title: ESCell_76_CTTTACC_amplified

description: PolyA RNA

value: CTTTACC


title: ESCell_73_CTAGGAA_amplified

status: Public on Dec 20 2013

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

description: PolyA RNA

library_source: transcriptomic

data_processing:
Read quality filtering and barcode extraction: Every read that was considered valid by the Illumina HiSeq control software was processed and filtered as follows: a) any 3' bases with a quality score of 'B' were removed; b) the well-identifying barcode was extracted from the 5' end of the read; c) if the read ended in a poly(A)-sequence leaving less than 25 transcript-derived bases, the read was discarded; d) the UMI was extracted and if any of the UMI bases had a Phred score less than 17 the read was discarded; e) a maximum of nine template-switching generated Gs were removed from the 5' end of the transcript-derived sequence; f) if the remaining sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment: The reads were aligned to the UCSC  mm10 genome using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. The genome included an artifical chromosome, containing a concatamer of the ERCC control sequences. Any reads with no alignments were re-aligned against another artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models22 were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incompete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation: The annotation step was performed barcode-by-barcode. For every unique mapping (genomic position and strand), the number of reads in each UMI was counted. Any multiread that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more mappings to exons, it was assigned at the exon where it was closest to the transcript model 5' end, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. After assigning reads, the number of molecules at each mapping position was determined by the number of distinct UMIs observed. To account for UMIs that stem from PCR-induced mutations or sequencing errors, any UMI that had fewer reads than 1/100 of the average of the non-zero UMIs was excluded. The raw UMI count was corrected for the UMI collision probability (important only at high UMI counts) as described. The expression level of each transcript model was taken as the total number of molecules at all its possible mapping positions.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file containing counts of detected cDNA molecules for each transcript model in each of the 96 cells, using data from all three sequencing lanes.

molecule: total RNA

organism: Mus musculus

source_name: R1 mouse embryonic stem cells, amplified

growth_protocol: R1 mouse embryonic stem cells were grown in ES1 medium on irradiated MEF feeder cells and harvested at confluency. After trypzinisation, the feeder cells were given time to settle in order to obtain a pure R1 ESC suspension. To reduce contamination with dead and dying cells, dead cells were subsequently stained with Red Fixable Dead Cell Stain (Life Technologies) and dead and early-apoptotic cells were depleted with AnnexinV-conjugated microbeads (Miltenyi Biotec). The cells were resuspended at a concentration of 400 cells/μl in ES1 medium with 10% DMSO, aliquoted and frozen at -80°C.

extract_protocol:
A 30 μL aliquot of ~12000 cells was thawed and 20 μL C1 Suspension Reagent was added (all "C1" reagents were from Fluidigm, Inc.). 5 μL of this mix was loaded according to the manufacturer's protocol on a C1 Single-Cell AutoPrep IFC microfludic chip designed for 10-17 μm cells, and the chip was then processed on a Fluidigm C1 instrument using the "mRNA Seq: Cell Load (1772x/1773x)" script. This captured one cell in each of up to 96 capture chambers, and took approximately 30 minutes. The plate was then transferred to an automated microscope (Nikon TE2000E) and an image was acquired from each site using μManager (http://micro-manager.org), which took less than 15 minutes.
20 μL lysis buffer (0.15% Triton X-100, 1 U/μL TaKaRa RNase inhibitor, 4 μM reverse transcription primer C1-P1-T31, 5% C1 Loading Reagent and 1:50,000 Life Technologies ERCC Spike-In Mix 1), reverse transcription mix (1x SuperScript II First-Strand Buffer supplemented with 3 mM MgCl2, 1.5 mM dNTP, 4 mM DTT, 3.3% C1 Loading Reagent, 1.8 μM template-switching oligo C1-P1-RNA-TSO, 1.5 U/μL TaKaRa RNase inhibitor and 18 U/μL Life Technologies Superscript II reverse transcriptase) and PCR mix (1.1x Clontech Advantage2 PCR buffer, 440 μM dNTP, 530 nM PCR primer C1-P1-PCR-2, 5% C1 Loading Reagent and 2x Advantage2 Polymerase Mix) were added to the designated wells according to the manufacturer's instructions, but using the indicated mixes in place of the corresponding commmercial reagents. The plate was then returned to the Fluidigm C1 and the "mRNA Seq: RT + Amp (1772x/1773x)" script was executed, which took about 8.5 hours and included lysis, reverse transcription and 21 cycles of PCR. When the run finished, the amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent and quantified on an Agilent BioAnalyzer. The typical yield was 1 ng/μL. Amplified cDNA was simultaneously fragmented and barcoded by 'tagmentation', i.e. using Tn5 DNA transposase to transfer adapters to the target DNA. 96 different 10x transposome stocks (6.25 μM barcoded adapter C1-TN5-x, 40% glycerol, 6.25 μM Tn5 transposase, where x denotes a well-specific barcode) were prepared, each with a different barcode sequence. 6 μL harvested cDNA was mixed with 5 μL tagmentation buffer (50 mM TAPS-NaOH pH 8.5, 25 mM MgCl2 and 50% DMF), 11.5 μL nuclease-free water and 2.5 μL 10x transposome stock. The mix was incubated for 5 minutes at 55°C then cooled on ice. 100 μL Dynabeads MyOne Streptavidin C1 beads were washed in 2xBWT (10 mM Tris HCl pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) then resuspended in 2 mL 2xBWT. 20 μL beads was added to each well and incubated at room temperature for 5 minutes. All fractions were pooled, the beads were immobilized and the supernatant removed (thus removing all internal fragments, and retaining only the 5'- and 3'-most fragments). The beads were then resuspended in 100 μL TNT (20 mM Tris pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, then twice in 100 μL TNT. The beads were then resuspended in 100 μL restriction mix (1x NEB NEBuffer 4, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3'  fragments carrying the PvuI recognition site. The mix was incubated for one hour at 37°C, then washed three times in TNT. Finally, the single-stranded library was eluted by resuspending the beads in 100 μL 100 mM NaOH, incubating for 5 minutes, removing the beads, then adding 100 μL 100 mM HCl and 50 μL Neutralization buffer (200 mM Tris pH 7.5, 0.05% Tween-20). At this point, the typical yield was 1-5 nM single-stranded library. Aliquots from these were run on the HiSeq 2000. Another aliquot was further amplified by 9 cycles of PCR to produce a double-stranded library as described in Islam, S. et al. Nat. Protoc. 7, 813-828 (2012). These were also run on the HiSeq 2000.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: barcode

value: CTAGGAA


title: ESCell_72_AACCCAT_amplified

description: PolyA RNA

value: AACCCAT


title: ESCell_75_AGGGAAG_amplified

description: PolyA RNA

value: AGGGAAG


title: ESCell_74_GCATGAT_amplified

description: PolyA RNA

value: GCATGAT


title: ESCell_67_GGAGTTA_amplified

description: PolyA RNA

value: GGAGTTA


title: ESCell_66_TCGCTAG_amplified

description: PolyA RNA

value: TCGCTAG


title: ESCell_68_CACTTCC_amplified

description: PolyA RNA

value: CACTTCC


title: ESCell_70_ATTGCGT_amplified

description: PolyA RNA

value: ATTGCGT


title: ESCell_69_GTACTCG_amplified

description: PolyA RNA

value: GTACTCG


title: ESCell_83_GGCAGAC_amplified

description: PolyA RNA

value: GGCAGAC


title: ESCell_65_GAATCAC_amplified

description: PolyA RNA

value: GAATCAC


title: ESCell_63_ACCATAG_amplified

description: PolyA RNA

value: ACCATAG


title: ESCell_60_TTCACCC_amplified

description: PolyA RNA

value: TTCACCC


title: ESCell_64_TAAGTCC_amplified

description: PolyA RNA

value: TAAGTCC


title: ESCell_62_GATTATG_amplified

description: PolyA RNA

value: GATTATG


title: ESCell_61_AAGATGG_amplified

description: PolyA RNA

value: AAGATGG


title: ESCell_59_CTACCCT_amplified

description: PolyA RNA

value: mouse embryonic stem cells

value: CTACCCT


title: ESCell_58_CGTCGCA_amplified

description: PolyA RNA

value: CGTCGCA


title: ESCell_57_TCCCATG_amplified

description: PolyA RNA

value: TCCCATG


title: ESCell_71_CTCCAGG_amplified

description: PolyA RNA

value: CTCCAGG


title: ESCell_53_ACAGCGA_amplified

description: PolyA RNA

value: ACAGCGA


title: ESCell_55_TGCCCAG_amplified

description: PolyA RNA

value: TGCCCAG


title: ESCell_54_AAGTCTT_amplified

description: PolyA RNA

value: AAGTCTT


title: ESCell_51_ACAATCC_amplified

description: PolyA RNA

value: ACAATCC


title: ESCell_52_CTACATC_amplified

description: PolyA RNA

value: CTACATC


title: ESCell_50_CAGCGTA_amplified

description: PolyA RNA

value: CAGCGTA


title: ESCell_49_TATAGGA_amplified

description: PolyA RNA

value: TATAGGA


title: ESCell_45_TTTCCGA_amplified

description: PolyA RNA

value: TTTCCGA


title: ESCell_46_ACACAAC_amplified

description: PolyA RNA

value: ACACAAC


title: ESCell_47_ATGTGCT_amplified

description: PolyA RNA

value: ATGTGCT


title: ESCell_42_CGTTCTA_amplified

description: PolyA RNA

value: CGTTCTA


title: ESCell_43_GTCAATC_amplified

description: PolyA RNA

value: GTCAATC


title: ESCell_44_GGATACG_amplified

description: PolyA RNA

value: mouse embryonic stem cells

value: GGATACG


title: ESCell_40_CGGAGTT_amplified

description: PolyA RNA

value: CGGAGTT


title: ESCell_41_CACGGTG_amplified

description: PolyA RNA

value: CACGGTG


title: ESCell_39_GGTTTGT_amplified

description: PolyA RNA

value: GGTTTGT


title: ESCell_38_AGTCCAC_amplified

description: PolyA RNA

value: AGTCCAC


title: ESCell_37_GCTGAGG_amplified

description: PolyA RNA

value: GCTGAGG


title: ESCell_34_TGGTGGC_amplified

description: PolyA RNA

value: TGGTGGC


title: ESCell_36_TGGACTG_amplified

description: PolyA RNA

value: TGGACTG


title: ESCell_35_TGATTAC_amplified

description: PolyA RNA

value: TGATTAC


title: ESCell_56_TCTAGTT_amplified

description: PolyA RNA

value: TCTAGTT


title: ESCell_31_GTGGCAA_amplified

description: PolyA RNA

value: GTGGCAA


title: ESCell_30_TCGGGTG_amplified

description: PolyA RNA

value: TCGGGTG


title: ESCell_32_TTGGTAC_amplified

description: PolyA RNA

value: TTGGTAC


title: ESCell_28_CTAATGA_amplified

description: PolyA RNA

value: CTAATGA


title: ESCell_27_TCATGCA_amplified

description: PolyA RNA

value: TCATGCA


title: ESCell_29_AAGGAGC_amplified

description: PolyA RNA

value: AAGGAGC


title: ESCell_48_AATGACA_amplified

description: PolyA RNA

value: mouse embryonic stem cells

value: AATGACA


title: ESCell_26_ACTTTGC_amplified

description: PolyA RNA

value: ACTTTGC


title: ESCell_24_AGCCACT_amplified

description: PolyA RNA

value: AGCCACT


title: ESCell_23_CAAACAG_amplified

description: PolyA RNA

value: CAAACAG


title: ESCell_19_TCAGTGT_amplified

description: PolyA RNA

value: TCAGTGT


title: ESCell_20_CCTGTAA_amplified

description: PolyA RNA

value: CCTGTAA


title: ESCell_25_TTGTACA_amplified

description: PolyA RNA

value: TTGTACA


title: ESCell_22_GAACGGA_amplified

description: PolyA RNA

value: GAACGGA


title: ESCell_14_ACCCGTA_amplified

description: PolyA RNA

value: ACCCGTA


title: ESCell_21_AAAGGTC_amplified

description: PolyA RNA

value: AAAGGTC


title: ESCell_33_ACCTCGT_amplified

description: PolyA RNA

value: ACCTCGT


title: ESCell_15_ATGCTGT_amplified

description: PolyA RNA

value: ATGCTGT


title: ESCell_9_GGTATTC_amplified

description: PolyA RNA

value: GGTATTC


title: ESCell_16_TGTCAAA_amplified

description: PolyA RNA

value: TGTCAAA


title: ESCell_18_CAGGACT_amplified

description: PolyA RNA

value: CAGGACT


title: ESCell_12_CCTATCG_amplified

description: PolyA RNA

value: CCTATCG


title: ESCell_17_CTTGAAG_amplified

description: PolyA RNA

value: mouse embryonic stem cells

value: CTTGAAG


title: ESCell_11_TACCAGT_amplified

description: PolyA RNA

value: TACCAGT


title: ESCell_13_TCGACAT_amplified

description: PolyA RNA

value: TCGACAT


title: ESCell_8_GAGCTCC_amplified

description: PolyA RNA

value: GAGCTCC


title: ESCell_6_GTCTGTA_amplified

description: PolyA RNA

value: GTCTGTA


title: ESCell_3_TGACGTG_amplified

description: PolyA RNA

value: TGACGTG


title: ESCell_4_GTCGTTG_amplified

description: PolyA RNA

value: GTCGTTG


title: ESCell_5_CGCTAAA_amplified

description: PolyA RNA

value: CGCTAAA


title: Small RNA_leaf

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

country: China

institute: Sichuan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
DGE sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Nicotiana benthamiana whole genome using SOAPdenovo. For small RNA sequencing data, the 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags. Length distribution of clean tags are then summarized. Afterwards, the standard bioinformatics analysis will annotate the clean tags into different categories and take those which can not be annotated to any category to predict the novel miRNA and base edit of potential known miRNA.
To compare the DE of gene across samples (N6H/NCK, N48H/NCK and N48H/N6H), the number of raw clean tags in each library was normalized to TPM (number of transcripts per million clean tags) to obtain normalized gene expression level. DE detection of gene or tag across samples was performed according to Audic S (Genome Research, 1997, 7:986-995). In addition to the P value, False Discovery Rate (FDR) was manipulated to determine differentially expressed genes. Brieﬂy, among R differentially expressed genes, S of those really indicates differential expression, and V actually indicates no difference, which are false positive. If the error ratio Q = V/R must remain below a cutoff (5%), FDR should not exceed 0.05. After multiple testing between pairwise comparisons, we use "FDR≤0.001 and the absolute value of log2Ratio≥1" as the threshold to judge the significance of gene expression difference. More stringent criteria with smaller FDR and bigger fold-change value can be used to identify DEGs.
The relative change of individual miRNA families of detected reads for root-ck and root-treat and P-values of the t-test were calculated; differentially detected miRNA families were those with P-values <0.01.
Genome_build: Nicotiana benthamiana genome database  (v.0.4.4)
Supplementary_files_format_and_content: *GeneExpression.txt: all expression genes in three DGE libraries for each Sample
Supplementary_files_format_and_content: *result_advance.txt: tab-delimited text files include clean tags values for each  Sample

organism: Nicotiana tabacum

source_name: control_leaf_small RNA

extract_protocol: Tag library preparation for three root samples (three tobacco roots tag-based DGE libraries treated at three time points (0, 6 and 48 h)  with 20% PEG6000) was performed in parallel by using the Illumina gene expression sample preparation kit. Each sample was sequenced in a single lane of a flow cell. Each lane includes library preparations from both DpnII and NlaIII digests for that sample. Sequences from DpnII digests start with GATC and those from NlaIII digests start with ATG.  The samples for four small RNA libraries was used based on the result of physiological index measurement as follows: equal quantities (10 ug) of total RNA isolated from tobacco roots treated with two time points (6 and 48 h) were mixed together to construct the drought -treated small RNA library (Root-treat), and total RNA prepared from the control roots sample was used to construct the control small RNA library (Root-ck). In addition, we also constructed another two libraries from leaves and stems of control plants, respectively. These libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as described by Tang et al.[PMID 22353177].

tag: cultivar

value: Honghua Dajinyuan

tag: tissue

value: leaves of six leaves plants


title: Small RNA_stem

source_name: control_stem_small RNA

value: stems of six leaves plants


title: DGE_N48H

value: roots of six leaves plants under 48h drought treatment


title: ESCell_10_GTGTGAG_amplified

description: PolyA RNA

value: GTGTGAG


title: DGE_N6H

value: roots of six leaves plants under 6h drought treatment


title: DGE_NCK

extract_protocol: Tag library preparation for three root samples (three tobacco roots tag-based DGE libraries treated at three time points (0, 6 and 48 h)  with 20% PEG6000) was performed in parallel by using the Illumina gene expression sample preparation kit. Each sample was sequenced in a single lane of a flow cell. Each lane includes library preparations from both DpnII and NlaIII digests for that sample. Sequences from DpnII digests start with GATC and those from NlaIII digests start with ATG.  The samples for four small RNA libraries was used based on the result of physiological index measurement as follows: equal quantities (10 ug) of total RNA isolated from tobacco roots treated with two time points (6 and 48 h) were mixed together to construct the drought -treated small RNA library (Root-treat), and total RNA prepared from the control roots sample was used to construct the control small RNA library (Root-ck). In addition, we also constructed another two libraries from leaves and stems of control plants, respectively. These libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as described by Tang et al. [PMID 22353177].

value: roots of six leaves plants


title: ESCell_95_TTCTCTG_single

description: PolyA RNA

source_name: R1 mouse embryonic stem cells, single

value: TTCTCTG


title: Small RNA_root-treat

source_name: drought-treated root_small RNA

value: mixed roots of six leaves plants under 6 and 48h drought treatment


title: ESCell_93_CACCTTT_single

description: PolyA RNA

value: mouse embryonic stem cells

value: CACCTTT


title: ESCell_1_ATTAGAC_amplified

description: PolyA RNA

value: ATTAGAC


title: ESCell_86_GTTGTCC_single

description: PolyA RNA

value: GTTGTCC


title: ESCell_89_GAGGCGT_single

description: PolyA RNA

value: GAGGCGT


title: ESCell_85_CAGCAAG_single

description: PolyA RNA

value: CAGCAAG


title: ESCell_96_CCAAATG_single

description: PolyA RNA

value: CCAAATG


title: Small RNA_root-ck

source_name: control roots_small RNA


title: ESCell_94_TACAACG_single

description: PolyA RNA

value: TACAACG


title: ESCell_91_TTAGCGG_single

description: PolyA RNA

value: TTAGCGG


title: ESCell_84_CGACTAT_single

description: PolyA RNA

value: CGACTAT


title: ESCell_83_GGCAGAC_single

description: PolyA RNA

value: GGCAGAC


title: ESCell_81_GCGTCTA_single

description: PolyA RNA

value: GCGTCTA


title: ESCell_2_ACGAGTC_amplified

description: PolyA RNA

value: ACGAGTC


title: ESCell_92_GGACCTT_single

description: PolyA RNA

value: GGACCTT


title: smRNA sequencing of of H1 BMP4 derived Trophoblast Cultured cells; smRNA-seq_h1-bmp4_r2a

status: Public on Dec 23 2013

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: smRNA sequencing of of H1 BMP4 derived Trophoblast Cultured cells
Library name: smRNA-seq_h1-bmp4_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18996
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12103
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

organism: Homo sapiens

source_name: H1 BMP4 Derived Trophoblast Cultured Cell Line, biological replicate 2 (r2); smRNA-seq_h1-bmp4_r2a

extract_protocol: Library construction protocol: Small RNAs were isolated using the miRNeasy Mini Kit (QIAGEN) as per manufacturer's instructions. Approximately one microgram of total RNA was used as input. Each sequencing library was constructed using the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer's instructions. The completed library was then gel size selected to approximately 145-160 bp using the QIAquick Gel Extraction Kit (QIAGEN). Libraries were pooled, and then sequenced using the Illumina HiSeq 2000 (Illumina) instrument as per manufacturer's instructions.

tag: sra sample accession

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

tag: passage

tag: medium

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

tag: Sex

value: Male

tag: batch

value: Replicate 2

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 1 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: total RNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: ESCell_90_GATAAGT_single

description: PolyA RNA

value: mouse embryonic stem cells

value: GATAAGT


title: ESCell_79_GACACAA_single

description: PolyA RNA

value: GACACAA


title: ESCell_88_GCTTAAC_single

description: PolyA RNA

value: GCTTAAC


title: ESCell_87_GGGAATA_single

description: PolyA RNA

value: GGGAATA


title: ESCell_7_CCTACGC_amplified

description: PolyA RNA

value: CCTACGC


title: ESCell_78_ATGCCTG_single

description: PolyA RNA

value: ATGCCTG


title: ESCell_82_AGCAAGC_single

description: PolyA RNA

value: AGCAAGC


title: Skin sample from young subjects

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

description: Young

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Transcriptome-mapping: tophat 2.0
Evaluation of differential expression: DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Matrix-format created by DESeq containing the expression levels and p-values for differential expression

molecule: polyA RNA

source_name: skin

extract_protocol:
Epidermal suction blister samples were collected according to the current version of the Declaration of Helsinki and the guideline of the International Conference on Harmonization Good Clinical Practice (ICH GCP) was observed as applicable to a non-drug study. All volunteers provided written, informed consent. Suction blister samples were obtained at the study center of Beiersdorf AG and approved by the Beiersdorf AG Legal Review Board. Briefly, epidermis samples were detached from the forearms of 10 healthy female volunteers by applying a negative pressure of 150–250 mmHg for 2 h. Subsequently, suction blister roofs were taken and immediately stored at -20 °C. Before RNA isolation, suction blister samples were homogenized using a TissueLyser (Retsch). Total RNA from suction blister samples was isolated using the Fibrous Tissue Kit (Qiagen) according to the manufacturer’s instructions. The Poly(A)Purist™ MAG Kit (Ambion) was used for mRNA selection.
Sequencing libraries were prepared using 1µg of DNAse-treated human total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.

tag: subjects

value: 10 healthy female volunteers

tag: age of subjects

value: about 25 years

value: skin (epidermal suction blister samples)


title: ESCell_80_TATGCTC_single

description: PolyA RNA

value: TATGCTC


title: Old

description: Sample 2

library_source: genomic

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph-format containing the genomic methylation ratios of the respective sample

molecule: genomic DNA

extract_protocol:
Epidermal suction blister samples were collected according to the current version of the Declaration of Helsinki and the guideline of the International Conference on Harmonization Good Clinical Practice (ICH GCP) was observed as applicable to a non-drug study. All volunteers provided written, informed consent. Suction blister samples were obtained at the study center of Beiersdorf AG and approved by the Beiersdorf AG Legal Review Board. Briefly, epidermis samples were detached from the forearms of 10 healthy female volunteers by applying a negative pressure of 150–250 mmHg for 2 h. Subsequently, suction blister roofs were taken and immediately stored at -20 °C. For nucleic acid isolation, suction blister samples were washed in DPBS (Cambrex) and homogenized using a TissueLyser (Retsch). DNA from suction blister samples was isolated using the QIAamp DNA Investigator Kit (Qiagen) and Fibrous Tissue Kit (Qiagen), respectively, according to the manufacturer’s instructions.
5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

value: about 60 years


title: ESCell_77_AGTTGTG_single

description: PolyA RNA

value: AGTTGTG


title: ChIP-seq_P13-WTMECs-Input

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

data_processing:
Basecalls performed using the CASAVA software.
Sequenced reads were aligned to the mm9 genome assembly using the Bowtie program (Langmead et al., Genome Biol., 2009). Total mapped reads per sample were normalized to 10 million and bedGraph files were generated by using the HOMER program (Heinz et al., Mol Cell, 2010).
Genome_build: MGSCv37
Supplementary_files_format_and_content: BedGraph files.

source_name: MECs (mammary epithelial cells), p13, input

growth_protocol: Animals were handled and housed in accordance with the guidelines of NIH and all experiments were approved by the Animal Care and Use Committee of NIDDK.

extract_protocol: The ChIP DNA fragments were blunt-ended and ligated to the Illumina Indexed DNA adaptors and sequenced using the Illumina HiSeq 2000.

treatment_protocol: Frozen-stored mammary tissues from p13 and L1 were broken into powder with mortar and pestle, and MECs were isolated from mammary tissues of the day 13 of pregnancy. Then, cells were cross-linked with 1% formaldehyde for 10 min at RT. Nuclei were extracted in Farnham lysis buffer (5mM PIPES PH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitor). Chromatin was fragmented to 200 to 300 bp by sonication using MSONIX Sonicator 3000 (QSonica, Newtown, CT). Antibodies against STAT5 (Santa Cruz Biotechnology, 10ug) and H3K4me3 (Millipore, 5ug) were used for ChIP.

tag: strain/background

tag: genotype/variation

value: wild type

value: MECs (mammary epithelial cells)

tag: developmental stage

value: day 13 of pregnancy

tag: chip antibody


title: ESCell_76_CTTTACC_single

description: PolyA RNA

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: barcode

value: CTTTACC


title: ESCell_75_AGGGAAG_single

description: PolyA RNA

value: AGGGAAG


title: negative control

city: hangzhou

first: jie

address: yuhangtang road 866

institute: zcni

data_processing:
Basecalls performed using OLB1.8.0 with default parameters
ChIP-seq reads were aligned to the hg19 genome database using bowtie version 0.12.7 with the following configurations: -S -l 28 -n 2 -e 70 -m 1
Redundancies of aligned sequences were removed with samtools version 0.1.18
peaks were called using MACS version 1.4.0alpha2 with the following setting: effective genome size = 2.70e+09 band width = 300 model fold = 10,30 pvalue cutoff = 1.00e-06
Genome_build: hg19

source_name: EPT1 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and p63-DNA complexes were isolated with anti-p63 antibody. The negative control experiment used IgG antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Primary antibodies p63 (Cat# ab53039), actin (Cat# ab11003), vimentin (Cat# ab8978) and keratin 5 (Cat# ab53121) from Abcam (Cambridge, UK). E-Cadherin (Cat# BD610182) and ITGB4 (Cat# BD611233) from (BD Transduction Labs., BD Biosciences, San Jose, CA, USA). LAMC2 (Cat# MAB19562) from Millipore (Billerica, MA, USA). GJB2 (Cat# 33-5800) from Invitrogen (Camarillo, CA, USA).

value: EPT1 cells

value: prostate cell model

value: IgG antibody


title: ESCell_71_CTCCAGG_single

description: PolyA RNA

value: CTCCAGG


title: Young

description: Sample 1

tag: tissue


title: ESCell_66_TCGCTAG_single

description: PolyA RNA

value: TCGCTAG


title: ESCell_73_CTAGGAA_single

description: PolyA RNA

value: CTAGGAA


title: p63_chipseq

source_name: EP156T cells

value: EP156T cells


title: ESCell_70_ATTGCGT_single

description: PolyA RNA

value: ATTGCGT


title: ESCell_64_TAAGTCC_single

description: PolyA RNA

value: TAAGTCC


title: ESCell_72_AACCCAT_single

description: PolyA RNA

value: AACCCAT


title: ESCell_61_AAGATGG_single

description: PolyA RNA

value: AAGATGG


title: ESCell_74_GCATGAT_single

description: PolyA RNA

value: GCATGAT


title: ESCell_69_GTACTCG_single

description: PolyA RNA

value: GTACTCG


title: Skin sample from old subjects

description: Old

value: 10 healthy female volunteers

value: about 60 years

value: skin (epidermal suction blister samples)


title: ESCell_62_GATTATG_single

description: PolyA RNA

value: mouse embryonic stem cells

value: GATTATG


title: ESCell_58_CGTCGCA_single

description: PolyA RNA

value: CGTCGCA


title: ESCell_56_TCTAGTT_single

description: PolyA RNA

value: TCTAGTT


title: ESCell_57_TCCCATG_single

description: PolyA RNA

value: TCCCATG


title: ESCell_55_TGCCCAG_single

description: PolyA RNA

value: TGCCCAG


title: ESCell_54_AAGTCTT_single

description: PolyA RNA

value: AAGTCTT


title: ESCell_59_CTACCCT_single

description: PolyA RNA

value: CTACCCT


title: ESCell_53_ACAGCGA_single

description: PolyA RNA

value: ACAGCGA


title: ESCell_52_CTACATC_single

description: PolyA RNA

value: CTACATC


title: ESCell_67_GGAGTTA_single

description: PolyA RNA

value: GGAGTTA


title: ESCell_68_CACTTCC_single

description: PolyA RNA

value: CACTTCC


title: ESCell_51_ACAATCC_single

description: PolyA RNA

value: ACAATCC


title: RBM5 Control IgG CLIP-Seq

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

data_processing:
Basecalling was performed using Illumina pipeline versions 1.6.0 within within SCS 2.6 for the RBM6 and RBM10 data, Illumina pipeline versions 1.7.0 within within SCS 2.8 for the RBM5 data.
Reads were mapped to the human genome using GEM (Marco-Sola et al. 2013), allowing for up to 2 mismatches and retaining only sequences that mapped uniquely to the genome.
All the unmapped reads were then trimmed 1 base from the 3’ end and remapped. This sequential trimming and mapping was continued up to 21nt length reads (15 bases of trimming).
Additional filtered datasets and analysis description can be found here: http://regulatorygenomics.upf.edu/Data/RBMs/
Genome_build: hg18
Supplementary_files_format_and_content: BED files containing all mapped reads.

source_name: HeLa cells

growth_protocol: HeLa cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol:
HeLa cells were grown in 150mm plates, rinsed once with ice-cold PBS and placed in a Stratalinker without the cover plate and irradiated once with an energy of 400mJ/cm. Cells were then scraped off the palte and centrifuged at 2500rpm for 5 min at 4°C and the pellet re-suspended in 3x the cells volume of PBS and distributed in two separate eppendorf tubes. Each tube of crosslinked lysate was resuspended in 700 μl of 1X PXL (PBS (tissue culture grade without Mg++ or Ca++) 0.1% SDS 0.5% deoxycholate 0.5% NP-40, supplemented with protease inhibitors and with 15 μl RNAsin (Promega)) and kept on ice for 10 min. 30 μl of RQ1 DNAse (Promega, M6101) were added to each tube and extracts were incubated at 37° for 5 min, centrifuged at 1000 rpm, followed by an incubation at 37° for 5 minutes with RNAse I. Extracts were the centrifuged at 12000 rpm for 10’ and then clarified on protein A Dynabeads  for 2 hours at 4°C,  before immunoprecipitation using protein A pre-adsorbed with either rabbit IgGs or EWS antibody (5μg) at 4 °C under constant rotation. After incubation for 3 hours, stringent washes were performed with ice-cold buffers as follows: 2 washes with 1X PXL, 2 washes with 5X PXL (High-salt Wash Buffer) and 2 washes with PNK Buffer (50 mM Tris-Cl pH 7.4 10 mM MgCl2 0.5% NP-40). Alkaline phosphatase (Roche) treatment (3μl) was performed at 37°C for 20’ in Thermomixer, followed by 4 washes in PNK buffer (one wash including 20mM EGTA). 3’ RNA linker ligation was carried out overnight at 16°C on beads using T4 RNA ligase (Fermentas) and radioactively-labeled linkers. Beads were extensively washed (1x PXL buffer, 1x 5XPXL buffer, 3x PNK buffer), before and after PNK treatment (T4, NEB, [40 units]) for 20’ at 37°C.  Finally, beads were resuspended in 30ml of PNK buffer, supplemeted with Novex loading buffer and loaded on a Novex NuPAGE 10% Bis-Tris gel. The gel was run at 175V in the cold room and subsequently transfered to nitrocellulose using the Novex wet transfer apparatus, for 1 h at 30V in NuPAGE Transfer Buffer with 10% methanol. After transfer, the nitrocellulose filter was rinsed in 1X PBS, and exposed to autoradiogram. The radioactively labeled RNA-protein complexes were excised and proteinase K treatment was performed (20’ at 37°C) before RNA extraction with Phenol-Chloroform and preciiptation overnight with 3M NaOAc pH 5.2, glycogen (Ambion, 9510) and 1:1 EtOH:isopropanol.
The RNA was resuspended in RNase free water and 5’ end linker ligation (containing also barcode sequences) was carried out with T4 RNA ligase at 16°C for 5 hours. RNAs were reverse-transcribed, PCR amplified with barcoded primers and sequenced using Solexa (Illumina) technology.

value: HeLa

tag: antibody

value: Non-specific rabbit IgG antibody


title: ESCell_65_GAATCAC_single

description: PolyA RNA

value: GAATCAC


title: ESCell_50_CAGCGTA_single

description: PolyA RNA

value: CAGCGTA


title: ESCell_47_ATGTGCT_single

description: PolyA RNA

value: mouse embryonic stem cells

value: ATGTGCT


title: ESCell_49_TATAGGA_single

description: PolyA RNA

value: TATAGGA


title: ESCell_63_ACCATAG_single

description: PolyA RNA

value: ACCATAG


title: ESCell_46_ACACAAC_single

description: PolyA RNA

value: ACACAAC


title: ESCell_45_TTTCCGA_single

description: PolyA RNA

value: TTTCCGA


title: ESCell_60_TTCACCC_single

description: PolyA RNA

value: TTCACCC


title: ESCell_43_GTCAATC_single

description: PolyA RNA

value: GTCAATC


title: ESCell_44_GGATACG_single

description: PolyA RNA

value: GGATACG


title: ESCell_42_CGTTCTA_single

description: PolyA RNA

value: CGTTCTA


title: ESCell_41_CACGGTG_single

description: PolyA RNA

value: CACGGTG


title: ESCell_39_GGTTTGT_single

description: PolyA RNA

value: GGTTTGT


title: ESCell_36_TGGACTG_single

description: PolyA RNA

value: TGGACTG


title: ESCell_40_CGGAGTT_single

description: PolyA RNA

value: CGGAGTT


title: ESCell_37_GCTGAGG_single

description: PolyA RNA

value: GCTGAGG


title: ESCell_33_ACCTCGT_single

description: PolyA RNA

value: ACCTCGT


title: ESCell_35_TGATTAC_single

description: PolyA RNA

value: TGATTAC


title: ESCell_34_TGGTGGC_single

description: PolyA RNA

value: mouse embryonic stem cells

value: TGGTGGC


title: ESCell_38_AGTCCAC_single

description: PolyA RNA

value: AGTCCAC


title: ESCell_31_GTGGCAA_single

description: PolyA RNA

value: GTGGCAA


title: ESCell_29_AAGGAGC_single

description: PolyA RNA

value: AAGGAGC


title: ESCell_30_TCGGGTG_single

description: PolyA RNA

value: TCGGGTG


title: ESCell_48_AATGACA_single

description: PolyA RNA

value: AATGACA


title: ESCell_22_GAACGGA_single

description: PolyA RNA

value: GAACGGA


title: ESCell_21_AAAGGTC_single

description: PolyA RNA

value: AAAGGTC


title: ESCell_24_AGCCACT_single

description: PolyA RNA

value: AGCCACT


title: ESCell_23_CAAACAG_single

description: PolyA RNA

value: CAAACAG


title: ESCell_25_TTGTACA_single

description: PolyA RNA

value: TTGTACA


title: ESCell_16_TGTCAAA_single

description: PolyA RNA

value: TGTCAAA


title: ESCell_27_TCATGCA_single

description: PolyA RNA

value: TCATGCA


title: ESCell_15_ATGCTGT_single

description: PolyA RNA

value: ATGCTGT


title: ESCell_20_CCTGTAA_single

description: PolyA RNA

value: CCTGTAA


title: ESCell_26_ACTTTGC_single

description: PolyA RNA

value: ACTTTGC


title: ESCell_19_TCAGTGT_single

description: PolyA RNA

value: mouse embryonic stem cells

value: TCAGTGT


title: ESCell_18_CAGGACT_single

description: PolyA RNA

value: CAGGACT


title: ESCell_14_ACCCGTA_single

description: PolyA RNA

value: ACCCGTA


title: ESCell_32_TTGGTAC_single

description: PolyA RNA

value: TTGGTAC


title: SS020812 R1.0 co-culture [Shewanella]

city: Richland

first: Lye Meng

last: Markillie

state: WA

address: 902 Battelle Blvd

department: Biosystems Dynamics & Simulation

institute: Environmental Molecular Sciences Laboratory

description: These are co-culture experiments, the raw data are shared with SS020812 R1.0 co-culture [Synechococcus] and SS020812 R1.0 co-culture [Synechococcus]

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD  sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters
Genome_build: Shewanella sp. W3-18-1: ASM1518v1; NC_008750
Genome_build: Synechococcus 7002: ASM1948v1;  NC_010474, NC_010475, NC_010476, NC_010477, NC_010478, NC_010479 and NC_010480
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Shewanella sp. W3-18-1

source_name: SS020812 R1.0 co-culture

growth_protocol: Shewanella W3-18-1 cultures were maintained at 30oC in tryptic soy broth or M1 defined medium amended with 20 mM D,L-Na lactate and 10 ml each of 10X Wolfe's vitamin and 10X mineral solutions (Kieft et al 1999). In chemostat cultures, Shewanella W3-18 was grown using 5 mM D,L-Na lactate as the sole source of C . Synechococcus 7002 was routinely grown in modified A+ media (Stevens and Porter 1980) at room temperature in 1-L Roux bottles sparged with 2% CO2-enriched air under continuous 50 µmolom-2os-1 illumination. Chemostat cultivation of Synechococcus 7002 was carried out using 8 mM NaHCO3 as the sole source of C in a white-light photobioreactor

extract_protocol:
RNA was extracted using Trizol following by DNAseI treatment using Qiagen RNAseay mini column
Template cDNA was prepared using the Applied Biosystems SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) according to manufacturer's protocol. Sequencing was carried using the SOLiDTM 5500XL protocol (Life Technologies).

treatment_protocol: The co-cultivation experiments were carried out in a modified A+ medium which was contained 17 mM NH4Cl and 10 µm FeCl3·6H2O. D,L-Na lactate or NaHCO3 were used as the sole source of carbon at 5 mM and 8 mM concentrations

tag: lactate and nahco3 as carbon source

value: Synechococcus 7002 (OG1+LK1)

tag: condition

value: Shew W3-18 co-culture 5mM lactate

tag: strain


title: ESCell_13_TCGACAT_single

description: PolyA RNA

value: TCGACAT


title: SS020812 R1.2 co-culture [Shewanella]

description: These are co-culture experiments, the raw data are shared with SS020812 R1.2 co-culture [Shewanella] and SS020812 R1.2 co-culture [Synechococcus]

source_name: SS020812 R1.2 co-culture

value: Synechococcus 7002 (OG1+LK1G)

value: Shew W3-18 co-culture 8mM NaHCO3, C-limited


title: ESCell_12_CCTATCG_single

description: PolyA RNA

value: CCTATCG


title: ESCell_28_CTAATGA_single

description: PolyA RNA

value: CTAATGA


title: ESCell_7_CCTACGC_single

description: PolyA RNA

value: CCTACGC


title: ESCell_8_GAGCTCC_single

description: PolyA RNA

value: GAGCTCC


title: ESCell_9_GGTATTC_single

description: PolyA RNA

value: GGTATTC


title: ESCell_6_GTCTGTA_single

description: PolyA RNA

value: GTCTGTA


title: ESCell_10_GTGTGAG_single

description: PolyA RNA

value: GTGTGAG


title: ESCell_5_CGCTAAA_single

description: PolyA RNA

value: mouse embryonic stem cells

value: CGCTAAA


title: ESCell_11_TACCAGT_single

description: PolyA RNA

value: TACCAGT


title: ESCell_3_TGACGTG_single

description: PolyA RNA

value: TGACGTG


title: ESCell_17_CTTGAAG_single

description: PolyA RNA

value: CTTGAAG


title: ESCell_1_ATTAGAC_single

description: PolyA RNA

value: ATTAGAC


title: ESCell_4_GTCGTTG_single

description: PolyA RNA

value: GTCGTTG


title: ESCell_2_ACGAGTC_single

description: PolyA RNA

value: ACGAGTC


title: B20 - Non-Supportive ISEMF

city: Los Angeles

first: Martin

middle: G

last: Martin

department: Pediatrics Gastroenterology

institute: University of California Los Angeles

data_processing:
Alignment to mm9 assembly using Tophat 2.0.4, using Ensembl annotation as junction library, allowing unique reads only and up to 2 mismatches
Counting and annotating reads through HTSeq 0.5.4p3, using "non-empty intersection" method
Calculating p-values using DESeq with default parameters, method of estimating dispersions to be "blind"
Calculating RPKM values by dividing raw reads as reported by HTSeq by total number of aligned reads as reported by Tophat (in millions) and the length of each gene as calculated by the union length of all possible exons (in kilobases)
Genome_build: mm9
Supplementary_files_format_and_content: Data tables containing common name of gene,ling name, Ensembl ID, genomic coordinates, gene function, type of coding region, location in cell as annotated experimentally and predicted in other annotations, calculated length of gene as union length of exons, counts per sample, RPKM per sample, log base 2 ratio, p-value, and p-value adjusted for false discovery rate

source_name: intestinal subepithelial myofibroblast

extract_protocol:
Cells were lysed and extracted for total RNA using Qiagen's RNeasy Mini Kit, following the manufacturer's protocol.
Libraries were contructed using Illumina's TruSeq RNA Sample Kit, following the manufacturer's protocol.

value: small intestine

value: adult

value: intestinal subepithelial myofibroblast


title: B19 - Supportive ISEMF

value: neonatal


title: Cerevisiae_RPF

status: Public on Dec 19 2013

city: San Francisco

first: David

middle: E

last: Weinberg

address: 600 16th Street, GH S572F

institute: University of California, San Francisco

description: cytoplasmically-enriched RNA

data_processing:
Raw read files were stripped of adaptor and mapped to the S. Cerevisiae genome and transcriptome.
RNA-seq and ribosome profiling reads mapping within the coding sequence of an annotated gene, excluding the first 50 nucleotides of the coding sequence, were assigned to that gene and used to calculate its RPKM value.
Genome_build: sacCer3
Supplementary_files_format_and_content: The processed data file contains abundance measurements for all genes

molecule: cytoplasmic RNA

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae cells

growth_protocol: Yeast were grown in YPD to mid-log phase in accordance with standard protocols.

extract_protocol: Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809).

treatment_protocol: RNA-seq: Cytoplasmically-enriched RNA was extracted, depleted of rRNA using Ribo-Zero, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation. Ribosome profiling: Cells were harvested and extracts were perpared and processed as described for S. pombe samples in Subtelny et al., 2014 (GSE52809).


title: Cerevisiae_RNA

description: cytoplasmically-enriched RNA


title: targets

city: Guangzhou

first: cunyi

last: yang

address: No. 483 Wushan Road, the Tianhe District of the city

department: College of Agriculture

institute: South China Agricultural University

data_processing:
We performed a genome-wide sequencing of miRNA-cleaved mRNA and CleaveLand 3 analysis based on recently developed high-throughput degradome sequencing technology (Addo-Quaye et al., 2008; German et al., 2008; Addo-Quaye et al., 2009)
As CleavLand 3 used bowtie as the alignment program, and we directly used raw data which is fastq format to do the alignment. We used RNA-Seq library construction protocol to obtain longer insertion fragments into sequencing adaptors, we only sequenced the first 36 nt of the insertion fragment, there is no 3' adaptor remaining, most sequences are expected degradome tags, and only tags fit bowtie alignment parameters could be counted in the hits abundance, so we don't need to do additional procession with the raw data. alignment results with G. max transcripts, if this could be considered as processed data,
Genome_build: JGI database ftp site: ftp.jgi-psf.org /pub/compgen/phytozome/v8.0/Gmax/assembly/Gmax_109_hardmasked.fa.gz.
Supplementary_files_format_and_content: degradome_density_output.txt: alignment results with G. max transcripts

organism: Glycine max

source_name: root of soybean

growth_protocol: Seeds of each cultivar were sown in sterile quartz sand and left for 4 days (d) to germinate. Then, seedlings were transferred into 1/2 full-strength nutrient solution containing 2.5 mM KNO3, 2.5 mM Ca(NO3)2.4H2O, 0.082 mM Fe(III)-EDTA, 4.57 μM MnCl2.4H2O, 0.25 mM K2SO4, 1.0 mM MgSO4.7H2O, 0.38 μM ZnSO4.7H2O, 1.57 mM CuSO4.5H2O, 0.09 μM (NH4)6MO7O2.4H2O, 23.13 μM H3BO3 and 0.5mM KH2PO4, and then were cultured in a growth chamber with the following settings: 70% relative humidity, 28 °C / 25 °C and a light regime of 14 h light / 10 h dark

extract_protocol: Degradome library was constructed following with methods previously described by German et al.(2008)

treatment_protocol: Two days after transplant, stress with different Cd concentrations (0 μM and 22.24 μM Cd added in culture solution) was carried out. The culture solutions, with or without Cd, were changed every two days. Roots were harvested at 6, 12, 24, 48, 96 and 144 h after the initiation of Cd treatment

value: root

tag: cultivation pattren

value: hydroponics

tag: concentration

value: 0 μM and 22.24 μM


title: Shew12222010.4

value: high light / high O2


title: ski2KO

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

data_processing:
Library strategy: Ribosome Profiling
Base calling was performed at UC Riverside or Johns Hopkins sequencing facilities with CASAVA 1.8
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence (or trimmed to 35 nt for RNA-Seq samples). Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie 0.12.7 (Langmead et al., 2009) and the parameters: -y -a -m 1 --best --strata. Reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all 4 of these alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
The wig files prefixed with wt_combined and ko_combined were created by combining data from samples 5f,7f,1w,2w,3w, and 6f,8f,1k,2k,3k, respectively. These combined files were used for more advanced analysis because each of the 5 replicates made with different ribosome stabilizing conditions were very similar.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

source_name: Whole cells

growth_protocol: Cells were generally grown from an OD600 of 0.02 to 0.6 and harvested in YPD.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome or disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with stabilizing agents added only in the lysis buffer as described for each sample. mRNA-Seq samples had cycloheximide added in culture.

tag: ribosome stabilization agent

value: cycloheximide

tag: assayed molecule

value: Ribosome-protected RNA 25-34 nt


title: dom34KO glucose starvation

tag: cell culture treatment

value: glucose starvation (1 min in YP media)


title: ski2KO dom34KO suppressor tRNA

value: ski2KO dom34KO SUP4-o

value: CSM-His media


title: dom34KO 3-AT

value: HIS3 dom34KO

value: 100 mM 3-AT for 2.5 doublings (CSM-His media)


title: dom34KO diamide

value: 2mM diamide (+0.3 mM CaCl2) for 2 hours


title: hbs1KO


title: ski2KO suppressor tRNA

value: ski2KO SUP4-o


title: wild-type 3-AT


title: dom34KO CHX+GMP-PNP

value: cycloheximide+GMP-PNP


title: dom34KO high Mg++

value: high [Mg++]


title: dom34KO GMP-PNP

value: GMP-PNP


title: wild-type high Mg++

value: wild-type (BY4741)


title: wild-type GMP-PNP


title: wild-type CHX+GMP-PNP


title: wild-type no additive

value: no additive


title: dom34KO no additive


title: wild-type diamide


title: dom34KO CHX


title: dom34KO mRNA-Seq

data_processing:
Base calling was performed at UC Riverside or Johns Hopkins sequencing facilities with CASAVA 1.8
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence (or trimmed to 35 nt for RNA-Seq samples). Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie 0.12.7 (Langmead et al., 2009) and the parameters: -y -a -m 1 --best --strata. Reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all 4 of these alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
The wig files prefixed with wt_combined and ko_combined were created by combining data from samples 5f,7f,1w,2w,3w, and 6f,8f,1k,2k,3k, respectively. These combined files were used for more advanced analysis because each of the 5 replicates made with different ribosome stabilizing conditions were very similar.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

extract_protocol: Total RNA was extraced from frozen cells by using SDS/hot phenol/chloroform. RNA was then polyA selected with oligodT beads and randomly fragmented with light base treatment. Fragments of 40-60 nt were retained for library preparation.

value: cycloheximide (2 min)

value: polyA RNA


title: wild-type mRNA-Seq


title: wild-type CHX


title: WT males 20°C mRNA

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Sample name: fog220mseq
WT males 20°C mRNA
mRNA profiling

data_processing:
Remove 5' barcode and 3' barcode (or called linker)
Map the reads to WS215 genome and annotation
A custom PERL pipeline is used to summarize reads and generate histogram at single nt level.
Generic genome browse is used to visualize the data
Genome_build: WBcel215 (WormBase WS215)
Supplementary_files_format_and_content: txt format table for sequence and read number mapping the genome

organism: Caenorhabditis elegans

source_name: fog-2(q71) males 20°C

growth_protocol: C. elegans worm grown at 20°C and 25°C

extract_protocol: 3' ligation followed by circularization

treatment_protocol: For mRNA sequencing, polyA RNA was purified from total RNA using the PolyATtract mRNA Isolation System (Promega); each sample was purified twice. The mRNA was fragmented by base hydrolysis at 95°C for 9.5 min in Sodium carbonate buffer, and 2’,3’-cyclic phosphates were resolved with T4 Polynucleotide Kinase (NEB). mRNA fragments with an average length of ~200 nt were purified from an 8% polyacrylamide/8M urea gel

value: 5' barcode (A) TGAC

value: 3' barcode (1) CTGTAGGCACCATCAAT

value: WT

tag: culture conditions


title: alg-3/4 males 25°C mRNA

description:
Sample name: alg3425mseq
alg-3/4 males 25°C mRNA
mRNA profiling

value: 5' barcode (D) ATCA

tag: genotype/variation


title: Liver P56 H3K27ac

city: Berkeley

first: Alex

middle: S

last: Nord

address: 1 Cyclotron Road, Mail Stop 84-171

department: Genomics Divsion

institute: Lawrence Berkeley National Laboratory

description: Liver P56  H3K27ac ChIP-seq

data_processing:
Basecalls performed using standard Illumina pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using BWA with the following call: bwa aln -t 6 -l 25  mm9 sample.fastq.gz
Peaks were called using MACS (version 1.4) incoporating matched input data with the following call: macs14 -t chip.bam --control=input.bam –name=chip_output --format=BAM --gsize=mm --tsize=50 --bw=300 --mfold=10,30 --nolambda --nomodel --shiftsize=150 -p 0.00001
Peaks were filtered to remove regions where a significant proportion of the reads mapped within repetitive regions
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated by extending reads to 300bp and calculating the number of reads per 25bp bins across the genome; .bed files represent filtered peaks ranked by significance

source_name: liver

growth_protocol: Tissues were collected from CD1 mice at each stage.  For all but P56 stage, samples represent pooled tissues from multiple embryos/mice.

extract_protocol:
Tissues were cross-linked, lysed, and sonicated and immunoprecipation was performed using H3K27ac (Abcam Ab4729).  Input samples represent sonicated DNA before immunoprecipitation
Libraries were constructed using standard protocols and the Illumina TruSeq kit with index barcodes.

tag: developmental stage

value: H3K27ac (Abcam 4729)


title: Liver P56 input

description: Liver P56 input

tag: chip antibody


title: Liver P21 H3K27ac

description: Liver P21  H3K27ac ChIP-seq


title: Liver P21 input

description: Liver P21 input


title: Liver P7 H3K27ac

description: Liver P7  H3K27ac ChIP-seq


title: Liver P0 H3K27ac

description: Liver P0  H3K27ac ChIP-seq


title: Liver P7 input

description: Liver P7 input


title: Liver E11.5 input

description: Liver E11.5 input


title: Heart P56 H3K27ac

description: Heart P56  H3K27ac ChIP-seq

source_name: heart


title: Liver E14.5 input

description: Liver E14.5 input


title: Heart P21 input

description: Heart P21 input


title: Liver P0 input

description: Liver P0 input


title: Liver E14.5 H3K27ac

description: Liver E14.5  H3K27ac ChIP-seq


title: Liver E17.5 input

description: Liver E17.5 input


title: Liver E17.5 H3K27ac

description: Liver E17.5  H3K27ac ChIP-seq


title: Liver E11.5 H3K27ac

description: Liver E11.5  H3K27ac ChIP-seq


title: Heart P56 input

description: Heart P56 input


title: Heart P7 H3K27ac

description: Heart P7  H3K27ac ChIP-seq


title: WT males 25°C mRNA

description:
Sample name: fog225mseq
WT males 25°C mRNA
mRNA profiling

source_name: fog-2(q71) males 25°C

value: 5' barcode (B) CAGT


title: Heart E17.5 H3K27ac

description: Heart E17.5  H3K27ac ChIP-seq


title: Heart E14.5 input

description: Heart E14.5 input


title: Heart P7 input

description: Heart P7 input


title: Heart P0 H3K27ac

description: Heart P0  H3K27ac ChIP-seq


title: Heart E17.5 input

description: Heart E17.5 input


title: Heart E14.5 H3K27ac

description: Heart E14.5  H3K27ac ChIP-seq


title: Heart E11.5 input Rep2

description: Heart E11.5 input Rep2


title: Heart E11.5 H3K27ac Rep1

description: Heart E11.5  H3K27ac ChIP-seq Rep1


title: Heart E11.5 input Rep1

description: Heart E11.5 input Rep1


title: Forebrain P56 input Rep2

description: Forebrain P56 input Rep2

source_name: forebrain


title: Forebrain P56 H3K27ac Rep2

description: Forebrain P56  H3K27ac ChIP-seq Rep2


title: Heart P21 H3K27ac

description: Heart P21  H3K27ac ChIP-seq


title: Forebrain P0 H3K27ac

description: Forebrain P0  H3K27ac ChIP-seq


title: Forebrain P0 input

description: Forebrain P0 input


title: Forebrain E17.5 input

description: Forebrain E17.5 input


title: Forebrain P7 input

description: Forebrain P7 input


title: Forebrain P7 H3K27ac

description: Forebrain P7  H3K27ac ChIP-seq


title: Forebrain P21 input

description: Forebrain P21 input


title: Forebrain E14.5 input

description: Forebrain E14.5 input


title: Forebrain E17.5 H3K27ac

description: Forebrain E17.5  H3K27ac ChIP-seq


title: Forebrain P56 H3K27ac Rep1

description: Forebrain P56  H3K27ac ChIP-seq Rep1


title: Heart P0 input

description: Heart P0 input


title: Forebrain P21 H3K27ac

description: Forebrain P21  H3K27ac ChIP-seq


title: Forebrain E14.5 H3K27ac

description: Forebrain E14.5  H3K27ac ChIP-seq


title: Forebrain E11.5 input Rep2

description: Forebrain E11.5 input Rep2


title: Forebrain E11.5 H3K27ac Rep2

description: Forebrain E11.5  H3K27ac ChIP-seq Rep2


title: Heart E11.5 H3K27ac Rep2

description: Heart E11.5  H3K27ac ChIP-seq Rep2


title: Forebrain E11.5 input Rep1

description: Forebrain E11.5 input Rep1


title: Forebrain E11.5 H3K27ac Rep1

description: Forebrain E11.5  H3K27ac ChIP-seq Rep1


title: HS RNASeq (biological replicate 1 and 2)

city: London

first: Gordon

last: Peters

address: 44 Lincolns Inn Fields

country: United Kingdom

institute: CRUK London Research Institute

data_processing:
ChipSeq: Duplicates were removed using the Picard MarkDuplicates program (picard-tools package version 1.48; http://picard.sourceforge.net) with default parameters.
RNASeq: Alignments were performed to the UCSC version of the human transcriptome (Illumina iGenomes resource) using RSEM (version 1.2.4; Li and Dewey 2011).

source_name: Cultured fibroblasts

growth_protocol: The BF and Hs68 strains of human fibroblasts (30 population doublings) were cultured in Dulbecco modified Eagles medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin, and 100 μ/ml streptomycin.

extract_protocol:
Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 36bp single end sequencing on the GAIIx analyser.
RNA-Seq: Total RNA was extracted using the High Pure RNA extraction Kit (Roche). RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent) and subjected to poly-A selection using Sera-Mag oligo dT beads (Thermo Fisher Scientific Inc.). Libraries were prepared using the Directional mRNA-Seq Library Prep. v1.0. Pre-Release Protocol from Illumina with minor adjustments. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix which reduced the overall volume of the PCR and the ratio for the Agencourt AMPure XP beads was adjusted accordingly.  The standard PCR cycling was also changed to match the concentration of the total RNA from the initial QC. After passing the final QC, the libraries were subjected to cluster formation and then 72bp single end sequencing on the GAIIx analyser.

treatment_protocol: Fibroblasts (8×105 cells per 10 cm dish) were infected with packaged LKO lentivirus vector containg CBX7shRNA (Sigma NM_175709.1-153s1c1).  Infected cells were selected in puromycin (0.5ug/ml) and harvested after 10-14 days

value: normal foreskin


title: CBX input HS Senescent ChipSeq biological replicate 1


title: H3K4me3 HS Senescent ChipSeq biological replicate 1

value: 07-449 from Millipore


title: alg-3/4 males 20°C  mRNA

description:
Sample name: alg3420mseq
alg-3/4 males 20°C  mRNA
mRNA profiling

value: 5' barcode (C) GCTG


title: CBX7 HS Senescent ChipSeq (biological replicate 1 and 2)

value: AB-21873 from ABCAM


title: CBX8 HS Senescent ChipSeq (biological replicate 1 and 2)

value: A300-882a from BETHYL


title: H3 input HS ChipSeq biological replicate 1


title: Forebrain P56 input Rep1

description: Forebrain P56 input Rep1


title: RING input HS ChipSeq (biological replicate 1 and 2)


title: H3K4me3 HS ChipSeq biological replicate 1


title: RING2 HS ChipSeq (biological replicate 1 and 2)

value: Mouse Mab from H. Koseki


title: H3K27me3 HS ChipSeq biological replicate 1


title: RING1 HS ChipSeq (biological replicate 1 and 2)

value: 2820 from Cell Signalling Lab, LRI


title: CBX input HS ChipSeq (biological replicate 1 and 2)


title: H3K27me3 BF ChipSeq biological replicate 1

value: normal breast

value: BF


title: H3 input BF ChipSeq biological replicate 1


title: CBX7 HS ChipSeq (biological replicate 1 and 2)


title: CBX8 HS ChipSeq (biological replicate 1 and 2)


title: RING2 input BF ChipSeq (biological replicate 1 and 2)


title: H3K4me3 BF ChipSeq biological replicate 1


title: RING1 BF ChipSeq (biological replicate 1 and 2)


title: CBX6 HS ChipSeq (biological replicate 1 and 2)

value: MRO19 - in house rabbit polyclonal


title: BF RNASeq (biological replicate 1 and 2)


title: RING1 input BF ChipSeq (biological replicate 1 and 2)


title: RING2 BF ChipSeq (biological replicate 1 and 2)


title: CBX input BF ChipSeq (biological replicate 1 and 2)


title: CBX7 BF ChipSeq (biological replicate 1 and 2)


title: CBX6 BF ChipSeq (biological replicate 1 and 2)


title: Cerevisiae_3Pseq

data_processing:
3P-Seq:
Data was processed exactly as described in Jan et al., 2011 (GSE24924)
Reads were reverse complemented and aligned to the  Saccharomyces cerevisiae genome (sacCer3) using Bowtie. Reads that aligned best to one genomic locus and had one or more mismatches at their 3' end within a terminal adenylate-run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file.
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed data is BED file containing 3P-seq clusters

extract_protocol:
3P-Seq library was prepared from 75 μg of isolated RNA as described previously (Jan et al., 2011).
Libraries were constructed exactly as described in Jan et al., 2011 (GSE24924). 3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html.


title: e6-8hr_rna (rep1 and rep2)

city: Chapel Hill

first: Daniel

middle: J

last: McKay

state: NC

address: 3344 Genome Sciences Building

department: Biology, Genetics

institute: The University of North Carolina at Chapel Hill

data_processing:
Basecalls performed with CASAVA version 1.7
FAIRE-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal Index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq signal files were generated by extending each read to a total of 110bp, and the number of reads overlapping each base in the genome was counted.
FAIRE data were normalized by subtracting Input signal from FAIRE at each base, and z-scores were generated using the mean and standard deviation for each chromosome arm.
FAIRE peaks were called using MACS2 with Input as control, a shift size of 125bp, and a q-value cutoff of 1.00e-2.
RNA-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
RNA-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
Genome_build: dm3
Supplementary_files_format_and_content: FAIRE processed data files are in wig format, and contain Input-subtracted FAIRE z-scores, smoothed with a 200bp sliding window average and 10bp step size.
Supplementary_files_format_and_content: RNA processed data files are matrices of gene names with their associated FPKM values calculated with Cuffdiff from the Tophat-aligned reads and using a RefSeq genome annotation file.

organism: Drosophila melanogaster

source_name: 6-8 hour embryos

growth_protocol: Following a pre-clearing step, embryos were collected for 2 hours and aged at 25C until the designated time.

extract_protocol:
Staged samples were homogenized in trizol, and total RNA was extracted, DNaseI treated, and purified. mRNA was purified with oligo(dT) beads and fragmented, followed by first and second strand cDNA synthesis.
1-100ng DNA was prepared for sequencing on an Illumina GAII or Hi-Seq machine at the UNC High-Throughput Sequencing Facility.

value: OregonR

value: 6-8 hours after egg laying

value: whole embryo


title: leg_disc_rna (rep1 and rep2)

source_name: 3rd instar larval imaginal disc

growth_protocol: Bottles were flipped every 12 hours, and aged at 25C until the designated time.

value: y;cn,bw,sp

value: 3rd instar larvae

value: T3 leg disc


title: e16-18hr_rna (rep1 and rep2)

source_name: 16-18 hour embryos

value: 16-18 hours after egg laying


title: e2-4hr_rna (rep1 and rep2)

source_name: 2-4 hour embryos

value: 2-4 hours after egg laying


title: wing_disc_rna (rep1 and rep2)

value: wing disc


title: haltere_disc_rna (rep1 and rep2)

value: haltere disc


title: ICM replicate13

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Illumina Casava1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat (v1.2.0) with parameters -r 120 -p 5
Differential expression was analyzed using edgeR
To identify novel transcripts, we used cufflinks to reconstruct all transcripts, and compared them to reference gene annotations.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in each sample.

extract_protocol:
RNA was extracted with Trizol (Invitrogen) and further purified on RNeasy columns (Qiagen) with on column DNase digestion. Ribosomal RNA was depleted using the RiboMinus kit (Invitrogen).  1 µg rRNA-depleted RNA was used for the construction of sequencing libraries
Illumina RNA-seq libraries were prepared from rRNA-depleted samples using the standard Illumina protocol. SOLiD RNA-seq libraries were prepared from a pool of all of 15 ICM samples and a pool of all of 15 Ctrl samples using the standard SOLiD strand-specific library protocol.

treatment_protocol: Left ventricular (LV) myocardial samples, remote from infarcted areas, were snap frozen in liquid nitrogen within 2 hours of explantation and stored at -80 °C.

value: heart

tag: diagnosis

value: ischemic cardiomyopathy (ICM)


title: ICM replicate15


title: ICM replicate12


title: ICM replicate10


title: ICM replicate14


title: ICM replicate11


title: ICM replicate9


title: ICM replicate7


title: CBX8 BF ChipSeq (biological replicate 1 and 2)

value: A300-882a from BETHYL


title: ICM replicate6


title: ICM replicate4


title: ICM replicate5


title: ICM replicate1


title: ICM replicate2


title: ICM replicate3


title: control rep10

value: control


title: control rep12


title: control rep13


title: control rep11


title: control rep14


title: control rep8


title: control rep4


title: control rep6


title: control rep5


title: control rep2


title: control rep3


title: control rep7


title: ICM replicate8


title: control rep1


title: H3_AzLo

city: Athens

first: Stephen

last: Dalton

state: GEORGIA

address: 500 D.W. Brooks drive Athens G

department: Biochemistry & Molecular Biology

institute: University of Georgia

data_processing:
Alignment of RNA-seq reads against known genomic annotations downloaded from the University of California Santa Cruz site (http://www.genome.ucsc.edu) was performed using Bowtie version 0.12.7 and TopHat version 1.3.3
Transcript-level expression analysis was performed using Cufflinks version 1.2.1 (Trapnell et al., 2010).
Transcripts that showed consistent patterns of change in all three biological replicate experiments were selected for downstream analysis.
Transcripts were filtered for Spearman correlation coefficients, with a cutoff of 0.5 between any two of the three replicates.
Genome_build: hg19

source_name: S human embryonic stem cells

growth_protocol: WA09 hESCs were grown as previously described in media containing HEREGULIN b1 (10 ng/ml; Peprotech), ACTIVIN A (10 ng/ml; R&D Systems), and human LONGR3 insulin-like growth factor 1 (IGF-1; 200 ng/ml; Sigma; Singh et al., 2012)

extract_protocol:
RNA was extracted using TriZol (Invitrogen)
Library construction was conducted by Hudson Alpha
RNAseq was performed using an Illumina HiSeq instrument (Hudson Alpha). For each biological replicate, 50 M reads per sample were obtained by 2 x 50 nucleotide paired-end sequencing.

treatment_protocol: Human Fucci ESCs were sorted into early-G1 (DN), late-G1 (KO2), S phase (AzL), and G2/M (AzH) fractions by FACS on a MoFlo (Beckman Coulter) in biological triplicate (three independent passages).

tag: replicate

tag: origin

value: WA09 human embryonic stem cells

tag: sorted fraction

value: S phase


title: H3_AzHi

source_name: G2/M human embryonic stem cells


title: control rep15

tag: tissue


title: H3_KO2

source_name: Late G1 human embryonic stem cells

value: Late G1


title: H3_DN

source_name: Early G1 human embryonic stem cells

value: Early G1


title: H2_AzHi


title: H1_AzHi


title: H1_AzLo


title: wild-type disome footprints

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome or disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification. Ribosomes from the disome peak were retained and footprints of 40-80 nt were sequenced.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos.

value: wild-type (BY4741)

value: cycloheximide

value: Double ribosome-protected RNA 40-80 nt


title: H1_DN


title: H2_DN


title: GM12878 native deproteinized replicate 2, V1

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: Double strand RNA structure probing and deep sequencing of double stranded regions in Human transcriptome GM12878

data_processing:
Raw reads were trimmed to 50bp (trimmed 51bp from the 3'end)
Trimmed reads were mapped to hg19 transcriptome using bowtie2, where the hg19 transcriptome was aggragated from UCSC RefSeq and Gencode v12 databases
The number of single and double strand reads were calculated by passing through the SAM file accordingly, and numbers were then normalized by sequencing depth
Genome_build: Hg19 Transcriptome, aggragated from UCSC RefSeq and Gencode v12 databases
Supplementary_files_format_and_content: The processed .tab file contains two tab-seprated columns, the first column is the transcript ID, and the second column is a list of semi-colon seprated numbers indicating the S1/V1 counts for each base of that transcript
Supplementary_files_format_and_content: On the Series record, a table of transcript-level normalized counts.

source_name: rRNA depleted RNA Rnase V1 at 37°C

growth_protocol: GM12878, GM12891 and GM12892 cells were grown at 37˚C to ~0.6million cells/ml in RPMI media supplemented with 15% FBS, 2mM L-glutamine and 1% PenStep

extract_protocol: The cleavage sites are captured and cloned using Ambion RNA sequencing kit compatible with the Illumina platform (Ambion)

treatment_protocol: RNA is isolated from the cells using 1) Trizol and poly(A)+ selected or 2)lysed with 0.1% SDS, 0.25% Na deoxycholate, phenol extracted, before structure probing at 37˚C

tag: sample type

value: rRNA depleted

tag: cell line


title: GM12878 native deproteinized replicate 2, S1

description: Single strand RNA structure probing and deep sequencing of double stranded regions in Human transcriptome GM12878

source_name: rRNA depleted RNA S1 nuclease at 37°C


title: ski2KO dom34KO short footprints

source_name: Whole cells

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome or disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification. Small footprints of 15-24 nt were retained during RNA size selection. These were later separated into 15-18 and 19-24 nt pools during data processing.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos.

tag: strain

value: ski2KO dom34KO

value: Ribosome-protected RNA 15-24 nt


title: H2_KO2


title: pharate_wing_rna (rep1 and rep2)

source_name: pharate appendage

value: y;cn,bw,sp

value: stage P14 pharate adult

value: pharate wing


title: H1_KO2


title: pharate_haltere_rna (rep1 and rep2)

value: pharate haltere


title: ski2KO short footprints


title: GM12878 native deproteinized followed by renatured RNA, V1


title: GM12892_iCLIP_rep2

description: AGO iCLIP in GM12892 cell replicate 2

data_processing:
Qaulity control using FASTX toolkit: low quality raw reads were removed; adapter sequence were trimmed off from the 3'end of raw reads; and PCR-duplicates' raw reads were then removed.
Reads pass through the quality control were mapped to hg19 genome using bowtie, and an extension of +/-10bp of the cross-linking position was performed to increase signal intensity.
Signals of each cell type was defined as the minimun signal of the replicates
Peaks were called by a 50bp sliding window and defined as the enrichment score of that window greater than 2
Genome_build: hg19
Supplementary_files_format_and_content: bed format with Transcript ID on the first column and peak start stop position relative to the first base of the transcript

extract_protocol: AGO iCLIP libraries were produced in biological duplicates for each individual (91, 92, and 78), barcoded, and pooled for sequencing. Samples were single-end sequenced for 75bp on an Illumina HiSeq2500 machine.

treatment_protocol: 2x10^7 GM cells (per biological replicate) were collected under log phase growth, washed in once in ice-cold 1xPBS, resuspended in 10x pellet volumes of ice-cold 1xPBS, plated out on 10cm tissue culture dishes. Cells were UV crosslinked at 254nm for 0.3J/cm^2, collected in ice-cold PBS and cell pellets were frozen on dry ice. Lysate preparation, RNaseA, and immunoprecipitation of AGO were performed as described by Chi et al. using the antiAGO antibody (clone 2A8, Millipore). To produce iCLIP libraries on-bead enzymatic steps and off-bead final library preparation was performed as described by Konig et al


title: GM12892_iCLIP_rep1

description: AGO iCLIP in GM12892 cell replicate 1


title: GM12878 native deproteinized replicate 1, S1


title: GM12878 native deproteinized replicate 1, V1


title: pharate_T3leg_rna (rep1 and rep2)

value: T3 pharate leg


title: GM12892 renatured V1

description: Double strand RNA structure probing and deep sequencing of double stranded regions in Human transcriptome GM12892

source_name: polyA RNA Rnase V1 at 37°C

value: polyA RNA


title: dom34KO disome footprints


title: GM12891_iCLIP_rep2

description: AGO iCLIP in GM12891 cell replicate 2


title: GM12891_iCLIP_rep1

description: AGO iCLIP in GM12891 cell replicate 1


title: H2_AzLo


title: GM12892 renatured S1

description: Single strand RNA structure probing and deep sequencing of double stranded regions in Human transcriptome GM12892

source_name: polyA RNA S1 nuclease at 37°C


title: GM12891 renatured V1

description: Double strand RNA structure probing and deep sequencing of double stranded regions in Human transcriptome GM12891


title: GM12878 native deproteinized followed by renatured RNA, S1


title: control rep9

source_name: heart

value: heart

value: control


title: GM12878_iCLIP_rep1

description: AGO iCLIP in GM12878 cell replicate 1


title: PRMT4-KD1

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned using Tophat 1.4.0 with Bowtie 1
Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings
Genome_build: hg19
Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample.

source_name: cord blood

growth_protocol: Purifed human cord blood derived CD34+ cells were cultured in Iscove`s modified Dulbecco`s medium (IMDM, Cellgro) containing 20% BIT 9500 medium (Stem Cell Technologies) supplemented with SCF (100 ng/ml), FLT-3 ligand (10 ng/ml), IL-6 (20 ng/ml) and TPO (100 ng/ml)

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols.

treatment_protocol: CD34+ cells were infected with lentiviruses carrying PRMT4KD or scramble control shRNAs in the presence of 8µg/ml polybrene and spin inoculation . Transduced cells were sorted based on GFP positivity 72h after transduction.

tag: cell type

value: primary CD34+ cell


title: GM12878 renatured S1


title: Col0

city: PARIS

first: Alexis

last: Sarazin

address: 46 rue d'Ulm

department: Ecole Normale Supérieure, Département de Biologie

country: France

institute: CNRS UMR 8186 - Biologie Moléculaire des Organismes Photosynthétiques

data_processing:
Basecalls performed using HiSeq Control Soft. v. 1.5.15.1, RTA 1.13.48.0 and CASAVA 1.8.2
Reads were aligned to the Arabidopsis thaliana genome (TAIR10) using MUMmer v3. Perfectly alignned reads from 15 to 30nt were used for further analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Sequence count for A. thaliana derived small RNAs

organism: Arabidopsis thaliana

source_name: Col0 WT

growth_protocol: Seedlings were grown in long day conditions subjected to a cycle of 8 h and 16 h of darkness and light, respectively, at a day/night temperature of 22.5/18.5°

extract_protocol:
Total RNA was isolated with Trizol
Libraries construction was contracted out to Fasteris SA.
Libraries were prepared according to Illumina's instructions accompanying the sequencing Kit TruSeq(TM) SBS v5.

tag: cultivar

value: 10 day-old seedlings

value: wildtype


title: miR472OE

source_name: Col0 miR472OE


title: Input males 25°C small RNA

description:
Sample name: inp030613
Input males 25°C small RNA
small RNA profiling

source_name: neSi1[cb-unc-119(+) 3xflag::csr-1]; csr-1(tm892); fog-2 (q71) males 25°C

extract_protocol: Small RNA cloning, 5' and 3' ligation dependent

treatment_protocol: Small RNAs of 10-40nt from total RNAs were resolved on a 15% polyacrylamide 7M Urea Gel, along with 2 picomoles of RNA standard (18- and 40-nt) in separate lanes. SYBR gold staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and isopropanol-precipitated with 20mg of glycogen as the carrier. The gel purified RNA was incubated with 0.25 U/µl TAP (Epicentre) and  1U/µl SuperRNaseIN (Ambion) in 10µl reaction containing 1X buffer at 37 oC for 1 hr, followed by phenol-chloroform extraction and isopropanol precipitation. The TAP-treated samples were then incubated with 5µM of 3’-end linker (1, 2, 3 from IDT DNA Technologies), 1 Unit/µl of SuperRNaseIN, 10% DMSO and 1 U/µl T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2,10mg/mL BSA, 10mM DTT).  The 3’ ligated products were gel purified, eluted, precipitated and then incubated with 5 µM of 5’ adapter oligonucleotide with 4nt barcode at the 5' end, 1 Unit/µl SuperRNaseIN (Ambion) and 2 U/µl of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% DMSO. The ligated products were gel purified and reverse transcribed in a standard 20µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 8% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing HiSeq platform (Illumina, Inc.) and single-end 50 nt reads were obtained.

tag: barcode

value: 5' barcode (A) TGAC

value: 3' barcode (1) CTGTAGGCACCATCAAT

tag: ip antibody

value: none (input)


title: GM12878 renatured V1


title: PRMT4-KD3


title: GM12891 renatured S1

description: Single strand RNA structure probing and deep sequencing of double stranded regions in Human transcriptome GM12891


title: control-2


title: control-1


title: PRMT4-KD2


title: control-3


title: FLAG::CSR-1 IP males 25°C small RNA

description:
Sample name: csr1IP030613
FLAG::CSR-1 IP males 25°C small RNA
small RNA profiling

value: 5' barcode (B) CAGT

value: anti-flag M2 antibody (Sigma, catalog# F1804)


title: alg-3/4 males 25°C small RNA

description:
Sample name: alg3425
alg-3/4 males 25°C small RNA
small RNA profiling

value: 5' barcode (C) GCTG


title: ICM pooled

value: ischemic cardiomyopathy (ICM)


title: alg-3/4 males 20°C small RNA

description:
Sample name: alg3420
alg-3/4 males 20°C small RNA
small RNA profiling


title: WT males 20°C small RNA

description:
Sample name: fog220
WT males 20°C small RNA
small RNA profiling

source_name: fog-2(q71) males 20°C

value: WT


title: SLE9-RNA-seq

status: Public on Dec 18 2013

city: Philadelphia

first: Kathleen

middle: E.

last: Sullivan

state: PA

address: 3615 Civic Center Blvd.

department: Immunology

institute: The Children's Hospital of Philadelphia

data_processing:
Build a colorspace Bowtie index, and align reads to hg19 using TopHat2
Assemble outputs of TopHat2 with Cufflinks 2.0.2, using RefSeq annotation as reference
Merge all the assemblies with CuffMerge
Create a reference Transcriptome based on CuffMerge output and a collection of non-coding RNAs, including lincRNA, small RNA, etc.
Run Novoalign to align reads again to the reference Transcriptome, and use the outputs to get read count mapped to each transcritpt
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with multiple worksheet, each with a type of RNAs and their annotation

source_name: primary monocytes

growth_protocol: Primary monocytes

extract_protocol:
Total RNA was isolated from 2-3 million purified  primary monocytes using the Qiagen RNeasy kit and DNA was removed by on-column DNase digestion.
1 ug of total RNA was used to prepare the RNA seq libraries with the SOLiDTM whole transcriptome analysis kit (Applied Biosystems). The procedure followed the instructions of the manufacturer.

tag: disease state

value: SLE patient

tag: gender

value: Female

value: primary monocytes


title: GM12878_iCLIP_rep2

description: AGO iCLIP in GM12878 cell replicate 2

value: rRNA depleted


title: SLE7-RNA-seq


title: SLE8-RNA-seq


title: SLE5-RNA-seq


title: SLE2-RNA-seq


title: SLE3-RNA-seq


title: SLE6-RNA-seq


title: control 8-RNA-seq

value: healthy control


title: SLE4-RNA-seq


title: SLE1-RNA-seq


title: control 1-RNA-seq


title: control 2-RNA-seq


title: H2R_d0

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
Off-Line Basecaller (OLB) was used for bcl to qseq conversion
Illumina paired-end adapter sequences were removed using Cutadapt version 0.9.3
Reads were mapped using Bismark version 0.5
Methylation calls from Bismark were extracted with a modified methylation_extractor script which removed 3’-MspI-sites
The extracted methylation data was further analyzed in R/Bioconductor with the BiSeq package
Genome_build: hg19
Supplementary_files_format_and_content: Extracted CpG methylation call files were generated using R/Bioconductor with help of the BiSeq package. Each processed file contains a column for chromosome, position and extracted methylation data for the respective sample. For each CpG position observed the number of methylated / unmethylated reads is listed.

source_name: RRBS HTB56 intermediate metastatic cell line

extract_protocol: 0.3 – 1 µg of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with Illumina TruSeq adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 280 bps insert size were purified from a SYBR gold (Invitrogen) pre-stained agarose gel (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). The libraries were sequenced on an Illumina HiScanSQ instrument with version 3 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.

tag: rounds of in vivo selection

tag: 5-azacytidine status

value: untreated


title: control 4-RNA-seq


title: control 7-RNA-seq


title: control 3-RNA-seq


title: H0R_d0_rep2

source_name: RRBS HTB56 cell line


title: A1R_d0

source_name: RRBS A459 intermediate metastatic cell line


title: control pooled

value: heart

value: control


title: H3R_d0_rep2

source_name: RRBS highly metastatic HTB56 cell line


title: control 6-RNA-seq


title: A3R_d0_rep2

source_name: RRBS highly metastatic A459 cell line


title: A0R_d0_rep2

source_name: RRBS A459 cell line


title: WT males 25°C small RNA

description:
Sample name: fog225
WT males 25°C small RNA
small RNA profiling

source_name: fog-2(q71) males 25°C

value: 5' barcode (D) ATCA

tag: genotype/variation

tag: culture conditions


title: H3R_d13_250

source_name: RRBS highly metastatic HTB56 cell line at day 13 after 6 days 5-Azacytidine treatment at 250 nM and 7 days release in normal media.

value: 7 days release after treatment with 250 nM


title: H0R_d0_rep1


title: H3R_d0_rep1


title: H3R_d6_250

source_name: RRBS highly metastatic HTB56 cell line after 6 days 5-Azacytidine treatment at 250 nM


title: control 5-RNA-seq


title: A3R_d13_250

source_name: RRBS highly metastatic A549 cell line at day 13 after 6 days 5-Azacytidine treatment at 250 nM and 7 days release in normal media.


title: A3R_d13_1000

source_name: RRBS highly metastatic A549 cell line at day 13 after 6 days 5-Azacytidine treatment at 1000 nM and 7 days release in normal media.

value: 7 days release after treatment with 1000 nM


title: A0R_d0_rep1


title: A2R_d0


title: A3R_d0_rep1


title: A3R_d6_1000

source_name: RRBS highly metastatic A459 cell line after 6 days 5-Azacytidine treatment at 1000 nM


title: A3R_d6_250

source_name: RRBS highly metastatic A459 cell line after 6 days 5-Azacytidine treatment at 250 nM