoclonal)


title: s_5_raw_MeDIP_7_1ZW


title: s_6_raw_MeDIP_8_1ZH


title: untagged_0hrs_beforetreatment_RapExpt_ChIP


title: ECM5_4hrs_DMSO_RapExpt_ChIP


title: s_4_raw_MeDIP_5_20G


title: untagged_4hrs_DMSO_RapExpt_ChIP


title: untagged_4hrs_RAP_RapExpt_ChIP


title: ECM5_0.5hrs_DMSO_RapExpt_ChIP


title: s_1_raw_MeDIP_9_1XT


title: untagged_0.5hrs_RAP_RapExpt_ChIP


title: s_6_raw_MeDIP_11_1ZB


title: ECM5_4hrs_DMSO_RapExpt_Input


title: s_5_raw_MeDIP_6_219


title: SNT2_4hrs_RAP_RapExpt_ChIP


title: RCNBH_+tam_Nanog

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 4C PCR product

data_processing:
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank HindIII sites (fragment ends), using custom perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse mm9.
Genome_build: mm9

organism: Mus musculus

source_name: ESC RCNBH

growth_protocol: Two independently derived mouse ES cell lines were used in this study: IB10 ESCs (129/Ola background) and 129/Cast ESCs (129SVJ/Casteneus background). IB10 ESCs were grown in BRL conditioned DMEM (high glucose, Gibco) supplemented with 15% FBS, 1X NEAA (Gibco), 1X Pen Strep (Gibco), 1:1000 β-mercaptoethanol (Invitrogen), 1X  L-Glutamine (Gibco) and 1000 U/ml LIF (Gibco).   129/Cast ESCs were grown on irradiated mouse embryonic fibroblasts (MEFs) in DMEM supplemented with 15% FBS, 1x NEAA, 1x Pen Strep, 1:1000  β-mercaptoethanol and 1000 U/ml LIF. NP cells (IB10 and 129/Cast) were grown in DMEM-F12 supplemented with 1:100 N2 (Gibco), 20 ng/ml bFGF (Peprotech), 20 ng/ml murine EGF (Peprotech). For the 129/Cast NP cells 1X B-27 (Gibco) was added 10. We generated astrocytes by growing IB10 NP cells to confluency and washing twice with DMEM before adding astrocyte medium (DMEM-F12 supplemented with 1:100 N2 and 2% FBS) 19. The culture medium was changed twice and cells were grown for 5 days to make sure differentiation was complete, which was confirmed by immunofluorescence.  NPCs were generated according to Conti and collogues (Conti et al. 2005) with slight modifications. In brief ES cells (129SVJ/CAST) were differentiated in N2B27 (StemCell Recourses) for 7 days, followed by the formation of neural spheres in N2B27 supplemented with EGF and FGF (10ng/ml). 3 day old spheres were allowed to attach to the culture dish to expand NPCs.(also see Splinter et al., 2011, Genes & Development).

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

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

value: ESC RCNBH

tag: barcode

value: GAGACGTAATTTTGGTAAGCTT

tag: bait

value: Nanog


title: SNT2_0hrs_beforetreatment_RapExpt_ChIP


title: ECM5_0.5hrs_RAP_RapExpt_ChIP

value: rapamycin


title: ECM5_4hrs_RAP_RapExpt_ChIP


title: s_2_raw_MeDIP_2_20W


title: s_1_raw_MeDIP_1_202


title: Nanog_LacR_targeted_B6

description: 4C PCR product

value: CTGGAACTAAATGGAGGATC

value: Nfix


title: s_4_raw_MeDIP_4_20D


title: SNT2_4hrs_DMSO_RapExpt_ChIP

value: DMSO


title: ZHBTc4_-dox_Nanog

description: 4C PCR product

source_name: ESC ZHBTc4

value: ESC ZHBTc4

value: TCGACGTAATTTTGGTAAGCTT


title: Nanog_vp_control_kd

description: 4C PCR product

source_name: ESC 129/Cast

value: ESC 129/Cast

value: GACGTAATTTTGGTAAGCTT


title: ecm5D_0.5hrs_rep3

data_processing:
RNA-seq reads were aligned to the SacCer2 genome assembly using TopHat v1.4 with 25 bp segment length
Aligned BAM files were converted to Wig files using IGVtools
Genome_build: sacCer2

source_name: S. cerevisiae ecm5 deletion strain

growth_protocol: Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.3).

extract_protocol:
Total RNA was obtained through hot acid phenol extraction (Collart, M. A., and S. Oliviero. 200; Current Prot. Mol. Bio.)
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit (cat # RS-122-2001). After adapter ligation 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 Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: One half of each yeast culture was taken for the 0 hour (T0) sample. H2O2 was added to remaining cultures at a final concentration of 0.4 mM. Samples were taken 0.5 hours after H2O2 addition for the 0.5 hour (T0.5) sample.

value: BY4741 ecm5D

tag: hours h2o2

tag: biol. replicate #


title: SNT2_0.5hrs_RAP_RapExpt_ChIP


title: ecm5D_0.5hrs_rep2


title: ECM5_0hrs_beforetreatment_RapExpt_ChIP

value: untreated (0 hour time-point)


title: Sox2_ESC_E14

description: 4C PCR product

source_name: ESC E14

value: ESC E14

value: GATTGGCAAATAACTCAAGCTT


title: ecm5D_0hrs_rep3


title: SNT2_0.5hrs_DMSO_RapExpt_ChIP


title: Ednrb_ESC_E14

description: 4C PCR product

value: GCCCAATTTTAGCTAAGC

value: Ednrb


title: RCNBH_-tam_Nanog

description: 4C PCR product

value: ESC RCNBH


title: Mybl2_ESC_E14

description: 4C PCR product

value: GATTTTGTACCCCAGGAAGCTT


title: s_3_raw_MeDIP_3_20K

value: Caucasion

value: female

value: Peripheral Blood Monocytes


title: Nanog_vp_Nanog_kd

description: 4C PCR product

value: AGGACGTAATTTTGGTAAGCTT

value: Nanog


title: snt2D_0.5hrs_rep3

source_name: S. cerevisiae snt2 deletion strain

value: BY4741 snt2D


title: ecm5D_0hrs_rep1


title: Nanog_LacR_targeted_129

description: 4C PCR product

value: CTGGAACTAAATGGAGGATC

value: Nfix


title: Tas2R110_NPC_129_Cast

description:
4C PCR product.
Barcode: AGATTTTATATGTCAAAAGCTT

data_processing:
Library strategy: 4C-seq
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank HindIII sites (fragment ends), using custom Perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome mm9.
Genome_build: mm9

source_name: NPC 129/Cast, Tas2R110

growth_protocol:
Two independently derived mouse ES cell lines were used in this study: IB10 ESCs (129/Ola background) and 129/Cast ESCs (129SVJ/Casteneus background). IB10 ESCs were grown in BRL conditioned DMEM (high glucose, Gibco) supplemented with 15% FBS, 1X NEAA (Gibco), 1X Pen Strep (Gibco), 1:1000 β-mercaptoethanol (Invitrogen), 1X  L-Glutamine (Gibco) and 1000 U/ml LIF (Gibco). 129/Cast ESCs were grown on irradiated mouse embryonic fibroblasts (MEFs) in DMEM supplemented with 15% FBS, 1x NEAA, 1x Pen Strep, 1:1000  β-mercaptoethanol and 1000 U/ml LIF. NP cells (IB10 and 129/Cast) were grown in DMEM-F12 supplemented with 1:100 N2 (Gibco), 20 ng/ml bFGF (Peprotech), 20 ng/ml murine EGF (Peprotech). For the 129/Cast NP cells, 1X B-27 (Gibco) was added. We generated astrocytes by growing IB10 NP cells to confluency and washing twice with DMEM before adding astrocyte medium (DMEM-F12 supplemented with 1:100 N2 and 2% FBS). The culture medium was changed twice and cells were grown for 5 days to make sure differentiation was complete, which was confirmed by immunofluorescence.
NPCs were generated according to Conti and colleagues (Conti et al. 2005) with slight modifications. In brief, ES cells (129SVJ/CAST) were differentiated in N2B27 (StemCell Resources) for 7 days, followed by the formation of neural spheres in N2B27 supplemented with EGF and FGF (10ng/ml). 3-day-old spheres were allowed to attach to the culture dish to expand NPCs (also see Splinter et al., 2011, Genes & Development).

extract_protocol: The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Cells are cross-linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with HindIII and subsequently ligated under diluted conditions. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (indicated in the sample description). After a second re-ligation step, the sample is purified and a 4C PCR is applied.

treatment_protocol: Cells were cross-linked using 2% formaldehyde for 10 minutes at room temperature in 10%FCS/PBS.

value: NPC 129/Cast


title: ZHBTc4_+dox_Nanog

description: 4C PCR product

value: ESC ZHBTc4

value: TCGACGTAATTTTGGTAAGCTT


title: snt2D_0.5hrs_rep2


title: Tas2R110_Fetal_Brain

description:
4C PCR product.
Barcode: ATTTTATATGTCAAAAGCTT

source_name: Fetal brain, Tas2R110

tag: tissue

value: fetal brain


title: snt2D_0hrs_rep3


title: ecm5D_0.5hrs_rep1

value: BY4741 ecm5D


title: snt2D_0.5hrs_rep1


title: snt2D_0hrs_rep2


title: Tas2R110_AC_E14

source_name: astrocytes E14, Tas2R110

value: AC E14


title: Tas2R110_ESC_E14

source_name: ESC E14, Tas2R110

value: ESC E14


title: Tas2R110_iPSC

description:
4C PCR product.
Barcode: GATTTTATATGTCAAAAGCTT

source_name: iPSC, Tas2R110

value: iPSC


title: Retsat_ESC_E14

description:
4C PCR product.
Barcode: AGTTCATAGAACTGAAGCTT

source_name: ESC E14, Retsat

value: Retsat


title: Retsat_NPC_129_Cast

description:
4C PCR product.
Barcode: AGAGTTCATAGAACTGAAGCTT

source_name: NPC 129/Cast, Retsat


title: Retsat_ESC_129_Cast

source_name: ESC 129/Cast, Retsat

value: ESC 129/Cast


title: snt2D_0hrs_rep1


title: WT_0hrs_rep3

source_name: S. cerevisiae wild-type (BY4741) strain


title: Retsat_AC_E14

description:
4C PCR product.
Barcode: CTAGTTCATAGAACTGAAGCTT

source_name: astrocytes E14, Retsat


title: WT_0.5hrs_rep3


title: WT_0hrs_rep2


title: Ptprz1_NPC_129_Cast

description:
4C PCR product.
Barcode: AGTAATGCTATTGTATAAGCTT

source_name: NPC 129/Cast, Ptprz1


title: Ptprz1_iPSC

description:
4C PCR product.
Barcode: GTAATGCTATTGTATAAGCTT

source_name: iPSC, Ptprz1


title: Ptprz1_ESC_E14

description:
4C PCR product.
Barcode: TAATGCTATTGTATAAGCTT

source_name: ESC E14, Ptprz1


title: ecm5D_0hrs_rep2


title: Ptprz1_AC_E14

source_name: astrocytes E14, Ptprz1


title: Nanog_NPC_129_Cast

description:
4C PCR product.
Barcode: AGGACGTAATTTTGGTAAGCTT

source_name: NPC 129/Cast, Nanog


title: untagged_0hrs__H2O2Expt_Input

source_name: S. cerevisiae untagged strain

extract_protocol:
Samples were crosslinked by adding formaldehyde (final conc 1%) at room temp for 20 minutes, and then quenched with glycine (final conc 125 mM).  ChIPs were performed as described (Aparicio et al. 2005 Curr Protoc Mol Biol). Briefly cells were lysed using glass beads, and chromatin was sheared to 150-500 bp. Chromatin was isolated and used for ChIP with the anti-Myc 9E10 antibody (Millipore #05-419) according to standard procedures.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Preparation Kit (cat # FC-121-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 20 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: One third of each yeast culture was taken for the 0 hour (T0) ChIP/Input samples. H2O2 was added to remaining cultures at a final concentration of 0.4 mM. Samples were taken 0.5 and 4 hours after H2O2 addition for ChIP/Inputs

value: no antibody


title: ECM5_4hrs__H2O2Expt_Input

source_name: S. cerevisiae Ecm5-13Myc strain


title: untagged_0.5hrs__H2O2Expt_Input


title: ECM5_0.5hrs__H2O2Expt_Input


title: WT_0.5hrs_rep2


title: ECM5_0hrs__H2O2Expt_Input


title: Nanog_Fetal_Brain

description:
4C PCR product.
Barcode: GACGTAATTTTGGTAAGCTT

source_name: Fetal brain, Nanog


title: Nanog_ESC_E14

source_name: ESC E14, Nanog


title: WT_0hrs_rep1


title: Nanog_AC_E14

source_name: astrocytes E14, Nanog


title: SNT2_4hrs__H2O2Expt_Input

source_name: S. cerevisiae Snt2-13Myc strain


title: Retsat_iPSC

description:
4C PCR product.
Barcode: CAGTTCATAGAACTGAAGCTT

source_name: iPSC, Retsat


title: WT_0.5hrs_rep1


title: Slitrk4_ESC_129_Cast

description:
4C PCR product.
Barcode: TTACATCCTATAGCAAGCTT

source_name: ESC 129/Cast, Slitrk4


title: Ptprz1_ESC_129_Cast

source_name: ESC 129/Cast, Ptprz1


title: Xist_ESC_129_Cast

description:
4C PCR product.
Barcode: AGTCCAGAAGCTAGGAAAGCTT

source_name: ESC 129/Cast, Xist

value: Xist


title: Rad23a_ESC_129_Cast

description:
4C PCR product.
Barcode: TCGTAGTATTCATGAAGCTT

source_name: ESC 129/Cast, Rad23a


title: ras_SUMO1_rep2_ChIPSeq

tag: cell line

value: primary fibroblasts

value: Ras induced senescent

value: infected with pBABE-puro-H-RasG12V

value: SUMO1 (non-commercial)


title: Tas2R110_ESC_129_Cast

source_name: ESC 129/Cast, Tas2R110


title: prolif_SUMO1_rep2_ChIPSeq

value: Proliferative

value: infected with pBABE-puro-empty


title: SNT2_0hrs__H2O2Expt_Input


title: Nanog_ESC_129_Cast

source_name: ESC 129/Cast, Nanog

value: Nanog


title: untagged_0.5hrs__H2O2Expt_ChIP

value: anti-Myc (9E10 monoclonal)


title: GeneDesert_44.5Mb_ESC_E14

description:
4C PCR product.
Barcode: GGAGTGTACCAGCAAGCTT

source_name: ESC E14, GeneDesert 44.5Mb


title: GeneDesert_44.5Mb_iPSC

description:
4C PCR product.
Barcode: CGGAGTGTACCAGCAAGCTT

source_name: iPSC, GeneDesert 44.5Mb


title: untagged_4hrs__H2O2Expt_ChIP


title: SNT2_0.5hrs__H2O2Expt_Input


title: Nanog_iPSC

description:
4C PCR product.
Barcode: GGACGTAATTTTGGTAAGCTT

source_name: iPSC, Nanog


title: Beta-globin_ESC_129_Ola

description:
4C PCR product.
Barcode: CAATGCCTCTTACCTCCATG

source_name: ESC 129/Ola, Beta-globin

value: ESC 129/Ola

value: Beta-globin


title: untagged_0hrs__H2O2Expt_ChIP

source_name: S. cerevisiae untagged strain


title: GeneDesert_44.5Mb_NPC_129_Cast

description:
4C PCR product.
Barcode: AGGGAGTGTACCAGCAAGCTT

source_name: NPC 129/Cast, GeneDesert 44.5Mb

value: NPC 129/Cast


title: GeneDesert_44.5Mb_ESC_129_Cast

source_name: ESC 129/Cast, GeneDesert 44.5Mb


title: ECM5_4hrs__H2O2Expt_ChIP

source_name: S. cerevisiae Ecm5-13Myc strain


title: GeneDesert_44.5Mb_AC_E14

description:
4C PCR product.
Barcode: CTGGAGTGTACCAGCAAGCTT

source_name: astrocytes E14, GeneDesert 44.5Mb

value: AC E14


title: AB_part_iPSC

description:
4C PCR product.
Barcode: CTGGATTTGAATGGTAAGCTT

source_name: iPSC, AB_parts

value: iPSC


title: ECM5_0.5hrs__H2O2Expt_ChIP


title: AB_part_ESC_129_Cast

description:
4C PCR product.
Barcode: TGGATTTGAATGGTAAGCTT

source_name: ESC 129/Cast, AB_parts


title: ECM5_0hrs__H2O2Expt_ChIP


title: AB_part_AC_E14

description:
4C PCR product.
Barcode: CTTGGATTTGAATGGTAAGCTT

source_name: astrocytes E14, AB_parts


title: AB_part_ESC_E14

source_name: ESC E14, AB_parts

value: ESC E14


title: SNT2_4hrs__H2O2Expt_ChIP

source_name: S. cerevisiae Snt2-13Myc strain


title: SNT2_0.5hrs__H2O2Expt_ChIP


title: untagged_4hrs__H2O2Expt_Input


title: Pctk_ESC_129_Cast

description:
4C PCR product.
Barcode: ACTCTTCTTTTGAGAAGCTT

source_name: ESC 129/Cast, Pctk

value: ESC 129/Cast

value: Pctk


title: KT2440_glucose

status: Public on Jul 23 2013

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
Filtering raw reads: Removal of adaptors; removal of reads with more than 10% of Ns; removal of reads with more than 50% of bases with Q<5.
Filtered reads alignment: Clean reads were mapped to a database of Pseudomonas genes (GenBank accession AE015451.1) sequences using SOAP2.21 (Li et al., 2009) allowing up to 5 mistmaches.
Expression values calculation: RPKM were calculated for each gene.
Genome_build: AE015451.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Pseudomonas putida KT2440

source_name: Pseudomonas putida, mid-exponential phase, glucose

growth_protocol: Wild type P. putida KT2440 strain (Bagdasarian et al., 1981) was used in all experiments. P. putida was cultivated in M9 minimal media (Sambrook et al., 1989) supplemented with 2 mM MgSO4 and one of the four carbon sources: glucose (10 mM), succinate (15 mM), glycerol (10 mM) and fructose (10 mM). In all experiments, cells were grown at 30 ºC with vigorous orbital shaking.

extract_protocol:
Total RNA was extracted by using miRNeasy kit (Qiagen) with some modifications. The collected pellets were resuspended into 0.3 ml Tris-HCl (pH 7.5) containing 2 mg/mL lysozyme and incubated for 10 min at 37 °C. Then, 0.1 mL of lysate was used according to the manufacturer's instructions. RNase-free DNase (Qiagen) treatment was performed during the isolation procedure to eliminate the residual DNA. Finally, the quality of RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Total RNA from the samples above were digested with DNase I in order to avoid DNA contamination. rRNA was then eliminated using the RiboZero rRNA removal kit (Epicenter Biotechnologies) for Gram-negative bacteria according to the manufacturer's protocol. Samples for sequencing were prepared with the mRNA-Seq Kit of Illumina. This involved first a treatment of the RNA of the samples in a reaction with 5X Fragmentation Buffer at 94°C for 5 minutes and further purification by ethanol precipitation. For cDNA synthesis, reverse transcription was performed for the first strand chain and then the buffer solution, dNTPs, RNase H. Next, DNA polymerase I was added for the second strand cDNA and the synthesized products were purified. Then cDNA was then end-repaired and phosphorylated, followed by adenylation of 3' ends and 5' adapter ligation. The ligated reaction was purified on a 2% agarose gel and the cDNA migrating in the 200 bp (± 25 bp) range eluted and enriched with a PCR reaction. The thereby prepared cDNA libraries were then sequenced using HiSeq 2000 to yield 91 paired-end reads.

treatment_protocol: After overnight grown, cells were washed twice and diluted 100-fold in fresh medium containing succinate, glucose, fructose or glycerol as the sole carbon source. Cultures were then allowed to grow until mid-exponential phase (OD600 ~ 0.4). At this point, the samples were transferred to 1:10 sample:volume of ice-cold ethanol/phenol solution (5% water-saturated phenol in ethanol) to protect bacteria from RNA degradation. Cells were then harvested by centrifugation (3,800 rpm for 15 min at 4 °C). After aspiration of supernatant, the pellets were frozen in liquid nitrogen and stored at -80 °C until required.

tag: strain

tag: genotype

value: wild type

tag: carbon source

value: glucose


title: KT2440_fructose

source_name: Pseudomonas putida, mid-exponential phase, fructose

value: fructose


title: SNT2_0hrs__H2O2Expt_ChIP


title: KT2440_succinate

source_name: Pseudomonas putida, mid-exponential phase, succinate

value: succinate


title: 1D11 Schisto-PH Mouse #3

city: Aurora

first: Brian

last: Graham

state: CO

department: Medicine

institute: University of Colorado Denver

description: 1D11 Schisto-PH 3

data_processing:
Groomer/Tophat/Bowtie/Cufflinks analysis performed using Galaxy (https://main.g2.bx.psu.edu/)
Groomer: map Illumina reads onto Sanger reads, using NCBI37/mm9 mouse genome database
Bowtie, Single-ended, Mapped to mouse mm9 genome, Maximum number of mismatches: 2, Maximum permitted total of quality values at mismatched read positions: 70, Seed length: 28, Alignment policy: MAQ-like, Alignments per read: 1, Maximum number of backtracks permitted when aligning a read: 125
Tophat v1.2.0, Anchor length: 8, Maximum number of mismatches that can appear in the anchor region of spliced alignment: 0, Minimum intron length: 70, Minimum intron length that may be found during split-segment (default) search: 50, Maximum intron length: 500,000, Max insertion length: 3, Max deletion length: 3, Minimum isoform fraction: 0.15, Maximum number of alignments allowed: 40, Number of mismatches allowed in the initial read mapping: 2, Number of mismatches allowed in each segment alignment for reads mapped independently: 2, Minimum length of read segments: 25, Minimum intron length that may be found during coverage search: 50, Maximum intron length that may be found during coverage search: 20,000
Cufflinks v1.0.3, Max Intron Length: 300,000, Min Isoform Fraction: 0.05, Pre MRNA Fraction: 0.05, Reference Annotation: mouse mm9 genome, Bias Correction: No
Separately, Illumina CASAVA v1.7 was used to generate gene expression data for each sample as well.
Genome_build: NCBI Build 37/mm9
Supplementary_files_format_and_content: Cufflinks output (gene expression data) .tabular files in gtf format
Supplementary_files_format_and_content: CASAVA output (Illumina gene expression data) .txt files.   [Column 1] Chromosome number-starting with a c. The chromosome on which the exon resides. [Column 2] Start-The start of the gene. [Column 3] End-The end of the gene. [Column 4] Genes-The gene symbol. [Column 5] Normalized count (RPKM)=(10^9 x raw count)/(feature length x number of mapped bases). [Column 6] Raw count=sum of coverages for each base within the feature.

source_name: Whole mouse lung

extract_protocol:
Qiagen RNAeasy kit
Illumina TruSeq RNA Sample Preparation kit

treatment_protocol: Control group: no exposure. Schisto-PH group: 240 S. mansoni eggs IP/gram body weight, followed 2 weeks later by 240 S. mansoni eggs IV/gram body weight (tail vein injection), followed 1 week later by tissue harvest. 1D11 treated mice (in both the control and schisto-PH groups) were additionally administered 2 doses of 1D11 at 0.5ug/g body weight IP on the day of IV egg administration and 3 days thereafter (4 days prior to catheterization).

value: Female

tag: schisto exposure

value: IP/IV eggs

tag: disease state

value: experimental Schistosoma-induced pulmonary hypertension

value: whole lung


title: 1D11 Schisto-PH Mouse #2

description: 1D11 Schisto-PH 2


title: 1D11 Schisto-PH Mouse #1

description: 1D11 Schisto-PH 1


title: AB_part_NPC_129_Cast

description:
4C PCR product.
Barcode: AGTGGATTTGAATGGTAAGCTT

source_name: NPC 129/Cast, AB_parts

tag: cell type


title: 1D11 Control Mouse #3

description: 1D11 Control 3

value: control

tag: treatment


title: 1D11 Control Mouse #2

description: 1D11 Control 2


title: Schisto-PH Mouse #5

description: Schisto-PH 5


title: MeCP2_ESC_129_Cast

description:
4C PCR product.
Barcode: GGTTGGACACGAAAGCTT

source_name: ESC 129/Cast, MeCP2


title: Schisto-PH Mouse #4

description: Schisto-PH 4


title: Schisto-PH Mouse #3

description: Schisto-PH 3


title: KT2440_glycerol

source_name: Pseudomonas putida, mid-exponential phase, glycerol

value: glycerol


title: Control Mouse #2

description: Control 2


title: Control Mouse #1

description: Control 1


title: Control Mouse #4

description: Control 4


title: Schisto-PH Mouse #1

description: Schisto-PH 1


title: miCLIP_NSUN2_HEK293_rep5

city: St Louis

first: Sabine

last: Dietmann

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: Sample 5

data_processing:
Library strategy: iCLIP-seq
Potential PCR duplicates were removed and reads with identical barcodes were counted to determine exact cDNA counts. Adapter and barcodes were removed and reads were aligned to the human reference genome (GRCh37/hg19) using bowtie (0.12.9). Only the reads uniquely aligning to the genome with one mismatch were considered for further analysis.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: iCLIP read counts per ncRNAs from ENSEMBL (release 68, October 2012) and tRNA gene loci (GtRNA, October 2012), tab-spaced

extract_protocol:
Total RNA was obtained using the standard Trizol extraction protocol and the mRNA fraction was subsequently purified using oligodT magnetic dynabeads.
Following stringent washing, 3’end dephosphorylation was performed with T4 polynucleotide kinase before addition of a 3’ pre-adenylated linker using RNA ligase. 5’end labelling was then performed using T4 PNK and 32P-ATP before protein-RNA complexes were eluted and run on denaturing gels. Nitrocellulose transfer was then performed and the radioactive signal was then used to dissect nitrocellulose pieces that contained NSUN2-partially digested RNA complexes. RNA was recovered by incubating the nitrocellulose pieces in a buffer containing ProteinaseK and 7M urea. Reverse transcription was performed next, with the oligonucleotides for reverse transcription containing two inversely oriented adaptor regions separated by a BamHI restriction site as well as a barcode region at their 5′ end containing a 5-nt random barcode to enable tracing of individual cDNAs. cDNAs were size-purified on TBE-Urea gels before being circularized by CircLigase II. Circularised cDNAs were then annealed to an oligonucleotide complementary to the BamHI site and then BamHI digested. Linearized cDNAs were then PCR-amplified using primers complementary to the adaptor regions using either 25 or 35 cycles of PCR.
Libraries were prepared using the Illumina TruSeq mRNA library prep kit.

treatment_protocol: myc-tagged NSUN2 C271A construct was transfected into HEK293 cells which were harvested 24 hours post-transfection. Cells were then lysed in lysis buffer and treated with high concentration of DNase and low concentration of RNaseI to partially fragment RNAs. Lysates were incubated with proteinG dynabeads in the presence of anti-myc antibody to isolate NSUN2-RNA complexes.

value: Embryonic kidney cells

tag: transfected with

value: myc-tagged NSUN2 C271A construct

tag: iclip antibody

value: anti-myc antibody


title: Control Mouse #3

description: Control 3


title: miCLIP_NSUN2_HEK293_rep4

description: Sample 4


title: miCLIP_NSUN2_HEK293_rep1

description: Sample 1


title: miCLIP_NSUN2_HEK293_rep2

description: Sample 2


title: Nsun_rep4

data_processing:
Reads were aligned to the  human reference genome (GRCh37/hg19) using tophat (version 2.0.4). Only the reads uniquely aligning to the genome and aligning without mismatch were considered for further analysis. Fragment counts were normalized and differential abundance of fragments was evaluated with the Bioconductor DESeq package (http://www-huber.embl.de/users/anders/DESeq).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

extract_protocol:
Total RNA was obtained using the standard Trizol extraction protocol and the mRNA fraction was subsequently purified using oligodT magnetic dynabeads.
Libraries were prepared using the Illumina TruSeq mRNA library prep kit.

treatment_protocol: HEK293 cells were transfected with siRNAs directed against NSUN2 or otherwise a scrambled control sequence as a negative control. 48 hours post-transfection, cells were harvested.

value: Human Embryonic Kidney cells

value: siRNA against Nsun2


title: Nsun_rep3


title: Nsun_rep1


title: Scr_rep4

value: scrambled control sequence


title: Schisto-PH Mouse #2

description: Schisto-PH 2


title: 1D11 Control Mouse #1

description: 1D11 Control 1


title: Scr_rep3


title: Scr_rep2


title: miCLIP_NSUN2_HEK293_rep6

description: Sample 6


title: Control Mouse #5

description: Control 5


title: Scr_rep1


title: miCLIP_NSUN2_HEK293_rep3

description: Sample 3


title: resting-R13

status: Public on Jul 22 2013

city: Wageningen

first: Bart

last: Pannebakker

address: Droevendaalsesteeg 1

institute: Wageningen University

description: Sample 13

data_processing:
Basecalls were performed using Illumina pipeline v1.3
Reads were aligned against the Nasonia vitripennis genome (Nvit1.0, ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Nvitripennis/fasta/Nvit_1.0/linearized_sequence  ) using MAQ 0.6.8, allowing for a 2bp mismatch between the 21bp tag and reference sequence.  The remaining tags were aligned to the Nasonia Official Gene Set (OGS) v.1.2 (http://hymenopteragenome.org/nasonia/) using MAQ 0.6.8 and the same mapping settings.
Tags were removed from the dataset: phred mapping quality < 30 , anti-sense tags, tags<16 reads in total.
Genome_build: Nvit1.0 and OGS1.2
Supplementary_files_format_and_content: comma separated value (csv) file include: TagID, location (either Nvit1.0 scaffold or Nasonia OGS1.2), position, tag sequence, and tag counts for each sample

organism: Nasonia vitripennis

source_name: adult wasp whole-bodies_resting

extract_protocol:
Females were flash frozen on dry ice, females were flash-frozen in liquid nitrogen and stored on dry-ice until the addition of RNAlater-ICE (Ambion, Austin, TX, USA). We pooled the F2 test females from each F1 mother according to treatment, generating a total of eight pooled samples per treatment (consisting of 8 females per pool) for RNA isolation and sequencing. RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol. We further purified our samples using Turbo DNase (Ambion, Austin, TX, USA) and tested the integrity and concentration of our samples using a NanoDrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
Tag library preparation was done using the DGE-Tag Profiling for NlaIII Sample Prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Single 2-day old mated Nasonia vitripennis females (ASymC strain) were isolated in a glass vial and provided with a single host to produce F1 daughters. Eight 2-day old mated F1 females were subsequently provided with three hosts to produce the F2 test females. We randomly selected one host from each F1 female, and isolated 16 2-day old mated F2 test females in glass tubes, of which eight were randomly allocated to the oviposition treatment and eight to the resting treatment. We provided the test females with a single host for 24 hours as pre-treatment to facilitate egg development. We then discarded the pre-treatment hosts and gave each female a piece of chromatography paper soaked in honey solution for a further 24 hours. For the experiment, we transferred the females to 1.5 mL Eppendorf tubes that contained a single host for the oviposition experiment, or were empty for the resting treatment. After 60 mins, females were flash frozen.

value: ASymC

value: adult wasp whole-bodies

tag: behaviour

value: resting

tag: sample id


title: oviposition-H11

description: Sample 11

source_name: adult wasp whole-bodies_ovipositing

value: ovipositing


title: oviposition-H7

description: Sample 7


title: resting-R8

description: Sample 8


title: oviposition-H10

description: Sample 10


title: oviposition-H14

description: Sample 14


title: resting-R9

description: Sample 9


title: resting-R15

description: Sample 15


title: resting-R6

description: Sample 6


title: oviposition-H16

description: Sample 16


title: oviposition-H4

description: Sample 4


title: ovipostion-H5

description: Sample 5


title: resting-R3

description: Sample 3


title: Nsun_rep2


title: oviposition-H1

description: Sample 1


title: resting-R2

description: Sample 2


title: Pcdh11x_ESC_129_Cast

description:
4C PCR product.
Barcode: TCCAGTTGTGTCAAAAGCTT

source_name: ESC 129/Cast, Pcdh11x

value: ESC 129/Cast


title: Bleomycin

city: Tokyo

first: Tatsuya

last: Tsukui

address: 7-3-1, Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
The PGM raw reads were aligned against the mouse refseq genes (UCSC, http/hgdownload.cse.ucsc.edu/goldenPath/mm9/  database/) using BWA 0.6.2 which uses the 25_1 mapping parameter.
We generated unique gene counts by excluding reads that mapped to contigs of more than one gene. Reads mapping to several contigs within an isogroup were only counted once.
Supplementary_files_format_and_content: Text file includes normalized numbers of read tags for each group (Saline and Bleomycin) and gene identifiers

source_name: Lung fibroblasts from 3 mice

extract_protocol:
Lungs were harvested and dissociated with protease sollution (collagenase, dispase, Dnase). Lineage- GFP+ cells were sorted by FACS and RNA were isolated using mirVana mirRNA Isolation kit (Ambion). 1ug of total RNA was used for the construction of sequencing libraries
SAGE libraries were constructed using the SOLiD SAGE kit from Life Technologies (Life Technologies) according to manufacturer’s protocol.

treatment_protocol: Saline or bleomycin were injected intratracheally

value: Lung

value: Day 14 post bleomycin


title: Saline

value: Day 14 post saline


title: 37C_2

city: Bern

first: Stefan

last: Wyder

address: Murtenstrasse 31

department: Dpt. Clinical Research

country: Switzerland

institute: University of Bern

data_processing:
Alignment: bwa 0.6.1 using default settings
Coverage Depth: BEDTools 2.16.2 based on PATRIC RAST genome annotation (http://patricbrc.vbi.vt.edu/))
Statistics of differential expression: DESeq package in R/Bioconductor
Genome_build: Moraxella catarrhalis O35E, Accession NZ_AERL00000000
Supplementary_files_format_and_content: Normalized Counts: tab-delimited text file including counts for each gene for all samples , bed files were created using BEDTools containing raw counts per gene

organism: Moraxella catarrhalis O35E

source_name: continuous growth at 37°C

growth_protocol: Bacteria were cultured at 37°C and 200 rpm in brain heart infusion (BHI) broth (Difco) or on BHI agar plates in an atmosphere containing 5% CO2.

extract_protocol:
M. catarrhalis cultures were fixed with 2 volumes of RNA protect (Qiagen) and harvested. RNA was isolated using the RNeasy kit (Qiagen). Residual DNA in the samples was removed using Dnase I. The integrity of the RNA was analyzed using an Agilent bioanalyzer (Agilent technologies)
Library construction was performed according to the TruSeq RNA sample preparation v2 guide (Illumina).

tag: growth temperature

tag: barcode

value: GCCAAT


title: 26C_3

source_name: 26°C cold shock

value: CAGATC


title: 26C_1

value: CGATGT


title: resting-R12

description: Sample 12


title: 37C_1

value: TGACCA


title: RGL58

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

description:
MFA wig file generated by taking the ratio between sample RGL58 and RGL56
processed data file: N6953_MFA.wig.gz

data_processing:
Sequence reads were mapped to the E. coli (MG1655) reference genome (Accession number: NC_000913) using BioScope (version 1.3.1).
Sequence reads mapping to a single genomic location were summed in 1 kb bins.
Normalised copy numbers were generated by dividing the sequence read counts from each sample by the counts from a stationary (non-replicating) wild-type sample.
Normalised copy numbers were manually adjusted to give a  ratio of ~1 at the origin, oriC.
Genome_build: eschColi_K12
Supplementary_files_format_and_content: wig files of marker frequency analysis (MFA) for indicated comparisons. These are not manually adjusted and therefore reflect the read number obtained for each sample.

organism: Escherichia coli

source_name: Genomic DNA

growth_protocol: Samples from cultures of a strain grown to an A650 of ~1.2 in LB broth were diluted 400-fold in fresh broth and incubated with vigorous aeration until the A650 reached 0.4 at the temperature indicated. Samples from these exponential phase cultures were frozen in liquid nitrogen at this point for subsequent DNA extraction. Incubation of the remaining culture was continued until several hours after the culture had saturated and showed no further increase in the A650. A further sample (stationary phase) was frozen at this point.

extract_protocol:
DNA was extracted using the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich).
Library preparation and sequencing was carried out according to SOLiD instructions.

tag: relevant genotype

value: ΔxonA::apra ΔxseA::dhfr ΔsbcCD::kan

tag: growth phase

value: Exponential


title: Maize hen1-1 mutant

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

data_processing:
Seven small RNA libraries were made from three rice hen1 alleles and their controls. Small RNA sequences were obtained after removing adapters and low-quality reads, with trimmed lengths between 15 and 34 nucleotides.
Genome_build: TAIR10 and AGPv2

organism: Zea mays

source_name: Seedling leaf

growth_protocol: Immature inflorescence tissues including inflorescence meristem and early stages floral buds (up to stage 11/12) were collected from Arabidopsis grown in a growth chamber with 16 hours of light for five weeks.  For the seedling materials from wildtype, and the ago1-11 and hen1-2 single mutants, as well as the ago1-11/hen1-2 double mutants, seeds were sterilized and plated on 1/2 Murashige and Skoog medium containing 1% (w/v) sucrose and 1% (w/v) agar. Plates were first kept in 4°C for 3 days and then moved to growth chamber and grown under continuous light. Whole plant tissue samples were harvested 12 days after germination.  Rice plants containing the Os-hen1 alleles waf1-1 and waf1-2 were grown in a growth chamber with 12 hours of light for five weeks and genotyped by PCR to identify homozygous plants. The Os-hen1-3 allele was identified from the Kyung Hee University T-DNA collection (Jeong et al., 2002) as line PFG_2C-00348; seeds were obtained and homozygous lines identified by PCR-based genotyping.  For library construction, homozygous mutant seedlings at the five week stage were collected and the entire plants used for RNA extraction.  The Zm-hen1-1 allele was isolated in W22 background with a Mu insertion (mu1007900) within the first exon of HEN1. This insertion was verified by PCR analysis, and introgressed into B73. Materials were obtained from the homozygous F2 progeny derived from the W22 x B73 cross.

extract_protocol: Small RNA libraries  were constructed using Illumina Tru-Seq Small RNA preparation kit  and sequenced on an Illumina GAIIx instrument at the Delaware Biotechnology Institute.

treatment_protocol: no treatment

tag: background

tag: tissue

value: Seedling leaf

tag: genotype/variation


title: Maize wildtype control for hen1-1 mutant

value: wild type


title: 26C_2

value: ACAGTG

tag: strain


title: RGL50

description:
MFA wig file generated by taking the ratio between sample RGL50 and RGL48
processed data file: WX296_MFA.wig.gz

value: oriZ-cat


title: RGL56

description: Used as a non-replicating control for MFA with samples RGL57 and RGL58

value: Δlac

value: Stationary


title: RGL51

description:
MFA wig file generated by taking the ratio between sample RGL51 and RGL48
processed data file: RCe455_MFA.wig.gz

value: oriZ-cat ΔrecG::apra


title: RGL57

description:
MFA wig file generated by taking the ratio between sample RGL57 and RGL56
processed data file: AM1581_MFA.wig.gz


title: RGL13

description:
MFA wig file generated by taking the ratio between sample RGL13 and RGL4
processed data file: RCe260_MFA.wig.gz

value: rpoB*35 Δtus::cat


title: RGL35

description:
MFA wig file generated by taking the ratio between sample RGL35 and RGL33
processed data file: N6576_stat_MFA.wig

value: ΔlacIZYA ΔrecG::apra


title: RGL15

description:
MFA wig file generated by taking the ratio between sample RGL15 and RGL4
processed data file: JJ1378_MFA.wig.gz

value: ΔlacIZYA tus1::dhfr


title: 37C_3

value: CTTGTA


title: RGL49

description:
MFA wig file generated by taking the ratio between sample RGL49 and RGL52
processed data file: AM2123_MFA.wig


title: RGL39

description:
MFA wig file generated by taking the ratio between sample RGL39 and RGL33
processed data file: JJ1268_MFA.wig

value: ΔlacIZYA srgA1 ΔrecG::apra


title: RGL40

description:
MFA wig file generated by taking the ratio between sample RGL40 and RGL33
processed data file: AM2018_MFA.wig

value: ΔlacIZYA ΔrecG::apra ΔpriB::dhfr


title: RGL47

description:
MFA wig file generated by taking the ratio between sample RGL47 and RGL52
processed data file: AB1157_MFA.wig

value: rec+


title: RGL33


title: RGL34

description:
MFA wig file generated by taking the ratio between sample RGL34 and RGL33
processed data file: N6576_MFA.wig


title: RGL32

description:
MFA wig file generated by taking the ratio between sample RGL32 and RGL33
processed data file: N5740_MFA.wig


title: RGL52

value: ΔlacIZYA<>frt


title: RGL42

description:
MFA wig file generated by taking the ratio between sample RGL42 and RGL33
processed data file: N4702_MFA.wig

value: ΔrecG263::kan recB268::Tn10


title: RGL48

description: Used as a non-replicating control for MFA with samples RGL50 and RGL51


title: RGL29


title: RGL26

description:
MFA wig file generated by taking the ratio between sample RGL26 and RGL29
processed data file: RCe399_MFA.wig

value: recG265::cat tos-kan N15 lysogen

value: Exponential


title: RGL22

description:
MFA wig file generated by taking the ratio between sample RGL22 and RGL29
processed data file: N7957_MFA.wig

value: ΔrecG::apra Δtus::cat


title: RGL24

description:
MFA wig file generated by taking the ratio between sample RGL24 and RGL29
processed data file: RCe391_MFA.wig

value: recG265::cat tos-kan


title: RGL23

description:
MFA wig file generated by taking the ratio between sample RGL23 and RGL29
processed data file: N7957_stat_MFA.wig


title: RGL18

description:
MFA wig file generated by taking the ratio between sample RGL18 and RGL29
processed data file: N8227_MFA.wig


title: Arabidopsis hen1-8 mutant rep3

description: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Arabidopsis thaliana

source_name: flower

value: Col

value: flower


title: Arabidopsis hen1-8 mutant rep2


title: RGL19

description:
MFA wig file generated by taking the ratio between sample RGL19 and RGL29
processed data file: N8227_stat_MFA.wig

value: Stationary


title: RGL38

description:
MFA wig file generated by taking the ratio between sample RGL38 and RGL33
processed data file: N6859_MFA.wig

value: priA300 ΔlacIZYA ΔrecG::apra


title: RGL16

description:
MFA wig file generated by taking the ratio between sample RGL16 and RGL29
processed data file: N8226_MFA.wig


title: Arabidopsis Col wildtype, control for hen1-8 rep3

value: wild type


title: RGL12

description:
MFA wig file generated by taking the ratio between sample RGL12 and RGL4
processed data file: RCe261_MFA.wig

value: rpoB*35 ΔrecG::apra Δtus::cat


title: Arabidopsis Col wildtype, control for hen1-8 rep2


title: Arabidopsis Col wildtype, control for hen1-8 rep1


title: RGL2

value: F– rph-1


title: RGL6

description:
MFA wig file generated by taking the ratio between sample RGL6 and RGL4
processed data file: RCe268_MFA.wig

value: rpoB*35 ΔrecG::apra Δtus::cat tnaA::Tn10 dnaA46


title: RGL10

description:
MFA wig file generated by taking the ratio between sample RGL10 and RGL4
processed data file: N6576_MFA.wig

value: ΔlacIZYA ΔrecG::apra


title: Arabidopsis hen1-1 mutant rep3

value: Ler


title: Arabidopsis hen1-1 mutant rep2


title: RGL4

description:
MFA wig file generated by taking the ratio between sample RGL2 and RGL4
processed data file: MG1655_MFA.wig


title: RGL28

description:
MFA wig file generated by taking the ratio between sample RGL28 and RGL29
processed data file: RCe475_MFA.wig

value: Δlac


title: Arabidopsis hen1-1 mutant rep1


title: Arabidopsis Ler wildtype, control for hen1-1 rep2


title: Arabidopsis Ler wildtype, control for hen1-1 rep1


title: Arabidopsis Ler wildtype, control for hen1-1 rep3


title: Segregating heterozygotes control for oshen1-3 mutant

description:
Seg_oshen1-3
small RNA

data_processing:
Seven small RNA libraries were made from three rice hen1 alleles and their controls. Small RNA sequences were obtained after removing adapters and low-quality reads, with trimmed lengths between 15 and 34 nucleotides.  ~136 million reads matched to the rice genome.
Processed data files: Distinct small RNAs with their raw abundance after removing the adapter sequences.

organism: Oryza sativa

source_name: leaf

extract_protocol: Small RNA libraries were constructed as previously described (Lu et al. 2007 PMID:17889797) and sequenced on an Illumina GAIIx instrument at the Delaware Biotechnology Institute.

tag: cultivar

value: Dongjin

value: leaf


title: Arabidopsis hen1-8 mutant rep1


title: WT control for oshen1-3 mutant

description:
Wt_oshen1-3
small RNA

source_name: leaf, WT


title: small RNAs from AGO1 IP - AGO1-IP in hen1-8

tag: antibody


title: Rice waf1-2 mutant

description:
waf1-2
small RNA

source_name: leaf, waf1-2 mutant

value: Kinmaze

value: waf1-2 mutant


title: Rice oshen1-3 mutant

description:
oshen1-3
small RNA

source_name: leaf, oshen1-3 mutant

value: oshen1-3 mutant


title: small RNAs from AGO1 IP - AGO1-IP in heso1-1/hen1-8 double mutant


title: Control for waf1-2 mutant

description:
WT_waf1-2
small RNA


title: Rice waf1-1 mutant

description:
waf1-1
small RNA

source_name: leaf, waf1-1 mutant

value: waf1-1 mutant


title: small RNAs from AGO1 IP - input control for heso1-1/hen1-8

value: Col

value: input control


title: Arabidopsis Ler wildtype, control for hen1-2 and ago1-11

source_name: Seedling

value: Seedling


title: Control for waf1-1 mutant

description:
WT_waf1-1
small RNA


title: small RNAs from AGO1 IP - Input control for hen1-8

value: flower


title: Arabidopsis ago1-11/hen1-2 double mutant


title: Arabidopsis hen1-2 mutant


title: Arabidopsis ago1-11 mutant


title: Arabidopsis thaliana wildtype Lersberg erecta (Ler)

description: small RNA

data_processing:
Four RNA libraries were made from Ler, hen1-1, Col and hen1-8. In total, ~64 million small RNA sequences were obtained after removing adapters and low-quality reads, with trimmed lengths between 15 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), ~29 million reads were mapped to the Arabidopsis genome (TAIR9). Processed data files: Distinct small RNAs with their raw abundance after removing the adapter sequences.
Genome Build:
Ler_b_chopped.txt: TAIR9

extract_protocol: Small RNA libraries  were constructed as previously described (Lu et al. 2007 PMID:17889797) and sequenced on an Illumina GAIIx instrument at the Delaware Biotechnology Institute.

value: wildtype


title: Arabidopsis thaliana hen1-1 mutant in Ler background

description: small RNA

data_processing:
Four RNA libraries were made from Ler, hen1-1, Col and hen1-8. In total, ~64 million small RNA sequences were obtained after removing adapters and low-quality reads, with trimmed lengths between 15 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), ~29 million reads were mapped to the Arabidopsis genome (TAIR9). Processed data files: Distinct small RNAs with their raw abundance after removing the adapter sequences.
Genome Build:
hen1-1_b_chopped.txt: TAIR9

value: hen1-1 mutant


title: Arabidopsis thaliana wildtype Columbia (Col)

description: small RNA

data_processing: Four RNA libraries were made from Ler, hen1-1, Col and hen1-8. In total, ~64 million small RNA sequences were obtained after removing adapters and low-quality reads, with trimmed lengths between 15 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), ~29 million reads were mapped to the Arabidopsis genome (TAIR9). Processed data files: Distinct small RNAs with their raw abundance after removing the adapter sequences.


title: Arabidopsis thaliana hen1-8 mutant in Col backgroud

description: small RNA

data_processing:
Four RNA libraries were made from Ler, hen1-1, Col and hen1-8. In total, ~64 million small RNA sequences were obtained after removing adapters and low-quality reads, with trimmed lengths between 15 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), ~29 million reads were mapped to the Arabidopsis genome (TAIR9). Processed data files: Distinct small RNAs with their raw abundance after removing the adapter sequences.
Genome Build:
hen1_8_bcm_chopped.txt: TAIR9

value: hen1-8 mutant


title: E14(wt)_RNA

city: Cambridge

first: Laurie

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
RNA-seq reads were aligned to the mm9 genome assembly using Bowtie 0.12.3, with the following parameters --solexa1.3-quals --best --strata -m 1 -n 2 -p 8 -S.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using an in-house perl script interacting with Bedtools (as described in Wamstadt et al. Cell 2012).

source_name: RNA-seq in wt ESCs

growth_protocol: ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates.  Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Cells were then preplated - plated on cell culture plates without gelatin for 20 minutes to allow the MEFs to attach and thus deplete the cell population of MEFs - before collection for RNA preparation.

extract_protocol: RNA was prepared using Trizol, according to the manufacturer's instructions. The RNA was examined for quality by Bioanalyzer (Agilent). RNA-seq libraries were then prepared as described in Wamstad et al., 2012. Briefly, mRNA was purified and fragmented, first strand cDNA was synthesized, and the second strand was synthesized. The SPRI-TE Nucleic Acid Extractor by Beckman Coulter was then used to automate library preparation. Each sample was amplified for 18 cycles. The samples were then examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.

value: Embryonic stem cells

value: wild-type


title: V6.5_H3K27me3

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 0.12.3, with the following parameters --solexa1.3-quals --best --strata -m 1 -n 2 -p 8 -S.
Sequences were extended +200 bp for histone marks and allocated in 25-bp bins.
A Poissonian model was used to determine statistically enriched bins with a P-value threshold set at 1x10-9 as described previously (Marson et al., 2008).  Additionally, we required that genomic bins were at least 5 fold over input to be considered enriched peaks.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using an in-house perl script interacting with Bedtools (as described in Wamstad et al. Cell 2012).

source_name: H3K27me3 ChIP-seq in wt ESCs

growth_protocol: ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates.  Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Cells were then preplated - plated on cell culture plates without gelatin for 20 minutes to allow the MEFs to attach and thus deplete the cell population of MEFs - before collection for ChIP.

extract_protocol: The ChIP protocol has been adapted from previous studies (Lee et al., 2006; Boyer et al., 2006, Creyghton et al., 2008) with the following modification: Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on (high), 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water. Millipore 07-449 antibody was used in the ChIP.  The ChIP DNA was then used to prepare sequencing libraries as described in Schmidt et al., 2009. For this study, a 1:40 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was amplified for 18 cycles. The samples were then examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.

tag: chip antibody

value: H3K27me3 [Millipore:07-449]


title: CiPS11 [CiPS11]

city: beijing

first: chun

last: liu

state: beijing

address: beijing

country: China

institute: Peking University

data_processing:
Tophat 1.3.0. to align the clean reads to the mm9 RefSeq, and gene expression was analyzed by the RPKM method.
FDR < 0.01 and the absolute ratio of log2 > 1 as the threshold for the differential expresion of genes.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text file. RPKM values and GeneIDs.

source_name: CiPS line 11

growth_protocol: MEFs were cultured in DMEM/High Glucose (Hyclone) containing 10% fetal bovine serum (Invitrogen). Mouse ESCs (R1 and TT2) and CiPSCs were maintained on feeder layers of mitomycin C-treated MEFs in ESC culture medium.

extract_protocol:
Total RNA extracted by QIAGEN Rneasy Kit following manufacturer's instructions.
RNA libraries were prepared and sequenced following Illumina protocol

treatment_protocol: GFP- cells, GFP+ clusters and GFP+ colonies were picked up and collected for RNA isolation.

tag: developmental stage

value: embryo

tag: cell type

value: pluripotent stem cell

tag: chemical treatment condition


title: 153-C_RNA_m0_0

city: Davis

first: Danielle

middle: G

last: Lemay

state: CA

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

data_processing:
Basecalls performed using Illumina software
Reads mapped to the genome using TopHat with these options: tophat -G hg19.gtf -o tophat -p 4 -r 0
Mapped reads were indexed using samtools: samtools index tophat/accepted_hits.bam
Normalized transcript abundances determined using Cufflinks: cufflinks -u -b hg19.fa -G hg19.gtf -p 4 -o cufflinks tophat/accepted_hits.bam
Genome_build: hg19
Supplementary_files_format_and_content: Compressed tab-delimited text files contain transcript abundance measurements (FPKM) summarized at the gene level

molecule: polyA RNA

source_name: Milk Fat Layer

extract_protocol:
Soft Spin: Whole milk samples were centrifuged at 300 g for 10 min at 4 degrees C. The milk fat layers from three, 2.0 mL aliquots were transferred into a single new tube to which 500 µL TRIzol® was added and stored at -80 degrees C
Hard Spin: Whole milk samples were centrifuged at 15000 g for 10 min at 4 degrees C. The milk fat layers from three, 2.0 mL aliquots were transferred into a single new tube to which 500 µL TRIzol® was added and stored at -80 degrees C
Wash: After a hard spin at a warmer temperature, (15,000 g at 12 degrees C) the milk fat layers were transferred to a clean set of 3 tubes and re-suspended in 1 mL PBS+10µM EDTA. After centrifuging again (15,000 g at 12 degrees C), the milk fat layers from all 3 tubes were transferred to a single tube, re-suspended in 1 mL PBS, and centrifuged a final time (15,000 g at 12 degrees C). The remaining milk fat layer was transferred into a single new tube to which 500 µL TRIzol® was added and stored at -80 degrees C.
RNA Isolation: Total RNA was extracted and purified in batches of 16 using the PROMEGA Maxwell 16™ integrated system (Promega Corporation, Madison, WI).
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Kit and standard Illumina Protocols

tag: subject id

tag: lactation stage

value: Mature

tag: extraction protocol

value: Hard spin, Unwashed


title: Eed--_H3K27me3

description: mutant cell line reference: Montgomery et al., 2005

source_name: H3K27me3 ChIP-seq in Eed-/- ESCs

value: Eed-/-


title: Suz12GT_H3K27me3

description: mutant cell line reference: Pasini et al., 2007

source_name: H3K27me3 ChIP-seq in Suz12GT (aka Suz12(Bgal/Bgal)) ESCs


title: 174-X_RNA_m2_0

value: Hard spin, Washed once


title: Suz12GT_RNA

source_name: RNA-seq in Suz12GT (aka Suz12(Bgal/Bgal)) ESCs


title: Embryonic stem cells [ESCs2]

source_name: Embryonic stem cell line R1

value: embryonic stem cell

value: no treatment


title: 183-G_RNA_m2_2

value: Hard spin, Washed twice


title: Embryonic stem cells [ESCs1]


title: Embryonic stem cells [R1 2]

description: R1 2


title: Embryonic stem cells [R1]


title: 359_RNA_m0_0

value: Soft spin, Unwashed


title: Oct4-GFPpositive cell colonies [GFP+ colonies]

description: GFP+ colonies

source_name: Mouse embryonic fibroblasts

value: fibroblast


title: 179-C_RNA_m0_0


title: 183-G_RNA_m0_0


title: Oct4-GFPpositive cell clusters [GFP+ clusters]

description: GFP+ clusters


title: 168-R_RNA_m2_2


title: Oct4-GFP negative cells2 [GFP- cells2]

description: GFP- cells2


title: 188-L_RNA_c2_0

value: Transitional


title: Oct4-GFP negative cells1 [GFP- cells1]

description: GFP- cells1


title: Mouse embryonic fibroblasts2 [MEFs2]


title: 183-G_RNA_c2_0

value: Colostrum


title: 187-K_RNA_c2_0


title: CiPS 6 [CiPS6]

source_name: CiPS line 6


title: Mouse embryonic fibroblasts1 [MEFs1]


title: Mouse embryonic fibroblasts [MEFs]

description: MEFs


title: 179-C_RNA_c2_0


title: 187-K_RNA_c0_0


title: 158-1_RNA_c0_0


title: 154-D_RNA_c0_0


title: 179-C_RNA_m2_2


title: M091_100-nM-27A_HSF1_R2

status: Public on Jul 21 2013

first: Marc

last: Mendillo

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Images analysis and base calling was done using the solexa pipeline. ChIP-Seq reads were aligned to HG18 using ELAND  software (Illumina).
Identification of enriched genomic regions was performed as described previously (Guenther et al., 2008). Briefly, each ChIP-Seq read (a maximum of two repeat reads were allowed) was extended 100 bp to approximate the middle of the sequenced fragment. The extended fragments were subsequently allocated to 25 bp bins across the genome. Read density for each bin was calculated and enriched bins were identified by comparison to a Poisson background model using a p-value threshold of 10-12. The minimum ChIP-seq read density required to meet this threshold for each dataset is indicated in Table S1. Enriched bins within 200 bp were combined to form enriched regions. Enriched regions less than 100 bp were removed. Because of the non-random nature of background reads, enriched bins and regions were also required to have an eight-fold greater ChIP-seq density versus a nonspecific control IgG immunoprecipitation performed under identical conditions. All RefSeq genes that were within 8 kb of enriched regions were considered to be enriched genes. Enriched genes and regions for all experiments are listed in Table S1.
Genome_build: HG18
Supplementary_files_format_and_content: Processed data is provided as .xls.  It contains the genes that are located within 8 Kb of each region (enriched genes) for each cell line and condition.

source_name: M0-91 cells

extract_protocol: Nuclear extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: acute myelogenous leukemia cell line

tag: cell line

value: M0-91 cells

tag: treatment


title: M091_100-nM-27A_IGG

value: IGG (Santa Cruz, sc-2027, Lot# C2210)


title: 160-J_RNA_c0_2


title: M091_10-uM-CHX_HSF1_R1

value: Cycloheximide (10 µM)


title: M091_10-uM-CHX_IGG


title: M091_100-nM-27A_HSF1_R1


title: M091_10-uM-CHX_HSF1_R2


title: M091_20-nM-27A_HSF1_R1


title: M091_20-nM-27A_HSF1_R2


title: M091_20-nM-27A_IGG


title: M091_DMSO_HSF1

value: DMSO


title: MCF7_10-uM-CHX_IGG

source_name: MCF7 cells

value: breast cancer cell line

value: MCF7 cells


title: M091_DMSO_IGG


title: MCF7_10-uM-CHX_RNAPOLII_R2

value: RNA Pol II (AB817, Abcam, Lot#36502-3)


title: MCF7_10-uM-CHX_HSF1_R2


title: MCF7_DMSO_IGG


title: MCF7_10-uM-CHX_RNAPOLII_R1


title: MCF7_DMSO_RNAPOLII_R2


title: MCF7_DMSO_RNAPOLII_R1


title: MCF7_DMSO_HSF1_R2


title: MCF7_DMSO_HSF1_R1


title: AT-winter (paired end)

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

institute: College of life sciences, Peking University

data_processing:
Base-calling is performed using Illumina's Genome Analyzer system software by Illumina's protocol
SOAPaligner is used for aligning reads on to A. thaliana genome.
Methylation information is gathered into a tabular format file cotaining seven columns: 1. name of the chromosome, 2. coordinate on the chromosome, 3. strand (+/-), 4. methylation type (CG/CHG/CHH), 5. detailed methylation type, 6. number of methylated reads, 7. number of non-methylated reads.
Genome_build: TAIR9
Supplementary_files_format_and_content: The processed data are tabular format files and each row contains seven columns: 1. name of the chromosome, 2. coordinate on the chromosome, 3. strand (+/-), 4. methylation type (CG/CHG/CHH), 5. detailed methylation type, 6. number of methylated reads, 7. number of non-methylated reads.

source_name: whole plant

growth_protocol: A. thaliana plants are grown in walk-in greenhouse at 23℃ with 16 h light and 8 h of darkness for 20 days

extract_protocol: Libraries were constructed according to a published protocol (Lister et al., 2008). Briefly, sonicated DNA (100-300 bp) after end-repair were treated with Klenow fragment and dATP to produce 3'-dA overhang for ligation of Illumina's adapters. Then after bisulfite sodium treatment, DNA was PCR amplified with Illumina primers for 15 cycles and fragments of 250~350 bp were band isolated from an agarose gel for cluster generation.

value: whole organism

tag: time

value: February

tag: age


title: AT-summer (single)

value: August


title: AT-summer (paired end)


title: 506_s_3

status: Public on Jul 20 2013

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

description: 506_s_3 serum

data_processing:
Sequenced reads from Solexa were first mapped onto human genome version hg18 using novoalign software and the expression level of mature miRNAs in the miRBase human miRNA database v15 was summarized.
Quantile normalization was applied to the counts data
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each miRNA

source_name: serum

extract_protocol:
TRIZOL LS reagent (Invitrogen) was used to extract total RNA from ~1.5 ml of serum, as described in the manufacturer’s protocol. RNA pellet was dissolved in 10 μl of RNase-free water, and subjected to library construction and deep sequencing.
Each serum sample was independently subjected to library preparation and deep sequencing. All small RNAs of 15–52 nts were selected and sequenced using the Solexa system, following the manufacturer’s protocol (Illumina Inc., San Diego, CA). Library preparation, as well as cluster generation and deep sequencing, was performed according to the 5' ligation-dependent (5′ monophosphate-dependent) manufacturer’s protocol (Digital Gene Expression for small RNA; Illumina). For each sample, 5 μl of total RNA extracted from serum was used for small RNA library preparation. Small RNAs were size-selected between 17 and 52 nt according to the single-stranded DNA marker in the small RNA sequencing kit (Illumina). The library was quantified using picoGreen and qPCR. Sequencing was performed on a Genome Analyzer IIx (Illumina), and image processing and base calling were conducted using Illumina’s pipeline.

treatment_protocol: Pre-treatment sera from BC patients were used.

tag: er status

value: neg

tag: pr status

tag: her2 status

tag: inflammatory

value: N

tag: Stage

tag: relapse

value: Y

tag: molecule subtype

value: miRNA


title: PM1_37_1

city: College Station

first: James

last: Cai

state: TX

address: 4458 TAMU

department: VIBS

institute: Texas A&M University

data_processing:
Raw data were trimmed by using fastx-trimmer
Mapping was done by using TopHat 2
FPKM were calculated by using Cufflinks
Genome_build: ASM22705v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene

organism: Talaromyces marneffei PM1

source_name: arthroconidia

extract_protocol:
Fresh cells were collected from SDA plates. Total RNAs were extracted using the EZNA fungal RNA kit (Omega Bio-Tek).
RNA libraries were prepared for sequencing using the standard Illumina protocol

value: arthroconidia

tag: temperature


title: AT-winter (single)

tag: tissue


title: 40_s_2

description: 40_s_2 serum


title: PM1_25_2

source_name: mycelia

tag: cell type

value: mycelia


title: 23_s_7

description: 23_s_7 serum

value: pos


title: 53_s_4

description: 53_s_4 serum


title: 502_s_2

description: 502_s_2 serum


title: PN97_s_7

description: PN97_s_7 serum


title: PM1_37_2


title: MCF7_10-uM-CHX_HSF1_R1

tag: antibody


title: 39_s_4

description: 39_s_4 serum


title: PM1_25_1


title: dcr1 delta

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

data_processing:
All samples were sequenced (together with other libraries) on one lane of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the TruSeq barcode. Illumina software Casava v 1.8 was used.
The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Genome_build: n/a
Supplementary_files_format_and_content: Tabular, Columns: unique id, sequence, sequence count, original id from raw files if sequence is unique, or from first occurence in the raw data file

organism: Schizosaccharomyces pombe

source_name: dcr1 delta

growth_protocol: Yeast strains were grown at 30°C in YES

extract_protocol:
Total RNA was isolated from exponentially growing cells using the hot phenol method (Leeds, 1991). The RNA was fractionated using RNeasy Midi columns (Qiagen) following the „RNA cleanup protocol“ provided by the manufacturer. The flow-through fraction was precipitated („small RNA“ fraction). 25 μg of the "small RNA" fraction were separated on a 17.5% PAGE and the 18 – 28 nt population was purified.
The isolated small RNA populations were prepared for sequencing using the Illumina® TruSeqTM small RNA preparation protocol (Cat.# RS-930-1012).

tag: strain

tag: genotype

value: dcr1 delta


title: 37_s_3

description: 37_s_3 serum


title: 537_s_8

description: 537_s_8 serum


title: swi6+

source_name: wt

value: wild type


title: NLS-swi6-KR25A


title: 525_s_1

description: 525_s_1 serum

value: net


title: 2021_s_2

description: 2021_s_2 serum