title: P(HCC)-P81

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P109

status: Public on Nov 16 2015

type: SRA

city: Beijing

first: xiaomeng

last: liu

state: Beijing

address: Yiheyuan Road No.5

country: China

institute: Biodynamics Optical Imaging Center (BIOPIC), Peking University

description:
protocol: MCTA-Seq
cell-free DNA

library_source: genomic

data_processing:
Adapters, first 6bp, last 12bp were trimmed.
Low quality reads were discarded (N bases more than 10%, phred33<5 more than 50% and phred score of first 5bp <20 after trimming) .
For plasma samples, reads with more than 3 CpH were discarded.
Clean reads were mapped to hg19 by Bismark and Bowtie
Reads were retained for subsequent analysis if there were more than 2 CG in the human genome around mapping site (-3~+3).
PCR duplicates were removed if reads had the same barcode and leftmost mapping position
Reads located in the CpG islands were normalized by total unique mapping reads
Genome_build: hg19
Supplementary_files_format_and_content: 5bp.cgcgmat.rmd.CGI.bed include reads number mapped  to each CpG Islands; CG.bed include 5mC level in each CpG site

molecule: genomic DNA

organism: Homo sapiens

source_name: plasma of HCC patient

growth_protocol: Standard condition for culture of HePG2 and Hela cells

extract_protocol:
Genomic DNA of tissue samples, WBC or cancer cell lines including the human liver hepatocellular carcinoma cell line (HePG2) and the human cervical cancer cell line (HeLa) were extracted using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s protocol.The fully methylated human genomic DNA is purchased (Chemicon/Millipore, CpGenome Universal Methylated DNA, S7821).The plasma cell-free DNAs were extracted using the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer’s protocol.
1) bisulfite treatment of the DNA, 2) a single-tube three-step amplification of methylated CpG islands, 3) gel-purification of the PCR product that serves as the final sequencing library, and 4) high-throughput sequencing using a next-generation sequencer.

treatment_protocol: Bisulfite conversion was performed using the MethyCode bisulfite conversion kit (Invitrogen) according to the manufacturer’s protocol. Briefly, the reaction containing the genomic or cell-free DNAs and the conversion reagent were incubated at 98°C for 10 min and then at 65°C for 2.5 h. After this, the converted DNAs along with 100 ng carrier tRNA (Roche) were purified using the Zymo-Spin columns (Zymo) with a step of on-column desulfonation, being finally eluted in 10 uL elution buffer.

tag: patient id

tag: tissue

value: plasma of HCC patient


title: P(HCC)-P80

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P74

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P92

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P60

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P62

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P58

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P59

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P50

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P51

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P57

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P54

description:
protocol: MCTA-Seq
cell-free DNA

source_name: plasma of cirrhosis patient

value: plasma of cirrhosis patient


title: P(HCC)-P44

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P39

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P113

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P36

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P10

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P3

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P29

description:
protocol: MCTA-Seq
cell-free DNA


title: T(NL)-P34

description: protocol: MCTA-Seq

source_name: normal liver tissue

value: normal liver tissue


title: T(NL)-P33

description: protocol: MCTA-Seq


title: P(HCC)-P37

description:
protocol: MCTA-Seq
cell-free DNA


title: T(Aj)-P50

description: protocol: MCTA-Seq

source_name: adjacent noncancerous liver tissue

value: adjacent noncancerous liver tissue


title: T(NL)-P32

description: protocol: MCTA-Seq


title: T(Aj)-P57

description: protocol: MCTA-Seq


title: P(HCC)-P77

description:
protocol: MCTA-Seq
cell-free DNA


title: T(Aj)-P37

description: protocol: MCTA-Seq


title: T(Aj)-P39

description: protocol: MCTA-Seq


title: T(Aj)-P29

description: protocol: MCTA-Seq


title: T(Aj)-P41

description: protocol: MCTA-Seq


title: P(HCC)-P41

description:
protocol: MCTA-Seq
cell-free DNA


title: T(Aj)-P28

description: protocol: MCTA-Seq


title: T(Aj)-P44

description: protocol: MCTA-Seq


title: T(Aj)-P25

description: protocol: MCTA-Seq


title: T(Aj)-P27

description: protocol: MCTA-Seq


title: T(Aj)-P24

description: protocol: MCTA-Seq


title: T(Aj)-P22

description: protocol: MCTA-Seq


title: T(Aj)-P20

description: protocol: MCTA-Seq


title: T(Aj)-P21

description: protocol: MCTA-Seq


title: T(Aj)-P23

description: protocol: MCTA-Seq


title: T(Aj)-P19

description: protocol: MCTA-Seq


title: T(Aj)-P12

description: protocol: MCTA-Seq


title: T(Aj)-P18

description: protocol: MCTA-Seq


title: T(Aj)-P15

description: protocol: MCTA-Seq


title: T(Aj)-P17

description: protocol: MCTA-Seq


title: T(Aj)-P36

description: protocol: MCTA-Seq


title: T(Aj)-P26

description: protocol: MCTA-Seq


title: T(Aj)-P10

description: protocol: MCTA-Seq


title: T(HCC)-P44

description: protocol: MCTA-Seq

source_name: hepatocellular carcinoma (HCC) tissue

value: hepatocellular carcinoma (HCC) tissue


title: T(HCC)-P58

description: protocol: MCTA-Seq


title: T(Aj)-P13

description: protocol: MCTA-Seq


title: T(Aj)-P11

description: protocol: MCTA-Seq


title: T(HCC)-P41

description: protocol: MCTA-Seq


title: T(HCC)-P50

description: protocol: MCTA-Seq


title: T(Aj)-P6

description: protocol: MCTA-Seq


title: T(HCC)-P57

description: protocol: MCTA-Seq


title: T(HCC)-P39

description: protocol: MCTA-Seq


title: T(HCC)-P37

description: protocol: MCTA-Seq


title: T(Aj)-P58

description: protocol: MCTA-Seq


title: T(HCC)-P29

description: protocol: MCTA-Seq


title: T(HCC)-P36

description: protocol: MCTA-Seq


title: T(HCC)-P28

description: protocol: MCTA-Seq


title: T(HCC)-P27

description: protocol: MCTA-Seq


title: T(HCC)-P26

description: protocol: MCTA-Seq


title: T(HCC)-P23

description: protocol: MCTA-Seq


title: T(HCC)-P21

description: protocol: MCTA-Seq


title: T(HCC)-P24

description: protocol: MCTA-Seq


title: T(HCC)-P22

description: protocol: MCTA-Seq


title: T(HCC)-P25

description: protocol: MCTA-Seq


title: T(HCC)-P19

description: protocol: MCTA-Seq


title: T(HCC)-P18

description: protocol: MCTA-Seq


title: T(HCC)-P17

description: protocol: MCTA-Seq


title: T(HCC)-P15

description: protocol: MCTA-Seq


title: T(HCC)-P12

description: protocol: MCTA-Seq


title: T(HCC)-P11

description: protocol: MCTA-Seq


title: T(HCC)-P6

description: protocol: MCTA-Seq


title: T(HCC)-P20

description: protocol: MCTA-Seq


title: T(HCC)-P10

description: protocol: MCTA-Seq


title: 22-734

city: Vancouver

first: James

middle: Daniel

last: Johnson

state: British Columbia

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

description: primary cells

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome using Tophat2
Expression levels were quantified with RNA-SeQC
Differential expression analysis was performed on the gene-level read count data using the limma empirical Bayes analysis pipeline
Analysed data are expressed in FPKM.
Genome_build: GRCm38_68
Supplementary_files_format_and_content: Analysed data are expressed in FPKM and stored in the .xlsx file in which the log fold changes represent KO/control.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy kit with the on-column Dnase treatment. Samples were stored at -80 C until use.
Libraries were generated using Illumina's Truseq V2 library kit, and each sample was given a unique identifier prior to sequencing on an Illumina HiSeq 2500 (150 bpx2, 20 million paired-end reads)

treatment_protocol: Mice were treated with tamoxifen 6 days prior to islet isolation to induce Ins2 gene deletion

tag: treatment

value: Cre-T

tag: genotype

tag: background strain

value: mixed but mostly C57Bl/6

value: pancreas

tag: tissue compartment

value: islets


title: 27-232

description: primary cells


title: 27-231

description: primary cells


title: 22-731

description: primary cells


title: 28-231

description: primary cells


title: 22-733

description: primary cells

value: Cre+T


title: 24-223

description: primary cells


title: 27-233

description: primary cells


title: 24-221

description: primary cells


title: 21-221

description: primary cells


title: 24-222

description: primary cells


title: 22-732

description: primary cells


title: 13-222

description: primary cells


title: 35 Genes experiment ES 3

city: Oxford

middle: Oliver Joshua

last: Davies

state: Oxon

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine, Oxford University

description:
Genes Analyzed: Hba-a1&2, Trp53, Mir144, Pnpo, Sp2, Isca1, Zcchc6, Slc25A37, Epb4.9, Nfe2, Myc, Pkdrej, Cd47, Pou5f1, Adrb2, Lmo2, Sox2, Tal1, Pdzk1ip1, Klf4, KLF3, Nanog, Hipk2, Hbb-b1&2, Klf1, Epor, Alas2, Gata7
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_30gH_Nor_PF_BF.gfc HbbCombined_30gH_Nor_PF_BF.gfc Hba-1_30gH_Nor_PF_BF.gfc Hba-2_30gH_Nor_PF_BF.gfc TP53_30gH_Nor_PF_BF.gfc Mir144145_30gH_Nor_PF_BF.gfc Pnpo_30gH_Nor_PF_BF.gfc Sp2_30gH_Nor_PF_BF.gfc ISCA1_30gH_Nor_PF_BF.gfc Zcchc6_30gH_Nor_PF_BF.gfc Slc25A37_30gH_Nor_PF_BF.gfc Epb4.9-Dematin_30gH_Nor_PF_BF.gfc NFE2_30gH_Nor_PF_BF.gfc cMyc-1_30gH_Nor_PF_BF.gfc cMyc-2_30gH_Nor_PF_BF.gfc Pkdrej_30gH_Nor_PF_BF.gfc CD47_30gH_Nor_PF_BF.gfc Oct-4_30gH_Nor_PF_BF.gfc Adrb2_30gH_Nor_PF_BF.gfc Lmo2-1_30gH_Nor_PF_BF.gfc Lmo2-2_30gH_Nor_PF_BF.gfc SOX2_30gH_Nor_PF_BF.gfc Tal1-1_30gH_Nor_PF_BF.gfc Tal1-2_30gH_Nor_PF_BF.gfc Pdzk1ip1_30gH_Nor_PF_BF.gfc Klf4_30gH_Nor_PF_BF.gfc KLF3a_30gH_Nor_PF_BF.gfc KLF3b_30gH_Nor_PF_BF.gfc nanog_30gH_Nor_PF_BF.gfc Hipk2_30gH_Nor_PF_BF.gfc Hbb-b1_30gH_Nor_PF_BF.gfc Hbb-b2_30gH_Nor_PF_BF.gfc KLF1_30gH_Nor_PF_BF.gfc EpoR_30gH_Nor_PF_BF.gfc ALAS2-1_30gH_Nor_PF_BF.gfc ALAS2-2_30gH_Nor_PF_BF.gfc GATA1_30gH_Nor_PF_BF.gfc

data_processing:
Library strategy: NG Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: ES cells

growth_protocol: E14 embryonic stem cells were grown on gelatin coated flasks in GMEM with fetal calf serum and LIF  (Leukaemia Inhibitory Factor).

extract_protocol:
A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter.  Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences)).  The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads.  Cells were then separated using an auto-MACS (miltenyi biotec).
The protocol used for generation of the 3C libraries was similar to previous methods with minor modifications. Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80.  Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer.  The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%.  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol.  Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments.  Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using  the Nimblegen SeqCap reagents and an adapted protocol.  The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using either the Illumina MiSeq (150bp paired end reads) or HiSeq (100bp paired end reads).
The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage).  Oligonucleotide capture technology was then used to pull down the restricion fragments containing the promoters of the genes of interest and their interacting partners, which were subsequently idendified by high throughput sequencing.  The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.

treatment_protocol: Mice were treated with 3 doses of Phenylhydrazine (40mg / g body weight) 12h apart and harvested on day 5 following the start of the treatment (Spivak et al., 1973).

tag: strain

value: Cultured ES cells


title: 35 Genes experiment ES 2

description:
Genes Analyzed: Hba-a1&2, Trp53, Mir144, Pnpo, Sp2, Isca1, Zcchc6, Slc25A37, Epb4.9, Nfe2, Myc, Pkdrej, Cd47, Pou5f1, Adrb2, Lmo2, Sox2, Tal1, Pdzk1ip1, Klf4, KLF3, Nanog, Hipk2, Hbb-b1&2, Klf1, Epor, Alas2, Gata6
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_30gH_Nor_PF_BF.gfc HbbCombined_30gH_Nor_PF_BF.gfc Hba-1_30gH_Nor_PF_BF.gfc Hba-2_30gH_Nor_PF_BF.gfc TP53_30gH_Nor_PF_BF.gfc Mir144145_30gH_Nor_PF_BF.gfc Pnpo_30gH_Nor_PF_BF.gfc Sp2_30gH_Nor_PF_BF.gfc ISCA1_30gH_Nor_PF_BF.gfc Zcchc6_30gH_Nor_PF_BF.gfc Slc25A37_30gH_Nor_PF_BF.gfc Epb4.9-Dematin_30gH_Nor_PF_BF.gfc NFE2_30gH_Nor_PF_BF.gfc cMyc-1_30gH_Nor_PF_BF.gfc cMyc-2_30gH_Nor_PF_BF.gfc Pkdrej_30gH_Nor_PF_BF.gfc CD47_30gH_Nor_PF_BF.gfc Oct-4_30gH_Nor_PF_BF.gfc Adrb2_30gH_Nor_PF_BF.gfc Lmo2-1_30gH_Nor_PF_BF.gfc Lmo2-2_30gH_Nor_PF_BF.gfc SOX2_30gH_Nor_PF_BF.gfc Tal1-1_30gH_Nor_PF_BF.gfc Tal1-2_30gH_Nor_PF_BF.gfc Pdzk1ip1_30gH_Nor_PF_BF.gfc Klf4_30gH_Nor_PF_BF.gfc KLF3a_30gH_Nor_PF_BF.gfc KLF3b_30gH_Nor_PF_BF.gfc nanog_30gH_Nor_PF_BF.gfc Hipk2_30gH_Nor_PF_BF.gfc Hbb-b1_30gH_Nor_PF_BF.gfc Hbb-b2_30gH_Nor_PF_BF.gfc KLF1_30gH_Nor_PF_BF.gfc EpoR_30gH_Nor_PF_BF.gfc ALAS2-1_30gH_Nor_PF_BF.gfc ALAS2-2_30gH_Nor_PF_BF.gfc GATA1_30gH_Nor_PF_BF.gfc


title: Cell numbers (ABM) Sample 1

description:
Genes Analyzed: Hba-a1&2, Hbb-b1&2, Slc25A37
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_Celln_Nor_PF_BF.gfc HbbCombined_Celln_Nor_PF_BF.gfc Slc25A37_Celln_Nor_PF_BF.gfc

source_name: Erythroid cells

value: F1 C57Bl6 / CBA

value: Phenylhydrazine treated spleen


title: 13-221

description: primary cells


title: Cell numbers (ABM) Sample 2


title: ABM Double Sample2

description:
Genes Analyzed: Hba-a1&2, Hbb-b1&2, Slc25A37
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_Best_Nor_PF_BF.gfc HbbCombined_Best_Nor_PF_BF.gfc Slc25A37_Best_Nor_PF_BF.gfc

source_name: Erythroid cells (ter119+)

value: Phenylhydrazine treated spleen with ter119 selection


title: ABM Double Sample1


title: 35 Genes experiment ES 1

description:
Genes Analyzed: Hba-a1&2, Trp53, Mir144, Pnpo, Sp2, Isca1, Zcchc6, Slc25A37, Epb4.9, Nfe2, Myc, Pkdrej, Cd47, Pou5f1, Adrb2, Lmo2, Sox2, Tal1, Pdzk1ip1, Klf4, KLF3, Nanog, Hipk2, Hbb-b1&2, Klf1, Epor, Alas2, Gata5
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_30gH_Nor_PF_BF.gfc HbbCombined_30gH_Nor_PF_BF.gfc Hba-1_30gH_Nor_PF_BF.gfc Hba-2_30gH_Nor_PF_BF.gfc TP53_30gH_Nor_PF_BF.gfc Mir144145_30gH_Nor_PF_BF.gfc Pnpo_30gH_Nor_PF_BF.gfc Sp2_30gH_Nor_PF_BF.gfc ISCA1_30gH_Nor_PF_BF.gfc Zcchc6_30gH_Nor_PF_BF.gfc Slc25A37_30gH_Nor_PF_BF.gfc Epb4.9-Dematin_30gH_Nor_PF_BF.gfc NFE2_30gH_Nor_PF_BF.gfc cMyc-1_30gH_Nor_PF_BF.gfc cMyc-2_30gH_Nor_PF_BF.gfc Pkdrej_30gH_Nor_PF_BF.gfc CD47_30gH_Nor_PF_BF.gfc Oct-4_30gH_Nor_PF_BF.gfc Adrb2_30gH_Nor_PF_BF.gfc Lmo2-1_30gH_Nor_PF_BF.gfc Lmo2-2_30gH_Nor_PF_BF.gfc SOX2_30gH_Nor_PF_BF.gfc Tal1-1_30gH_Nor_PF_BF.gfc Tal1-2_30gH_Nor_PF_BF.gfc Pdzk1ip1_30gH_Nor_PF_BF.gfc Klf4_30gH_Nor_PF_BF.gfc KLF3a_30gH_Nor_PF_BF.gfc KLF3b_30gH_Nor_PF_BF.gfc nanog_30gH_Nor_PF_BF.gfc Hipk2_30gH_Nor_PF_BF.gfc Hbb-b1_30gH_Nor_PF_BF.gfc Hbb-b2_30gH_Nor_PF_BF.gfc KLF1_30gH_Nor_PF_BF.gfc EpoR_30gH_Nor_PF_BF.gfc ALAS2-1_30gH_Nor_PF_BF.gfc ALAS2-2_30gH_Nor_PF_BF.gfc GATA1_30gH_Nor_PF_BF.gfc


title: T(HCC)-P13

description: protocol: MCTA-Seq


title: 35 Genes experiment Erythroid 4

description:
Genes Analyzed: Hba-a1&2, Trp53, Mir144, Pnpo, Sp2, Isca1, Zcchc6, Slc25A37, Epb4.9, Nfe2, Myc, Pkdrej, Cd47, Pou5f1, Adrb2, Lmo2, Sox2, Tal1, Pdzk1ip1, Klf4, KLF3, Nanog, Hipk2, Hbb-b1&2, Klf1, Epor, Alas2, Gata4
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_30gH_Nor_PF_BF.gfc HbbCombined_30gH_Nor_PF_BF.gfc Hba-1_30gH_Nor_PF_BF.gfc Hba-2_30gH_Nor_PF_BF.gfc TP53_30gH_Nor_PF_BF.gfc Mir144145_30gH_Nor_PF_BF.gfc Pnpo_30gH_Nor_PF_BF.gfc Sp2_30gH_Nor_PF_BF.gfc ISCA1_30gH_Nor_PF_BF.gfc Zcchc6_30gH_Nor_PF_BF.gfc Slc25A37_30gH_Nor_PF_BF.gfc Epb4.9-Dematin_30gH_Nor_PF_BF.gfc NFE2_30gH_Nor_PF_BF.gfc cMyc-1_30gH_Nor_PF_BF.gfc cMyc-2_30gH_Nor_PF_BF.gfc Pkdrej_30gH_Nor_PF_BF.gfc CD47_30gH_Nor_PF_BF.gfc Oct-4_30gH_Nor_PF_BF.gfc Adrb2_30gH_Nor_PF_BF.gfc Lmo2-1_30gH_Nor_PF_BF.gfc Lmo2-2_30gH_Nor_PF_BF.gfc SOX2_30gH_Nor_PF_BF.gfc Tal1-1_30gH_Nor_PF_BF.gfc Tal1-2_30gH_Nor_PF_BF.gfc Pdzk1ip1_30gH_Nor_PF_BF.gfc Klf4_30gH_Nor_PF_BF.gfc KLF3a_30gH_Nor_PF_BF.gfc KLF3b_30gH_Nor_PF_BF.gfc nanog_30gH_Nor_PF_BF.gfc Hipk2_30gH_Nor_PF_BF.gfc Hbb-b1_30gH_Nor_PF_BF.gfc Hbb-b2_30gH_Nor_PF_BF.gfc KLF1_30gH_Nor_PF_BF.gfc EpoR_30gH_Nor_PF_BF.gfc ALAS2-1_30gH_Nor_PF_BF.gfc ALAS2-2_30gH_Nor_PF_BF.gfc GATA1_30gH_Nor_PF_BF.gfc


title: 28-232

description: primary cells


title: Hba-a1&2 Double Sample2

description:
Genes Analyzed: Hba-a1&2
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_Best_Nor_PF_BF.gfc


title: 35 Genes experiment Erythroid 3

description:
Genes Analyzed: Hba-a1&2, Trp53, Mir144, Pnpo, Sp2, Isca1, Zcchc6, Slc25A37, Epb4.9, Nfe2, Myc, Pkdrej, Cd47, Pou5f1, Adrb2, Lmo2, Sox2, Tal1, Pdzk1ip1, Klf4, KLF3, Nanog, Hipk2, Hbb-b1&2, Klf1, Epor, Alas2, Gata3
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_30gH_Nor_PF_BF.gfc HbbCombined_30gH_Nor_PF_BF.gfc Hba-1_30gH_Nor_PF_BF.gfc Hba-2_30gH_Nor_PF_BF.gfc TP53_30gH_Nor_PF_BF.gfc Mir144145_30gH_Nor_PF_BF.gfc Pnpo_30gH_Nor_PF_BF.gfc Sp2_30gH_Nor_PF_BF.gfc ISCA1_30gH_Nor_PF_BF.gfc Zcchc6_30gH_Nor_PF_BF.gfc Slc25A37_30gH_Nor_PF_BF.gfc Epb4.9-Dematin_30gH_Nor_PF_BF.gfc NFE2_30gH_Nor_PF_BF.gfc cMyc-1_30gH_Nor_PF_BF.gfc cMyc-2_30gH_Nor_PF_BF.gfc Pkdrej_30gH_Nor_PF_BF.gfc CD47_30gH_Nor_PF_BF.gfc Oct-4_30gH_Nor_PF_BF.gfc Adrb2_30gH_Nor_PF_BF.gfc Lmo2-1_30gH_Nor_PF_BF.gfc Lmo2-2_30gH_Nor_PF_BF.gfc SOX2_30gH_Nor_PF_BF.gfc Tal1-1_30gH_Nor_PF_BF.gfc Tal1-2_30gH_Nor_PF_BF.gfc Pdzk1ip1_30gH_Nor_PF_BF.gfc Klf4_30gH_Nor_PF_BF.gfc KLF3a_30gH_Nor_PF_BF.gfc KLF3b_30gH_Nor_PF_BF.gfc nanog_30gH_Nor_PF_BF.gfc Hipk2_30gH_Nor_PF_BF.gfc Hbb-b1_30gH_Nor_PF_BF.gfc Hbb-b2_30gH_Nor_PF_BF.gfc KLF1_30gH_Nor_PF_BF.gfc EpoR_30gH_Nor_PF_BF.gfc ALAS2-1_30gH_Nor_PF_BF.gfc ALAS2-2_30gH_Nor_PF_BF.gfc GATA1_30gH_Nor_PF_BF.gfc


title: 35 Genes experiment Erythroid 2

description:
Genes Analyzed: Hba-a1&2, Trp53, Mir144, Pnpo, Sp2, Isca1, Zcchc6, Slc25A37, Epb4.9, Nfe2, Myc, Pkdrej, Cd47, Pou5f1, Adrb2, Lmo2, Sox2, Tal1, Pdzk1ip1, Klf4, KLF3, Nanog, Hipk2, Hbb-b1&2, Klf1, Epor, Alas2, Gata2
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_30gH_Nor_PF_BF.gfc HbbCombined_30gH_Nor_PF_BF.gfc Hba-1_30gH_Nor_PF_BF.gfc Hba-2_30gH_Nor_PF_BF.gfc TP53_30gH_Nor_PF_BF.gfc Mir144145_30gH_Nor_PF_BF.gfc Pnpo_30gH_Nor_PF_BF.gfc Sp2_30gH_Nor_PF_BF.gfc ISCA1_30gH_Nor_PF_BF.gfc Zcchc6_30gH_Nor_PF_BF.gfc Slc25A37_30gH_Nor_PF_BF.gfc Epb4.9-Dematin_30gH_Nor_PF_BF.gfc NFE2_30gH_Nor_PF_BF.gfc cMyc-1_30gH_Nor_PF_BF.gfc cMyc-2_30gH_Nor_PF_BF.gfc Pkdrej_30gH_Nor_PF_BF.gfc CD47_30gH_Nor_PF_BF.gfc Oct-4_30gH_Nor_PF_BF.gfc Adrb2_30gH_Nor_PF_BF.gfc Lmo2-1_30gH_Nor_PF_BF.gfc Lmo2-2_30gH_Nor_PF_BF.gfc SOX2_30gH_Nor_PF_BF.gfc Tal1-1_30gH_Nor_PF_BF.gfc Tal1-2_30gH_Nor_PF_BF.gfc Pdzk1ip1_30gH_Nor_PF_BF.gfc Klf4_30gH_Nor_PF_BF.gfc KLF3a_30gH_Nor_PF_BF.gfc KLF3b_30gH_Nor_PF_BF.gfc nanog_30gH_Nor_PF_BF.gfc Hipk2_30gH_Nor_PF_BF.gfc Hbb-b1_30gH_Nor_PF_BF.gfc Hbb-b2_30gH_Nor_PF_BF.gfc KLF1_30gH_Nor_PF_BF.gfc EpoR_30gH_Nor_PF_BF.gfc ALAS2-1_30gH_Nor_PF_BF.gfc ALAS2-2_30gH_Nor_PF_BF.gfc GATA1_30gH_Nor_PF_BF.gfc

value: F1 (S57Bl6 / CBA)


title: Hba-a1&2 Double Sample1 (same as Hba-a1&2 Single Capture)


title: 22-222

description: primary cells


title: Hba-a1&2 Single Capture

description:
Genes Analyzed: Hba-a1&2
molecule: Capture-C products
3C library preparation followed by single oligonucleotide capture
Processed data file: HbaCombined_Single_capture_PF_BF.gfc


title: 35 Genes experiment Erythroid 1

description:
Genes Analyzed: Hba-a1&2, Trp53, Mir144, Pnpo, Sp2, Isca1, Zcchc6, Slc25A37, Epb4.9, Nfe2, Myc, Pkdrej, Cd47, Pou5f1, Adrb2, Lmo2, Sox2, Tal1, Pdzk1ip1, Klf4, KLF3, Nanog, Hipk2, Hbb-b1&2, Klf1, Epor, Alas2, Gata1
molecule: Next generation Capture-C products
3C library prepartion followed by double oligonucleotide capture
Processed data file: HbaCombined_30gH_Nor_PF_BF.gfc HbbCombined_30gH_Nor_PF_BF.gfc Hba-1_30gH_Nor_PF_BF.gfc Hba-2_30gH_Nor_PF_BF.gfc TP53_30gH_Nor_PF_BF.gfc Mir144145_30gH_Nor_PF_BF.gfc Pnpo_30gH_Nor_PF_BF.gfc Sp2_30gH_Nor_PF_BF.gfc ISCA1_30gH_Nor_PF_BF.gfc Zcchc6_30gH_Nor_PF_BF.gfc Slc25A37_30gH_Nor_PF_BF.gfc Epb4.9-Dematin_30gH_Nor_PF_BF.gfc NFE2_30gH_Nor_PF_BF.gfc cMyc-1_30gH_Nor_PF_BF.gfc cMyc-2_30gH_Nor_PF_BF.gfc Pkdrej_30gH_Nor_PF_BF.gfc CD47_30gH_Nor_PF_BF.gfc Oct-4_30gH_Nor_PF_BF.gfc Adrb2_30gH_Nor_PF_BF.gfc Lmo2-1_30gH_Nor_PF_BF.gfc Lmo2-2_30gH_Nor_PF_BF.gfc SOX2_30gH_Nor_PF_BF.gfc Tal1-1_30gH_Nor_PF_BF.gfc Tal1-2_30gH_Nor_PF_BF.gfc Pdzk1ip1_30gH_Nor_PF_BF.gfc Klf4_30gH_Nor_PF_BF.gfc KLF3a_30gH_Nor_PF_BF.gfc KLF3b_30gH_Nor_PF_BF.gfc nanog_30gH_Nor_PF_BF.gfc Hipk2_30gH_Nor_PF_BF.gfc Hbb-b1_30gH_Nor_PF_BF.gfc Hbb-b2_30gH_Nor_PF_BF.gfc KLF1_30gH_Nor_PF_BF.gfc EpoR_30gH_Nor_PF_BF.gfc ALAS2-1_30gH_Nor_PF_BF.gfc ALAS2-2_30gH_Nor_PF_BF.gfc GATA1_30gH_Nor_PF_BF.gfc


title: cortex CLEAR-CLIP, biological rep 19

status: Public on Nov 15 2015

city: New York

first: Michael

middle: John

last: Moore

state: NY

address: 1230 York Ave Box 226

department: Molecular Neuro-Oncology

country: USA

institute: The Rockefeller University

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: TGCA
false ligation test with spiked E. coli RNA at 1:6 ratio

data_processing:
base calling: Casava 1.8.2
quality filtering: minimum quality filter applied for barcode and insert; fastq_filter.pl;  -if sanger -f min:0-3:20,mean:20-40:20 -maxN -1 -v -of fasta ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
collapse exact sequences: exact duplicate sequences removed; fasta2collapse.pl; ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
remove 3' adapter sequene: 3' adapter GTGTCAGTCACTTCCAGCGG clipped; fastx Clipper; -l 20 -a GTGTCAGTCACTTCCAGCGG -n; http://hannonlab.cshl.edu/fastx_toolkit/
trim 5' adapter sequence: 5' 20 nucleotides trimmed (NNNNAGGGAGGACGATGCGG, where NNNN is 4 nucleotide index for multiplexing); fastx Trimmer; -f 21; http://hannonlab.cshl.edu/fastx_toolkit/
strip 5' degenerate linker: 5 nucleotide (NNNNG) degenerate barcode stripped and appended to read IDs; stripBarcode.pl; -linker 5 ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
alignment against micoRNA database: microRNA database mapped against sample file (treated as reference genome) to identify potential chimeric reads containing microRNA sequence; Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml
extract chimeric read: extract potential chimeric sequence 5' or 3' of mapped microRNA sequence; text manipulation in R; ;
alignment against genome reference: alignment ofpotential chimeric reads against reference genome to identify target sites; Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml
collapse PCR duplicates: mapped reads with same 5' end and same degenerate barcode consolidated; tag2collapse.pl; keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
clustering : chimera interactions with the same ligated microRNA and overlapping genomic coordinates were clustered; Genome_Intervals R package; ;
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet with gene coordinate information and additional annotations for chimera-identified interactions
Supplementary_files_format_and_content: Excel spreadsheet gene coordinate information for standard CLIP AGO binding peaks, and overlapping microRNA seed matches and chimera interactions

source_name: cortex + E. Coli RNA (1:6)

growth_protocol: Mice were sacrificed at indicated age.

extract_protocol:
Cortex was dissected into ice cold PBS, triturated by passing twice though an 18G needle, and UV-irradiated.  AGO-cross-linked RNA was isolated with the CLEAR-CLIP protocol described in detail in the accompanying publication.
AGO-cross-linked RNA was cloned by addition of pre-adenylated 3' linker and RNA 5' linker, then RT-PCR, as described in the published CLEAR-CLIP protocol. Products were amplified in a second round of PCR that added a 4 nt index (for multiplexing, see above) and 16 nt common primer sequence.  Raw files are demultiplexed on the basis of this index, but have not been further modified.

tag: age

value: cortex


title: cortex CLEAR-CLIP, biological rep 17

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: CGTA
false ligation test with spiked E. coli RNA at 1:1 ratio

source_name: cortex + E. Coli RNA (1:1)


title: cortex CLEAR-CLIP, biological rep 20

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: ATGC
false ligation test with spiked E. coli RNA at 1:6 ratio


title: cortex CLEAR-CLIP, biological rep 21

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: GATC

source_name: cortex

value: 6 weeks


title: cortex CLEAR-CLIP, biological rep 23

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: GCAT
false ligation test with mixed cortex and Drosophila lysates (1:1 RNA ratio)

source_name: cortex + Drosophila S2 cells


title: cortex CLEAR-CLIP, biological rep 22

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: CGTA
false ligation test with mixed cortex and Drosophila lysates (1:1 RNA ratio)


title: cortex CLEAR-CLIP, biological rep 16


title: cortex CLEAR-CLIP, biological rep 18

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: GCAT
false ligation test with spiked E. coli RNA at 1:1 ratio


title: cortex CLEAR-CLIP, biological rep 14

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: TAGC


title: cortex CLEAR-CLIP, biological rep 15

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: CTAG


title: cortex CLEAR-CLIP, biological rep 13

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: ATGC


title: resting Treg, rep2

first: Willey

last: Liao

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

data_processing:
Short reads were aligned with STAR v2.4.0c
GENCODE v2 genes were quantified with featureCounts (subhead package, v1.4.3-p1)
Differential gene expression was determined using DESeq2
Genome_build: mm10, GENCODE v2
Supplementary_files_format_and_content: DEseq2 log2 transformed matrix and feature counts

source_name: spleen

extract_protocol:
miRNeasy Mini Kit
Clontech SMART-seq v4 Ultra low input RNA Kit

tag: cell type

value: rTreg (CD4+Foxp3+CD62LhiCD44lo)

tag: phenotype

value: resting


title: resting Treg, rep1


title: cortex CLEAR-CLIP, biological rep 11

description:
protocol: CLEAR-CLIP
complex MW (kD): 150-180
multiplex index: CCGA


title: cortex CLEAR-CLIP, biological rep 6, Miseq run

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-150
multiplex index: TCAC


title: activated Treg, rep1

value: aTreg (CD4+Foxp3+CD62LhiCD44lo)

value: activated


title: activated Treg, rep2


title: cortex CLEAR-CLIP, biological rep 12b

description:
protocol: CLEAR-CLIP
complex MW (kD): 180-200
multiplex index: AACC


title: cortex CLEAR-CLIP, biological rep 10a

description:
protocol: CLEAR-CLIP
complex MW (kD): 150-180
multiplex index: CGTA


title: cortex CLEAR-CLIP, biological rep 10b

description:
protocol: CLEAR-CLIP
complex MW (kD): 180-200
multiplex index: GCAT


title: cortex CLEAR-CLIP, biological rep 9

description:
protocol: CLEAR-CLIP with denaturation
complex MW (kD): 130-150
multiplex index: GATC


title: cortex CLEAR-CLIP, biological rep 6, Hiseq run


title: cortex CLEAR-CLIP, biological rep 4

description:
protocol: CLEAR-CLIP
complex MW (kD): 150-180
no-ligase control


title: cortex CLEAR-CLIP, biological rep 5


title: cortex CLEAR-CLIP, biological rep 3

description:
protocol: CLEAR-CLIP
complex MW (kD): 150-180
multiplex index: TGCA


title: cortex CLEAR-CLIP, biological rep 8

description:
protocol: CLEAR-CLIP
complex MW (kD): 180-200
multiplex index: TACG


title: cortex CLEAR-CLIP, biological rep 1

description:
protocol: CLEAR-CLIP
complex MW (kD): 150-180
multiplex index: ACCG


title: cortex CLEAR-CLIP, biological rep 2

description:
protocol: CLEAR-CLIP
complex MW (kD): 150-180
multiplex index: CATG


title: Huh-7.5 CLEAR-CLIP12

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: TGAG
RNAse T1, HSPC117 over-expression no T4 RNA ligase

data_processing:
base calling: Casava 1.8.2
quality filtering: minimum quality filter applied for barcode and insert: fastq_filter.pl;  -if sanger -f min:0-3:20,mean:20-40:20 -maxN -1 -v -of fasta ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
collapse exact sequences: exact duplicate sequences removed: fasta2collapse.pl; ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
remove 3' adapter sequene: 3' adapter GTGTCAGTCACTTCCAGCGG clipped: fastx Clipper; -l 20 -a GTGTCAGTCACTTCCAGCGG -n; http://hannonlab.cshl.edu/fastx_toolkit/
trim 5' adapter sequence: 5' 20 nucleotides trimmed (NNNNAGGGAGGACGATGCGG, where NNNN is 4 nucleotide index for multiplexing): fastx Trimmer; -f 21; http://hannonlab.cshl.edu/fastx_toolkit/
strip 5' degenerate linker: 5 nucleotide (NNNNG) degenerate barcode stripped and appended to read IDs: stripBarcode.pl; -linker 5 ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
alignment against micoRNA database: microRNA database mapped against sample file (treated as reference genome) to identify potential chimeric reads containing microRNA sequence: Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml
extract chimeric read: extract potential chimeric sequence 5' or 3' of mapped microRNA sequence: text manipulation in R; ;
alignment against genome reference: alignment ofpotential chimeric reads against reference genome to identify target sites: Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml
collapse PCR duplicates: mapped reads with same 5' end and same degenerate barcode consolidated: tag2collapse.pl; keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
clustering : chimera interactions with the same ligated microRNA and overlapping genomic coordinates were clustered: Genome_Intervals R package; ;
Genome_build: hg18
Supplementary_files_format_and_content: Excel spreadsheet with gene coordinate information and additional annotations for chimera-identified interactions

source_name: Huh-7.5 hepatoma cells

growth_protocol: Huh-7.5 cell culture

extract_protocol:
Huh-7.5 cells were UV-irradiated.  AGO-cross-linked RNA was isolated with the Std. AGO-CLIP or CLEAR-CLIP protocol described in detail in the accompanying publication.
AGO-cross-linked RNA was cloned by addition of pre-adenylated 3' linker and RNA 5' linker, then RT-PCR, as described in the published CLEAR-CLIP protocol. Products were amplified in a second round of PCR that added a 4 nt index (for multiplexing, see above) and 16 nt common primer sequence.  Raw files are demultiplexed on the basis of this index, but have not been further modified.

treatment_protocol: LNA-122, miravirsen or siRNA treatment, or HSPC117 over-expression according to protocol described in accompanying publication.

tag: cell line


title: Huh-7.5 CLEAR-CLIP10

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: ACTC
RNAse A (high), HSPC117 over-expression no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP4

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: ATGC
RNAse A (low), no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP9

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: AACC
RNAse A (high), HSPC117 over-expression no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP5

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: CCGA
RNAse A (low), with T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP2

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: AGTG
RNAse A (low), HSPC117 siRNA, no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP11

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: TTGG
RNAse T1, HSPC117 over-expression no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP8

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: GAGG
RNAse A (low), HSPC117 over-expression no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP7

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: GGCT
RNAse A (low), HSPC117 over-expression no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP3

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: TACG
RNAse A (low), no T4 RNA ligase


title: Huh-7.5 CLEAR-CLIP6

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: CTCC
RNAse A (low), with T4 RNA ligase


title: Huh-7.5 std.-CLIP miR-122 exp., miravirsen-2

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: TCAC
Std. AGO-CLIP miR-122 exp.: MockmiR-122 exp.: LNA-122miR-122 exp.: miravirsen


title: Huh-7.5 CLEAR-CLIP1

description:
protocol: CLEAR-CLIP
complex MW (kD): 130-180
multiplex index: TCAC
RNAse A (low), HSPC117 siRNA, no T4 RNA ligase


title: Huh-7.5 std.-CLIP miR-122 exp., miravirsen-1


title: Huh-7.5 std.-CLIP miR-122 exp., LNA-122-4

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: TGCA
Std. AGO-CLIP miR-122 exp.: MockmiR-122 exp.: LNA-122


title: cortex CLEAR-CLIP, biological rep 12a

description:
protocol: CLEAR-CLIP
complex MW (kD): 150-180
multiplex index: GAGG


title: Huh-7.5 std.-CLIP miR-122 exp., LNA-122-2

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: CATG
Std. AGO-CLIP miR-122 exp.: MockmiR-122 exp.: LNA-122


title: Huh-7.5 std.-CLIP miR-122 exp., LNA-122-3


title: Huh-7.5 std.-CLIP miR-122 exp., LNA-122-1


title: Huh-7.5 std.-CLIP miR-122 exp., miravirsen-3

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: AGTG
Std. AGO-CLIP miR-122 exp.: MockmiR-122 exp.: LNA-122miR-122 exp.: miravirsen


title: cortex CLEAR-CLIP, biological rep 7

description:
protocol: CLEAR-CLIP
complex MW (kD): 180-200
multiplex index: AGTG


title: Huh-7.5 std.-CLIP miR-122 exp., Mock-1

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: GTGC
Std. AGO-CLIP miR-122 exp.: Mock


title: Huh-7.5 std.-CLIP miR-122 exp., Mock-2


title: Huh-7.5 std.-CLIP miR-122 exp., Mock-4

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: ACCG
Std. AGO-CLIP miR-122 exp.: Mock


title: Huh-7.5 std.-CLIP 7

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: GCAT
Std. AGO-CLIP on Huh-7.5 cells


title: Huh-7.5 std.-CLIP miR-122 exp., Mock-3


title: Huh-7.5 std.-CLIP 5

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: CTCC
Std. AGO-CLIP on Huh-7.5 cells


title: Huh-7.5 std.-CLIP 4

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: CTAG, GATC, CGTA, GCAT, GTGC, ACCG
Std. AGO-CLIP on Huh-7.5 cells


title: Huh-7.5 std.-CLIP 6

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: GATC
Std. AGO-CLIP on Huh-7.5 cells


title: Huh-7.5 std.-CLIP miR-122 exp., miravirsen-4


title: Huh-7.5 std.-CLIP 2

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: GTG, CAC
Std. AGO-CLIP on Huh-7.5 cells


title: Huh-7.5 std.-CLIP 3

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: GTG, CAC, AGC, GCT
Std. AGO-CLIP on Huh-7.5 cells


title: Huh-7.5 std.-CLIP 1

description:
protocol: Std. AGO-CLIP
complex MW (kD): 130-180
multiplex index: N/A: Not multiplexed. No index or RL5 sequence present. Sequences start with NNNNG.
Std. AGO-CLIP on Huh-7.5 cells


title: mir-11~998 RMCE-1 biological replicate 2

city: Chicago

first: Mary

last: Truscott

state: IL

address: 900 S Ashland Ave, room 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: 30-50 discs/sample

data_processing:
Control software: HiSeq Control Software 2.2.38
Primary Analysis: RTA 1.18.61.0
Secondary Analysis: CASAVA-1.8.2
Read Quality Assessment and Filtering was done with FastQC program
TopHat2 was used for mapping of reads. "featureCount" of SubRead package was used to count the reads of exons for each gene abundance measurement. (Ensembl gene v.77)
Genome_build: D. melanogaster ENSEMBL (v77)
Supplementary_files_format_and_content: tab-delimited text files include absolute count values for each sample

organism: Drosophila melanogaster

source_name: 3rd instar larval eye disc

growth_protocol: Flies were cultured on standard medium at 25 degrees Celcius

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
Library construction was performed using standard Illumina protocols; Illumina HiScanSQ Instrument; Total RNA directional; incl. rRNA depletion
Single end 50 bp sequencing 2-lane flowcell

treatment_protocol: Different genotypes were compared: Canton S, mir-11 KO(w-), mir-11~998 RMCE-1 and mir-11~998 RMCE-2

tag: developmental stage

value: 3rd instar larval

tag: tissue type

value: eye disc

tag: stock


title: mir-11~998 RMCE-2 biological replicate 1

description: 30-50 discs/sample


title: Canton S biological replicate 2

description: 30-50 discs/sample

value: Canton S


title: mir-11 KO(w-) biological replicate 2

description: 30-50 discs/sample

value: mir-11 KO (w-)


title: mctl_6

status: Public on Nov 14 2015

city: Worcester

first: Helene

last: Tran

address: 55 North Lake Avenue

department: Neurology

institute: UMASS

data_processing:
We performed QC using trimmomatic removing PCR primers and low quality bases.
We aligned cleaned read to the mm10 genome using Bowtie2.
Using DESeq, we determined differentially expressed genes.
Genome_build: MM10
Supplementary_files_format_and_content: csv file output of DESEQ2

extract_protocol:
RNA was extracted from mouse brain with Trizol
libraries were prepared according Zhang et al protocol (PMID: 23273270)
Strand Specific libraries prepared without poly(A) selection

tag: strain background

tag: gender

value: male

tag: genotype/variation

value: wild type

value: brain


title: mC9_5

value: expressing a human C9ORF72 BAC including 500 G4C2 repeats


title: mC9_3


title: mir-11~998 RMCE-2 biological replicate 2

description: 30-50 discs/sample


title: mctl_4


title: mC9_1


title: Canton S biological replicate 1

description: 30-50 discs/sample


title: mC9_8


title: mir-11 KO(w-) biological replicate 1

description: 30-50 discs/sample


title: mC9_2


title: Hom_WT1_CT10

city: Zurich

first: Steven

middle: A.

last: Brown

address: Winterthurerstrasse 190

country: Switzerland

institute: University Zurich

data_processing:
RNA-seq reads were quality-checked with fastqc which computes various quality metrics for the raw reads. Reads were aligned to the genome and transcriptome with tophat v 1.3.3. Before mapping the low quality ends of the reads were clipped (3 bases from the read start and 10 bases from the read end). Tophat was run with default options. The fragment length parameter was set to 100 bases with a standard deviation of 100 bases. Based on these alignments the distribution of the reads across genomic features was assessed.Isoform expression was quantified with the RSEM algorithm
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20).  Sequence alignment of the resulting high-quality reads to the Mus musculus reference genome (build mm10) and quantification of gene level expression was carried out using RSEM (Version 1.2.5) [1].
To detect differentially expressed genes we applied count based negative binomial model implemented in the software package edgeR (R version: 2.15.2, edgeR version: 3.0.6) [2], in which the normalization factor was calculated by trimmed mean of M values (TMM) method [3].
The gene-wise dispersions were estimated by conditional maximum likelihood and an empirical Bayes procedure was used to shrink the dispersions towards a consensus value.
The differential expression was assessed using an exact test adapted for over-dispersed data. Genes showing altered expression with adjusted (Benjamini and Hochberg method) p-value < 0.05 were considered as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM output files

source_name: Whole Brain

extract_protocol:
In brief, mouse brains were homogenized in 5 ml homogenization buffer (0.32 M sucrose, 1 mM EDTA pH 7.4, 1 mM dithiothreitol, phenylmethanesulfonyl fluoride solution (Sigma, 93482-50ML-F), complete mini-protease inhibitor (Roche Diagnostics) for 10 sec using a polytron. The homogenate was centrifuged at 1,000g for 10 min at 4 °C yielding the nuclear fraction (Nuc) and the supernatant (Sup). The supernatant was centrifuged at 31,000g for 5 min at 4°C using a discontinuous Percoll gradient. The layer between 3% and 10% of Percoll were collected, washed in 30 ml of homogenization buffer and further centrifuged at 22,000 × g for 15 min at 4°CT. The pellet was resuspended in in EBC buffer (50 mM Tris-HCl pH 8.0, 120 mM NaCl and 0.5% NP-40) containing complete mini-protease inhibitor (Roche Diagnostics) and phosphatase inhibitor cocktail 1 and 2 (Sigma–Aldrich)) for Western blot analysis or lysis buffer for RNA extraction (GenElute Mammalian Total RNA Miniprep Kit, Sigma).
For transcriptome analysis using RNA-Seq, the quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). RNAs were then processed using The TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc, California, USA) according to the manufacturer recommendations. The TruSeq SR Cluster Kit v3-cBot-HS or TruSeq PE Cluster Kit v3-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on a Illumina HiSeq 2000 system using the TruSeq SBS Kit v3-HS (Illumina, Inc, California, USA) with paired end 2 X100 reads or single end 1X100 reads.

value: WT

value: whole brain

tag: rna source

value: total homogenate


title: Syn_WT1_CT10

tag: tissue

value: synaptosomes-enriched fraction


title: KO3 CT10

source_name: Hippocampus

extract_protocol:
Extract hippocampal total RNA  extraction (GenElute Mammalian Total RNA Miniprep Kit, Sigma).
For transcriptome analysis using RNA-Seq, the quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). RNAs were then processed using The TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc, California, USA) according to the manufacturer recommendations. The TruSeq SR Cluster Kit v3-cBot-HS or TruSeq PE Cluster Kit v3-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on a Illumina HiSeq 2000 system using the TruSeq SBS Kit v3-HS (Illumina, Inc, California, USA) with paired end 2 X100 reads or single end 1X100 reads.

value: Hippocampus

value: NONO KO


title: WT3 CT22


title: mir-11~998 RMCE-1 biological replicate 1

description: 30-50 discs/sample


title: KO1 CT22


title: KO2 CT22


title: KO2 CT10


title: WT1 CT22


title: WT2 CT22


title: mctl_7


title: WT2 CT10


title: KO1 CT10


title: WT1 CT10


title: WT3 CT10


title: KO3 CT22


title: RNA-seq_CRISPR_scr_A

city: Bethesda

first: Tineke

middle: Laura

last: Lenstra

state: MD

address: 41 Library Drive, Bldg 41, B302

department: Laboratory of Receptor Biology and Gene Expression

institute: National Cancer Institute, Center for Cancer Research

data_processing:
Basecalling, RTA 1.18.64,  Illumina instrument run time analysis software
Demultiplexing, Bcl2fastq 1.8.4, Barcode demultiplexed allowing 1 mismatch
Filtering (Adaptor and quality), Trimmomatic 0.30, PE -threads 16 -phred33 ILLUMINACLIP:TruSeq_and_nextera_adapters.fa:3:50:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MAXINFO:50:0.8 MINLEN:25
Alignment, TopHat v2.0.8, tophat -G annonation.gtf -o ./ -r 10 --mate-std-dev 200 -p 16 --library- type fr-firststrand bowtie2_annoatation/prefix read1.fastq read2.fastq
RNAStatistics, Picard 1.84, CollectRnaSeqMetrics.jar REF_FLAT=annotation_refFlat.txt INPUT=sample.bam OUTPUT= RnaSeqMetrics.txt RIBOSOMAL_INTERVALS= ribosome_interval_list.txt STRAND_SPECIFICITY=NONE VALIDATION_STRINGENCY=LENIENT
Duplication Statistics, Picard 1.84, MarkDuplicates.jar INPUT=sample.bam OUTPUT=sample.MKDUP.bam METRICS_FILE=sample.bam.metric ASSUME_SORTED=true MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 VALIDATION_STRINGENCY=LENIENT
Genome_build: Yeast (scEF4_mod), Ensembl_YeastS288C_EF4 modified with plasmid sequences
Supplementary_files_format_and_content: Cvs file containing normalized read counts for all genes for all 4 samples, acquired from the R package DESeq2

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae BY4741

growth_protocol: SC -LEU -URA + glucose

extract_protocol:
hot phenol total RNA extraction and cleanup + DNAse treatment with Qiagen RNAeasy mini
TruSeq Stranded mRNA LT, RS-122-2101,
multiplex: index sample_RNA_1: GTCCGC, index sample_RNA_2: ATGTCA, index sample_RNA_3: GCCAAT, index sample_RNA_4: CGATGT

treatment_protocol: growth to midlog, from OD 0.1 to 0.4

tag: crispri guiderna

value: scrambled

tag: condition

value: glucose mid-log


title: 5'-end sequencing after Syn9 infection of WH7803 at 2h TAP treated. [WH7803_inf_III_2h_race_TAP]

status: Public on Nov 13 2015

city: Rehovot

first: Shany

last: Doron

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science,

description: Synechococcus sp. strain WH7803 infected with theT4-like myovirus Syn9

data_processing:
RNA-seq reads were aligned separately for each sample to the reference genomes of the Syn9 cyanophage (Genbank: NC_008296) and the matching host (Genbank: NC_009481, NC_005070 and CP006882 for WH7803, WH8102 and WH8109, respectively), and analyzed according to the library type. Reads that mapped to more than one position were discarded from further analyses.
Reads from the whole-transcriptome libraries were aligned using Novoalign 2.08.01 (Novocraft Technologies Sdn Bhd, http://www.novocraft.com) with the default parameters and [-c 1 -r Random]. reads covering each gene were counted (in-house script), and normalized by gene length and by the number of reads mapped to the RNA component of the RNase P gene (rnpB) from the respective hosts.
Reads from the bisulfite strand-specific libraries were aligned using Novoalign 2.08.01 with the parameters [-b] for the indexing step, and [-r Random] for the alignment. Reads were used to estimate asRNA length, based on the sharp decline in coverage of bisulfite sequencing reads.
Reads from the 5’-end libraries were used for determining TSSs across the phage genome, and were analyzed as previously described (Wurtzel et al., 2012a) with some minor modifications. Briefly, TSS determination relies on the enrichment of TSSs within libraries treated by the Tobacco Acid Pyrophosphatase (TAP), which specifically cleaves primary 5’ triphosphate containing ends, compared to untreated ones, which provides both primary and processed 5’ ends. To differentiate between reads initiating from TSSs versus RNA processing sites, a set of 5’ ends most likely representing real TSSs (positive set) was deﬁned and compared with a group of 5’ ends most likely representing processed sites (negative set). For each time point, the positive set included the 5’ ends located upstream of genes (up to 100 nt) that were reproducible in the phage while infecting all 3 hosts. If multiple genomic positions were found for a gene within this distance, the position with the highest number of supporting reads was selected as the TSS for the positive set. Additional 5’ ends farther than 100nt upstream of genes, for which a sharp increase (>5 fold) in the measured expression produced from the whole-transcript sequencing was observed, were also added to the positive set. The negative set was defined as genomic positions located more than 150 nt inside ORFs.    The TAP enrichment threshold for a TSS was calculated for each sample separately based on the distribution of the TAP+/TAP- ratio in the positive and negative sets (Wurtzel et al., 2012a). A genomic position was considered a real TSS at a specific time point, if it was above the TAP+/TAP- threshold in all three hosts or when found in two hosts for multiple time points. Also, positions supported by a sharp increase in coverage were added.    The dominant TSS upstream of each gene (up to 400 bp) at each time point was considered to be that gene’s primary TSS. TSSs internal to ORFs were associated with the gene only if they were supported by an increase in coverage, affecting the expression level of that gene. When no TSS was associated with a gene at a certain time point the gene was considered to be part of an operon with the upstream gene under the condition that it was both positioned on the same strand and expressed at the same levels (less than 2 fold change in the median coverage).
Genome_build: Genbank: NC_008296, NC_009481, NC_005070 and CP006882 for Syn9 cyanophage, Synechococcus WH7803, WH8102 and WH8109, respectively.
Supplementary_files_format_and_content: 3 tab-delimited text files, one per host including all time points (controls, ~5 min, 0.5h, 1h, 2h):  (A-H)      Gene information. Col H is feature - 1/8 for coding/tRNA  (I-S)       raw reads  (T-AD)    rnpB normalized reads. Expression of all genes is normalized by the expression of rnpB gene, and by their length.  (AE-AH) averages of duplicates.  Aabbreviations:  controls: c05, c1, c2  7803: a=rep I,  b=rep III  8102: a=rep II, b=rep III  8109: a=rep II, b=rep III

organism: Synechococcus sp. WH 7803

source_name: Synechococcus sp. strain WH7803  infected by Syn9

growth_protocol: Synechococcus strains were grown in an artificial sea water-based medium (ASW) (Wyman et al., 1985) with modifications as described in Lindell et al. (1998), at 22 °C under cool white light with a 14:10 h light:dark cycle at an intensity of 30 μmol photon·m-2·s-1 during the light period

extract_protocol:
Synechococcus cells (50-75 ml of each infected or control culture) were collected on 0.4 μm pore-sized polycarbonate filters (GE) by filtration at a vacuum pressure of 10 inch Hg and snap frozen at -80 ºC in 2 ml PGTX buffer (40 ml liquid phenol 95%, 6.9 ml glycerol, 0.1 g 8-hydroxyquinoline, 0.58 g EDTA, 0.8 g sodium acetate, 0.5 g guanidine thiocyanate and 4.6 g guanidine hydrochloride at final pH = 4.2 in a final volume of 100ml) as described in Pinto et al (2009) but without Triton X-100. Each culture was sampled a minute apart such that WH8102-infected cells were sampled 1 and 2 minutes after WH8109- and WH8109-infected cells, respectively. Total RNA was extracted by the PGTX 95 method (Pinto et al. 2009) with some minor modifications. Briefly, the samples were thawed on ice and subjected to a 5-min incubation at 95 °C followed by a further 5-min on ice. The aqueous phase was extracted with an equal volume of chloroform:isoamyl alcohol (24:1, vol/vol). RNA was precipitated with 1 volume of isopropanol and washed in 75% ethanol. Total nucleic acids were quantified based on absorption at 260 nm and RNA integrity was verified by gel electrophoresis. DNA was removed by DNase I digestion using the Turbo DNA-free kit (Ambion). This treatment was repeated  to digest residual DNA. RNA samples were then treated with MICROBExpres Bacterial mRNA Purification Kit (Ambion) to remove rRNA. If necessary the rRNA treatment was repeated.  Samples were stored at -80°C.
The whole-transcriptome cDNA libraries were prepared using Illumina’s TruSeq RNA Sample Preparation Kit without the polyA isolation step. cDNA libraries for bisulfite strand-specific sequencing were prepared as previously described (Edelheit et al., 2013). 5’-end sequencing libraries were prepared as previously described, with some modifications (Wurtzel et al., 2012a, 2012b): For each sample, 1.5 μg of rRNA-depleted RNA was incubated with or without 5 U of TAP for 2 h at 37°C to generate 5′ monophosphate RNAs (TAP+ and TAP- samples, respectively). The 3′ ends were blocked with NaIO4 (10 mM) for 1.5 h at 4°C in the dark and saturated by adding 1/10 volume of 1 M lysine for 10 min at room temperature. Each reaction was passed through NucAway spin columns (Ambion). Illumina 5′ adapters (in single-strand RNA form), with addition of a unique 4-base index sequence, were ligated to the resultant RNA using 25 units of T4 RNA ligase (Epicentre) in the presence of 40 units of RNase inhibitor (Promega) in a final volume of 50 μL. The reaction was incubated at 37°C for 2 h and precipitated with 1/10 volume of 5 M NH4OAc and 100% ethanol, at 13,000 rpm for 15 min at 4°C. The ethanol was removed after chilling at -80°C for 1 h. The RNA pellet was washed twice with 70% ethanol, resuspended in RNase-free water and washed twice with ultra-pure water on YM-30 microcon columns (Millipore). First strand cDNA was synthesized using random hexamer primers attached to the Illumina 3′ adapter with the SuperScript First Strand Synthesis system (Invitrogen). Adaptors and primer dimers were removed from the resultant cDNA using a PCR purification kit (Qiagen). The cDNA was then PCR amplified using primers matching the 5′ and 3′ Illumina adapters for 20 cycles. Fragments 250-500 bp long were extracted from 3% low melting point agarose gels and quantified with the Bioanalyzer. 5'-end cDNA libraries of 2-10 subsamples were mixed in equal amounts and sent for Illumina sequencing.

treatment_protocol: Synechococcus cultures were infected at a multiplicity of infection (MOI) of 2-3 approximately 2 h after “lights on” in the morning and incubated under growth conditions. The infection cycle was complete 4 h before darkness. Samples were collected at different time points during the lytic cycle for RNA-sequencing (5 min, 0.5 h, 1 h and 2 h after infection).

tag: infection

value: Infected by Syn9

tag: time

tag: replicate

tag: tap treated


title: 5'-end sequencing after Syn9 infection of WH7803 at 2h NO TAP. [WH7803_inf_III_2h_race_NOTAP]


title: 5'-end sequencing after Syn9 infection of WH7803 at 1h TAP treated. [WH7803_inf_III_1h_race_TAP]


title: RNA-seq_CRISPR_116_A

tag: strain


title: 5'-end sequencing after Syn9 infection of WH7803 at 0.5h TAP treated. [WH7803_inf_III_0.5h_race_TAP]


title: 5'-end sequencing after Syn9 infection of WH7803 at 0.5h NO TAP. [WH7803_inf_III_0.5h_race_NOTAP]


title: RNA-seq_CRISPR_scr_B


title: 5'-end sequencing after Syn9 infection of WH7803 at 2h TAP treated. [WH7803_inf_I_2h_race_TAP]


title: 5'-end sequencing after Syn9 infection of WH7803 at 0.5h TAP treated. [WH7803_inf_I_0_5h_race_TAP]


title: Whole transcriptome at 120 min after Syn9 infection of WH7803 [WH7803_inf_2h_III_whole_transcr]

value: Not Applicable


title: Whole transcriptome at 120 min after Syn9 infection of WH7803 [WH7803_inf_2h_I_whole_transcr]


title: DNA input control

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

data_processing:
HiSeq Control Software 2.2.68
Reads were mapped to mm9 using Bowtie v1.1.0 (Langmead et al., 2009)
Peaks were detected using MACS v1.4 (Zhang et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: xls file detected peaks annotated to the two nearest genes

source_name: Whole Intestine

extract_protocol:
ChIP was performed following a previously described protocol (Vokes et. Al, 2007). Intestines wer snap-frozen in liquid and ground in a mortar and pestle to dissociate the tissue to single cells. DNA and protein were then crosslinked and sonicated to an average 500 bp fragment size. cJUN bound regions were immunoprecipitated overnight using anti cJUN Polyclonal Rabbit antibody (Santa Cruz sc-44) bound to Protein G Dyanabeads). Input control consisted of sonicated DNA.
ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: none, DNA input control

tag: age

tag: genotype


title: Whole transcriptome at 30 min after Syn9 infection of WH7803 [WH7803_inf_0.5h_III_whole_transcr]


title: RNA-seq_CRISPR_116_B


title: Whole transcriptome at 5 min after Syn9 infection of WH7803 [WH7803_inf_0h_I_whole_transcr]


title: ELR_chx_rep2

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

description: Cycloheximide Treatment

data_processing:
Library strategy: ribosome profiling
We trimmed 3’ adapters from sequencing reads and then aligned the trimmed reads to human rRNA sequences and removed reads mapping to rRNAs (5S, 5.8S, 18S, and 28S. We then aligned remaining reads to the union of human reference transcript sequences: defined RefSeq; GENCODE lncRNAs; human body Mpap lncRNAs. The unmapped reads were then aligned to human reference genome sequence (hg19) using Tophat (Trapnell et al., 2009). We counted number of reads in canonical ORFs of protein coding genes, excluding 15aa downstream start codon and 5aa upstream stop codon.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts of sequencing reads

source_name: Fibroblast cell

growth_protocol: All cultures were performed at 37°C under 5% CO2. BJ fibroblast cell lines (EH, EL and ELR) were cultured on Knockout DMEM (Invitrogen) with 10% FBS, medium 199, glutamine and penicillin-streptomycin(Hahn et al., 1999).  The breast epithelial cell line (MCF-10A-ER-Src) was grown in DMEM/F12 with 5% charcoal-stripped fetal bovine serum (Invitrogen) and supplements(Iliopoulos et al., 2009). Cells were seeded at 1 × 106 cells per 10-cm culture dish and cultured overnight. MCF-10A-ER-Src cells were treated by 1 µM 4-hydroxy-tamoxifen for various time points (1, 4, and 24 hr) to induce transformation.

extract_protocol:
For ribosome profiling, cells were pretreated with cycloheximide (100 µg/ml; Sigma-Aldrich) for 90 seconds or harringtonine (2 µg/ml; Santa Cruz) for 5 minutes, and detergent lysis was then performed with flash-freezing in liquid nitrogen. DNase I-treated lysates were then treated with RNase I, and ribosome-protected fragments were purified as previously described (Ingolia et al., 2012).
For ribosome profiling, ribosome-protected fragments were subjected to Illumina TruSeq library construction as previously described (Ingolia et al., 2012).

tag: cell line

value: BJ

tag: cell type

value: Fibroblast

tag: rna type

value: Ribosome protected fragments


title: Whole transcriptome at 30 min after Syn9 infection of WH7803 [WH7803_inf_0.5h_I_whole_transcr]


title: EL_chx_rep2

description: Cycloheximide Treatment


title: ELR_harr_rep2

description: Harringtonine Treatment


title: EL_harr_rep2

description: Harringtonine Treatment


title: 5'-end sequencing after Syn9 infection of WH7803 at 1h NO TAP. [WH7803_inf_III_1h_race_NOTAP]


title: Whole transcriptome at 60 min after Syn9 infection of WH7803 [WH7803_inf_1h_I_whole_transcr]


title: Whole transcriptome at 5 min after Syn9 infection of WH7803 [WH7803_inf_0h_III_whole_transcr]


title: 5'-end sequencing after Syn9 infection of WH7803 at 1h TAP treated. [WH7803_inf_I_1h_race_TAP]


title: EH_chx_rep2

description: Cycloheximide Treatment


title: ELR_harr_rep1

description: Harringtonine Treatment


title: EL_harr_rep1

description: Harringtonine Treatment


title: LCLOlaparib72hr_2

city: Philadelphia

first: Italo

last: Tempera

state: PA

address: 3307 N. Broad Street, PAHB, Room 206

department: Fels Institute

institute: Temple University

data_processing:
Illumina Casava1.7 software used for basecalling.
Tophat2
Cuffdiff v2.2.1: cuffdiff -u
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Olaparib 72hr.

growth_protocol: Lymphoblastoid cell lines (LCLs) were cultured in suspension in RPMI 1640 medium supplemented with 15% fetal bovine serum and antibiotics in 5% CO2 at 37°C.

extract_protocol:
RNA was extracted from 5 × 106 cells using a Qiagen RNeasy Plus Mini Kit according to the manufacturer’s protocol. Total RNA was depleted of the ribosomal RNA component using RiboZero (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Olaparib was dissolved in DMSO and cells were treated with 2.5 μM olaparib for 24 or 72 hrs in the appropriate media.

value: LCLs B-cells


title: EH_harr_rep1

description: Harringtonine Treatment


title: LCLOlaparib24hr_2

source_name: Olaparib 24hr.


title: LCLOlaparib72hr_1


title: EH_chx_rep1

description: Cycloheximide Treatment


title: Whole transcriptome at 60 min after Syn9 infection of WH7803 [WH7803_inf_1h_III_whole_transcr]


title: cJUN IP

value: cJUN Polyclonal Rabbit antibody (Santa Cruz sc-44)

value: wild type


title: EH_harr_rep2

description: Harringtonine Treatment


title: ELR_rna

data_processing:
We trimmed 3’ adapters from sequencing reads and then aligned the trimmed reads to human rRNA sequences and removed reads mapping to rRNAs (5S, 5.8S, 18S, and 28S. We then aligned remaining reads to the union of human reference transcript sequences: defined RefSeq; GENCODE lncRNAs; human body Mpap lncRNAs. The unmapped reads were then aligned to human reference genome sequence (hg19) using Tophat (Trapnell et al., 2009). We counted number of reads in canonical ORFs of protein coding genes, excluding 15aa downstream start codon and 5aa upstream stop codon.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts of sequencing reads

extract_protocol:
For RNA-seq, total RNA was purified from DNase-treated lysates, and ribosomal RNA was depleted with RiboMinus Eukaryote Kit (Invitrogen).
RNA-seq libraries were prepared with a tagging-based workflow(Pease and Kinross, 2013). In brief, rRNA-depleted RNA was fragmented at 85°C for 5 min, followed by cDNA synthesis, terminal tagging and PCR amplification with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre).

value: Total RNA


title: EL_rna


title: EH_rna


title: ERSrcTAM01hr_chx_rep2

description: Cycloheximide Treatment

source_name: Breast epithelial cell

value: breast epithelial


title: ERSrcTAM24hr_chx_rep2

description: Cycloheximide Treatment


title: LCLTime0_1

source_name: Control


title: ERSrcEtOH24hr_chx_rep2

description: Cycloheximide Treatment


title: ERSrcEtOH04hr_chx_rep2

description: Cycloheximide Treatment


title: LCLTime0_2


title: ERSrcTAM04hr_chx_rep2

description: Cycloheximide Treatment


title: LCLTime0_0


title: LCLOlaparib72hr_0


title: ERSrcTAM24hr_harr_rep1

description: Harringtonine Treatment


title: ELR_chx_rep1

description: Cycloheximide Treatment


title: ERSrcEtOH01hr_chx_rep2

description: Cycloheximide Treatment


title: ERSrcTAM04hr_harr_rep1

description: Harringtonine Treatment


title: EL_chx_rep1

description: Cycloheximide Treatment


title: 5'-end sequencing after Syn9 infection of WH8103 at 2h TAP treated. [WH8109_inf_III_2h_race_TAP]

description: Synechococcus sp. strain WH8109 infected with theT4-like myovirus Syn9

organism: Synechococcus sp. WH 8109

source_name: Synechococcus sp. strain WH8109  infected by Syn9


title: Bisulfite sequencing 30 min after Syn9 infection of WH8109 [WH8109_inf_0.5h_bisulfite]

value: Pooled


title: Bisulfite sequencing 60 min after Syn9 infection of WH8109 [WH8109_inf_1h_bisulfite]


title: ERSrcTAM00hr_harr_rep1

description: Harringtonine Treatment


title: SUC2

city: East Lansing

first: Benli

last: Chai

state: Michigan

address: 567 Wilson Road Rm 2225 A

department: Center for Microbial Ecology

institute: Michigan State University

description: early-to-mid log phase cultures  grown on 20mM succinate at 30 C using defined mineral DSMZ medium 457 (Brunner medium) (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, http://www.dsmz.de/).

data_processing:
reads were quality trimmed at the 3' end to the position marked by Read Segment Quality Control Indicator
reads were aligned to RW1 genome using Bowtie with the parameters: -n 2 -e 70 -l 28 --best.
read counts were tallied with a python script
differential expressions were called using DESeq.
Genome_build: NC_009507, NC_009508, NC_009511
Supplementary_files_format_and_content: normalized abundance of mapped reads to each gene feature.

organism: Rhizorhabdus wittichii

source_name: RW1, SUC, rep 2

growth_protocol: RW1 was grown at 30 oC using defined mineral DSMZ medium 457 (Brunner medium) (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, http://www.dsmz.de/).

extract_protocol:
Total RNA was isolated from early-to-mid log phase cultures (CFU of 1.0x109 to 1.5x109 cells/mL) using PureLink Mini Kit (Life Technologies, Carlsbad, CA). To ensure complete removal of DNA, RNA samples underwent a two-step DNAse I treatment, first with DNAse I (amplification grade, Life Technologies) followed by TURBO DNAse I (Life Technologies). RNA concentration was measured using Qubit (Life Technologies) and its quality was validated using BioAnalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatments comparised of using different carbon sustrates: SUC was added to a final 20 mM concentration. DD and DF were added to sterile flasks from acetone stocks to a final nominal concentration of 3 mM and left open in a sterile hood for 5 h to allow acetone to completely evaporate. Brunner medium was then added and flasks were sonicated for 10 s to dislodge and break up substrate crystals. SAP was added to 0.7% (w/v) final concentration in Brunner medium with succinate and sonicated to obtain a suspension with homogenized clay particles.

tag: medium


title: LCLOlaparib24hr_1


title: SUC1

source_name: RW1, SUC, rep 1

value: grown on 20mM succinate at 30 C using defined mineral DSMZ medium 457


title: Bisulfite sequencing 120 min after Syn9 infection of WH8109 [WH8109_inf_2h_bisulfite]


title: 5'-end sequencing after Syn9 infection of WH8103 at 1h TAP treated. [WH8109_inf_III_1h_race_TAP]


title: ERSrcTAM04hr_chx_rep1

description: Cycloheximide Treatment


title: LCLOlaparib24hr_0


title: SAP2

description: early-to-mid log phase cultures  grown on 20mM succinate and  0.7% (w/v) smectite clay at 30 C using defined mineral DSMZ medium 457 (Brunner medium) (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, http://www.dsmz.de/).

source_name: RW1, clay + SUC, rep 2


title: 5'-end sequencing after Syn9 infection of WH8103 at 0.5h TAP treated. [WH8109_inf_III_0.5h_race_TAP]


title: ERSrcTAM01hr_harr_rep1

description: Harringtonine Treatment


title: SAP1

source_name: RW1, clay + SUC, rep 1

value: 20mM succinate and  0.7% (w/v) smectite clay at 30 C using defined mineral DSMZ medium 457


title: ERSrcTAM24hr_chx_rep1

description: Cycloheximide Treatment


title: ERSrcTAM01hr_chx_rep1

description: Cycloheximide Treatment


title: 5'-end sequencing after Syn9 infection of WH8103 at 2h TAP treated. [WH8109_inf_II_2h_race_TAP]


title: ERSrcTAM24hr_rna


title: 5'-end sequencing after Syn9 infection of WH8103 at 0.5h TAP treated. [WH8109_inf_II_0.5h_race_TAP]


title: ERSrcTAM00hr_chx_rep1

description: Cycloheximide Treatment


title: DF2

description: early-to-mid log phase cultures  grown on 3mM dibenzofuran at 30 C using defined mineral DSMZ medium 457 (Brunner medium) (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, http://www.dsmz.de/).

source_name: RW1, 3mM DF, rep 2


title: 5'-end sequencing after Syn9 infection of WH8103 at 2h NO TAP. [WH8109_inf_II_2h_race_NOTAP]


title: ERSrcTAM04hr_rna


title: 5'-end sequencing after Syn9 infection of WH8103 at 1h NO TAP. [WH8109_inf_II_1h_race_NOTAP]


title: 5'-end sequencing after Syn9 infection of WH8103 at 0.5h NO TAP. [WH8109_inf_II_0.5h_race_NOTAP]


title: ERSrcTAM01hr_rna


title: DD3

description: early-to-mid log phase cultures  grown on 3mM dibenzo-p-dioxin at 30 C using defined mineral DSMZ medium 457 (Brunner medium) (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, http://www.dsmz.de/).

source_name: RW1, 3mM DD, rep 3


title: DF1

source_name: RW1, 3mM DF, rep 1

value: 3mM dibenzofuran at 30 C using defined mineral DSMZ medium 457


title: DF3

source_name: RW1, 3mM DF, rep 3


title: ERSrcEtOH24hr_rna


title: 5'-end sequencing after Syn9 infection of WH8103 at 1h TAP treated. [WH8109_inf_II_1h_race_TAP]


title: 5'-end sequencing after Syn9 infection of WH8102 at2h TAP treated. [WH8102_inf_III_2h_race_TAP]

description: Synechococcus sp. strain WH8102 infected with theT4-like myovirus Syn9

organism: Parasynechococcus marenigrum WH 8102

source_name: Synechococcus sp. strain WH8102  infected by Syn9


title: DD2

source_name: RW1, 3mM DD, rep 2

value: 3mM dibenzo-p-dioxin at 30 C using defined mineral DSMZ medium 457


title: Whole transcriptome at 120 min after Syn9 infection of WH8109 [WH8109_inf_2h_II_whole_transcr]


title: ERSrcEtOH01hr_rna


title: 5'-end sequencing after Syn9 infection of WH8102 at 1h TAP treated. [WH8102_inf_III_1h_race_TAP]


title: ERSrcEtOH04hr_rna


title: Whole transcriptome at 120 min after Syn9 infection of WH8109 [WH8109_inf_2h_III_whole_transcr]


title: Whole transcriptome at 60 min after Syn9 infection of WH8109 [WH8109_inf_1h_II_whole_transcr]


title: 5'-end sequencing after Syn9 infection of WH8102 at 0.5h TAP treated. [WH8102_inf_III_0.5h_race_TAP]


title: Whole transcriptome at 60 min after Syn9 infection of WH8109 [WH8109_inf_1h_III_whole_transcr]


title: 5'-end sequencing after Syn9 infection of WH8102 at 2h TAP treated. [WH8102_inf_II_2h_race_TAP]


title: 5'-end sequencing after Syn9 infection of WH8102 at 2h NO TAP. [WH8102_inf_II_2h_race_NOTAP]


title: DD1

source_name: RW1, 3mM DD, rep 1


title: 5'-end sequencing after Syn9 infection of WH8102 at 1h TAP treated. [WH8102_inf_II_1h_race_TAP]


title: Whole transcriptome at 30 min after Syn9 infection of WH8109 [WH8109_inf_0.5h_III_whole_transcr]


title: 5'-end sequencing after Syn9 infection of WH8102 at 1h NO TAP. [WH8102_inf_II_1h_race_NOTAP]


title: Whole transcriptome at 5 min after Syn9 infection of WH8109 [WH8109_inf_0h_II_whole_transcr]


title: Whole transcriptome at 30 min after Syn9 infection of WH8109 [WH8109_inf_0.5h_II_whole_transcr]


title: Whole transcriptome at 5 min after Syn9 infection of WH8109 [WH8109_inf_0h_III_whole_transcr]


title: 5'-end sequencing after Syn9 infection of WH8102 at 0.5h TAP treated. [WH8102_inf_II_0.5h_race_TAP]


title: 664a_input_2

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

data_processing:
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2 with default setting
Data were filtered using samtools to keep only uniquely mapped reads
peaks were called using MACS2 version 2.1 with p value threshold at 0.01
Genome_build: Zv9
Supplementary_files_format_and_content: bedGraph file with score representing the read count within the corresponding region

organism: Danio rerio

source_name: Neural progenitor cells

growth_protocol: ChIP assays were performed in duplicate using cells derived from ~100 zebrafish heads at 48 hpf essentially as previously described.

extract_protocol:
Sonication was performed using on a Bioruptor instrument (Diagenode) using 7 cycles of 30s “ON”, 30s “OFF” on the “High” setting.
ChIP was performed using the Millipore EZ-ChIP kit according to the manufacturer protocol. ChIP DNA was sequenced by Illumina Hi-Seq sequencer with multiplex.
An anti-H3K9me2 (AbCam) and an isotype control (AbCam) antibodies were used at 2μg per sample.

treatment_protocol: Head region cells were cross-linked using 1% formaldehyde for 15min and quenched by treating with 0.125M glycine for 10min.

value: cells derived from retina and midbrain cell populations

tag: chip antibody

value: AB

tag: genotype/variation

value: 664a mutant


title: Whole transcriptome at 120 min after Syn9 infection of WH8102 [WH8102_inf_2h_III_whole_transcr]

value: Infected by Syn9

value: Not Applicable


title: Whole transcriptome at 120 min after Syn9 infection of WH8102 [WH8102_inf_2h_II_whole_transcr]


title: WT_H3K9me2_2

value: anti-H3K9me2 (AbCam)

value: WT


title: 5'-end sequencing after Syn9 infection of WH8102 at 0.5h NO TAP. [WH8102_inf_II_0.5h_race_NOTAP]


title: 664a_H3K9me2_1


title: Whole transcriptome at 60 min after Syn9 infection of WH8102 [WH8102_inf_1h_III_whole_transcr]


title: MIN6 Nuc2

first: Keren

last: Bahar-Halpern

address: Herzl St 234

institute: Weizmann Institute

data_processing:
Mapping the reads to the genome using TopHat
Quantification of RPKMs using CuffDiff and a filtered (with only last 500bp from the 3’ end of the gene) gtf file of the mm10 ensemble
Supplementary_files_format_and_content: RPKM

source_name: total MIN6 cytoplasmic mRNA

growth_protocol: MIN6 cells were maintained and expanded in DMEM media (Biological Industries) supplemented with 15% fetal bovine serum (Biological Industries), 1% of Penicillin-Streptomycin (Biological Industries), 1% L-Glutamine (Biological Industries) and 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Isolation of nuclear and cytoplasmic liver mRNA was performed according to the Nascent-SEQ protocol (Menet et al., 2012) except for minor modifications. In order to isolate cytoplasmic mRNA the supernatant was collected following nuclei isolation by sucrose gradient. For isolation of nuclear mRNA the supernatant was collected following chromatin isolation. 1/50 volumes of 5M Nacl and 2.5 volumes of 100% EtOH were added to the supernatants collected, and the mixture was incubated at -200C for 1 hour and then centrifuged for 20 minutes at full speed. The pellet was resuspended in 0.5 ml 0.5% SDS buffer (0.5% SDS, 0.1M NaCl, 1mM EDTA, 10mM Tris-HCl). Similar volume of acid phenol:chloroform (Ambion AM9722) mixture was added. The mixture was then vortexed and centrifuged at full speed for 5 minutes at RT. The aqueous phase was transferred to a new tube and 1 ml of 0.5% SDS buffer was added to the phenol phase for re-extraction. The two aqueous phases were combined and re-extracted with acid phenol:chloroform. The RNA from the aqueous phase was then isolated using standard EtOH precipitation.
For isolation of nuclear and cytoplasmic RNA from MIN6, the cells (~2x106) were first trypsinized and washed with cold PBS. Cell pellet was then treated with 175 µl RLN buffer (Tris pH8.0 50mM, NaCl 140mM, MgCl2 1.5mM, NP-40 0.15mM, EDTA 10mM, DTT 1mM, RNase inhibitor 10U/ml) and incubated for 5 minutes on ice. Lysate was centrifuged at 300g for 5 minutes in a cold centrifuge. The supernatant (cytoplasmic fraction) was separated and the pellet was resuspended with same volume of RLN buffer and immediately centrifuged at 500g for 1 minute. Pellet was resuspended in 1 ml S1 buffer (sucrose 250mM, MgCl2 10mM, RNase inhibitor 10U/ml), layered over 3 ml of S3 buffer (sucrose 880mM, MgCl2 10mM, RNase inhibitor 10U/ml) and centrifuged for 10 minutes in cold centrifuge at 2800g. RNA from the pellet (nuclear fraction) and the cytoplasmic fraction was isolated using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Libraries were prepared with Illumina TrueSeq kits and sequenced on Illumina HiSeq.


title: MIN6 Cyto1

source_name: total MIN6 nuclear mRNA


title: MIN6 Cyto2


title: WT_IgG_2

value: isotype control (AbCam)


title: MIN6 Nuc1


title: Whole transcriptome at 60 min after Syn9 infection of WH8102 [WH8102_inf_1h_II_whole_transcr]


title: Whole transcriptome at 30 min after Syn9 infection of WH8102 [WH8102_inf_0.5h_III_whole_transcr]


title: Liver Cyto2

source_name: total liver cytoplasmic mRNA

tag: tissue

value: Liver


title: ERSrcTAM00hr_rna

source_name: Breast epithelial cell


title: Whole transcriptome at 30 min after Syn9 infection of WH8102 [WH8102_inf_0.5h_II_whole_transcr]


title: WT_input_2


title: 664a_input_1


title: Liver Cyto1


title: Whole transcriptome at 5 min after Syn9 infection of WH8102 [WH8102_inf_0h_III_whole_transcr]


title: 664b_H3K9me2_2

value: 664b mutant


title: Liver Nuc2

source_name: total liver nuclear mRNA


title: 664b_input_2


title: WT_input_1


title: 664a_H3K9me2_2


title: Liver Nuc1


title: 664b_input_1


title: WT_IgG_1


title: WT_H3K9me2_1


title: X. laevis oviduct input replicate 1

status: Public on Nov 12 2015

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
DIP-Seq
All reads were trimmed using sickle and the fastx toolkit (removing bases with <Q20).
M. musculus reads were mapped to mm9 with variations as in publication using bwa 0.6.2
X. laevis reads were mapped to LAEVIS7.1 with variaitions as in publication using bwa 0.6.2
E. coli reads were mapped to the K12 genome (NCBI Reference NC_000913.2) using bwa 0.6.2
bigwigs were generated by extending the reads to 300 bases and binned to 50 bases.
Genome_build: E.coli NC_000913.2; mm9;
X. laevis 7.1 at ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla7.1/
Supplementary_files_format_and_content: bigwigs - binned tracks for visualisation

organism: Xenopus laevis

source_name: X. laevis oviduct input

growth_protocol: Freshly isolated tissue was used

extract_protocol:
genomic DNA was extracted using Phenol and Quiagen Dneasy Blood and Tissue Kit
Libraries were prepared accroding to Ford et al (BMC Res. Notes 7, 312, 2014). 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 12-18 cycles and library fragments of 250-350 bp ) were band isolated with Agencourt beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: pigmented, from eNASCO

tag: gender

value: female

tag: developmental stage

value: adult

value: oviduct


title: X. laevis oviduct input replicate 2


title: X. laevis testes IP** replicate 2

source_name: X. laevis testes IP**

value: male

value: testes

value: m6A (N6-methyladenosine) mouse monoclonal, purified IgG

tag: antibody vendor

value: Synaptic Systems GmbH

tag: cat. #


title: X. laevis fat input replicate 2

source_name: X. laevis fat input

value: fat


title: X. laevis fat input replicate 1


title: X. laevis fat IP replicate 2

source_name: X. laevis fat IP

value: m6A (N6-methyladenosine)


title: 1170Glc3

city: Gainesville

first: Lin

last: Zeng

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description:
enriched mRNA
repeat 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: 1009Glc-Scr-Fru Limma 1e-3.xlsx - diifferential expression data generated at http://vicbioinformatics.com/degust/index.html, using Limma
Supplementary_files_format_and_content: counts

organism: Streptococcus mutans

source_name: Bacterial batch culture

growth_protocol: Bacterial cells used for extraction of RNA were grown in tryptone (3%), yeast extract (0.1%) medium supplemented with 0.5% glucose, fructose or sucrose. Bacterial cultures were incubated aerobically without agitation in the presence of 5% CO2 at 37°C until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from the enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

tag: parental strain

value: gtfABCD ftf fruA fruBM1stop scrA::km

tag: media

value: Tryptone(3%)-yeast(0.1%), 0.5% glucose


title: 1170Glc2

description:
enriched mRNA
repeat 2


title: X. laevis fat IP replicate 1

tag: strain


title: X. laevis oviduct IP replicate 1

source_name: X. laevis oviduct IP

tag: antibody


title: 1170Glc1

description:
enriched mRNA
repeat 1


title: 1009Scr3

description:
enriched mRNA
repeat 3 of sucrose

value: gtfA:em gtfBCD ftf fruAB:km

value: Tryptone(3%)-yeast(0.1%), 0.5% sucrose


title: X. laevis testes IP* replicate 2

source_name: X. laevis testes IP*


title: X. laevis oviduct IP replicate 2


title: X. laevis testes IP** replicate 1


title: 664b_H3K9me2_1

value: cells derived from retina and midbrain cell populations

value: anti-H3K9me2 (AbCam)

value: AB


title: X. laevis testes IP replicate 2

source_name: X. laevis testes IP

value: pigmented, from eNASCO

value: m6A (N6-methyladenosine) rabbit polyclonal, affinity purified


title: X. laevis testes IP* replicate 1

value: adult


title: 1009Scr1

description:
enriched mRNA
repeat 1 of sucrose


title: Whole transcriptome at 5 min after Syn9 infection of WH8102 [WH8102_inf_0h_II_whole_transcr]

source_name: Synechococcus sp. strain WH8102  infected by Syn9

tag: infection

value: Infected by Syn9

tag: time

tag: replicate

tag: tap treated

value: Not Applicable


title: X. laevis testes IP IgG replicate 1

source_name: X. laevis testes IP IgG

value: male

value: testes

value: Rabbit IgG, polyclonal - Isotype Control (ChIP Grade)

value: Abcam


title: 1009Fru1

description:
enriched mRNA
repeat 1 of fructose

tag: genotype

value: Tryptone(3%)-yeast(0.1%), 0.5% fructose


title: 1009Fru2

description:
enriched mRNA
repeat 2 of fructose


title: 1009Fru3

description:
enriched mRNA
repeat 3 of fructose


title: X. laevis testes IP IgG replicate 2


title: X. laevis testes IP replicate 1

value: Synaptic Systems GmbH


title: 1009Glc2

description:
enriched mRNA
repeat 2 of glucose

value: Tryptone(3%)-yeast(0.1%), 0.5% glucose


title: X. laevis testes input replicate 2

source_name: X. laevis testes input


title: 1009Glc3

description:
enriched mRNA
repeat 3 of glucose

value: gtfA:em gtfBCD ftf fruAB:km


title: X. laevis testes input replicate 1


title: 1009Glc1

description:
enriched mRNA
repeat 1 of glucose


title: 5mC-WT-2

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

description: 5mC Profiling (MeDIP-seq)

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Genome_build: mm9
Supplementary_files_format_and_content: 5hmc/5mc peaks in bed file; RNAseq gene expression value in cufflink fpkm_tracking file format

source_name: LK Cells

extract_protocol:
DNA was extracted by phenol/choloroform method.
RNA was isolated using Trizol.
5hmC enrichment was performed using a previously described procedure with an improved selective chemical labeling method (Song et al, Nature Biotechnology, 2011). DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25-50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. [Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., Wang, J., Zhang, L., Looney, T.J., Zhang, B., Godley, L.A., Hicks, L.M., Lahn, B.T., Jin, P., and He, C. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature Biotechnology, 29(1): 68-72.]
Enriched DNA from MeDIP were subjected to library construction using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina according the manufacturer’s protocol.
RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol.

value: WT

tag: cell type

value: LK


title: ChIPSeq_H3K9me2_E8.5 WT-Rep2

city: Illkirch

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

description: ChIPSeq_H3K9m2_E8.5_WT_noDup_25_ext300.bw

data_processing:
Because of the broad distribution of H3K9me2, we merged the Fastq files from the three experiments.
Raw reads were aligned to the mm10 genome with bowtie2 v2.2.4 using default parameters.
We flagged PCR duplicates with Picard MarkDuplicates v1.136 and generated density tracks in wig format with igvtools count v2.3.3.2 using the parameters -w 25 -e 300 --minMapQuality 30.
Genome_build: mm10
Supplementary_files_format_and_content: We provide browser tracks in bigwig format.

source_name: E8.5 whole embryos

extract_protocol:
8 embryos collected at E8.5 were dissociated in Trypsin 0.25% EDTA 1mM for 5 min at RT, washed in PBS and cross-linked with 1 % formaldehyde for 10 min at RT. After sonication with a Bioruptor waterbath sonicator (Diagenode), we performed ChIP with the LowCell ChIP kit (Diagenode).
ChIP-Seq libraries were prepared with the NEXTflex ChIP-Seq Kit (Bioo Scientific) according to the manufacturer’s instructions.

value: embryo

tag: age

value: wild type

tag: chip antibody

value: anti-H3K9me2 (Abcam ab1220)

value: whole embryo


title: ChIPSeq_Input_E8.5 WT-Rep3

description: ChIPSeq_Input_E8.5_WT_noDup_25_ext300.bw

tag: tissue


title: ChIPSeq_H3K9me2_E8.5 WT-Rep3


title: ChIPSeq_Input_E8.5 WT-Rep2


title: 1009Scr2

description:
enriched mRNA
repeat 2 of sucrose

value: Tryptone(3%)-yeast(0.1%), 0.5% sucrose


title: 5mC-Tet2KO-2

description: 5mC Profiling (MeDIP-seq)

tag: genotype/variation

value: Tet2 KO


title: RNA-Seq_E8.5 G9aKO-Rep2

data_processing:
We aligned reads to the mouse mm10 genome with TopHat2 v2.0.13 using default parameters plus --no-coverage-search --library-type fr-firststrand using a transcriptome index built from RefSeq mm10.
We generated browser tracks in bigwig format with bam2wig.py from the RSeQC package v2.4 using the parameters -u -t 5000000000.
We calculated raw read counts in genes with HTseq-count v0.6.0 using the parameters –t exon –s no and a RefSeq mm10 annotation gtf file.
We used DESeq2 v1.4.5 to identify differentially expressed genes between WT and KO samples using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: We provide browser tracks of gene expression in bigwig format.

extract_protocol:
Total RNA was extracted from the embryos with the RNeasy Protect Mini Kit (Qiagen).
RNA-Seq libraries were prepared with the Ovation RNA-Seq System V2 (NuGEN) according to the manufacturer’s instructions.

tag: developmental stage

tag: gender


title: 5mC-WT-1

description: 5mC Profiling (MeDIP-seq)


title: Cyclopamine Intestine 2

data_processing:
HiSeq Control Software 2.2.68
Reads were mapped to mm9 using TopHat v2.0.13 (Trapnell et al., 2009)
Differential expression of RNA samples was determined using DESeq (Anders and Huber, 2010)
Genome_build: mm9
Supplementary_files_format_and_content: xls file contains read counts per sample and fold change between conditions

source_name: Whole Intestine

extract_protocol:
Total RNA was collected for each sample using the Life Technologies mirVanaTM miRNA Isolation Kit following the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: Cyclopamine

value: Whole Intestine


title: RNA-Seq_E8.5 G9aKO-Rep1

value: male


title: Cyclopmaine Intestine 3


title: Cyclopamine Intestine 1


title: 5mC-DKO-2

description: 5mC Profiling (MeDIP-seq)

value: DKO


title: ChIPSeq_H3K9me2_E8.5 WT-Rep1


title: RNA-Seq_E8.5 WT-Rep2

value: female


title: Intestinal Mesenchyme 3

source_name: Mesenchyme tissue

value: Mesenchyme tissue


title: 5mC-DKO-1

description: 5mC Profiling (MeDIP-seq)


title: Intestinal Mesenchyme 1


title: Intestinal Mesenchyme 2


title: RNA-Seq_E8.5 WT-Rep1


title: Intestinal Epithelium 3

source_name: Epithelial tissue

value: Epithelial tissue


title: RRBS_E8.5 G9aKO-Rep3

data_processing:
We cleaned sequencing reads with Trim Galore v0.2.1 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired.
We aligned reads to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: We provide igv files containing methylation scores calculated for all CGs with at least 8x sequencing depth.

extract_protocol:
Genomic DNA was extracted by proteinase K digestion followed by phenol/chloroform extraction.
We prepared RRBS libraries using a published protocol (Gu et al., Nat Protoc 6:468-81, 2011) with some modifications. Briefly, we digested 70 ng of genomic DNA 5 hours with MspI (Thermo Scientific), followed by end-repair and A-tailing (Klenow fragment, Thermo Scientific) and ligation to methylated adapters (T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR.


title: Intestinal Epithelium 2


title: 5hmC-WT-2

description: 5hmC Profiling (hMe-Seal)

data_processing:
library strategy: 5hmC capture (hMe-Seal)
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Genome_build: mm9
Supplementary_files_format_and_content: 5hmc/5mc peaks in bed file; RNAseq gene expression value in cufflink fpkm_tracking file format

tag: strategy

value: 5hmC capture


title: 5hmC-WT-1

description: 5hmC Profiling (hMe-Seal)


title: Intestinal Epithelium 1


title: ChIPSeq_Input_E8.5 WT-Rep1


title: RRBS_E8.5 G9aKO-Rep2


title: 5hmC-DKO-2

description: 5hmC Profiling (hMe-Seal)


title: 5hmC-DKO-1

description: 5hmC Profiling (hMe-Seal)


title: RRBS_E8.5 WT-Rep1


title: 5hmC-Tet2KO-1

description: 5hmC Profiling (hMe-Seal)


title: RRBS_E8.5 WT-Rep4


title: RRBS_E8.5 G9aKO-Rep1


title: RRBS_TT2 ESCs G9aKO+G9a

source_name: ES cells

value: C57BL/6xCBA F1

value: ES cells


title: 5hmC-Tet2KO-2

description: 5hmC Profiling (hMe-Seal)

value: LK


title: RRBS_E8.5 WT-Rep2

value: embryo


title: RNAseq-WT-2-B-ALL

description: RNA-seq

source_name: Control Cells

value: WT

value: non tumor cells (control for B-ALL cells)


title: RNAseq-Tet2KO-B-ALL-2

description: RNA-seq

source_name: B-ALL

value: B-ALL


title: RNAseq-WT-1-B-ALL

description: RNA-seq


title: RRBS_TT2 ESCs G9aKO


title: RRBS_TT2 ESCs WT

value: wild type


title: RRBS_E8.5 WT-Rep3

value: whole embryo


title: RNAseq-Tet2KO-B-ALL-1

description: RNA-seq

value: Tet2 KO


title: RNAseq-DKO-B-ALL-3

description: RNA-seq


title: RNAseq-DKO-B-ALL-2

description: RNA-seq


title: E. coli Dam+ IP

organism: Escherichia coli

source_name: E. coli Dam+ IP

tag: strain info

value: Dam+ bacteria

value: m6A (N6-methyladenosine)

tag: antibody vendor

value: Synaptic Systems GmbH

tag: cat. #


title: RNAseq-WT-2

description: RNA-seq

tag: strain


title: RNAseq-Tet2KO-Preleukemic-1

description: RNA-seq

source_name: Preleukemic Cells

value: Preleukemic


title: RNAseq-DKO-B-ALL-1

description: RNA-seq

value: DKO


title: RNAseq-Tet2KO-Preleukemic-2

description: RNA-seq


title: E. coli Dam+ input

source_name: E. coli Dam+ input


title: RNAseq-WT-1

description: RNA-seq


title: RNAseq-Tet2KO-LK-1

description: RNA-seq


title: RNAseq-DKO-LK-2

description: RNA-seq


title: RNAseq-DKO-LK-1

description: RNA-seq


title: E. coli Dam- input

source_name: E. coli Dam- input

value: Dam- bacteria