title: ape1l-1_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

source_name: Seedlings

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

value: ape1l-1 mutant

tag: tissue

value: whole seedlings


title: arp-1_MethylC-Seq

status: Public on Nov 21 2014

type: SRA

country: USA

description: treated with bisulfite

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

tag: genotype

value: arp-1 mutant


title: Emoy2_0ddpi_biorep2_lane1_lib1

city: Norwich

first: Ghanasyam

last: Rallapalli

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

description: tag-seq; Sample 5

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded. Read qualities are converted from Illumina fastq to sanger fastq format
EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
Quality-filtered libraries were aligned to the combined genome of Arabidopsis TAIR10 and Hpa Emoy2 v8.3 [7] or Waco9-SNVs-corrected v8.3 using Bowtie version 0.12.8, and reads with up to 10 reportable alignments were selected. Unaligned reads from previous steps were used to align to transcript sequences of Arabidopsis Col-0 (ftp://ftp.Arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214_updated) using Bowtie version 0.12.8. Linking of each sequenced read (Tag) to gene was carried out using the following considerations: reads aligning to each gene limits were assigned to that gene; reads aligning to genes with overlapping gene limits were split equally between them; and reads aligning to more than 10 genes were discarded. Differential expression analysis was performed using the R statistical language version 2.11.1 with the Bioconductor package, edgeR version 1.6.15 with the exact negative binomial test using tagwise dispersions.
Genome_build: Arabidopsis TAIR10 and Hpa Emoy2 v8.3
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

molecule: total RNA

source_name: aerial shoots_Hpa Emoy2_0 dpi

growth_protocol: Arabidopsis plants were grown at 22°C and 60% humidity under a 10-h photoperiod and a 14-h dark period in environmentally controlled growth cabinets.

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.
[EXPRSS]Typically 3 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library
Each biological replicate set of samples were sequenced as one batch and each batch was sequenced in 4 individual Illumina flowcell lanes. Four sequecing lanes of each three biological repliates resulted in 12 sequencing libraries. 'The unassigned read_*' samples are for 'nobarcode_biorep[x]_lanne[x].fq'  file containing sequences unassigned to any barcode from respective bioreplicate sequencing lanes.

treatment_protocol: Three week old arabidopsis plants were spray-inoculated to saturation with a spore suspension of 5 x 10^4 conidiospores/ml. Water sprayed and hpa infected plants were harvested at 1, 3 and 5 days post-inoculation (dpi). Tissue collected from intact plants and conidiospores of Emoy2 and Waco9 were considered as 0 dpi time points for H2O, Emoy2 and Waco9 treatment, respectively.

tag: ecotype

value: Columbia (Col-0)

value: Wild type

value: aerial shoots

tag: age

value: 3 weeks

tag: inoculated with

value: Hyaloperonospora arabidopsidis (Hpa) Emoy2

tag: time point

value: 0 dpi

tag: barcode sequence

value: GCTCT

tag: barcode position

value: 5' end of the read


title: Emoy2_0ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 7


title: ELAV 6-8h rep1

city: Berkeley

first: Wei

last: Zhang

address: University of California at Berkeley

institute: UC Berkeley

data_processing:
Standard FASTQ files were outputed by CASAVA_v1.8.0
All sequencing reads were aligned to the Drosophila melanogaster reference genome (UCSC dm3 release) using Bowtie version 0.12.7 with parameters -k 1 -m 1 -n 2 --best --strata.
We used the model-based analysis of ChIP-Seq (MACS) peak-finding algorithm version 1.4.1 with default parameters to identify the regions of ELAV ChIP-Seq enrichment over input DNA.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated using HOMER software; Scores represent reads per 10 million total reads.

organism: Drosophila melanogaster

source_name: whole embryos

growth_protocol: Drosophila melanogaster yw flies were reared in standard cornmeal food at 25C, embryos were collected on apple juice plates.

extract_protocol:
Whole embryo nuclei extracts were sonicated and ChIP assays were done using a mix of two anti-ELAV antibodies raised against the entire ELAV protein: mouse anti-ELAV-9F8A9 (DSHB) and rat anti-ELAV-7E8A10 (DSHB).
ChIP-seq libraries were constructed with the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina using NEBNext Multiplex Oligos.

tag: hours after fertilization

tag: chip antibody

value: ELAV

tag: chip antibody vendor

value: Developmental Studies Hybridoma Bank (DSHB)

tag: chip catalog number

value: mouse anti-ELAV-9F8A9

value: rat anti-ELAV-7E8A10


title: Ws_WT_MethylC-Seq

description: treated with bisulfite

value: WT


title: Emoy2_1ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 15

source_name: aerial shoots_Hpa Emoy2_1 dpi

value: 1 dpi

value: GTACT


title: zdp-1_MethylC-Seq

description: treated with bisulfite

extract_protocol: Libraries were prepared according to a published protocol (Lister et al., 2008). Briefly, Genomic DNA was extracted from 14-d-old seedlings. Sonicated DNA was end-repaired by using End Repair Enzyme Mix (NEB, #E6041A). The blunt end DNA were treated with Klenow fragment (NEB, #E6044A) 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. Unmethylated cytosine residues were converted to uracil by EpiTect bisulfite Kit (Qiagen, 59104) after adaptor ligation. After bisufite treated DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 250~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols in KAUST(King Abdullah University of Science and Technology)

value: zdp-1 mutant

value: whole seedlings


title: Emoy2_0ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 4

value: Columbia (Col-0)


title: Emoy2_0ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 2

value: Wild type


title: Emoy2_0ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 3

value: aerial shoots


title: Emoy2_0ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 1

value: 3 weeks


title: Exp2_slh1_19C_24h

description:
Barcode sequence: TCGT
Barcode position: 5' end of the read

data_processing:
library strategy: Tag-Seq
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded. Read qualities are converted from Illumina fastq to sanger fastq format
EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
Quality filtered library was aligned to the Arabidopsis thaliana Col-0 genome sequences (TAIR10) using Bowtie version 0.12.8 (-a -m 10 --best --strata) and selected reads with up to 10 reportable alignments. Unaligned reads from previous step are used to align to transcript sequences of Arabidopsis using Novoalign V2.08.03 (-s 1 -r A 100). Tag to gene association is carried out using following considerations. Reads aligning in sense orientation with in each gene limits are assigned to that gene. A read aligning to all splice variant of a gene is counted once, and the reads uniquely aligning to various splice variants of a gene are pooled. Reads aligning to genes with overlapping gene limits are split equally between them. Reads aligning to more than 10 genes are discarded. Reads aligning to up to 10 genes are split equally between them. Reads aligning on the anti-sense strand of any gene are tested for if the read falls within 500bp from 3’ end of another gene in sense direction. Otherwise reads are assigned as antisense tags for the specific gene. The tag assignment process was implemented in perl and scripts are available on request. Differential expression analysis was performed using the R statistical language version 2.15.3 with the Bioconductor package edgeR version 2.6.12 with the exact negative binomial test using tagwise dispersions.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

growth_protocol: Arabidopsis No-0 and slh1 plants were grown for 4 weeks at 28°C under short-day conditions (10 hr light/14 hr dark cycles).

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.
EXPRSS: Typically 5 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity - 5, Duty cycle - 20%, Cycles/Burst - 200, Duration - 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library

treatment_protocol: Four weeks old plants were transferred to 19°C growth chamber at the beginning of the light cycle and leaves were harvested at 0 h, 9 h, 12 h, 16 h and 24 h after transfer

value: Nossen (No-0)

tag: genotype/variation

value: 4 weeks old

tag: harvested at

value: 24 h at 19°C

value: Leaf


title: unassigned reads

description: All 16 samples submitted for this study were sequenced in one lane of Illumina GAIIx  and the "No-0_slh1_tempshift_nobarcode.fq" ('unassigned reads' sample raw data) contains unassigned sequence reads to any barcode, once sample de-multiplexing has been carried out based on barcode.

source_name: sequence information of unassigned reads to any barcode from the sequencing run


title: Exp2_slh1_19C_16h

description:
Barcode sequence: AGCT
Barcode position: 5' end of the read

value: 16 h at 19°C


title: Exp2_slh1_19C_09h

description:
Barcode sequence: AACAGAGT
Barcode position: 5' end of the read

value: 09 h at 19°C


title: Exp2_slh1_19C_12h

description:
Barcode sequence: TGTGCGAT
Barcode position: 5' end of the read

value: 12 h at 19°C


title: Exp2_slh1_28C

description:
Barcode sequence: TTGCGCT
Barcode position: 5' end of the read

value: 00 h at 19°C


title: Exp2_No-0_19C_16h

description:
Barcode sequence: CAGAGT
Barcode position: 5' end of the read


title: Exp2_No-0_19C_12h

description:
Barcode sequence: GACACT
Barcode position: 5' end of the read


title: Exp2_No-0_19C_24h

description:
Barcode sequence: CATACGT
Barcode position: 5' end of the read


title: Exp2_No-0_19C_09h

description:
Barcode sequence: CGAGAT
Barcode position: 5' end of the read


title: Exp2_No-0_28C

description:
Barcode sequence: TTGGAT
Barcode position: 5' end of the read


title: Emoy2_0ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 8

value: Hyaloperonospora arabidopsidis (Hpa) Emoy2

value: 0 dpi

value: GCTCT

value: 5' end of the read


title: Emoy2_0ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 6


title: Waco9_1ddpi_biorep1_lane4_lib2

description: tag-seq; Sample 152

source_name: aerial shoots_Hpa Waco9_1 dpi

value: Hyaloperonospora arabidopsidis (Hpa) Waco9

value: 1 dpi

value: TGTGCGAT


title: Exp1_slh1_19C_09h

description:
Barcode sequence: ACTGT
Barcode position: 5' end of the read


title: Exp1_slh1_28C

description:
Barcode sequence: GTACT
Barcode position: 5' end of the read


title: Exp1_No-0_19C_24h

description:
Barcode sequence: GCTCT
Barcode position: 5' end of the read

value: Wild type


title: Exp1_No-0_19C_09h

description:
Barcode sequence: GCAT
Barcode position: 5' end of the read


title: Exp1_No-0_28C

description:
Barcode sequence: CGGT
Barcode position: 5' end of the read


title: Rep3_rrs1-1_PopP2-2hr.fq

description:
Tag-seq
Barcode sequence: ACTGT
Barcode position: 5' end of the read

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded. Read qualities are converted from Illumina fastq to sanger fastq format
EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
Quality filtered library was aligned to the Arabidopsis thaliana Col-0 genome sequences (TAIR10) using Bowtie version 0.12.8 (-a -m 10 --best --strata) and selected reads with up to 10 reportable alignments. Unaligned reads from previous step are used to align to transcript sequences of Arabidopsis using Novoalign V2.08.03 (-s 1 -r A 100). Tag to gene association is carried out using following considerations. Reads aligning in sense orientation with in each gene limits are assigned to that gene. A read aligning to all splice variant of a gene is counted once, and the reads uniquely aligning to various splice variants of a gene are pooled. Reads aligning to genes with overlapping gene limits are split equally between them. Reads aligning to more than 10 genes are discarded. Reads aligning to up to 10 genes are split equally between them. Reads aligning on the anti-sense strand of any gene are tested for if the read falls within 500bp from 3’ end of another gene in sense direction. Otherwise reads are assigned as antisense tags for the specific gene. The tag assignment process was implemented in perl and scripts are available on request. Differential expression analysis was performed using the R statistical language version 2.15.3 with the Bioconductor package edgeR version 2.6.12 with the exact negative binomial test using tagwise dispersions.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

source_name: Leaf discs

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown under short-day conditions (10 hr light/14 hr dark cycles).

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.
Typically 5 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library

treatment_protocol: Leaves from 5-week-old Ws-2 or rrs1-1 plants were infiltrated with Pf0-1 carrying either PopP2 or PopP2C321A at density of 0.2 OD600. Leaf discs from centre of each half of leaf were harvested at 2, 4, 6 and 8 hpi.

value: Wassilewskija-2 (Ws-2)

value: 5 weeks old

tag: treatment

value: Pf0-1 PopP2


title: Rep3_rrs1-1_PopP2-6hr.fq

description:
Tag-seq
Barcode sequence: CATACGT
Barcode position: 5' end of the read


title: Rep3_rrs1-1_NT-0hr.fq

description:
Tag-seq
Barcode sequence: GCAT
Barcode position: 5' end of the read

value: No treatment (NT)


title: Rep3_rrs1-1_PopP2-4hr.fq

description:
Tag-seq
Barcode sequence: CGAGAT
Barcode position: 5' end of the read

value: Leaf


title: Unassigned Reads

description:
Replicate 1 samples were sequenced in one lane. Rep1_nobarcode-in-sequence.fq is the file containing sequences unassigned to any barcode
Replicate 2 samples were sequenced in one lane. Rep2_nobarcode-in-sequence.fq is the file containing sequences unassigned to any barcode
Replicate 3 samples were sequenced in one lane. Rep3_nobarcode-in-sequence.fq is the file containing sequences unassigned to any barcode


title: Rep3_Ws-2_C321A-8hr.fq

description:
Tag-seq
Barcode sequence: AACAGAGT
Barcode position: 5' end of the read

value: Pf0-1 PopP2C321A


title: Rep3_rrs1-1_PopP2-8hr.fq

description:
Tag-seq
Barcode sequence: TGTGCGAT
Barcode position: 5' end of the read


title: Rep3_Ws-2_C321A-6hr.fq

description:
Tag-seq
Barcode sequence: CAGAGT
Barcode position: 5' end of the read


title: Rep3_Ws-2_C321A-4hr.fq

description:
Tag-seq
Barcode sequence: TTGGAT
Barcode position: 5' end of the read


title: Rep3_Ws-2_C321A-2hr.fq

description:
Tag-seq
Barcode sequence: GTACT
Barcode position: 5' end of the read


title: Emoy2_5ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 61

source_name: aerial shoots_Hpa Emoy2_5 dpi

value: Columbia (Col-0)

value: aerial shoots

value: 3 weeks

value: 5 dpi

value: ATCCT


title: Exp1_slh1_19C_24h

description:
Barcode sequence: ATCCT
Barcode position: 5' end of the read

value: Nossen (No-0)

value: 4 weeks old

value: 24 h at 19°C


title: Rep3_Ws-2_PopP2-2hr.fq

description:
Tag-seq
Barcode sequence: GCTCT
Barcode position: 5' end of the read


title: Genital tubercle 4C Hoxa13

city: Lausanne

first: Nicolas

last: Lonfat

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL - Ecole Polytechnique Fédérale de Lausanne

description: library strategy: 4C

data_processing:
De-multiplexing, mapping and 4C-seq were done through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/).
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 and http://htsstation.epfl.ch/).
4C figures were made using a running mean algorithm with a window size of eleven fragments.
4C-seq was performed as previously described (Noordermeer et al. 2011)
Genome_build: mm9
Supplementary_files_format_and_content: Signal/restriction fragment or smoothed (bedGraph) for each viewpoint

organism: Mus musculus

source_name: 4C E15.5 mouse genital tubercle (GT)

extract_protocol:
Tissue were made single cell by collagenase treatment. Chromatin was crosslinked in the presence of 2% formaldehyde. Cross-linked chromatin was digested with NlaIII, ligated, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.
PCR amplification using primers with included adapter sequences (for Illumina HiSeq) as described before (Noordermeer et al. 2011, Science).

treatment_protocol: 4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science).

value: Genital tubercle

tag: viewpoint


title: Rep3_Ws-2_PopP2-4hr.fq

description:
Tag-seq
Barcode sequence: ATCCT
Barcode position: 5' end of the read


title: HCT116 Input DNA

first: Krassimira

middle: I

last: Botcheva

state: CA

address: One Cyclotron Rd MS977

department: Cell and Molecular Biology

institute: Lawrence Berkeley National Laboratory

description: Input (non-immunoprecipitated chromatin)

data_processing:
Alignment: Sequence reads were mapped using in-house developed software. All reads were mapped at 36 nt length allowing one mismatch.
Peak detection was performed using in-house developed software. Briefly, enriched locations were identified by adapting published methods whereby distinct uniquely mapped reads were used to construct a coverage map at each nucleotide at each genome position, yielding peaks at the enriched locations. These were then filtered by applying statistical confidence tests.
Fragment coverage was calculated by extending reads by 350nt in the appropriate direction. Coverage files are in bedGraph format.
Genome_build: hg18

organism: Homo sapiens

source_name: Input DNA

growth_protocol: HCT116 cells were grown in McCoy's 5A Medium supplemented with 10% fetal bovine serum, at 37oC, in a humidified atmosphere containing 5% CO2.

extract_protocol: ChIP and Input DNA libraries for single end sequencing were prepared with the Illumina ChIP-Seq DNA Sample Prep kit according to the manufacturer’s instructions. DNA was purified using QIAGEN PCR clean up kit, DNA fragments were 3’ A-tailed and ligated to Illumina adapters. Adapter-ligated DNA was purified using Agencourt AMPure kit, and the entire amount of eluted DNA was used for PCR amplification (10-12 cycles). The PCR amplified ChIP and Input libraries were subjected to electrophoresis and fragments with average size ~200-400 bp were recovered using the QIAGEN gel extraction kit. Libraries was quantified on Agilent 2100 Bioanalyzer using the High Sensitivity DNA kit and single end sequencing was performed on Illumina Genome Analyzer 2x.

treatment_protocol: Cultures were treated with 375 μM 5-fluorouracil (SIGMA) for 6 hrs.

tag: cell line

tag: cell type

value: colorectal cancer cell

tag: antibody


title: Rep3_Ws-2_PopP2-8hr.fq

description:
Tag-seq
Barcode sequence: TTGCGCT
Barcode position: 5' end of the read

tag: ecotype

tag: genotype

value: Wild type

tag: tissue


title: Rep3_Ws-2_PopP2-6hr.fq

description:
Tag-seq
Barcode sequence: GACACT
Barcode position: 5' end of the read

value: Wassilewskija-2 (Ws-2)

tag: age


title: Genital tubercle 4C Hoxd13

description: library strategy: 4C


title: HCT116 p53 ChIP-seq

description: Chromatin IP against p53

source_name: p53 ChIP-seq

value: p53-specific DO1


title: GRO-seq Rev-erbA WT Liver ZT10

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

description:
nascent RNA
library strategy: GRO-seq

data_processing:
PolyA tail was trimmed off each sequencing read. Reads longer than 20bp were then mapped to the mouse genome (mm9) using Bowtie v0.12.8 (Langmead et al., 2009) with parameters ‘-n 1 -l 20 -m 1 –f’. Uniquely mapped reads were extended to 150bp in the 5’ to 3’ direction and used for downstream analysis. Bigwig files were generated using HOMER v4.3 (Heinz et al., 2010) and visualized using Integrative Genomics Viewer (Robinson et al., 2011). Enriched eRNA signal was identified using HOMER v4.3 (0.1% FDR).
Genome_build: mm9
Supplementary_files_format_and_content: UCSC genome browser tracks (bigwig files) and ChIP-seq peak calls (bed files) were generated by HOMER.

source_name: liver

extract_protocol:
Mouse liver was harvested at indicated time and washed with cold swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In). Nuclear extract was prepared by dounce homogenization in cold swelling buffer and filtered using the cell strainer (100 µm, BD Biosciences). Lysate was centrifuged at 400g for 10 min, then resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% Igepal) and incubated on ice for 5 min. Nuclei were washed twice with lysis buffer, and resuspended at the concentration of 10 x 10-7 nuclei/ ml in freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA).
The nuclear run-on assay was performed as previously described (Core et al., 2008; Step, 2014; Wang et al., 2011). Synthesis of cDNA from RNA was performed as described previously (Wang et al., 2011). cDNA was denatured at 70°C for 3 min then products from 105-400 nucleotides size were excised and eluted from shredded gel pieces for 4h in TE + 0.1% Tween and precipitated by adding 1 µl of glycogen, 300 mM NaCl and 2 volumes of ethanol and incubated overnight at -20°C. cDNA was resuspended into circularization reaction and circularized with CircLigase (Epicentre) for 1 hour at 60°C, denatured for 10 min at 80°C, and relinearized by adding relinearization mix (25 mM KCl, 500 µM DTT) and APE I (15U; New England Biolabs). Linearized DNA was amplified by PCR using Phusion Hot Start II Kit. The PCR product from 150-305 nucleotides size were eluted from shredded gel pieces and purified using ChIP DNA Clean and Concentrator Kit (Genesee Scientific).

tag: strain

tag: zt

value: GRO-seq


title: Rep3_Ws-2_NT-0hr.fq

description:
Tag-seq
Barcode sequence: CGGT
Barcode position: 5' end of the read

value: 5 weeks old

value: No treatment (NT)


title: GRO-seq Rev-erbA KO Liver ZT10

description:
nascent RNA
library strategy: GRO-seq


title: GRO-seq WT Liver ZT22 replicate

description:
nascent RNA
library strategy: GRO-seq


title: Rep2_rrs1-1_PopP2-6hr.fq

value: Leaf

value: Pf0-1 PopP2


title: Rep2_rrs1-1_NT-0hr.fq


title: Rep2_rrs1-1_PopP2-2hr.fq

description:
Tag-seq
Barcode sequence: ACTGT
Barcode position: 5' end of the read


title: GRO-seq WT Liver ZT10 replicate

description:
nascent RNA
library strategy: GRO-seq


title: Rep2_Ws-2_C321A-8hr.fq

value: Pf0-1 PopP2C321A


title: Rep2_Ws-2_C321A-6hr.fq


title: GRO-seq WT Liver ZT22

description:
nascent RNA
library strategy: GRO-seq


title: Rep2_rrs1-1_PopP2-8hr.fq


title: GRO-seq WT Liver ZT19

description:
nascent RNA
library strategy: GRO-seq


title: Rep2_Ws-2_C321A-4hr.fq


title: Rep2_Ws-2_PopP2-8hr.fq


title: Rep2_Ws-2_C321A-2hr.fq


title: Rep2_Ws-2_PopP2-6hr.fq


title: Rep2_rrs1-1_PopP2-4hr.fq


title: Rep2_Ws-2_PopP2-4hr.fq


title: GRO-seq WT Liver ZT10

description:
nascent RNA
library strategy: GRO-seq


title: GRO-seq WT Liver ZT13

description:
nascent RNA
library strategy: GRO-seq

tag: genome build


title: Rep1_rrs1-1_PopP2-8hr.fq


title: GRO-seq WT Liver ZT7

description:
nascent RNA
library strategy: GRO-seq


title: RORalpha Liver ZT22 ChIP-seq

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie v0.12.8 (Langmead et al., 2009) with parameters with parameters ‘-n 2 -l 34 --best --strata -m 1’. Only one uniquely aligning read per genomic position was kept for further analysis. Aligned reads from biological replicates were pooled together and peak calling was performed with HOMER (Heinz et al., 2010), using previously published liver input controls (Feng et al., 2011).
Genome_build: mm9
Supplementary_files_format_and_content: UCSC genome browser tracks (bigwig files) and ChIP-seq peak calls (bed files) were generated by HOMER.

extract_protocol:
ChIP experiments were performed as previously described (Feng et al., 2011) with minor changes. Mouse liver was harvested, minced and cross-linked in 1% formaldehyde for 20min, followed by quenching with 1/20 volume of 2.5M glycine solution for 5 minutes, and two washes with 1× PBS. Nuclear extracts were prepared by Dounce homogenization in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC). Chromatin fragmentation was performed by sonication in lysis buffer (50mM Tris-HCl pH 8.0, 1%SDS, 10mM EDTA), using the Bioruptor (Diagenode). Proteins were immunoprecipitated in ChIP buffer, and cross-linking was reversed overnight at 65°C in lysis buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS, pH 8), and DNA isolated using phenol/chloroform/isoamyl alcohol.
DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina, using adaptor oligo and primers from Illumina, enzymes from New England Biolabs and PCR Purification Kit and MinElute Kit from Qiagen.

value: ChIP-seq

tag: target

value: ROR alpha

tag: antibodies

value: RORalpha (Santa Cruz, sc-6062)


title: GRO-seq WT LiverZT16

description:
nascent RNA
library strategy: GRO-seq


title: GRO-seq WT Liver ZT1

description:
nascent RNA
library strategy: GRO-seq


title: Rep1_rrs1-1_NT-0hr.fq


title: Rep1_rrs1-1_PopP2-6hr.fq

description:
Tag-seq
Barcode sequence: CATACGT
Barcode position: 5' end of the read


title: E4BP4 Liver ZT22 ChIP-seq

description: this sample represents 3 replicates

value: E4BP4 (Santa Cruz, sc-9550 and sc-9549, mixed in 1:1 ratio.)


title: Rep2_Ws-2_NT-0hr.fq


title: Rep1_Ws-2_C321A-6hr.fq


title: Rep1_Ws-2_C321A-2hr.fq


title: Rep1_Ws-2_C321A-4hr.fq


title: Rep1_Ws-2_C321A-8hr.fq


title: Rep1_Ws-2_PopP2-8hr.fq


title: Rep2_Ws-2_PopP2-2hr.fq


title: Rep1_Ws-2_PopP2-6hr.fq


title: GRO-seq WT Liver ZT4

description:
nascent RNA
library strategy: GRO-seq


title: Rep1_rrs1-1_PopP2-4hr.fq


title: Rep1_Ws-2_NT-0hr.fq


title: Rep1_Ws-2_PopP2-4hr.fq


title: NOTCH1_GA2

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM

description: these cells are MCF10A cells overexpressing the intracellular domain of NOTCH1

data_processing:
The fast splice junction mapper Tophat (v2.0.8b) in combination with the short read aligner Bowtie (v2.1.0) were used to align NGS reads to the GRCh37 (hg19) reference genome and concurrently identify exon splice junctions. Ensembl (e70) Homo sapiens transcript annotation served as the reference transcriptome, while characterisation of novel splice junctions was permitted
For each replicate, spliced alignments were assembled into transcripts and their abundance estimated via Cufflinks (v2.1.1), again using Ensembl (e70) transcriptome annotation as a guide and de-novo assembly of transcripts was permitted
Transcriptome assemblies of replicates were merged with Cuffmerge, before testing for significant differential expression with Cuffdiff (v2.1.1) taking replicates into account
Genome_build: hg19
Supplementary_files_format_and_content: Each file refers to one cell line and describes ID and locus of transcripts together with average FPKM values for the DMSO-treated sample and the ginkgolic acid-treated sample

source_name: MCF10A_NOTCH_ cells_ginkgolic acid

growth_protocol: MCF10A and NOTCH1 cells were cultured in Dulbecco’s modified Eagle’s medium/F12 supplemented with 5% horse serum, 1% penicillin–streptomycin, insulin (10 μg/ml), cholera toxin (100 ng/ml), epidermal growth factor (20 ng/ml) and hydrocortisone (500 ng/ml)

extract_protocol:
Rneasy Kit from Qiagen
ScriptSeq Complete Gold Kit, Epicentre, Illumina

treatment_protocol: Cells were treated with either DMSO or ginkgolic acid 30 uM for 3 days

value: breast


title: NOTCH1_GA1


title: NOTCH1_DMSO1

source_name: MCF10A_NOTCH_ cells_DMSO


title: Rep1_Ws-2_PopP2-2hr.fq


title: Lateral seeds 20DAPF Rep1

city: Milan

first: Sergio

last: Ferrero

address: Via Celoria 26

department: Dipartimento di Bioscienze

country: Italy

institute: Università degli Studi di Milano

data_processing:
Quality control on the raw sequence data was done using FastQC (Babraham Bioinformatics)
Reads were aligned to whole genome sequences from the Malus x domestica genome v1.0 (www.rosaceae.org) and analyzed using the CLC Genomics workbench (www.clcbio.com)
RPKM was considered as expression values
Genome_build: Malus x domestica genome v1.0 (www.rosaceae.org)
Supplementary_files_format_and_content: tab-delimited text files include gene model (http://www.rosaceae.org/malus/malus_x_domestica/), RPKM values for each sample

organism: Malus domestica

source_name: apple seeds

growth_protocol: Adult trees on experimental field

extract_protocol:
Seeds of fruitlets at 20DAPF were dissected and RNA extracted using CTAB buffer according to the method of Yang et al. (2013)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Golden Delicious

tag: type of fruit

value: Lateral

tag: developmental stage

value: 20 DAPF


title: Lateral seeds 20DAPF Rep3


title: Central seeds 20DAPF Rep3

value: Central


title: MCF10A_GA1

source_name: MCF10A cells_ginkgolic acid


title: Lateral seeds 20DAPF Rep2


title: Central seeds 20DAPF Rep1


title: Central seeds 20DAPF Rep2


title: MCF10A_DMSO2

source_name: MCF10A cells_DMSO


title: MCF10A_DMSO1


title: MCF10A_GA2


title: DICER1 KD siRNA1

status: Public on Nov 20 2014

city: Berlin

first: Marvin

last: Jens

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

description: adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTA

data_processing:
demultiplexing by CASAVA, and removal of custom 3'adapter sequence with FLEXBAR
collapsing distinct read-sequences with custom script
alignment with BOWTIE2 2.1.0 to hg19
coverage track building and read counting with custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: coverage wig files

source_name: cell culture

extract_protocol:
NP40 lysis buffer, FLAG magnetic beads, proteinase K, phenol chloroform
Illumina small RNA (truseq)

value: Flp-In HEK293 T-Rex

tag: knockdown

value: DICER1 siRNA


title: DROSHA KD siRNA2

description: adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTA

value: DROSHA siRNA


title: DICER1 KD siRNA2

description: adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTA


title: hek_mock_18h

data_processing:
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment to hg19 with STAR
quantification of GENCODE transcript expression with HT-seq
normalized log2 fold-changes computed with edgeR
Genome_build: hg19
Supplementary_files_format_and_content: text file (tab-separated), with read counts (HT-Seq) and normalized log2 fold-changes by edgeR
Supplementary_files_format_and_content: tab-separated text: gene, log(CPM) [counts per million], normalized Log2 fold-change, P-value estimate (in absence of replicates this is unreliable and was not used).

molecule: polyA RNA

extract_protocol:
TRIZOL
Default Illumina RNA-Seq for HiSeq2000 (TruSeq)

treatment_protocol: RNAi by transfection

value: HEK293 T-Rex FLAG:DICER1 FLP-IN

tag: transfection

value: control sample


title: hek_dicer1_siRNA2_18h

tag: cell line

value: DICER1 siRNA2, 18h


title: hek_drosha_siRNA2_18h

value: DROSHA siRNA2, 18h


title: NOTCH1_DMSO2


title: hek_drosha_siRNA1_18h

value: DROSHA siRNA1, 18h


title: hek_dicer1_siRNA1_18h

value: DICER1 siRNA1, 18h


title: PAR-CLIP of PACT (PRKRA), extra elution step

description: library strategy: PAR-CLIP

data_processing:
removal of default 3'adapter sequence with FLEXBAR (see supplementary methods) and random dinucleotides on 5' and 3' ends with custom script
collapsing distinct read-sequences with custom script
alignment with BWA 0.7.5a-r405  to hg19 and decoy
scanning around DICER1 binding sites or control binding sites for aligned reads
Genome_build: hg19
Supplementary_files_format_and_content: fixed width WIG files with depth-of-coverage

extract_protocol:
PAR-CLIP (Hafner et al. 2010)
Illumina small RNA

value: FLAG:PRKRA Flp-In HEK293 T-Rex


title: negative control

description: adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTA


title: PAR-CLIP of PACT (PRKRA), replicate 2

description: library strategy: PAR-CLIP


title: PAR-CLIP of TRBP (TARBP), replicate 1

description: library strategy: PAR-CLIP

value: FLAG:TARBP Flp-In HEK293 T-Rex


title: PAR-CLIP of TRBP (TARBP), replicate 2

description: library strategy: PAR-CLIP


title: NBM_1_errbs

city: New York

first: Ari

last: Melnick

state: New York

address: 1305 York Ave.

institute: Weill Cornell Medical College

description: ERRBS

data_processing:
For ERRBS:Adaptors are trimmed with cutadapt,then we aligned trimmed reads to genome (hg18) with Bismark aligner (v 0.6.3). We called for methylation percentage for each CpG with at least 10X coverage and each base on the reads that cover the C must have at least phred Quality score of 20.
For hMe-Seal: reads are aligned to genome using eland (from CASAVA 1.8 pipeline) and peaks are called using Chipseeqer (arguments: -t 15 -fold_t 2 - uniquereads 1 )
Genome_build: hg18
Supplementary_files_format_and_content: For ERRBS, text files for location of CpGs and their methylation information:   column 1: base id   column 2: chromosome     column 3: base position  column 4: strand  column 5: coverage   column 6: number of methylated Cs on that position  column 7: number of unmethylated Cs on that position    For hMeSeal, text file containing peak locations and statistics Chromosome  :   column 1  : the first (genomic) coordinate of the peak  column 2 : the second (genomic) coordinate of the peak  column 3  : average log p-value of the nucleotides in the normalized peak region  column 4  : score estimated as the average ChIP reads/length of peak (minus the average INPUT reads/length of peak - if INPUT is available)  column 5      : the position of the maximum height of the peak  column 6   : the maximum peak height (in reads)  column 7  : the relative position of the maximum height of the peak, e.g., 50% means the highest point is at the middle of the peak  column 8  : the size of the peak (in bp)  column 9    : the middle position of the peak  column 10  : the distance of the maximum height from the middle of the peak
Supplementary_files_format_and_content: peak locations and statistics from Chipseeqer
Supplementary_files_format_and_content: CpG methylation information: location, number of methylated Cs(freqCs),number of unmethylated Cs(freqTs) and coverage

source_name: Normal CD34+ bone marrow cells

extract_protocol:
DNA was extracted using Qiagen Puregene kit protocol;
hMe-seal 5hmC labelling: Genomic DNA (gDNA) was sonicated into 200-400bp long fragments (set up: high, 30 times, 30s interval pulse followed by 30 s pause).  Subsequently 2 g units are wrong of gDNA were labeled with chemically modified uridine diphosphoglucose glucose (UDP-6-N3-Glu) by viral β-glucosyltransferase (β-GT) as described previously(Song et al., 2011, Nature Biotech.). Afterwards the labeled DNA was purified by QIAquick PCR Purification Kit (Qiagen Inc.,Valencia CA) and eluted in water.  The click chemistry reaction was performed by addition of 150 μM dibenzocyclooctyne modified biotin into the eluted DNA, the reaction mixture was incubated for 2 h at 37 °C.  The DNA samples were then purified by MinElute Reaction Cleanup Kit (Qiagen Inc., Valencia CA) and the amount of eluted DNA was determined by Nanodrop UV spectroscope (Thermo, Wilmington, DE)
ERRBS:  Library construction protocol: Genomic DNA was purified from cell lines and primary human samples, digested with MspI restriction enzyme (200U MspI per reaction), subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors (2000U T4 DNA ligase per reaction). Fragments of 150-250 bp (reduced representation bisulfite sequencing) and 150-400 bp (for enhanced reduced representation bisulfite sequencing) were isolated after agarose gel electrophoresis and subjected to bisulfite conversion (single conversion round using Zymo Research EZ DNA Methylation Kit) and PCR amplification using paired-end Illumina primers (18 cycles).  Libraries were sequenced using an Illumina Genome Analyzer II or HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read runs.
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

tag: cell type

value: Normal CD34+ bone marrow cells

tag: experiment type

value: ERRBS


title: NBM_3_hmeSeal_input

description: input DNA

value: input DNA


title: PAR-CLIP of PACT (PRKRA), replicate 1

description: library strategy: PAR-CLIP


title: NBM_5_hmeSeal_input

description: input DNA


title: NBM_1_hmeSeal_input

description: input DNA


title: NBM_4_hmeSeal_input

description: input DNA


title: NBM_1_hmeSeal

description: hMe-seal

value: hMe-seal


title: NBM_3_errbs

description: ERRBS


title: NBM_2_hmeSeal_input

description: input DNA


title: DROSHA KD siRNA1

description: adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTA


title: NBM_3_hmeSeal

description: hMe-seal


title: NBM_5_hmeSeal

description: hMe-seal


title: hek_drosha_2.5d

data_processing:
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment to hg19 with TOPHAT2 2.06
quantification of GENCODE17 transcript expression with cuffdiff 2.1.1 from CUFFLINKS suite
building coverage tracks with samtools and custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: wig files with coverage, text file (tab-separated), with FPKM expression values
hek.isoforms.fpkm_tracking cuffdiff output, tab-separated text
hek.polya.lfc tab-separated text: gene, mock FPKM, DICER1 KD FPKM, DROSHA KD FPKM, Log2 fold-change (DICER1/MOCK), Log2 fold-change (DROSHA/MOCK)


title: NBM_2_hmeSeal

description: hMe-seal


title: PAR-CLIP with T1, replicate 2

description:
Dicer bound RNA fragments, custom 3'adapter TCTCCATTCGTATGCCGTCTTCTGCTTG
dicer1_4su_1_BC5.qseq.txt.gz 3' adapter TCTCACGTCGTATGCCGTCTTCTGCTTG
dicer1_4su_1_reseq_BC5.qseq.txt.gz 3' adapter TCTCACGTCGTATGCCGTCTTCTGCTTG
dicer1_4su_2_BC6.qseq.txt.gz 3' adapter TCTCCATTCGTATGCCGTCTTCTGCTTG
dicer1_4su_2_reseq_BC6.qseq.txt.gz 3' adapter TCTCCATTCGTATGCCGTCTTCTGCTTG
dicer1_4su_3_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dicer1_4su_3_reseq_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG

data_processing:
removal of default Illumina 3'adapter sequence with FLEXBAR (see supplementary methods)
collapsing distinct read-sequences with custom script
alignment with BOWTIE2 2.1.0 to hg19
cluster building and quality filtering to limit false-discovery rate with custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: GFF with genomic regions covered by filtered clusters (binding sites)

value: FLAG:DICER Flp-In HEK293 T-Rex


title: hek_mock_2.5d


title: hek_dicer1_2.5d


title: PAR-CLIP with T1, replicate 3

description:
Dicer bound RNA fragments, custom 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dicer1_4su_1_BC5.qseq.txt.gz 3' adapter TCTCACGTCGTATGCCGTCTTCTGCTTG
dicer1_4su_1_reseq_BC5.qseq.txt.gz 3' adapter TCTCACGTCGTATGCCGTCTTCTGCTTG
dicer1_4su_2_BC6.qseq.txt.gz 3' adapter TCTCCATTCGTATGCCGTCTTCTGCTTG
dicer1_4su_2_reseq_BC6.qseq.txt.gz 3' adapter TCTCCATTCGTATGCCGTCTTCTGCTTG
dicer1_4su_3_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dicer1_4su_3_reseq_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG


title: NBM_2_errbs

description: ERRBS


title: FLAG:AGO2 loaded small RNA

description:
small RNA
5' adapter introduces NN random barcode in the beginning of each raw read. 3' adapter sequence is TCTCGTATCGTATGCCGTCTTCTGCTTG

data_processing:
demultiplexing by, and removal of custom 3'adapter sequence with FLEXBAR (see supplementary methods)
collapsing distinct read-sequences with custom script
trimming of 5' NN
alignment with BOWTIE2 2.1.0 to either miRBASE v.20 or hg19
coverage track building and read counting with custom scripts
pooling of alignments and cluster building
Genome_build: hg19
Supplementary_files_format_and_content: coverage wig files, flat files with mirbase read counts, GFF with genomic regions covered by clusters

extract_protocol:
NP40 lysis buffer, FLAG magnetic beads, proteinase K, phenol chloroform
Illumina small RNA. 3' and 5' ligation of custom RNA adapters before RT

value: HEK293 T-Rex


title: FLAG:AGO3 loaded small RNA

description:
small RNA
5' adapter introduces NN random barcode in the beginning of each raw read. 3' adapter sequence is TCTCACGTCGTATGCCGTCTTCTGCTTGTCTCGTATCGTATGCCGTCTTCTGCTTG


title: PAR-CLIP with T1, replicate 1

description:
Dicer bound RNA fragments, custom 3'adapter TCTCACGTCGTATGCCGTCTTCTGCTTG
dicer1_4su_1_BC5.qseq.txt.gz 3' adapter TCTCACGTCGTATGCCGTCTTCTGCTTG
dicer1_4su_1_reseq_BC5.qseq.txt.gz 3' adapter TCTCACGTCGTATGCCGTCTTCTGCTTG
dicer1_4su_2_BC6.qseq.txt.gz 3' adapter TCTCCATTCGTATGCCGTCTTCTGCTTG
dicer1_4su_2_reseq_BC6.qseq.txt.gz 3' adapter TCTCCATTCGTATGCCGTCTTCTGCTTG
dicer1_4su_3_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dicer1_4su_3_reseq_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG


title: WT1mut_2_errbs

description:
ERRBS
ERRBS
16253
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

data_processing:
For ERRBS:Adaptors are trimmed with cutadapt,then we aligned trimmed reads to genome (hg18) with Bismark aligner (v 0.6.3). We called for methylation percentage for each CpG with at least 10X coverage and each base on the reads that cover the C must have at least phred Quality score of 20.
For hMe-Seal: reads are aligned to genome using eland (from CASAVA 1.8 pipeline) and peaks are called using Chipseeqer (arguments: -t 15 -fold_t 2 - uniquereads 1 )
Genome_build: hg18
Supplementary_files_format_and_content: For ERRBS, text files for location of CpGs and their methylation information:   column 1: base id   column 2: chromosome     column 3: base position  column 4: strand  column 5: coverage   column 6: number of methylated Cs on that position  column 7: number of unmethylated Cs on that position    For hMeSeal, text file containing peak locations and statistics Chromosome  :   column 1  : the first (genomic) coordinate of the peak  column 2 : the second (genomic) coordinate of the peak  column 3  : average log p-value of the nucleotides in the normalized peak region  column 4  : score estimated as the average ChIP reads/length of peak (minus the average INPUT reads/length of peak - if INPUT is available)  column 5      : the position of the maximum height of the peak  column 6   : the maximum peak height (in reads)  column 7  : the relative position of the maximum height of the peak, e.g., 50% means the highest point is at the middle of the peak  column 8  : the size of the peak (in bp)  column 9    : the middle position of the peak  column 10  : the distance of the maximum height from the middle of the peak

source_name: WT1 mutated Acute Myeloid Leukemia patient sample

extract_protocol:
DNA was extracted using Qiagen Puregene kit protocol;
hMe-seal 5hmC labelling: Genomic DNA (gDNA) was sonicated into 200-400bp long fragments (set up: high, 30 times, 30s interval pulse followed by 30 s pause).  Subsequently 2 g units are wrong of gDNA were labeled with chemically modified uridine diphosphoglucose glucose (UDP-6-N3-Glu) by viral β-glucosyltransferase (β-GT) as described previously(Song et al., 2011, Nature Biotech.). Afterwards the labeled DNA was purified by QIAquick PCR Purification Kit (Qiagen Inc.,Valencia CA) and eluted in water.  The click chemistry reaction was performed by addition of 150 μM dibenzocyclooctyne modified biotin into the eluted DNA, the reaction mixture was incubated for 2 h at 37 °C.  The DNA samples were then purified by MinElute Reaction Cleanup Kit (Qiagen Inc., Valencia CA) and the amount of eluted DNA was determined by Nanodrop UV spectroscope (Thermo, Wilmington, DE)
ERRBS:  Library construction protocol: Genomic DNA was purified from cell lines and primary human samples, digested with MspI restriction enzyme (200U MspI per reaction), subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors (2000U T4 DNA ligase per reaction). Fragments of 150-250 bp (reduced representation bisulfite sequencing) and 150-400 bp (for enhanced reduced representation bisulfite sequencing) were isolated after agarose gel electrophoresis and subjected to bisulfite conversion (single conversion round using Zymo Research EZ DNA Methylation Kit) and PCR amplification using paired-end Illumina primers (18 cycles).  Libraries were sequenced using an Illumina Genome Analyzer II or HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read runs.

value: Acute Myeloid Leukemia cells

value: WT1 mutated


title: WT1mut_1_errbs

description:
ERRBS
ERRBS
15182
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: AML1ETO_3_errbs

description:
ERRBS
ERRBS
20806
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

source_name: AML1ETO Acute Myeloid Leukemia patient sample


title: WT1mut_4_errbs

description:
ERRBS
ERRBS
18086
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_3_errbs

description:
ERRBS
ERRBS
17919
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: NBM_4_hmeSeal

description: hMe-seal


title: AML1ETO_2_errbs

description:
ERRBS
ERRBS
19537
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

value: AML1ETO Acute Myeloid Leukemia patient sample


title: AML1ETO_4_errbs

description:
ERRBS
ERRBS
15835
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: AML1ETO_1_errbs

description:
ERRBS
ERRBS
16426
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_2_errbs

description:
ERRBS
ERRBS
19211
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

source_name: TET2 mutated Acute Myeloid Leukemia patient sample

value: TET2 mutated


title: IDH2mut_2_errbs

description:
ERRBS
ERRBS
15800
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

source_name: IDH2 mutated Acute Myeloid Leukemia patient sample

value: IDH2 mutated


title: IDH2mut_1_errbs

description:
ERRBS
ERRBS
17781
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: AML1ETO_3_hmeSeal_input

description:
input DNA
input DNA
20806
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_4_errbs

description:
ERRBS
ERRBS
15065
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

source_name: IDH1 mutated Acute Myeloid Leukemia patient sample

value: IDH1 mutated


title: AML1ETO_2_hmeSeal_input

description:
input DNA
input DNA
19537
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: AML1ETO_1_hmeSeal_input

description:
input DNA
input DNA
16426
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_4_hmeSeal_input

description:
input DNA
input DNA
18086
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_5_hmeSeal_input

description:
input DNA
input DNA
18407
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_3_hmeSeal_input

description:
input DNA
input DNA
17919
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_2_hmeSeal_input

description:
input DNA
input DNA
16253
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_3_hmeSeal_input

description:
input DNA
input DNA
20058
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_1_hmeSeal_input

description:
input DNA
input DNA
15544
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_1_hmeSeal_input

description:
input DNA
input DNA
15182
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_2_hmeSeal_input

description:
input DNA
input DNA
19211
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH2mut_2_hmeSeal_input

description:
input DNA
input DNA
15800
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH2mut_1_hmeSeal_input

description:
input DNA
input DNA
17781
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH2mut_3_hmeSeal_input

description:
input DNA
input DNA
20655
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_4_hmeSeal_input

description:
input DNA
input DNA
15065
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH2mut_3_errbs

description:
ERRBS
ERRBS
20655
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_1_hmeSeal_input

description:
input DNA
input DNA
20623
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_4_errbs

description:
ERRBS
ERRBS
15746
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_5_hmeSeal

description:
hMe-seal
hMe-seal
18407
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: AML1ETO_1_hmeSeal

description:
hMe-seal
hMe-seal
16426
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: AML1ETO_2_hmeSeal

description:
hMe-seal
hMe-seal
19537
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: AML1ETO_3_hmeSeal

description:
hMe-seal
hMe-seal
20806
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_2_hmeSeal_input

description:
input DNA
input DNA
19616
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_4_hmeSeal

description:
hMe-seal
hMe-seal
18086
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_2_hmeSeal

description:
hMe-seal
hMe-seal
16253
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: WT1mut_3_hmeSeal

description:
hMe-seal
hMe-seal
17919
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_3_hmeSeal

description:
hMe-seal
hMe-seal
20058
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH2mut_2_hmeSeal

description:
hMe-seal
hMe-seal
15800
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_1_hmeSeal

description:
hMe-seal
hMe-seal
15544
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: TET2mut_2_hmeSeal

description:
hMe-seal
hMe-seal
19211
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH2mut_3_hmeSeal

description:
hMe-seal
hMe-seal
20655
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_3_hmeSeal_input

description:
input DNA
input DNA
19515
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH2mut_1_hmeSeal

description:
hMe-seal
hMe-seal
17781
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_2_hmeSeal

description:
hMe-seal
hMe-seal
19616
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_4_hmeSeal

description:
hMe-seal
hMe-seal
15065
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_3_hmeSeal

description:
hMe-seal
hMe-seal
19515
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: IDH1mut_1_hmeSeal

description:
hMe-seal
hMe-seal
20623
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )


title: irrelevant siRNA 2

city: Urbana

first: Stephanie

last: Ceman

state: IL

address: 601 S. Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois-Urbana Champaign

data_processing:
The libraries were quantitated by qPCR, pooled all together and sequenced on two lanes for 101 cycles from one end of the cDNA fragments on a HiSeq2000 using a TruSeq SBS sequencing kit version 3
Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2.
Each of the two fastq files per sample were individually trimmed for quality using trimmomatic 0.22 with parameters TRAILING:20 MINLEN:30 (minimum PHRED quality score accepted 20, read length accepted 30). Each pair of technical replicates had similar quality and percent reads removed, so they were concatenated into one fastq file per sample before alignment.
Alignments to UCSC hg19 were done using Tophat2 2.0.8 with parameters --coverage-search -p 8 -N 7 --read-edit-dist 7 --library-type fr-firststrand.
Read counts for each gene were generated using htseq-count (version 0.5.3p9 from samtools 0.1.18) with parameters -s reverse -m intersection-nonempty and combined into one tab-delimited text file for all 20 samples
Genome_build: UCSC hg19
Supplementary_files_format_and_content: a single tab-delimited text file of raw read counts were used directly in edgeR 3.2.1for statistical analysis and thus are the "normalized" data.

source_name: Human Embryonic Kidney cell lines

growth_protocol: Cells were grown in serum containing DMEM  at 37C

extract_protocol:
Cells were lysed and RNA was extracted using Trizol
Illumina's TruSeq Stranded RNAseq Sample Prep kit was used with 1 ug of total RNA for the construction of sequencing libraries. Indices (barcodes) were included to be able to differentiate the sequences from each sample. The adapter sequence used was AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNN = 6 nt barcode index in .fastq file name)

treatment_protocol: MOV10 and irrelevant siRNA treatments were performed at 24 hr intervals three times, overexpression studies involved a single myc-MOV10 transfection

value: Human Embryonic Kidney cells

tag: treatment

value: control

tag: mov expression

value: normal


title: MOV10 overexpression 2

value: MOV10 overexpression

value: high


title: MOV10 overexpression 3


title: irrelevant siRNA 1


title: MOV10 knockdown 2

value: MOV10 knockdown

value: low


title: C7 experiment

description:
Replicate 2 - experimental pull down
processed data file: all_regions.exptC7.bed

data_processing:
library strategy: CLIP-Seq (libraries were pooled and sequenced)
Basecalls performed using CASAVA version 1.8.2
Quality trimming (phred score 30) performed followed by adapter trimming. PCR duplicates were collapsed to a single fasta entry (duplicate count was tracked) for each lane of sequencing on the pooled data.
Bar codes were used to separate out the 4 samples (2 replicates) into 4 fasta file for each lane of sequencing, i.e. for each sample there were 3 sets of fasta files, one for each lane. These were combined for each sample to get a consolidated fasta dataset per sample (4 fasta files, 1 per sample, generated for alignment).
NOTE- The raw fastq files for each sample were generated specifically for the purposes of submission. For the actual analysis, the samples were separated into individual files only after trimming and de-duplication.
These 4 fasta files were then mapped to hg19 using Novoalign and allowing for only 2 (-t 60) mismatches. Only uniquely mapped reads were utilized for downstream analysis.
Using bedtools and samtools the alignment files was then used to determine location of MOV10 binding. All locations with an overlap of 1 or more nucleotides were combined into a single longer region. For both C5 and C7, any regions identified in the experimental samples that had any overlap with regions identified in the control samples were not considered as aMOV10 binding region.
Gene annotation information along with bedtools was used to determine the gene feature where the MOV10 binding location
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using samtools and bedtools to represent the location of MOV10 binding

source_name: HEK293F_MOV10 pull down

extract_protocol:
A published iCLIP protocol was followed (Konig et al., 2010, 2011) with the following exceptions: phosphatase treatment was performed using shrimp alkaline phosphatase (SAP), the irrelevant immunoprecipitation was performed with a rabbit affinity purified antibody to zebra finch FMRP, described in (Winograd et al., 2008).
During the iCLIP protocol, once the RNA was isolated, primers containing unique sequences as bar codes for each sample were utilized for the priming of the reverse transcription reaction. These primers also contained sequences complementary to Solexa P5 and P3 primers that were subsequently utilized for second strand synthesis and eventual PCR amplification. The tagged and amplified cDNA was then put on the HiSeq2000 for sequencing.

tag: bar code

value: NNNGGCCNN…cDNA

tag: antibody for pull-down

tag: antibody vendor

value: Bethyl Laboratories Inc.

tag: antibody cat. #

tag: antibody lot #


title: WT1mut_1_hmeSeal

description:
hMe-seal
hMe-seal
15182
Bisulfite-seq (RRBS) and OTHER (hMe-Seal: chemical labeling,biotnylation and pulldown of regions with 5hmC )

tag: genotype

value: hMe-seal


title: MOV10 knockdown 3


title: MOV10 overexpression 1


title: C5 experiment

description:
Replicate 1 - experimental pull down
processed data file: all_regions.exptC5.bed

value: NNNTGGANN…cDNA


title: lbl1, small RNA, rep2

city: Cold Spring Harbor

first: Molly

last: Gale Hammell

state: NY

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Lab

description:
Small RNA, 15-30 nt.
DatasetS1_smallRNA_counts.xls

data_processing:
Small RNA reads 18 to 26 nt in length were filtered, trimmed, and aligned to the maize B73 RefGen_v2 genome (release 5a.57) using Bowtie v0.12.7, allowing no mismatches and up to 20 potential alignments per read. Reads matching known structural RNAs (rRNAs, tRNAs, sn-RNAs and sno-RNAs) from Rfam 10.0 were removed from further analysis.
The abundances of small RNA reads were calculated using sliding, non-overlapping 500 nt windows. Any windows with fewer than 10 reads total, across all libraries were removed from further analysis. For the remaining windows, edgeR (Robinson, McCarthy & Smyth, 2010) was used to model the counts distribution using a negative binomial model with common dispersion estimate. Differentially expressed loci were defined as windows with at least a 2-fold difference in abundance between the wild-type and lbl1 samples, and an adjusted P-value < 0.05 (corrected according to the method of Benjamini & Hochberg, 1990). Differentially expressed 24-nt small RNAs derived from the lbl1 introgression interval were excluded from further analysis.
Genome_build: Maize B73 RefGen_v2 genome (release 5a.57) and the annotated exon junctions (version 5b_AGPv2).
Supplementary_files_format_and_content: Small RNA: DatasetS1_smallRNA_counts.xls: All counts, fold changes and P-values are given for the hundreds of DE species (rather than the 100,000s of all small RNAs mapped).
Supplementary_files_format_and_content: mRNA: rnaseq-lbl1-Cuffdiff_gene_expression.txt: Cuffdiff output of RPKM values is given for all RNA-seq data.

organism: Zea mays

source_name: maize vegetative apex, lbl1 mutant, small RNA

growth_protocol: Families segregating the lbl1-rgd1 allele (Nogieira, et al., 2007) introgressed at least three times into B73 were grown in growth-chambers at 16 hour 28 C/light and 8 hour 24 C/dark cycles. Shoot apices including the meristem and up to 5 leaf primordia were dissected from 2-week-old plants.

extract_protocol:
Total RNA was prepared using the mirVana RNA isolation kit (Life Techologies).
1ug total RNA per sample was used to generate smRNA-seq libraries using the smRNA-seq kit (Illumina). RNA 3'  and 5'  adapters were ligated in consecutive reactions with T4 RNA ligase. Ligated RNA fragments were primed with an adapter-specific RT primer and reverse transcribed with Superscript II reverse transcriptase (Life Technologies), followed by eleven cycles of amplification with adapter-specific primers. Resulting cDNA libraries were separated on a 6% TBE gel and library fragments with inserts of 18-25p were excised. Recovered cDNA libraries were validated by QC on an Agilent Bioanalyzer HiSens DNA chip (Agilent Technologies Inc.)

tag: line/background

tag: age

value: 2 weeks

tag: tissue

value: leaf apex


title: WT, small RNA, rep1

source_name: maize vegetative apex, WT, small RNA

value: WT


title: lbl1, small RNA, rep1


title: WT, small RNA, rep3


title: WT, small RNA, rep2


title: lbl1, small RNA, rep3


title: trf4D_2_T0

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Biological replicate 2

data_processing:
Reads were mapped to the S. cerevisiae S288C reference genome (retrieved from SGD) using the version 1.4.1 of TopHat, with a tolerance of 4 mismatches and a maximum size for introns of 2 Kb.
Subsequent analysis used reads uniquely mapped on the reference genome.
Tags densities were normalized on the total number of reads mapped on ORFs.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each gene in each sample

organism: Saccharomyces cerevisiae

extract_protocol:
Total RNA was extracted using standard hot phenol procedure. rRNAs were depleted from total RNA using the RiboMinus Eukaryote Kit for RNA-Seq (Life Technologies).
Strand-specific total RNA-Seq libraries were prepared from 125 ng of rRNA-depleted RNA using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Paired-end sequencing (2x50 nt) of the libraries was performed on a HiSeq 2500 sequencer.

tag: strain background

tag: genotype/variation

value: trf4D derivative of JKM139

tag: induction status

value: No HO induction


title: C7 control

description:
Replicate 2 - control/irrelevant pull down
processed data file: all_regions.exptC7.bed

source_name: HEK293F_control pull down

tag: cell line

value: irrelevant (ir)


title: C5 control

description:
Replicate 1 - control/irrelevant pull down
processed data file: all_regions.exptC5.bed

tag: cell type

value: Human Embryonic Kidney cells


title: rrp6D_1_T0

description: Biological replicate 1

value: rrp6D derivative of JKM139


title: xrn1D_2_T0

description: Biological replicate 2

value: xrn1D derivative of JKM139


title: xrn1D_1_T0

description: Biological replicate 1


title: irrelevant siRNA 3

value: control

value: normal


title: JKM139_1_T240

description: Biological replicate 1

value: wild type

value: 240 min after HO induction


title: JKM139_2_T60

description: Biological replicate 2

value: 60 min after HO induction


title: C21

city: Yangling

first: Yongzhen

last: Huang

state: Shaanxi

address: No.22 Xinong Road

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

data_processing:
Images generated by sequencers are converted by base calling into nucleotide sequences
using clean-fastq_v1.pl to remove adapters and low quality tags as well as contaminants
clean reads were perfect matched to the bovine reference genome  UMD 3.1 for the assembly using SOAP2 software and not allowed to mismatches in reads.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: wig

organism: Bos taurus

source_name: Longissimus Muscle

growth_protocol: All animal protocols were approved by the Review Committee for the Use of Animal Subjects of Northwest A&F University.

extract_protocol:
The experimental animals used in this study were of a famous elite native breed of Chinese Qinchuan cattle. Two tissue samples were collected from fetal bovine (FB, day 90 bovine embryos),  and adult bovine (AB, 2-year-old). Day 90 fetal bovine (FB) embryos (gestation period 280 days). These tissues were rapidly separated from each carcass, immediately frozen in liquid nitrogen and stored at − 80 °C unti DNA extraction.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Chinese Qinchuan cattle

value: Longissimus Muscle


title: T23

value: day 90 bovine embryos


title: JKM139_1_T0

description: Biological replicate 1


title: lbl1, mRNA, rep2

data_processing:
The mRNA sequencing data were aligned to the B73 RefGen_v2 genome (release 5a.57) and the annotated exon junctions (version 5b_AGPv2) using TopHat v1.2.0.
mRNA differential expression was determined using Cuffdiff v1.0.3 with default parameters, except that the "minimum alignment count" (-c) which was set to 50.
Genome_build: Maize B73 RefGen_v2 genome (release 5a.57) and the annotated exon junctions (version 5b_AGPv2).
Supplementary_files_format_and_content: Small RNA: DatasetS1_smallRNA_counts.xls: All counts, fold changes and P-values are given for the hundreds of DE species (rather than the 100,000s of all small RNAs mapped).
Supplementary_files_format_and_content: mRNA: rnaseq-lbl1-Cuffdiff_gene_expression.txt: Cuffdiff output of RPKM values is given for all RNA-seq data.

source_name: maize vegetative apex, lbl1 mutant, mRNA

extract_protocol:
Total RNA was prepared using the mirVana RNA isolation kit (Life Techologies).
Libraries were prepared using TruSeq RNA Sample Prep Kits (Illumina).

value: 2 weeks


title: JKM139_2_T0

description: Biological replicate 2


title: lbl1, mRNA, rep1

description: rnaseq-lbl1-Cuffdiff_gene_expression.txt

value: leaf apex


title: JKM139_1_T60

description: Biological replicate 1


title: WT, mRNA, rep2

source_name: maize vegetative apex, WT, mRNA

value: WT


title: monophosphate_smallrna_cel

description: small RNA

data_processing:
removal of default Illumina 3'adapter sequence with FLEXBAR (see supplementary methods)
collapsing distinct read-sequences with custom script
alignment with BOWTIE2 2.1.0 to either miRBASE v.20 or ce6
coverage track building and read counting with custom scripts
cluster building from NR_AR_0037 reads of length 18..26 nt (inclusive)
Genome_build: ce6
Supplementary_files_format_and_content: coverage wig files, GFF with genomic regions covered by clusters

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
TRIZOL
Illumina small RNA


title: WT, mRNA, rep1


title: cel_dcr1_4

data_processing:
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment to ce6 with STAR
quantification of wormbase transcript expression with HT-seq
normalized log2 fold-changes computed with edgeR
Genome_build: ce6 (WS190)
Supplementary_files_format_and_content: text file (tab-separated), with read counts (HT-Seq) and normalized log2 fold-changes by edgeR
Supplementary_files_format_and_content: lfc files: tab-separated text: gene, log(CPM) [counts per million], normalized Log2 fold-change, P-value estimate (in absence of replicates this is unreliable and was not used).

source_name: young adult nematodes

growth_protocol: fem-1 strain, sterile control animals to compare to dcr-1 loss of function animals (induces sterility)

treatment_protocol: RNAi by feeding

tag: developmental stage

value: young adult

value: dcr-1 knockdown


title: polyphosphatase_smallrna_cel

description: small RNA


title: trf4D_1_T0

description: Biological replicate 1

value: trf4D derivative of JKM139

value: No HO induction


title: cel_dcr1_2.5d

data_processing:
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2
alignment to ce6 with TOPHAT2 2.06
quantification of wormbase transcript expression with cuffdiff 2.1.1 from CUFFLINKS suite
building coverage tracks with samtools and custom scripts
correction for different coverage along transcript length (see Suppl. methods) with custom script
Genome_build: ce6 (WS190)
Supplementary_files_format_and_content: wig files with coverage, text file (tab-separated), with FPKM expression values
cel.isoforms.fpkm_tracking cuffdiff output, tab-separated text
dcr1_2.5.fpkm.lfc tab-separated text: gene, mock FPKM (corrected), dcr-1 KD FPKM (corrected), Log2 fold-change
drosha_2.5.fpkm.lfc tab-separated text: gene, mock FPKM (corrected), drsh1 KD FPKM (corrected), Log2 fold-change


title: cel_mock_2.5d


title: rrp6D_2_T0

description: Biological replicate 2

value: rrp6D derivative of JKM139


title: PAR-CLIP with T1/V1, replicate 1

description:
Dicer bound RNA fragments, custom 3'adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dcr-1_4su_1_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dcr-1_4su_2_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dcr-1_4su_3_noBC.qseq.txt.gz 3' adapter TCGTATGCCGTCTTCTGCTTGT

data_processing:
removal of default Illumina 3'adapter sequence with FLEXBAR (see supplementary methods)
collapsing distinct read-sequences with custom script
alignment with BOWTIE2 2.1.0 to ce6
cluster building and quality filtering to limit false-discovery rate with custom scripts
Genome_build: ce6
Supplementary_files_format_and_content: GFF with genomic regions covered by filtered clusters (binding sites)

source_name: young adult whole worm

extract_protocol:
in vivo PAR-CLIP (Jungkamp et al. 2011)
Illumina small RNA


title: single secretagogin+ cell 9

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read quality filtering and barcode extraction: Every read that was considered valid by the Illumina HiSeq control software was processed and filtered as follows: a) any 3' bases with a quality score of 'B' were removed; b) the well-identifying barcode was extracted from the 5' end of the read; c) if the read ended in a poly(A)-sequence leaving less than 25 transcript-derived bases, the read was discarded; d) the UMI was extracted and if any of the UMI bases had a Phred score less than 17 the read was discarded; e) a maximum of nine template-switching generated Gs were removed from the 5' end of the transcript-derived sequence; f) if the remaining sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment:the reads were aligned to the genome using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. The genome included an artifical chromosome, containing a concatamer of the ERCC control sequences. Any reads with no alignments were re-aligned against another artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models22 were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incompete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation: The annotation step was performed barcode-by-barcode. For every unique mapping (genomic position and strand) the number of reads in each UMI was counted. Any multiread that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more mappings to exons, it was assigned at the exon where it was closest to the transcript model 5' end, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. After assigning reads, the number of molecules at each mapping position was determined by the number of distinct UMIs observed. To account for UMIs that stem from PCR-induced mutations or sequencing errors, any UMI that had fewer reads than 1/100 of the average of the non-zero UMIs was excluded. The raw UMI count was corrected for the UMI collision probability (important only at high UMI counts) as described10. The expression level of each transcript model was taken as the total number of molecules at all its possible mapping positions.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file containing counts of detected cDNA molecules for each transcript model in each of the 9 cells.

source_name: hypothalamic paraventricular nucleus

extract_protocol:
The PVN region of juvenile mice was isolated from 300-μm-thick coronal slices under microscopy guidance and dissociated using the Papain Dissociation System (Worthington). Isolated single cells were concentrated by centrifugation to a density of 300–500 cells/μL and loaded according to the manufacturer’s protocol on a C1 Single-Cell AutoPrep IFC microfludic chip , and the chip was then processed on a Fluidigm C1 instrument using the “mRNA Seq: Cell Load (1772x/1773x)” script. This captured one cell in each of up to 96 capture chambers, and took approximately 30 minutes.
20 μL lysis buffer (0.15% Triton X-100, 1 U/μL TaKaRa RNase inhibitor, 4 μM reverse transcription primer C1-P1-T31, 5% C1 Loading Reagent and 1:50,000 Life Technologies ERCC  Spike-In Mix 1), reverse transcription mix (1x SuperScript II First-Strand Buffer supplemented with 3 mM MgCl2, 1.5 mM dNTP, 4 mM DTT, 3.3% C1 Loading Reagent, 1.8 μM template-switching oligo C1-P1-RNA-TSO, 1.5 U/μL TaKaRa RNase inhibitor and 18 U/μL Life Technologies Superscript II reverse transcriptase) and PCR mix (1.1x Clontech Advantage2 PCR buffer, 440 μM dNTP, 530 nM PCR primer C1-P1-PCR-2, 5% C1 Loading Reagent and 2x Advantage2 Polymerase Mix) were added to the designated wells according to the manufacturer’s instructions, but using the indicated mixes in place of the corresponding commmercial reagents. The plate was then returned to the Fluidigm C1 and the “mRNA Seq: RT + Amp (1772x/1773x)” script was executed, which took about 8.5 hours and included lysis, reverse transcription and 21 cycles of PCR. When the run finished, the amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent and quantified on an Agilent BioAnalyzer. The typical yield was 1 ng/μL. Amplified cDNA was simultaneously fragmented and barcoded by ‘tagmentation’, i.e. using Tn5 DNA transposase to transfer adapters to the target DNA. 96 different 10x transposome stocks (6.25 μM barcoded adapter C1-TN5-x, 40% glycerol, 6.25 μM Tn5 transposase, where x denotes a well-specific barcode) were prepared, each with a different barcode sequence.  6 μL harvested cDNA was mixed with 5 μL tagmentation buffer (50 mM TAPS-NaOH pH 8.5, 25 mM MgCl2 and 50% DMF), 11.5 μL nuclease-free water and 2.5 μL 10x transposome stock. The mix was incubated for 5 minutes at 55°C then cooled on ice. 100 μL Dynabeads MyOne Streptavidin C1 beads were washed in 2xBWT (10 mM Tris HCl pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) then resuspended in 2 mL 2xBWT. 20 μL beads was added to each well and incubated at room temperature for 5 minutes. All fractions were pooled, the beads were immobilized and the supernatant removed (thus removing all internal fragments, and retaining only the 5'- and 3'-most fragments). The beads were then resuspended in 100 μL TNT (20 mM Tris pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, then twice in 100 μL TNT. The beads were then resuspended in 100 μL restriction mix (1x NEB NEBuffer 4, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3' fragments carrying the PvuI recognition site. The mix was incubated for one hour at 37°C, then washed three times in TNT. Finally, the single-stranded library was eluted by resuspending the beads in 100 μL 100 mM NaOH, incubating for 5 minutes, removing the beads, then adding 100 μL 100 mM HCl and 50 μL Neutralization buffer (200 mM Tris pH 7.5, 0.05% Tween-20). At this point, the typical yield was 1-5 nM single-stranded library. Aliquots from these were run on the Hiseq2000 (rawdata file names prefixed with 187ss_ and 187ss-2_). Another aliquot was further amplified by 9 cycles of PCR to produce a double-stranded library as described in Islam, S. et al. Nat. Protoc. 7, 813-828 (2012). These were also run on the Hiseq2000 (rawdata file names prefixed with 187ds_).

value: single secretagogin+ cell


title: single secretagogin+ cell 6


title: single secretagogin+ cell 7


title: single secretagogin+ cell 2


title: single secretagogin+ cell 3


title: single secretagogin+ cell 5


title: cel_drsh1_4

value: drsh-1 knockdown


title: Input Miwi +/- 2

city: NewHaven

first: Toshiaki

last: Watanabe

state: CT

address: 10 Amistad

institute: Yale University

description: ribosomal RNA minus

data_processing:
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis.The unique reads extracted after mapping with Tophat were further mapped to the mRNAs of Ensemble genes with Bowtie software. Reads Per Kilobase of transcript per Million (RPKM) values were calculated for each gene by using (1) A = the number of reads perfectly mapped to either of mRNA variants in sense orientation, (2) B = the mean length of the mRNA variants, and (3) C = the number of unique reads extracted after mapping with Tophat (RPKM = A(103/B)(106/C)).
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [MIWI IP Miwi ADH/- RPKM] [MIWI IP Miwi +/- RPKM] [MIWI IP Miwi -/- RPKM] [Input Miwi ADH/- RPKM] [Input Miwi +/- RPKM] [Input Miwi -/- RPKM]

source_name: Late spermatocyte

extract_protocol:
RNA was harvested using Trizol reagent from testes or FACS-purified cells.
Libraries were prepared for sequencing using standard Illumina protocols

value: Miwi +/-

value: late spermatocyte


title: cel_mock_4

value: control


title: Input Miwi -/- 2

description: ribosomal RNA minus

value: Miwi -/-


title: MIWI IP Miwi ADH/- 2

description: ribosomal RNA minus

value: Miwi ADH/-


title: single secretagogin+ cell 1


title: single secretagogin+ cell 8


title: single secretagogin+ cell 4


title: Input Miwi ADH/- 1

description: ribosomal RNA minus


title: MIWI IP Miwi -/- 1

description: ribosomal RNA minus


title: cel_drsh1_2.5d


title: MIWI IP Miwi +/- 1

description: ribosomal RNA minus


title: Input Miwi +/- 1

description: ribosomal RNA minus


title: MIWI IP Miwi -/- 2

description: ribosomal RNA minus


title: PAR-CLIP with T1 (replicate 3)

description:
Dicer bound RNA fragments, default 3' adapter TCGTATGCCGTCTTCTGCTTGT
dcr-1_4su_1_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dcr-1_4su_2_BC2.qseq.txt.gz 3' adapter TCTCCCATCGTATGCCGTCTTCTGCTTG
dcr-1_4su_3_noBC.qseq.txt.gz 3' adapter TCGTATGCCGTCTTCTGCTTGT


title: PAR-CLIP with T1/V1, replicate 2


title: Input Miwi ADH/- 2

description: ribosomal RNA minus


title: MIWI IP Miwi +/- 2

description: ribosomal RNA minus


title: Input Miwi -/- 1

description: ribosomal RNA minus


title: MIWI IP Miwi ADH/- 1

description: ribosomal RNA minus


title: Mov10l1 s fl/- rep1

description: Directional

data_processing:
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis.The unique reads extracted after mapping with Tophat were further mapped to the mRNAs of Ensemble genes with Bowtie software. Reads Per Kilobase of transcript per Million (RPKM) values were calculated for each gene by using (1) A = the number of reads perfectly mapped to either of mRNA variants in sense orientation, (2) B = the mean length of the mRNA variants, and (3) C = the number of unique reads extracted after mapping with Tophat (RPKM = A(103/B)(106/C)).
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [Mov10l1_fl_+ rep1 RPKM] [Mov10l1_fl_+ rep2 RPKM] [Mov10l1_fl_+ rep3 RPKM] [Mov10l1_s_fl_- rep1 RPKM] [Mov10l1_s_fl_- rep2 RPKM] [Mov10l1_s_fl_- rep3 RPKM]

value: Mov10l1 s fl/-


title: Mov10l1 fl/+ rep3

description: Directional

value: Mov10l1 fl/+


title: Mov10l1 s fl/- rep2

description: Directional


title: Mov10l1 fl/+ rep2

description: Directional


title: Mov10l1 fl/+ rep1

description: Directional


title: Miwi+/- late sc rep3

description: Directional

data_processing:
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis.The unique reads extracted after mapping with Tophat were further mapped to the mRNAs of Ensemble genes with Bowtie software. Reads Per Kilobase of transcript per Million (RPKM) values were calculated for each gene by using (1) A = the number of reads perfectly mapped to either of mRNA variants in sense orientation, (2) B = the mean length of the mRNA variants, and (3) C = the number of unique reads extracted after mapping with Tophat (RPKM = A(103/B)(106/C)).
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [Miwi+-rep1 RPKM] [Miwi+-rep2 RPKM] [Miwi+-rep3 RPKM] [Miwi--rep1 RPKM] [Miwi--rep2 RPKM] [Miwi--rep3 RPKM]

value: Miwi+/-

tag: genetic background

value: mixed C57BL/6 and 129


title: Miwi-/- late sc rep2

description: Directional

value: Miwi-/-


title: Miwi+/- late sc rep1

description: Directional


title: Miwi+/- late sc rep2

description: Directional


title: Miwi-/- late sc rep1

description: Directional


title: Mov10l1 s fl/- rep3

description: Directional


title: 18 dpp

description: Directional

data_processing:
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis.The unique reads extracted after mapping with Tophat were further mapped to the mRNAs of Ensemble genes with Bowtie software. Reads Per Kilobase of transcript per Million (RPKM) values were calculated for each gene by using (1) A = the number of reads perfectly mapped to either of mRNA variants in sense orientation, (2) B = the mean length of the mRNA variants, and (3) C = the number of unique reads extracted after mapping with Tophat (RPKM = A(103/B)(106/C)).
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [6dpp RPKM] [10dpp RPKM] [15dpp RPKM] [18dpp RPKM] [22dpp RPKM] [28dpp RPKM] [40dpp RPKM]

source_name: 18 dpp testis

value: 18 dpp

value: testis


title: 10 dpp

description: Directional

source_name: 10 dpp testis

value: 10 dpp


title: 28 dpp

description: Directional

source_name: 28 dpp testis

value: 28 dpp


title: 40 dpp

description: Directional

source_name: 40 dpp testis

value: 40 dpp


title: 15 dpp

description: Directional

source_name: 15 dpp testis

value: 15 dpp


title: 6 dpp

description: Directional

source_name: 6 dpp testis

value: 6 dpp


title: Stambp-ps1+/- small RNA

description:
Directional
linker TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC

data_processing: Linker sequences were trimmed. Genome build not applicable. Supplementary file contains small RNA sequence and read number

source_name: 23 dpp testes

extract_protocol:
RNA was harvested using Trizol reagent from testes.
Total RNAs were isolated from testes of 23 dpp Stambp-ps1+/- and Stambp-ps1-/- mice, and then 20 μg of the total RNAs were loaded on 15% denaturing polyacrylamide gels. Small RNAs ranging in size between from 15 to 40 nt were gel purified and used for library construction with TruSeq Small RNA Sample Prep Kit (Illumina).

value: 23 dpp


title: early-P

description: Unstranded

data_processing:
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis. RPKM values of Ensemble genes were calculated by using Cufflinks software.
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [L/Z RPKM] [early-P RPKM] [mid-P RPKM] [late-P/D RPKM] [RS RPKM]

source_name: early-Pachytene spermatocytes

value: early-Pachytene spermatocytes


title: mid-P

description: Unstranded

source_name: mid-Pachytene spermatocytes

value: mid-Pachytene spermatocytes


title: Stambp-ps1-/- small RNA


title: L/Z

description: Unstranded

source_name: Leptotene/Zygotene spermatocytes

value: Leptotene/Zygotene spermatocytes


title: Miwi-/- early RS rep3

description: Unstranded

data_processing:
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis. RPKM values of Ensemble genes were calculated by using Cufflinks software.
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [Miwi+-rep1 RPKM] [Miwi+-rep2 RPKM] [Miwi+-rep3 RPKM] [Miwi--rep1 RPKM] [Miwi--rep2 RPKM] [Miwi--rep3 RPKM]

source_name: early round spermtid

value: early round spermatid


title: 22 dpp

description: Directional

source_name: 22 dpp testis

value: 22 dpp


title: RS

description: Unstranded

source_name: Round spermatids

value: Round spermatids


title: Miwi-/- early RS rep1

description: Unstranded


title: late-P/D

description: Unstranded

source_name: late-Pachytene/Diplotene spermatocytes

value: Miwi+/-

value: late-Pachytene/Diplotene spermatocytes


title: Miwi+/- early RS rep3

description: Unstranded

value: mixed C57BL/6 and 129


title: Miwi-/- early RS rep2

description: Unstranded

value: Miwi-/-


title: Miwi+/- early RS rep1

description: Unstranded


title: Miwi+/- early RS rep2

description: Unstranded


title: Miwi-/- late sc rep3

description: Directional

value: late spermatocyte


title: AV-R10

status: Public on Nov 19 2014

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: FPKM

source_name: Thymic Lymphoma

extract_protocol:
RNA from the thymic lymphoma tissues were extracted using the TRIZOL LS method
Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Mice at 10 weeks were injected with Ad-mCherry or Ad-CRE-mCherry virus directly into the lymphoma and sample tissue was collected 48 hours after infection for RNA extraction

tag: mice age

value: 10 weeks

tag: treatment

value: Ad-CRE-mCherry


title: AV-R9


title: AV-R4

value: Ad-mCherry


title: AV-R8


title: AV-R5


title: AV-R6


title: AV-R7


title: AV-R3


title: Del_SCR_Cast_11 [Illumina HiSeq 2000]

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description:
Del_SCR_Cast_11.bedgraph
Del_SCR_Cast_11(129).bedgraph
Del_SCR_Cast_11(Cast).bedgraph

data_processing:
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/) on 14/02/2014
Reads were aligned to in silico constructed versions of the 129S1 and CastEiJ genomes using Tophat2 running Bowtie2.
Mapped reads were split into 129, Cast or unknown using custom scripts and variant data, only variant bases sequenced with Phred score > 20 (on standard 33 offset) were considered for allele calling
BedGraphs were generated using bedtools v2.17.0 genomecov script with standard settings.
genome build:mm9

source_name: embryonic stem cells

growth_protocol: All cells were maintained on gelatin-coated plates in ES media supplemented with LIF and two inhibitors (2i, CHIR99021 and PD0325901).

extract_protocol:
RNA was isolated using Trizol (Life Technologies) and DNase treated prior to library construction.
NEBNext mRNA Library Prep Reagent Set for Illumina

treatment_protocol: SCR deleted clones contain a deletion of the Sox2 downstream enhancer which lies between Chr3:34653922-34661217 in the M. musculus genome build mm9.  Deletions were generated in F1 ES cells using gRNA104 (TAGCATACGTCACGCCGGAA) and gRNA112 (ACTGTTCTCGAACACTCTGT) to target the Cas9 nuclease.

value: ΔSCR(Cast), clone 11

tag: passage

value: 5 after colony seletion


title: Del_SCR_129/Cast_1_p5 [Illumina HiSeq 2000]

description:
Del_SCR_129Cast_1_p5.bedgraph
Del_SCR_129Cast_1_p5(129).bedgraph
Del_SCR_129Cast_1_p5(Cast).bedgraph

value: ΔSCR(129/Cast), clone 1


title: Del_SCR_129_37 [Illumina HiSeq 2000]

description:
Del_SCR_129_37.bedgraph
Del_SCR_129_37(129).bedgraph
Del_SCR_129_37(Cast).bedgraph

value: ΔSCR(129), clone 37