title: A0514_Male_Input

city: College Station

first: Kory

last: Douglas

address: 4458 TAMU

institute: Texas A&M University

description: Illumina ChIP-seq

data_processing:
Illumina CASAVA 1.7 software was used for basecalling.
Adapter sequences were removed from the raw reads by custom scripts.
The short reads were aligned to the opossum reference genome (UCSC monDom5) using Bowtie v. 1.1.2.
Significant Peaks were called using MACS v. 1.0.1.
Genome_build: MonDom5
Supplementary_files_format_and_content: BED files containing peaks, peak coordinates, and -10*log10(pvalue) of each peak.

organism: Monodelphis domestica

source_name: ear fibroblasts, input

growth_protocol: Primary fibroblasts were isolated from ear clips and grown/expanded in complete culture media (IMDM, FBS, ITS, CaCl2, L-glutamine, and Penicillin/Streptomycin) at 33 degrees Celsius.

extract_protocol:
Chromatin was extracted, digested with micrococcal nuclease, pooled (sisters only), and quantified using Qubit. Chromatin was equally divided and ChIP was performed using the indicated antibodies. Samples were purified using the Minelute PCR Purification Kit by Qiagen. Enrichment was checked by qPCR.
ChIP-seq libraries were constructed using a modified version of the Illumina TruSeq RNA Sample Prep protocol. All libraries were constructed at Global Biologics, Columbia, MO.

tag: strain/background

value: LL1 Mother (A0359) X LL2 Father (A0342)

tag: developmental stage

value: adult

value: male

value: ear fibroblasts

value: 4 to 6

tag: chip antibody


title: aPD1_mLama4_pos_rep1

status: Public on Nov 07 2014

type: SRA

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

country: USA

institute: Washington University in St.Louis

library_source: transcriptomic

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 50bpX25bp pair-end! 10 sequencing. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm9 genome using TopHat with following options -G mm9.mrna.10.31.gtf --prefilter-multihits --segment-length 20 --max-multihits 15. Geneexpression was obtained using ESAT software tool(http://garberlab.umassmed.edu/software/esat/) focused on analysis of 3’end targetedRNA-Seq. The following parameters were used: -task "score3P" –normalizedOutput -window 1000 -maxExtension 3000 -maxIntoGene 2000 -stranded –collapseIsoforms.
Genome_build: mm9
Supplementary_files_format_and_content: comma delimited file that includes normalized count data for each sample and tab delimited file with barcode annotations

molecule: total RNA

organism: Mus musculus

source_name: tumor infiltrating lymhpocytes

extract_protocol:
For sorting of mLama4-specific cells, tumour-infiltrating cells were enriched for CD45+ cells using CD45 cell purification magnetic beads (Miltenyi Biotec). CD45 enriched cells were then sorted gating for PI- CD3ε+ CD8α+ mLama4-tetramer-PE+ or PI- CD3ε+ CD8α+ mLama4-tetramer-PE- cells. Sorting was performed on a BD FACSAria II (BD Biosciences). Sorted cells were pelleted and processed for RNA analysis. All flow cytometry was performed on the FACSCalibur (BD Biosciences) or LSR Fortessa (BD Biosciences) and analysed using FlowJo software (TreeStar).
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded using consecutive acid-alkali treatment. Then, second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (New EnglandBiolabs, Ipswich, MA) and after SPRI clean-up, mixture was PCR enriched 14 cycles andSPRI purified to yield final strand specific 3'end RNA-seq libraries
3'end DGE

tag: strain

tag: cell type

value: tumor infiltrating lymhpocytes

tag: treatment


title: M_phase_synchronized_GCC biological replicate #2

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
Fission yeast cells synchronized in the M phase of the cell cycle
M_combined_ra.out, M_combined_ra.out.datmult

library_source: genomic

data_processing:
Library strategy: Genome conformation capture
Paired-end reads were aligned using the SOAP algorithm not allowing any mismatches or unassigned bases (http://soap.genomics.org.cn/)
The dimensional interaction networks were constructed using the topography suit Rodley et al. 2009.
genome build: ASM294v2

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: nuc2-663 (M phase) synchronized Schizosaccharomyces pombe

growth_protocol: Schizosaccharomyces pombe strains were recovered from -80°C on YES (2% agar) plates (26°C, 4 days). YES medium (12 ml) starter cultures were inoculated and incubated (26°C, 200 rpm) until the OD595 measured ~0.8 (~24 h).

extract_protocol:
Chromatin isolation and GCC were performed as in Rodley et al. 2009 and Cagliero et al. 2013, with modifications; Following synchronization, cultures (200 ml) were cross-linked, washed, and suspended in FA-lysis buffer. Aliquots containing ~9.5*108 cells were made up to a volume of 330 μl with FA-lysis buffer and the cell walls were digested with T20 Zymolyase (70 μl at 75mg/ml; 35°C, 40 min with periodic inversion) before heat inactivation (60°C, 5 min). Acid washed glass beads (500 μl) were added to each sample before disruption in a Geno/Grinder (-20°C; 1,750 rpm, 2 x 30 sec on 60 sec off; SPEX sample prep 2010). Glass beads were removed by the centrifugation of chromatin through a pin hole into a clean tube (2,000 rpm, 1 min). Chromatin was pelleted (13,000 rpm, 15 min, 4°C), washed with FA-lysis buffer, suspended in chromatin digestion buffer and stored (-80°C).
AseI (100U, New England Biolabs, 37°C, 2 h). A ligation control (sees below and Supplementary Table S8) was added to the AseI digested chromatin, samples were diluted (~20-fold) and ligated with T4 DNA ligase (20U, Invitrogen). Following ligation, cross-links, protein and RNA were removed. pUC19 plasmid (27.4pg/2ml) was added as a sequence library preparation ligation control before phenol:chloroform (1:1) extraction and column purification.

treatment_protocol: Synchronization cultures (125 ml EMM2, in baffled flasks) were inoculated with starter culture to an OD595 = ~0.05 and incubated (26°C, 120 rpm). Cultures were grown for four generations (OD595 ~0.8) before synchronization was induced by the addition of pre-warmed EMM2 medium (125 ml, 46°C), instantly rising the temperature of the culture to the restrictive temperature (36°C). Cultures were incubated in a hot water bath (36°C, 140 rpm, for 4 h) to complete synchronization.

tag: cell cycle

value: M phase


title: A0514_Male_H3K9Ac

state: TX

description: Illumina ChIP-seq

source_name: ear fibroblasts, H3K9Ac ChIP

tag: Sex

tag: passages

value: H3K9Ac (Upstate-Millipore #CS200583; Lot DAM1601913)


title: A0514_Male_H3K27me3

description: Illumina ChIP-seq

source_name: ear fibroblasts, H3K27me3 ChIP

value: H3K27me3 (Upstate-Millipore #07-449; Lot JBC1873477)


title: aPD1_mLama4_neg_rep1


title: M_phase_synchronized_GCC biological replicate #1


title: A0514_Male_H3K9me3

description: Illumina ChIP-seq

source_name: ear fibroblasts, H3K9me3 ChIP

value: H3K9me3 (Upstate-Millipore #07-442; Lot JBC1865906)


title: rox_MOF

city: Umeå

first: Jan

last: Larsson

state: Västerbotten

address: University Hospital, buildings 6 K and 6 L

department: Molecular Biology

country: Sweden

institute: Umeå University

description: ChIP-seq

data_processing:
Alignment to : Applied Biosystems Bioscope software v1.2.1
Enrichment ratio calculation: Average read-count per nucleotide was calculated for IP and input samples. For regions where the IP sample had at least the average read-count, a ratio of IP-input (in log2 scale) was calculated. If the read count in the input was below the average read-count (in the input sample) it was set to the average. All ratio values were then adjusted by reducing each value with the average read-count in IP minus the average read-count in input. This linear adjustment was to normalize for differences in sequencing depth of IP and input. Ratio values every 10bp were extracted across the genome.
Ratio values every 10bp were extracted across the genome, median smoothed using a window size of 500bp and windows with fewer than 25 data points were discarded.
Genome_build: Drosophila melanogaster reference sequence: release 5. Drosophila simulans reference sequence: release 2.
Supplementary_files_format_and_content: BED files with ratio IP/input

organism: Drosophila melanogaster

source_name: salivary glands from 3rd instar larvae

growth_protocol: larvae were grown at 25°C in potato mash

extract_protocol:
We used 125 salivary glands for each sample. The glands were dissected in PBS and directly transferred to 2% formaldehyde in PBS with 0.1% Triton X-100 for 1–2 min for fixation. The glands were then washed in PBS and glycine was added to a final concentration of 0.125 M. The glands were then washed once in PBS, 1 mM PMSF, protease inhibitor cocktail (Roche) followed by two washes in TBS, 1 mM PMSF, and protease inhibitor cocktail. The samples were homogenized in 250 μl lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1]). Approximately 60 μl glass beads were added prior to sonication for 2 × 10 sec at output level 1, 2 × 10 sec at output level 2, 2 × 10 sec at output level 3 and finally 2 × 10 s at output level 4 (Misonix XL2020, microtip). The samples were cleared by centrifuging for 10 min at 16,000 g. 150 μl of cell lysate was diluted by a factor of ten in ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.0], 167 mM NaCl), and protein inhibitors were added. The diluted lysate was precleared by incubation with 30 μl (60 μl for salivary glands) of Dynabeads conjugated to Protein A (Dynal) and preblocked by equilibration in 150 μl ChIP buffer containing 12 μg (24 μg for salivary glands) sonicated herring sperm DNA. The cleared lysates were then incubated with 3 μl anti-MSL1 , 2 μl anti-MSL2, or 3 μl anti-MOF (from Mitzi Kuroda, Harvard Medical School) antibodies overnight at 4 °C. The antibody complexes were precipitated by incubation with DNA-blocked Protein A Dynabeads for 1 h at 4 °C. The beads were washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl [pH 8.0], 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl [pH 8.0], 500 mM NaCl), once with LiCl-containing buffer (250 mM LiCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate), and twice with TE Buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA). The protein/DNA complexes were eluted from the antibodies by incubating them for 2 × 15 min at room temperature in 250 μl Elution buffer (1% SDS, 0.1 M NaHCO3) with rotation. NaCl was added to a final concentration of 200 mM, and protein/DNA crosslinks were reversed by heating at 65 °C for 4 h. A total of 10 μl of 0.5 M EDTA, 20 μl of 1M Tris-HCl [pH 6.5], and 1 μl of 20 mg/ml proteinase K were added before an additional incubation at 45 °C for 1 h. The DNA was recovered by phenol/chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA was then dissolved in 24 μl water.
SOLiD (TM) Library Preparation - Uppsala Genome Center ; Size selection (100-150 bp + adapters 90bp < 250bp)

tag: genotype

value: rox1 rox2 mutants (y w roX1[ex6] Df(1)roX2[52] P[w+ 4Δ4.3]/Y)

value: MOF

tag: tissue

value: salivary gland


title: aCTLA4_mLama4_pos_rep3


title: A0514_Male_H3K4me3

description: Illumina ChIP-seq

source_name: ear fibroblasts, H3K4me3 ChIP

value: H3K4me3 (Upstate-Millipore #07-473; Lot JBC1888194)


title: aPD1_mLama4_neg_rep2


title: rox_MSL2

description: ChIP-seq


title: G2_phase_synchronized_GCC biological replicate #1

description:
Fission yeast cells synchronized in the G2 phase of the cell cycle
G2_combined_ra.out, G2_combined_ra.out.datmult

source_name: cdc25-22 (G2 phase) synchronized Schizosaccharomyces pombe

value: G2 phase


title: G1_phase_synchronized_GCC biological replicate #2

description:
Fission yeast cells synchronized in the G1 phase of the cell cycle
G1_combined_ra.out, G1_combined_ra.out.datmult

source_name: cdc10-129 (G1 phase) synchronized Schizosaccharomyces pombe

value: G1 phase


title: aCTLA4_mLama4_neg_rep3


title: G1_phase_synchronized_RNA-seq biological replicate #2

data_processing:
RNA sequences (90 bp) were quality assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
RNA sequence analysis was performed using the cufflinks suite  and -T operator
Genome_build: ASM294v2

extract_protocol: For RNA extraction, cells were harvested from 12 ml of each synchronized cell culture prior to cross-linking (4,000 rpm, 2 min, RT), washed with 5 ml of AE buffer (50 mM Sodium Acetate, 10 mM EDTA, pH 5.3), and suspended in AE buffer (400 μl). Cell suspensions were transferred to tubes containing an equal volume of phenol/chloroform/isoamyl alcohol (24/24/1 Ambion) and 400 μl of acid washed glass beads (Invitrogen). Tubes were transferred to a chilled block (-20°C) in a Geno/Grinder (SPEX sample prep 2010) and the cells were lysed (1,750 rpm, 8 x 30 sec on 60 sec off). Lysis was completed by freeze (-80oC, ~15 min), thaw before centrifugation (14,500 rpm, 5 min, 4°C). The aqueous phase was extracted three times with an equal volume of phenol/chloroform/isoamyl alcohol. RNA was isolated by precipitation with 1/10th volume ammonium acetate (5 M) and 2 volumes of 100% ethanol at -80°C (>30 min/over-night) before centrifugation (14,500 rpm, 10 min, 4°C). RNA was washed with 70% ethanol (350 μl; 14,500 rpm, 5 min, 4°C) and air dried (37°C, ~15 min). RNA pellets were suspended in RNASecure (80 μl; Ambion) and dissolved by heating (60°C, 10 min).


title: aCTLA4_mLama4_pos_rep2


title: RM30 revertant from RM55

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: Sample 2

data_processing: Processed data files not available.

organism: Glycine max

source_name: shoot tips

growth_protocol: Soybean plants were grown in the greenhouse and the shoot tips were harvested 2-3 weeks after germination.

extract_protocol:
Genomic DNA was isolated from freeze dried shoot tips dissected using a microprep method (Dellaporta, 1993) with minor modifications (Zabala and Vodkin,  2003).
Library construction and high-throughput sequencing was carried out using DNA-Seq technology with Illumina HiSeq2000 at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.
The shotgun libraries were constructed using the Kapa Biosystems kit with one modification: after adaptor ligation, libraries were treated with the EZ DNA Methylation-Lightning kit (Zymo Research). Bisulfite-treated libraries were amplified with the Kapa HiFi Uracil+ DNA Polymerase. Each library was sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000 using a TruSeq SBS sequencing kit version 3. The sequence reads were 100-nt in length. Fastq files were generated with the software Casava 1.8.2 (Illumina).

treatment_protocol: optimal green house growth conditions

tag: genotype/variation

value: RM30-R* seed color line

value: shoot tips


title: rox_MSL1

description: ChIP-seq


title: aCTLA4_mLama4_neg_rep2


title: RM55 (PI547559)

description: Sample 1

value: RM55-rm seed color line


title: G1_phase_synchronized_GCC biological replicate #1


title: aCTLA4_mLama4_neg_rep1


title: SCNT2C_Kdm4dmutOE_2_RNAseq

city: Brookline

first: Yuting

last: Liu

state: MA

address: 82 Walnut St. Unit 3

department: Department of Genetics

institute: Harvard Medical School

data_processing:
Sequence reads were mapped against the mouse genome (mm9) with Novoalign. All programs were performed with default setting (unless otherwise specified). The unique mapped reads (about 70% of total reads) were subsequently assembled into transcripts guided by reference annotation (UCSC gene models) with Cufflinks v2.0.2. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Kdm4dmut-OE 2-cell SCNT embryos

growth_protocol: Cumulus cells were collected from adult BDF1 females through superovulation by injecting 7.5 IU of pregnant mare serum gonadotropin (PMSG; Harbor) and 7.5 IU of human chroinic gonadotropin (hCG; Millipore). Fifteen hours after the hCG injection, cumulus-oocyte complexes (COCs) were collected from the oviducts and briefly treated with Hepes-buffered potassium simplex-optimized medium (KSOM) medium containing 300 U/ml bovine testicular hyaluronidase (Calbiochem # 385931) to obtain dissociated cumulus cells.

extract_protocol: The embryos were directly lysed and used for cDNA synthesis using SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech). After amplification, the cDNA samples were fragmented using Covaris sonicator (Covaris). Sequencing libraries were made with the fragmented DNA using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer’s instruction (New England Biolabs). Single end 50 bp sequencing was done on Hiseq 2500 (Illumina).

value: Kdm4dmut-OE 2-cell SCNT embryos

tag: cell/embryos number

value: 25 embryos

value: donor cell:(C57BL/6J x CAST/EiJ) F1, recipient oocyte:B6D2F1


title: G2_phase_synchronized_GCC biological replicate #2


title: aCTLA4_mLama4_pos_rep1

value: tumor infiltrating lymhpocytes


title: RM30-R* (R155_RM30_400)

description: Sample 13

data_processing:
75 or 100bp (from HiSeq2000) reads were aligned to soybean reference genome cv. Williams 82 (Gmax_109 version 1.0), using BOWTIE v1 (Langmead et al., Genome Biology, 2009) with up to 3 mismatches and 25 alignments allowed.
RNA-Seq data was normalized in Reads per Kilobase of Gene Model Per Million Mapped Reads (RPKM) (Mortazavi et al., Nat Met 5:621-628, 2008).
Genome_build: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)
Supplementary_files_format_and_content: tab-delimited text file with RPKM values

source_name: Seed coat

growth_protocol: Soybean plants were grown in the greenhouse and the seeds were harvested at different stages of development based on pod/seed size. Seed coats were dissected from seeds weighing betwen 100-500 mg fresh weight and separated in subgroups at 100 mg intervals. All tissues were fast frozen in liquid nitrogen, lyophillized and stored at -70C untill further use.

extract_protocol:
Extrction of total RNA from seed coats with dark pigmentation required the use of a modified extraction protocol which prevents procyanidins from binding the RNA and is based on the procedure from Wang et al. Plant Physiology, 1994.
Library construction and high-throughput sequencing was carried out using RNA-Seq technology with Illumina HiSeq2000 at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.

value: 400-500mg seed weight stage

value: seed coat


title: SCNT2C_Kdm4dOE_2_RNAseq

source_name: Kdm4d-OE 2-cell SCNT embryos

value: Kdm4d-OE 2-cell SCNT embryos


title: RM38-r (R156_RM38_300)

description: Sample 12

value: RM38-r seed color line

value: 300-400mg seed weight stage


title: SCNT2C_Kdm4dOE_1_RNAseq


title: RM38-r (R112_RM38_300)

description: Sample 10

value: 300-400mg seed weight stage (desiccating)


title: RM30-R* (R110_RM30_300)

description: Sample 9


title: wt_input

description: ChIP-seq

value: wild type (Oregon R)

value: none (input)

value: salivary gland


title: wt_MOF

description: ChIP-seq

value: MOF


title: wt_MSL2

description: ChIP-seq


title: rox_input

description: ChIP-seq

value: rox1 rox2 mutants (y w roX1[ex6] Df(1)roX2[52] P[w+ 4Δ4.3]/Y)


title: SCNT2C_1_RNAseq

source_name: 2-cell SCNT embryos

value: 2-cell SCNT embryos

value: 40 embryos


title: SCNT2C_2_RNAseq


title: RM38-r (R113_RM38_400)

description: Sample 8


title: SCNT1C_2_RNAseq

source_name: 1-cell SCNT embryos

value: 1-cell SCNT embryos

value: 36 embryos


title: RM38-r (R125_RM38_300)

description: Sample 6


title: RM30-R* (R111_RM30_400)

description: Sample 7

value: RM30-R* seed color line


title: IVF2C_2_RNAseq

source_name: 2-cell IVF embryos

value: 2-cell IVF embryos

value: 25 embryos

value: C57BL/6J oocyte x CAST/EiJ sperm


title: IVF2C_1_RNAseq


title: RM30-R* (R122_RM30_200)

description: Sample 3

value: 200-300mg seed weight stage

value: seed coat


title: RM30-R* (R123_RM30_300)

description: Sample 5

value: 300-400mg seed weight stage


title: RM38-r (R124_RM38_200)

description: Sample 4

value: RM38-r seed color line


title: IVF1C_2_RNAseq

source_name: 1-cell IVF embryos

value: 1-cell IVF embryos

value: 31 embryos


title: SCNT2C_Kdm4dmutOE_1_RNAseq

value: Kdm4dmut-OE 2-cell SCNT embryos

value: donor cell:(C57BL/6J x CAST/EiJ) F1, recipient oocyte:B6D2F1


title: st10.5_Smad23_ChIP_rep2

city: Irvine

first: William

last: Chiu

state: CA

address: Room 4410 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California, Irvine

description: processed data file: st_10.5_Smad2_peaks_MACS_SISSRs_overlap.txt

data_processing:
Raw ChIP-seq reads from the replicates were pooled and mapped to an indexed Xenopus tropicalis genome using Bowtie (v. 0.12.9) (Langmead et al. 2009), only uniquely mapped reads were retained, i.e. parameters: -m 1
MACS (v. 2.0.10) (Zhang et al. 2008) and SISSRs (v. 1.4) (Jothi et al. 2008) were used for peak calling. Effective genome size is 1.16e+09. MACS was run with default setting, Sissrs was run with parameter -a
Peaks were assigned to the nearest genes, using BEDTools (v 2.16.2) (Quinlan and Hall 2010), based on the following criteria:  peak summits need to lie within 10 kb upstream of the 5’ end, within the gene body (5’ UTRs, exons, introns, and 3’UTRs), or 10 kb downstream of the 3’ end of the gene.
Genome_build: Xenopus tropicalis genome build v 7.1
Supplementary_files_format_and_content: bed format of peaks only called by both MACS and Sissrs

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were cultured in 1/9X MMR at 25°C until the indicated stage.

extract_protocol:
The fixed embryos were homogenized with an Eppendorf tube pestle and microfuged at 14,000rpm, 4°C for 15 minutes. The pellets, which contain chromatin, were re-suspended in 750ul RIPA buffer and sonicated on ice using a Branson Digital Sonifier 450 (18% power output, 20 sec per pulse, 10 pulses) resulting in DNA fragmentation with a maximum between 200-500bp long. The resulting samples were microfuged at 4°C and 14,000 rpm for 20 minutes to remove insoluble cellular debris. Supernatant containing fragmented chromatin was “pre-cleared” by incubating with 20μl Protein A-coated Dynabeads (Invitrogen) for 2 hour at 4°C. 50 embryo equivalent (eeq) volume of the chromatin supernatant was frozen for use as “input control”. Antibodies were pre-bound to 20μl of Protein A Dynabeads (per batch of 200 embryos) by incubating at 4°C for 30 min. Sonicated chromatin fragments were then added to antibody-bound Dynabeads and incubated overnight at 4°C on an end-over-end rotator. The next day, supernatants were discarded, the recovered beads were washed once with ice-cold ChIP wash solution I (50mM HEPES-KOH pH7.5, 2mM EDTA, 150mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100, 1mM DTT, and 0.4mM PMSF), ChIP wash solution II (50mM HEPES-KOH pH7.5, 2mM EDTA, 500mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100, 1mM DTT, and 0.4mM PMSF), and ChIP wash solution III (0.25 M LiCl, 1 mM EDTA, 10 mM Tris-HCl pH 8.0, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM DTT, and 0.4 mM PMSF), and finally ice-cold TE (10mM Tris, 1mM EDTA, 1 mM DTT, and 0.4 mM PMSF). The DNA was then eluted with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C for 6 hours to overnight. Frozen sonicated input control chromatin frozen was diluted with elution buffer (3-fold) and also incubated at 65°C. On the following day the samples were treated with RNAse A (0.2μg/μl) for 2hr at 37°C, followed by Proteinase K (0.2μg/μl) for 2hr at 55°C, followed by phenol/chloroform extraction and ethanol precipitation. DNA pellets were resuspended in Qiagen EB solution. For ChIP-qPCR analyses on enriched chromatin fragments, immunoprecipitated DNA was amplified using specific primers to detect enrichment in the denoted genomic regions. Results were normalized against input DNA.
Libraries were prepared using Bioo Scientific NEXTflex™ ChIP-seq Kit (Cat# 5143-01)

treatment_protocol: Two thousand embryos were cultured until early gastrula (stage 10.5). Embryos were crosslinked in batches of 200 embryos with 1ml 1% formaldehyde in 1/9XMMR at room temperature for 45 minutes with gentle rocking. Crosslinking reactions were neutralized by removal of the formaldehyde solution and incubation in 1ml 0.125M glycine for 5 minutes at room temperature. Processed embryos were washed twice with ice-cold RIPA buffer (50 mM Tris-HCl pH7.4, 150mM NaCl, 1mM EDTA, 0.25% sodium deoxycholate, 1% NP40, 0.1% SDS, 0.5 mM DTT, and Roche cOmplete protease inhibitor cocktail). The samples can be flash-frozen in liquid nitrogen and stored at -80°C

value: Nigerian

value: mid-gastrula stage (st10.5)

value: mouse anti-Smad2/3 antibody

tag: chip antibody vendor

value: BD

tag: chip antibody cat. #


title: RM38-r (R43_RM38_100)

description: Sample 2

value: 100-200mg seed weight stage


title: RM30-R* (R154_RM30_300)

description: Sample 11

value: RM30-R* seed color line


title: IVF1C_1_RNAseq

value: 32 embryos


title: st10.5_Smad23_ChIP_rep1


title: Donor_2_RNAseq

source_name: cumulus cells

value: cumulus cells

value: (C57BL/6J x CAST/EiJ) F1


title: RM38-r (R157_RM38_400)

description: Sample 14

value: 400-500mg seed weight stage


title: Donor_1_RNAseq


title: RM30-R* (R42_RM30_100)

description: Sample 1

value: seed coat


title: TIL25_TGGAT.PL19

status: Public on Nov 06 2014

city: Madison;

first: John

last: Doebley

state: WI

address: 425-G Henry Mall

department: Genetics Department

institute: University of Wisconsin - Madison

description: Tissue captured from stem of parent TIL25

data_processing:
Illumina Casava1.8 software used for basecalling.
Pseudotranscriptomes were constructed for all parents by inserting SNPs and short indels into the B73 reference transcriptome (AGP v2).
RNA-Seq reads were aligned to pseudotranscriptomes using Bowtie 1
Counts of reads perfectly aligning to different alleles  were obtained for each gene within each pair of species
Read counts were used in downstream statisctical analysis
Genome_build: B73_Refgenv2
Supplementary_files_format_and_content: Files *.snpspt_trn list maize- and teosinte-specific read counts (columns 11 and 12, respectively) at sites segregating between the two parents in a cross (the cross is specified in the beginning of the file name). Columns 1-10 contain: gene, transcript, position on B73 transcript, allele on B7 3 transcript, position on maize pseudotranscript, allele on maize pseudotranscript, position on teosinte pseudotranscript, allele on teosinte pseudotranscript, chromosome, position on the chromosome,
Supplementary_files_format_and_content: Files *.snpspt_unnorm list read counts (column 9) for a given parent at all sites segregating between this parent and any other parent it is crossed with in this study. Columns 1-8 contain: gene, transcript, position on B73 transcript, allele on B7 3 transcript, position on parent's pseudotranscript, allele on parent's pseudotranscript, chromosome, position on the chromosome

molecule: polyA RNA

organism: Zea mays

source_name: stem tissue from parent TIL25,biological replicate 2

growth_protocol: Plants were grown in growth chambers with a 12 hour dark-light cycle for up to 6 weeks, after which they were moved to a greenhouse.

extract_protocol:
Total RNA was extracted from the plant tissues using a standard TRIzol protocol, quantified by spectrophotometer, and normalized to 1 Ã¬Ã¬in nuclease free water.
We generated polyA selected, strand specific, barcoded RNAseq libraries using a five minute fragmentation time and 12 PCR amplification cycles. Library adapters used balanced barcode sequences of four and five base pairs. Pools of 14 (F1s) or 15 (parents) libraries were sequenced on one Illumina lane each

treatment_protocol: Fifty to 100 milligram samples of the immature ear, leaf, and seedling stem were harvested for RNA extraction during this time. Leaf and seedling stem (including the shoot apical meristem) tissue was collected at the v4 leaf stage. Single ears from maize and F1 hybrid plants were collected when the ears weighed 50 to 100 milligrams with silks just beginning to be visible. Teosinte ears were also collected when silks just started to appear, however, due to the small size of teosinte ears 7 to 16 ears (average of 11.27) from each plant were pooled to obtain ~50 milligrams of tissue.

tag: cultivar

value: teosinte

value: stem


title: TIL15_GCTAT.PL19

description: Tissue captured from stem of parent TIL15

source_name: stem tissue from parent TIL15,biological replicate 1


title: TIL25_ATGCT.PL18

source_name: stem tissue from parent TIL25,biological replicate 1


title: W22_CACTA.PL18

description: Tissue captured from stem of parent W22

source_name: stem tissue from parent W22,biological replicate 2

value: maize


title: TIL15_TGGAT.PL18

source_name: stem tissue from parent TIL15,biological replicate 2


title: TIL14_GCTAT.PL18

description: Tissue captured from stem of parent TIL14

source_name: stem tissue from parent TIL14,biological replicate 2


title: TIL14_ATCGT.PL19

source_name: stem tissue from parent TIL14,biological replicate 1


title: SCNT1C_1_RNAseq

value: 1-cell SCNT embryos

value: 36 embryos


title: TIL11_CGATT.PL19

description: Tissue captured from stem of parent TIL11

source_name: stem tissue from parent TIL11,biological replicate 2


title: TIL10_GTTCT.PL19

description: Tissue captured from stem of parent TIL10

source_name: stem tissue from parent TIL10,biological replicate 2


title: TIL11_ATCGT.PL18

source_name: stem tissue from parent TIL11,biological replicate 1


title: TIL09_TAGCT.PL19

description: Tissue captured from stem of parent TIL09

source_name: stem tissue from parent TIL09,biological replicate 2


title: TIL09_GTTCT.PL18

source_name: stem tissue from parent TIL09,biological replicate 1


title: Pure_invitro_PA14

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

description: PA14 anaerobic in vitro growth

data_processing:
RNA-seq reads were mapped to a hybrid genome containing both PA14 and Vpa sequences using the Stampy aligner with default settings.
Only high-quality mapped reads (Phred-score mapping quality of at least 20) were assigned to the corresponding species
Differential expression was estimated using the R library DESeq
Supplementary_files_format_and_content: TXT files containing the recorded reads-per-gene

organism: Pseudomonas aeruginosa PA14

source_name: PA14 planktonic culture

growth_protocol: Anaerobic growth of P. aeruginosa PA14 and V. parvula (DSM 2008) was performed in an anaerobic workstation (D. Whitley) at 37°C. The growth media used for all experiments was a modified DSMZ medium No. 104 supplemented with 100 mM KNO3 (PYG-KNO3).

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, eukariotic RNA was depleted using MICROBEnrich Kit, subsequently bacterial rRNA was depleted using MICROBExpress kit and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells were harvested after addition of RNA protect buffer (Qiagen) and RNA was isolated from cell pellets using the RNeasy plus kit (Qiagen).

tag: culture

value: Pseudomonas aeruginosa PA14


title: TIL03_TCCAT.PL18

description: Tissue captured from stem of parent TIL03

source_name: stem tissue from parent TIL03,biological replicate 1


title: TIL05_TCCAT.PL19

description: Tissue captured from stem of parent TIL05

source_name: stem tissue from parent TIL05,biological replicate 2


title: TIL01_CAGGT.PL18

description: Tissue captured from stem of parent TIL01

source_name: stem tissue from parent TIL01,biological replicate 1


title: Oh43_TCCTC.PL19

description: Tissue captured from stem of parent Oh43

source_name: stem tissue from parent Oh43,biological replicate 2


title: Mo17_GTAAG.PL18

description: Tissue captured from stem of parent Mo17

source_name: stem tissue from parent Mo17,biological replicate 1


title: Mo17_GTAAG.PL19

source_name: stem tissue from parent Mo17,biological replicate 2


title: st10.5_Foxh1_ChIP_rep2

description: processed data file: st_10.5_Foxh1_peaks_MACS_SISSRs_overlap.txt

source_name: whole embryo

value: Nigerian

value: rabbit anti-Foxh1 antibody

value: custom-made


title: Oh43_TCCTC.PL18

source_name: stem tissue from parent Oh43,biological replicate 1


title: W22_ATGCT.PL19

description: Tissue captured from stem of parent W22

source_name: stem tissue from parent W22,biological replicate 1


title: Ki3_AGTCA.PL19

description: Tissue captured from stem of parent Ki3

source_name: stem tissue from parent Ki3,biological replicate 2


title: TIL01_CAGGT.PL19

source_name: stem tissue from parent TIL01,biological replicate 2


title: CML103_TGTGC.PL18

description: Tissue captured from stem of parent CML103

source_name: stem tissue from parent CML103,biological replicate 1


title: W22_TIL25_CGATT.PL12

description: Tissue captured from stem of cross W22_TIL25

source_name: stem tissue from cross W22_TIL25,biological replicate 2

value: F1 cross


title: B73_GCATG.PL18

description: Tissue captured from stem of parent B73

source_name: stem tissue from parent B73,biological replicate 1


title: W22_TIL25_CGATT.PL12_1


title: B73_GCATG.PL19

description: Tissue captured from stem of parent B73

source_name: stem tissue from parent B73,biological replicate 2


title: TIL10_CGATT.PL18

source_name: stem tissue from parent TIL10,biological replicate 1


title: W22_TIL25_CGATT.PL10

source_name: stem tissue from cross W22_TIL25,biological replicate 1


title: W22_TIL14_CAGGT.PL13_1

description: Tissue captured from stem of cross W22_TIL14

source_name: stem tissue from cross W22_TIL14,biological replicate 2


title: W22_TIL14_CAGGT.PL11

source_name: stem tissue from cross W22_TIL14,biological replicate 1


title: TIL05_TAGCT.PL18

source_name: stem tissue from parent TIL05,biological replicate 1


title: Ki3_AGTCA.PL18

description: Tissue captured from stem of parent Ki3

source_name: stem tissue from parent Ki3,biological replicate 1


title: CML103_TGTGC.PL19

source_name: stem tissue from parent CML103,biological replicate 2


title: W22_TIL14_CAGGT.PL13


title: W22_TIL25_CGATT.PL10_1


title: W22_TIL11_GTTCT.PL10

description: Tissue captured from stem of cross W22_TIL11

source_name: stem tissue from cross W22_TIL11,biological replicate 2


title: 1018-iPS-B

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Reads were mapped to the human reference genome (NCBI/build37.2) using Tophat (version 2.0.4)
Fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks (version 2.0.2)
Genome_build: NCBI/build 37.2
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample

organism: Homo sapiens

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone B

extract_protocol:
RNA was isolated using the Total RNA Purification Micro Kit (Norgen). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (200 ng–1 µg per sample, RIN > 8)
Libraries were prepared using the Illumina TruSeq RNA prep kit

tag: cell line

value: Undifferentiated induced pluripotent stem cells


title: 1018-iPS-C

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone C


title: 1018-iPS-A

source_name: RNA-reprogrammed induced pluripotent stem cell line from adult fibroblasts of a type 1 diabetic subject (ID 1018), clone A


title: W22_TIL11_GCATG.PL13

source_name: stem tissue from cross W22_TIL11,biological replicate 1


title: BJ-iPS-O

source_name: RNA-reprogrammed induced pluripotent stem cell line derived from neonatal BJ fibroblasts, clone O

value: BJ-iPS-O


title: W22_TIL03_TCCAT.PL11

description: Tissue captured from stem of cross W22_TIL03

source_name: stem tissue from cross W22_TIL03,biological replicate 2


title: W22_TIL03_TCCAT.PL11_1


title: BJ-iPS-M

source_name: RNA-reprogrammed induced pluripotent stem cell line derived from neonatal BJ fibroblasts, clone M

value: BJ-iPS-M


title: W22_TIL03_TAGCT.PL12

source_name: stem tissue from cross W22_TIL03,biological replicate 1


title: W22_TIL03_TAGCT.PL12_1


title: BJ-NT-ES-8 rep 2

description: Used for allele-specific gene expression analysis

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 8

value: Undifferentiated nuclear-transfer embryonic stem cells


title: BJ-NT-ES-6 rep 2

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 6


title: W22_TIL14_CAGGT.PL11_1


title: 1018-NT-ES

source_name: Nuclear-transfer embryonic stem cell line derived from adult fibroblasts of a type 1 diabetic subject (ID 1018)


title: W22_TIL01_GTAAG.PL12_1

description: Tissue captured from stem of cross W22_TIL01

source_name: stem tissue from cross W22_TIL01,biological replicate 2


title: W22_TIL01_CGATT.PL11

source_name: stem tissue from cross W22_TIL01,biological replicate 1


title: NYSCF1-ES

source_name: Embryonic stem cell line

value: Undifferentiated embryonic stem cells


title: W22_TIL01_GTAAG.PL12


title: W22_TIL01_CGATT.PL11_1


title: Oh43_TIL25_TGTGC.PL10

description: Tissue captured from stem of cross Oh43_TIL25

source_name: stem tissue from cross Oh43_TIL25,biological replicate 2


title: Oh43_TIL25_GTTCT.PL12

source_name: stem tissue from cross Oh43_TIL25,biological replicate 1


title: BJ-NT-ES-5 rep 2

source_name: Nuclear-transfer embryonic stem cell line derived from neonatal BJ fibroblasts, clone 5


title: BJ fibroblasts

source_name: BJ fibroblast cell line

value: BJ-Fib

value: Fibroblasts


title: W22_TIL11_GTTCT.PL10_1

source_name: stem tissue from cross W22_TIL11,biological replicate 2


title: 1018 fibroblasts

source_name: ID 1018 fibroblast cell line


title: BJ-NT-ES-5 rep 1


title: BJ-NT-ES-6 rep 1


title: W22_TIL11_GCATG.PL13_1

source_name: stem tissue from cross W22_TIL11,biological replicate 1


title: Oh43_TIL25_GTTCT.PL12_1


title: 150_day_Quiescence_3

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.p6
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample

source_name: total RNA extracted from MRC-5 fibroblasts

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

treatment_protocol: MRC-5 fibroblastswere subjected to quiescence using 150 days contact inhibition

tag: population doublings

value: MRC-5 fibroblasts


title: Oh43_TIL15_TGTGC.PL12

description: Tissue captured from stem of cross Oh43_TIL15

source_name: stem tissue from cross Oh43_TIL15,biological replicate 2

value: stem


title: BJ-NT-ES-8 rep 1


title: 150_day_Quiescence_1

value: subjected to quiescence using 150 days contact inhibition


title: 150_day_Quiescence_2


title: Oh43_TIL15_TCCTC.PL11

source_name: stem tissue from cross Oh43_TIL15,biological replicate 1


title: Oh43_TIL15_TGTGC.PL12_1


title: Oh43_TIL15_TCCTC.PL11_1


title: Hen-16-Input2

city: Chicago

first: Guan-Zheng

last: Luo

address: 929 E 57th St

department: Chemistry

institute: UChicago

description: Sample 7

data_processing:
library strategy: m6A-seq (N6-methyladenosine–sequencing)
Align the input and IP sequenced samples to the Columbia reference genome and annotation file (Tair10) by Tophat.
The BEDTools utility GenomeBED was used to divide the aligned accepted hits into 1bp intervals. The read depth was then averaged for each 25 nt discrete, non-overlapping genomic window using an ad hoc R program.
To identify 25 nt windows enriched for m6A editing, the number of reads that mapped to each window for the IP and input sample, and the total reads for each, were compared using Fisher’s exact tests and corrected for multiple testing using Benjamini-Hochberg to reduce FDR to 5%.
Peaks that shared more than 50% overlapping length were defined as recurrent peaks.
Consensus sequences were found by Homer. Gene expression was calculated by Cufflinks using the input sequencing reads.  Gene function analysis (GO enrichment) was performed by DAVID tool. Plant miRNA targets were predicted by psRobot.
Genome_build: Tair10
Supplementary_files_format_and_content: tdf files were generated by IGVTools which can be loaded into IGV for visulization.

organism: Arabidopsis thaliana

source_name: Hen 16_input

growth_protocol: Seedlings were germinated in controlled-environment growth chambers at the University of Chicago greenhouses on a 16-hour light, 8-hour dark cycle.

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq and library preparation were performed according to previous protocols (Dan et. al., 2012) . RNA-Seq was done at UChicago on an Illumina HiSeq machine with 100 bp single end sequencing.

treatment_protocol: Plants were thinned between days 5-7 of growth. Above-ground tissue was harvested between the fifth and seventh hour of the light cycle on day 21. The tissue was flash frozen in liquid nitrogen, ground using a mortar and pestle, and stored at -80 °C.

tag: ecotype

value: whole plant

tag: antibody


title: Oh43_TIL11_TGGAT.PL6

description: Tissue captured from stem of cross Oh43_TIL11

source_name: stem tissue from cross Oh43_TIL11,biological replicate 1


title: Oh43_TIL11_TGGAT.PL12_1

source_name: stem tissue from cross Oh43_TIL11,biological replicate 2


title: Hen-16-IP2

description: Sample 8

source_name: Hen 16_IP

tag: antibody vendor

value: SYSY

tag: antibody cat.#

tag: antibody lot #


title: Oh43_TIL11_TGGAT.PL12


title: Can-0-IP2

description: Sample 4


title: Oh43_TIL25_TGTGC.PL10_1


title: Hen-16-IP1

description: Sample 6


title: Can-0-Input2

description: Sample 3


title: Can-0-IP1

description: Sample 2


title: Oh43_TIL11_TGGAT.PL6_1


title: Can-0-Input1

description: Sample 1


title: Oh43_TIL10_AGTCA.PL13

description: Tissue captured from stem of cross Oh43_TIL10

source_name: stem tissue from cross Oh43_TIL10,biological replicate 1


title: Oh43_TIL09_ATGCT.PL13

description: Tissue captured from stem of cross Oh43_TIL09

source_name: stem tissue from cross Oh43_TIL09,biological replicate 2


title: Oh43_TIL09_ATGCT.PL10_1

source_name: stem tissue from cross Oh43_TIL09,biological replicate 1


title: Oh43_TIL10_TCCTC.PL10_1

source_name: stem tissue from cross Oh43_TIL10,biological replicate 2


title: Oh43_TIL10_TCCTC.PL10


title: Oh43_TIL10_AGTCA.PL13_1


title: Oh43_TIL09_ATGCT.PL13_1


title: Oh43_TIL03_TGTGC.PL13

description: Tissue captured from stem of cross Oh43_TIL03

source_name: stem tissue from cross Oh43_TIL03,biological replicate 2


title: Oh43_TIL03_TGTGC.PL13_1


title: Oh43_TIL03_GTAAG.PL10

source_name: stem tissue from cross Oh43_TIL03,biological replicate 1


title: Oh43_TIL01_TCCTC.PL13

description: Tissue captured from stem of cross Oh43_TIL01

source_name: stem tissue from cross Oh43_TIL01,biological replicate 2


title: Oh43_TIL01_TCCTC.PL13_1


title: Hen-16-Input1

description: Sample 5


title: Oh43_TIL01_TAGCT.PL10_1

source_name: stem tissue from cross Oh43_TIL01,biological replicate 1


title: Oh43_TIL01_TAGCT.PL10


title: Mo17_TIL25_GCTAT.PL12

description: Tissue captured from stem of cross Mo17_TIL25

source_name: stem tissue from cross Mo17_TIL25,biological replicate 2


title: Oh43_TIL09_ATGCT.PL10


title: Mo17_TIL25_CAGGT.PL10_1

source_name: stem tissue from cross Mo17_TIL25,biological replicate 1


title: Mo17_TIL25_GCTAT.PL12_1


title: Mo17_TIL14_ATCGT.PL12

description: Tissue captured from stem of cross Mo17_TIL14

source_name: stem tissue from cross Mo17_TIL14,biological replicate 1


title: Mo17_TIL14_ATCGT.PL12_1


title: Mo17_TIL09_TGGAT.PL13

description: Tissue captured from stem of cross Mo17_TIL09

source_name: stem tissue from cross Mo17_TIL09,biological replicate 2


title: Mo17_TIL14_GTTCT.PL13

source_name: stem tissue from cross Mo17_TIL14,biological replicate 2


title: Oh43_TIL03_GTAAG.PL10_1


title: Mo17_TIL09_TGGAT.PL13_1


title: Mo17_TIL01_TCCAT.PL13

description: Tissue captured from stem of cross Mo17_TIL01

source_name: stem tissue from cross Mo17_TIL01,biological replicate 2


title: Mo17_TIL09_AGTCA.PL11_1

source_name: stem tissue from cross Mo17_TIL09,biological replicate 1


title: Mo17_TIL09_AGTCA.PL11


title: Mo17_TIL01_TCCAT.PL13_1


title: Mo17_TIL01_ATCGT.PL11_1

source_name: stem tissue from cross Mo17_TIL01,biological replicate 1


title: Ki3_TIL14_TAGCT.PL13

description: Tissue captured from stem of cross Ki3_TIL14

source_name: stem tissue from cross Ki3_TIL14,biological replicate 1


title: Ki3_TIL14_TAGCT.PL13_1


title: Ki3_TIL11_ATGCT.PL11

description: Tissue captured from stem of cross Ki3_TIL11

source_name: stem tissue from cross Ki3_TIL11,biological replicate 1


title: Ki3_TIL11_CAGGT.PL12

source_name: stem tissue from cross Ki3_TIL11,biological replicate 2


title: Ki3_TIL11_CAGGT.PL12_1


title: Ki3_TIL14_TCCAT.PL12_1

source_name: stem tissue from cross Ki3_TIL14,biological replicate 2


title: Ki3_TIL09_TAGCT.PL11_1

description: Tissue captured from stem of cross Ki3_TIL09

source_name: stem tissue from cross Ki3_TIL09,biological replicate 2


title: Ki3_TIL11_ATGCT.PL11_1


title: Ki3_TIL09_ATCGT.PL6_1

source_name: stem tissue from cross Ki3_TIL09,biological replicate 1


title: Mo17_TIL14_GTTCT.PL13_1


title: Ki3_TIL09_ATCGT.PL6


title: Ki3_TIL03_GCATG.PL12

description: Tissue captured from stem of cross Ki3_TIL03

source_name: stem tissue from cross Ki3_TIL03,biological replicate 2


title: Ki3_TIL03_AGTCA.PL10

source_name: stem tissue from cross Ki3_TIL03,biological replicate 1


title: Ki3_TIL03_GCATG.PL12_1


title: Ki3_TIL03_AGTCA.PL10_1


title: CML103_TIL25_TCCTC.PL12_1

description: Tissue captured from stem of cross CML103_TIL25

source_name: stem tissue from cross CML103_TIL25,biological replicate 2


title: CML103_TIL25_TCCTC.PL12


title: CML103_TIL14_TGGAT.PL10

description: Tissue captured from stem of cross CML103_TIL14

source_name: stem tissue from cross CML103_TIL14,biological replicate 2


title: CML103_TIL25_GCTAT.PL11_1

source_name: stem tissue from cross CML103_TIL25,biological replicate 1


title: Mo17_TIL01_ATCGT.PL11


title: CML103_TIL25_GCTAT.PL11


title: CML103_TIL14_TGGAT.PL10_1


title: CML103_TIL14_GCTAT.PL13_1

source_name: stem tissue from cross CML103_TIL14,biological replicate 1


title: Ki3_TIL14_TCCAT.PL12


title: CML103_TIL11_GCTAT.PL10

description: Tissue captured from stem of cross CML103_TIL11

source_name: stem tissue from cross CML103_TIL11,biological replicate 2


title: CML103_TIL11_GCTAT.PL10_1


title: CML103_TIL11_ATCGT.PL13

source_name: stem tissue from cross CML103_TIL11,biological replicate 1


title: CML103_TIL11_ATCGT.PL13_1


title: CML103_TIL03_TCCAT.PL10_1

description: Tissue captured from stem of cross CML103_TIL03

source_name: stem tissue from cross CML103_TIL03,biological replicate 2


title: B73_TIL25_CGATT.PL13

description: Tissue captured from stem of cross B73_TIL25

source_name: stem tissue from cross B73_TIL25,biological replicate 2


title: Ki3_TIL09_TAGCT.PL11


title: CML103_TIL03_GTTCT.PL11

source_name: stem tissue from cross CML103_TIL03,biological replicate 1


title: CML103_TIL03_TCCAT.PL10


title: Mo17_TIL25_CAGGT.PL10

source_name: stem tissue from cross Mo17_TIL25,biological replicate 1


title: B73_TIL25_AGTCA.PL12_1

source_name: stem tissue from cross B73_TIL25,biological replicate 1


title: B73_TIL25_CGATT.PL13_1


title: B73_TIL25_AGTCA.PL12


title: B73_TIL14_GCATG.PL11

description: Tissue captured from stem of cross B73_TIL14

source_name: stem tissue from cross B73_TIL14,biological replicate 2


title: B73_TIL14_GCATG.PL10

source_name: stem tissue from cross B73_TIL14,biological replicate 1


title: B73_TIL11_TGGAT.PL11_1

description: Tissue captured from stem of cross B73_TIL11

source_name: stem tissue from cross B73_TIL11,biological replicate 2


title: B73_TIL11_TGGAT.PL11


title: CML103_TIL14_GCTAT.PL13


title: B73_TIL14_GCATG.PL10_1


title: B73_TIL11_GCTAT.PL6

source_name: stem tissue from cross B73_TIL11,biological replicate 1


title: CML103_TIL03_GTTCT.PL11_1


title: B73_TIL11_GCTAT.PL6_1


title: B73_TIL03_TGTGC.PL11

description: Tissue captured from stem of cross B73_TIL03

source_name: stem tissue from cross B73_TIL03,biological replicate 1


title: B73_TIL05_ATGCT.PL6

description: Tissue captured from stem of cross B73_TIL05

source_name: stem tissue from cross B73_TIL05,biological replicate 2


title: B73_TIL05_ATGCT.PL6_1


title: B73_TIL09_ATCGT.PL10_1

description: Tissue captured from stem of cross B73_TIL09

source_name: stem tissue from cross B73_TIL09,biological replicate 1


title: B73_TIL01_GTAAG.PL13_1

description: Tissue captured from stem of cross B73_TIL01

source_name: stem tissue from cross B73_TIL01,biological replicate 2


title: B73_TIL05_ATGCT.PL12_1

source_name: stem tissue from cross B73_TIL05,biological replicate 1


title: B73_TIL03_TGTGC.PL11_1


title: B73_TIL09_ATCGT.PL10


title: W22_CACTA.PL16

description: Tissue captured from leaf of parent W22

source_name: leaf tissue from parent W22,biological replicate 2

value: maize

value: leaf


title: B73_TIL01_GTAAG.PL11

source_name: stem tissue from cross B73_TIL01,biological replicate 1


title: B73_TIL01_GTAAG.PL13


title: W22_ATGCT.PL17

description: Tissue captured from leaf of parent W22

source_name: leaf tissue from parent W22,biological replicate 1


title: B73_TIL01_GTAAG.PL11_1


title: TIL25_ATGCT.PL16

description: Tissue captured from leaf of parent TIL25

source_name: leaf tissue from parent TIL25,biological replicate 1

value: teosinte


title: TIL14_GCTAT.PL16

description: Tissue captured from leaf of parent TIL14

source_name: leaf tissue from parent TIL14,biological replicate 2


title: TIL15_GCTAT.PL17

description: Tissue captured from leaf of parent TIL15

source_name: leaf tissue from parent TIL15,biological replicate 1


title: TIL15_TGGAT.PL16

source_name: leaf tissue from parent TIL15,biological replicate 2


title: TIL11_CGATT.PL17

description: Tissue captured from leaf of parent TIL11

source_name: leaf tissue from parent TIL11,biological replicate 2


title: TIL11_ATCGT.PL16

source_name: leaf tissue from parent TIL11,biological replicate 1


title: B73_TIL14_GCATG.PL11_1

source_name: stem tissue from cross B73_TIL14,biological replicate 2


title: B73_TIL05_ATGCT.PL12


title: TIL10_CGATT.PL16

description: Tissue captured from leaf of parent TIL10

source_name: leaf tissue from parent TIL10,biological replicate 1


title: TIL09_TAGCT.PL17

description: Tissue captured from leaf of parent TIL09

source_name: leaf tissue from parent TIL09,biological replicate 2


title: TIL09_GTTCT.PL16

source_name: leaf tissue from parent TIL09,biological replicate 1


title: TIL05_TAGCT.PL16

description: Tissue captured from leaf of parent TIL05

source_name: leaf tissue from parent TIL05,biological replicate 1


title: TIL05_TCCAT.PL17

source_name: leaf tissue from parent TIL05,biological replicate 2


title: TIL03_TCCAT.PL16

description: Tissue captured from leaf of parent TIL03

source_name: leaf tissue from parent TIL03,biological replicate 1


title: TIL01_CAGGT.PL17

description: Tissue captured from leaf of parent TIL01

source_name: leaf tissue from parent TIL01,biological replicate 2


title: TIL10_GTTCT.PL17

source_name: leaf tissue from parent TIL10,biological replicate 2


title: TIL25_TGGAT.PL17

source_name: leaf tissue from parent TIL25,biological replicate 2


title: Oh43_TCCTC.PL16

description: Tissue captured from leaf of parent Oh43

source_name: leaf tissue from parent Oh43,biological replicate 1


title: TIL01_CAGGT.PL16

source_name: leaf tissue from parent TIL01,biological replicate 1


title: Mo17_GTAAG.PL17

description: Tissue captured from leaf of parent Mo17

source_name: leaf tissue from parent Mo17,biological replicate 2


title: Mo17_GTAAG.PL16

source_name: leaf tissue from parent Mo17,biological replicate 1


title: Ki3_AGTCA.PL17

description: Tissue captured from leaf of parent Ki3

source_name: leaf tissue from parent Ki3,biological replicate 2


title: Ki3_AGTCA.PL16

description: Tissue captured from leaf of parent Ki3

source_name: leaf tissue from parent Ki3,biological replicate 1


title: CML103_TGTGC.PL16

description: Tissue captured from leaf of parent CML103

source_name: leaf tissue from parent CML103,biological replicate 1


title: CML103_TGTGC.PL17

source_name: leaf tissue from parent CML103,biological replicate 2


title: B73_GCATG.PL17

description: Tissue captured from leaf of parent B73

source_name: leaf tissue from parent B73,biological replicate 2


title: B73_GCATG.PL16

description: Tissue captured from leaf of parent B73

source_name: leaf tissue from parent B73,biological replicate 1


title: TIL14_ATCGT.PL17

source_name: leaf tissue from parent TIL14,biological replicate 1


title: W22_TIL25_TAGCT.PL5_1

description: Tissue captured from leaf of cross W22_TIL25

source_name: leaf tissue from cross W22_TIL25,biological replicate 2


title: W22_TIL25_ATCGT.PL8

source_name: leaf tissue from cross W22_TIL25,biological replicate 1


title: W22_TIL25_TAGCT.PL5


title: W22_TIL25_ATCGT.PL8_1


title: W22_TIL14_TGTGC.PL9_1

description: Tissue captured from leaf of cross W22_TIL14

source_name: leaf tissue from cross W22_TIL14,biological replicate 2


title: W22_TIL14_CGATT.PL7_1

source_name: leaf tissue from cross W22_TIL14,biological replicate 1


title: W22_TIL14_CGATT.PL7


title: W22_TIL11_TCCTC.PL5_1

description: Tissue captured from leaf of cross W22_TIL11

source_name: leaf tissue from cross W22_TIL11,biological replicate 2


title: Oh43_TCCTC.PL17

source_name: leaf tissue from parent Oh43,biological replicate 2


title: W22_TIL11_TCCTC.PL5


title: W22_TIL11_TCCAT.PL7_1

source_name: leaf tissue from cross W22_TIL11,biological replicate 1


title: W22_TIL03_GTTCT.PL8

description: Tissue captured from leaf of cross W22_TIL03

source_name: leaf tissue from cross W22_TIL03,biological replicate 2


title: W22_TIL11_TCCAT.PL7


title: W22_TIL03_ATCGT.PL7

source_name: leaf tissue from cross W22_TIL03,biological replicate 1


title: W22_TIL01_TCCTC.PL8

description: Tissue captured from leaf of cross W22_TIL01

source_name: leaf tissue from cross W22_TIL01,biological replicate 2


title: W22_TIL03_GTTCT.PL8_1


title: W22_TIL01_TCCTC.PL8_1


title: W22_TIL03_ATCGT.PL7_1


title: W22_TIL01_ATGCT.PL7

source_name: leaf tissue from cross W22_TIL01,biological replicate 1


title: Oh43_TIL25_TCCAT.PL9

description: Tissue captured from leaf of cross Oh43_TIL25

source_name: leaf tissue from cross Oh43_TIL25,biological replicate 2


title: Oh43_TIL25_CGATT.PL8_1

source_name: leaf tissue from cross Oh43_TIL25,biological replicate 1


title: W22_TIL01_ATGCT.PL7_1


title: Oh43_TIL15_GTTCT.PL7

description: Tissue captured from leaf of cross Oh43_TIL15

source_name: leaf tissue from cross Oh43_TIL15,biological replicate 2


title: Oh43_TIL25_CGATT.PL8


title: Oh43_TIL15_GTTCT.PL7_1


title: W22_TIL14_TGTGC.PL9


title: Oh43_TIL25_TCCAT.PL9_1


title: Oh43_TIL11_TAGCT.PL9_1

description: Tissue captured from leaf of cross Oh43_TIL11

source_name: leaf tissue from cross Oh43_TIL11,biological replicate 2


title: Oh43_TIL15_ATGCT.PL5_1

source_name: leaf tissue from cross Oh43_TIL15,biological replicate 1


title: Oh43_TIL11_ATGCT.PL8

source_name: leaf tissue from cross Oh43_TIL11,biological replicate 1


title: Oh43_TIL11_ATGCT.PL8_1


title: Oh43_TIL10_GTAAG.PL7_1

description: Tissue captured from leaf of cross Oh43_TIL10

source_name: leaf tissue from cross Oh43_TIL10,biological replicate 2


title: Oh43_TIL15_ATGCT.PL5


title: Oh43_TIL11_TAGCT.PL9


title: Oh43_TIL10_GTAAG.PL7


title: Oh43_TIL10_GCATG.PL5

source_name: leaf tissue from cross Oh43_TIL10,biological replicate 1


title: Oh43_TIL10_GCATG.PL5_1


title: Oh43_TIL09_CGATT.PL6

description: Tissue captured from leaf of cross Oh43_TIL09

source_name: leaf tissue from cross Oh43_TIL09,biological replicate 2


title: Oh43_TIL09_CGATT.PL6_1


title: Oh43_TIL03_GTAAG.PL5

description: Tissue captured from leaf of cross Oh43_TIL03

source_name: leaf tissue from cross Oh43_TIL03,biological replicate 2


title: Oh43_TIL09_ATGCT.PL9_1

source_name: leaf tissue from cross Oh43_TIL09,biological replicate 1


title: Oh43_TIL03_GTAAG.PL5_1


title: Oh43_TIL09_ATGCT.PL9


title: Oh43_TIL03_AGTCA.PL7

source_name: leaf tissue from cross Oh43_TIL03,biological replicate 1


title: Oh43_TIL03_AGTCA.PL7_1


title: Oh43_TIL01_GCATG.PL8

description: Tissue captured from leaf of cross Oh43_TIL01

source_name: leaf tissue from cross Oh43_TIL01,biological replicate 2


title: Oh43_TIL01_CAGGT.PL7

source_name: leaf tissue from cross Oh43_TIL01,biological replicate 1


title: Mo17_TIL25_TGGAT.PL8_1

description: Tissue captured from leaf of cross Mo17_TIL25

source_name: leaf tissue from cross Mo17_TIL25,biological replicate 2


title: Mo17_TIL25_CAGGT.PL5

source_name: leaf tissue from cross Mo17_TIL25,biological replicate 1


title: Mo17_TIL25_TGGAT.PL8


title: Mo17_TIL25_CAGGT.PL5_1


title: Mo17_TIL14_CAGGT.PL9

description: Tissue captured from leaf of cross Mo17_TIL14

source_name: leaf tissue from cross Mo17_TIL14,biological replicate 1


title: Oh43_TIL01_CAGGT.PL7_1


title: Mo17_TIL14_GCTAT.PL8

source_name: leaf tissue from cross Mo17_TIL14,biological replicate 2


title: Mo17_TIL14_GCTAT.PL8_1


title: Mo17_TIL09_TGGAT.PL9_1

description: Tissue captured from leaf of cross Mo17_TIL09

source_name: leaf tissue from cross Mo17_TIL09,biological replicate 2


title: Mo17_TIL14_CAGGT.PL9_1


title: Mo17_TIL09_ATCGT.PL5

source_name: leaf tissue from cross Mo17_TIL09,biological replicate 1


title: Mo17_TIL01_TGGAT.PL7

description: Tissue captured from leaf of cross Mo17_TIL01

source_name: leaf tissue from cross Mo17_TIL01,biological replicate 2


title: Mo17_TIL01_AGTCA.PL8_1

source_name: leaf tissue from cross Mo17_TIL01,biological replicate 1


title: Ki3_TIL14_TAGCT.PL8

description: Tissue captured from leaf of cross Ki3_TIL14

source_name: leaf tissue from cross Ki3_TIL14,biological replicate 1


title: Mo17_TIL01_AGTCA.PL8


title: Ki3_TIL14_TAGCT.PL8_1


title: Ki3_TIL11_TCCAT.PL8

description: Tissue captured from leaf of cross Ki3_TIL11

source_name: leaf tissue from cross Ki3_TIL11,biological replicate 2


title: Ki3_TIL11_TCCAT.PL8_1


title: Ki3_TIL11_GTAAG.PL9

source_name: leaf tissue from cross Ki3_TIL11,biological replicate 1


title: Ki3_TIL11_GTAAG.PL9_1


title: Ki3_TIL09_TGTGC.PL8

description: Tissue captured from leaf of cross Ki3_TIL09

source_name: leaf tissue from cross Ki3_TIL09,biological replicate 2


title: Ki3_TIL09_GCTAT.PL7

source_name: leaf tissue from cross Ki3_TIL09,biological replicate 1


title: Ki3_TIL09_TGTGC.PL8_1


title: Ki3_TIL09_GCTAT.PL7_1


title: Ki3_TIL03_AGTCA.PL5

description: Tissue captured from leaf of cross Ki3_TIL03

source_name: leaf tissue from cross Ki3_TIL03,biological replicate 1


title: Ki3_TIL03_AGTCA.PL5_1


title: Ki3_TIL03_TGTGC.PL7

source_name: leaf tissue from cross Ki3_TIL03,biological replicate 2


title: Ki3_TIL03_TGTGC.PL7_1


title: CML103_TIL25_AGTCA.PL9_1

description: Tissue captured from leaf of cross CML103_TIL25

source_name: leaf tissue from cross CML103_TIL25,biological replicate 1


title: CML103_TIL25_CAGGT.PL8

source_name: leaf tissue from cross CML103_TIL25,biological replicate 2


title: Mo17_TIL01_TGGAT.PL7_1


title: CML103_TIL25_AGTCA.PL9


title: CML103_TIL14_GCTAT.PL9

description: Tissue captured from leaf of cross CML103_TIL14

source_name: leaf tissue from cross CML103_TIL14,biological replicate 1


title: CML103_TIL14_GTTCT.PL6_1

source_name: leaf tissue from cross CML103_TIL14,biological replicate 2


title: CML103_TIL14_GCTAT.PL9_1


title: CML103_TIL14_GTTCT.PL6


title: CML103_TIL25_CAGGT.PL8_1


title: Mo17_TIL09_ATCGT.PL5_1


title: CML103_TIL11_ATCGT.PL9

description: Tissue captured from leaf of cross CML103_TIL11

source_name: leaf tissue from cross CML103_TIL11,biological replicate 1


title: CML103_TIL11_ATCGT.PL9_1


title: CML103_TIL03_TCCTC.PL7

description: Tissue captured from leaf of cross CML103_TIL03

source_name: leaf tissue from cross CML103_TIL03,biological replicate 2


title: CML103_TIL11_TAGCT.PL6_1

source_name: leaf tissue from cross CML103_TIL11,biological replicate 2


title: CML103_TIL03_TCCAT.PL5_1

source_name: leaf tissue from cross CML103_TIL03,biological replicate 1


title: CML103_TIL03_TCCTC.PL7_1


title: B73_TIL25_TCCAT.PL6_1

description: Tissue captured from leaf of cross B73_TIL25

source_name: leaf tissue from cross B73_TIL25,biological replicate 3


title: B73_TIL25_GCTAT.PL5_1

source_name: leaf tissue from cross B73_TIL25,biological replicate 2


title: B73_TIL25_CGATT.PL9

source_name: leaf tissue from cross B73_TIL25,biological replicate 1


title: B73_TIL25_TCCAT.PL6


title: CML103_TIL03_TCCAT.PL5


title: B73_TIL25_GCTAT.PL5


title: B73_TIL14_TGTGC.PL5

description: Tissue captured from leaf of cross B73_TIL14

source_name: leaf tissue from cross B73_TIL14,biological replicate 2


title: B73_TIL14_GCATG.PL7

source_name: leaf tissue from cross B73_TIL14,biological replicate 1


title: B73_TIL14_TGTGC.PL5_1


title: B73_TIL14_GCATG.PL7_1


title: B73_TIL11_GTAAG.PL8

description: Tissue captured from leaf of cross B73_TIL11

source_name: leaf tissue from cross B73_TIL11,biological replicate 1


title: B73_TIL11_TCCTC.PL9_1

source_name: leaf tissue from cross B73_TIL11,biological replicate 2


title: Mo17_TIL09_TGGAT.PL9

source_name: leaf tissue from cross Mo17_TIL09,biological replicate 2


title: B73_TIL09_GTTCT.PL5_1

description: Tissue captured from leaf of cross B73_TIL09

source_name: leaf tissue from cross B73_TIL09,biological replicate 1


title: B73_TIL05_GTTCT.PL9

description: Tissue captured from leaf of cross B73_TIL05

source_name: leaf tissue from cross B73_TIL05,biological replicate 2


title: B73_TIL11_GTAAG.PL8_1


title: B73_TIL09_GTTCT.PL5


title: B73_TIL09_TAGCT.PL7

source_name: leaf tissue from cross B73_TIL09,biological replicate 2


title: B73_TIL03_CGATT.PL5_1

description: Tissue captured from leaf of cross B73_TIL03

source_name: leaf tissue from cross B73_TIL03,biological replicate 1


title: B73_TIL05_CAGGT.PL6_1

source_name: leaf tissue from cross B73_TIL05,biological replicate 1


title: B73_TIL05_GTTCT.PL9_1


title: B73_TIL25_CGATT.PL9_1


title: B73_TIL01_GCATG.PL9

description: Tissue captured from leaf of cross B73_TIL01

source_name: leaf tissue from cross B73_TIL01,biological replicate 1


title: B73_TIL01_TGGAT.PL5

source_name: leaf tissue from cross B73_TIL01,biological replicate 2


title: W22_ATGCT.PL14

description: Tissue captured from ear of parent W22

source_name: ear tissue from parent W22,biological replicate 1

value: ear


title: TIL25_ATGCT.PL15

description: Tissue captured from ear of parent TIL25

source_name: ear tissue from parent TIL25,biological replicate 1


title: CML103_TIL11_TAGCT.PL6

source_name: leaf tissue from cross CML103_TIL11,biological replicate 2

value: F1 cross


title: W22_CACTA.PL15

description: Tissue captured from ear of parent W22

source_name: ear tissue from parent W22,biological replicate 2


title: B73_TIL11_TCCTC.PL9


title: TIL25_TGGAT.PL14

source_name: ear tissue from parent TIL25,biological replicate 2


title: TIL15_GCTAT.PL14

description: Tissue captured from ear of parent TIL15

source_name: ear tissue from parent TIL15,biological replicate 1


title: TIL14_ATCGT.PL14

description: Tissue captured from ear of parent TIL14

source_name: ear tissue from parent TIL14,biological replicate 1


title: TIL15_TGGAT.PL15

source_name: ear tissue from parent TIL15,biological replicate 2


title: TIL14_GCTAT.PL15

source_name: ear tissue from parent TIL14,biological replicate 2


title: B73_TIL05_CAGGT.PL6


title: TIL11_ATCGT.PL15

description: Tissue captured from ear of parent TIL11

source_name: ear tissue from parent TIL11,biological replicate 1


title: TIL09_CACTA.PL14

description: Tissue captured from ear of parent TIL09

source_name: ear tissue from parent TIL09,biological replicate 1


title: TIL09_GTTCT.PL15

source_name: ear tissue from parent TIL09,biological replicate 2


title: TIL11_CGATT.PL14

source_name: ear tissue from parent TIL11,biological replicate 2


title: TIL10_GTTCT.PL14

description: Tissue captured from ear of parent TIL10

source_name: ear tissue from parent TIL10,biological replicate 2


title: TIL05_TAGCT.PL15

description: Tissue captured from ear of parent TIL05

source_name: ear tissue from parent TIL05,biological replicate 2


title: TIL03_TCCAT.PL15

description: Tissue captured from ear of parent TIL03

source_name: ear tissue from parent TIL03,biological replicate 2


title: TIL03_TCCAT.PL14

source_name: ear tissue from parent TIL03,biological replicate 1


title: TIL05_TAGCT.PL14

source_name: ear tissue from parent TIL05,biological replicate 1


title: B73_TIL01_GCATG.PL9_1

source_name: leaf tissue from cross B73_TIL01,biological replicate 1


title: B73_TIL03_CGATT.PL5

source_name: leaf tissue from cross B73_TIL03,biological replicate 1


title: B73_TIL01_TGGAT.PL5_1

source_name: leaf tissue from cross B73_TIL01,biological replicate 2


title: TIL01_CAGGT.PL15

description: Tissue captured from ear of parent TIL01

source_name: ear tissue from parent TIL01,biological replicate 2


title: TIL01_CAGGT.PL14

source_name: ear tissue from parent TIL01,biological replicate 1


title: Oh43_TCCTC.PL14

description: Tissue captured from ear of parent Oh43

source_name: ear tissue from parent Oh43,biological replicate 1


title: Mo17_GTAAG.PL15

description: Tissue captured from ear of parent Mo17

source_name: ear tissue from parent Mo17,biological replicate 2


title: Ki3_AGTCA.PL14

description: Tissue captured from ear of parent Ki3

source_name: ear tissue from parent Ki3,biological replicate 1


title: Ki3_AGTCA.PL15

description: Tissue captured from ear of parent Ki3

source_name: ear tissue from parent Ki3,biological replicate 2


title: Mo17_GTAAG.PL14

description: Tissue captured from ear of parent Mo17

source_name: ear tissue from parent Mo17,biological replicate 1


title: CML103_TGTGC.PL15

description: Tissue captured from ear of parent CML103

source_name: ear tissue from parent CML103,biological replicate 2


title: B73_GCATG.PL15

description: Tissue captured from ear of parent B73

source_name: ear tissue from parent B73,biological replicate 2


title: B73_GCATG.PL14

description: Tissue captured from ear of parent B73

source_name: ear tissue from parent B73,biological replicate 1


title: TIL10_CGATT.PL15

source_name: ear tissue from parent TIL10,biological replicate 1


title: CML103_TGTGC.PL14

source_name: ear tissue from parent CML103,biological replicate 1


title: W22_TIL25_TCCTC.PL2

description: Tissue captured from ear of cross W22_TIL25

source_name: ear tissue from cross W22_TIL25,biological replicate 2


title: W22_TIL25_ATGCT.PL4

source_name: ear tissue from cross W22_TIL25,biological replicate 1


title: W22_TIL25_TCCTC.PL2_1


title: W22_TIL11_TGTGC.PL4

description: Tissue captured from ear of cross W22_TIL11

source_name: ear tissue from cross W22_TIL11,biological replicate 2


title: W22_TIL14_CGATT.PL3

description: Tissue captured from ear of cross W22_TIL14

source_name: ear tissue from cross W22_TIL14,biological replicate 1


title: W22_TIL11_TGTGC.PL4_1


title: Oh43_TIL01_GCATG.PL8_1

description: Tissue captured from leaf of cross Oh43_TIL01

source_name: leaf tissue from cross Oh43_TIL01,biological replicate 2


title: W22_TIL03_CAGGT.PL2

description: Tissue captured from ear of cross W22_TIL03

source_name: ear tissue from cross W22_TIL03,biological replicate 2


title: W22_TIL03_CAGGT.PL2_1


title: W22_TIL01_TGTGC.PL3

description: Tissue captured from ear of cross W22_TIL01

source_name: ear tissue from cross W22_TIL01,biological replicate 2


title: W22_TIL11_GTAAG.PL3_1

source_name: ear tissue from cross W22_TIL11,biological replicate 1


title: W22_TIL03_AGTCA.PL3

source_name: ear tissue from cross W22_TIL03,biological replicate 1


title: W22_TIL01_TGTGC.PL3_1


title: Oh43_TCCTC.PL15

description: Tissue captured from ear of parent Oh43

source_name: ear tissue from parent Oh43,biological replicate 2


title: W22_TIL01_GTAAG.PL2

source_name: ear tissue from cross W22_TIL01,biological replicate 1


title: W22_TIL01_GTAAG.PL2_1


title: Oh43_TIL25_TGTGC.PL2

description: Tissue captured from ear of cross Oh43_TIL25

source_name: ear tissue from cross Oh43_TIL25,biological replicate 3


title: Oh43_TIL25_TGTGC.PL2_1


title: Oh43_TIL25_TGGAT.PL2_1

source_name: ear tissue from cross Oh43_TIL25,biological replicate 2


title: Oh43_TIL15_TCCTC.PL3_1

description: Tissue captured from ear of cross Oh43_TIL15

source_name: ear tissue from cross Oh43_TIL15,biological replicate 2


title: W22_TIL25_ATGCT.PL4_1


title: Oh43_TIL25_TGGAT.PL2


title: W22_TIL03_AGTCA.PL3_1


title: Oh43_TIL25_TAGCT.PL2

source_name: ear tissue from cross Oh43_TIL25,biological replicate 1


title: Oh43_TIL15_GCTAT.PL1

source_name: ear tissue from cross Oh43_TIL15,biological replicate 1


title: W22_TIL11_GTAAG.PL3


title: Oh43_TIL11_TAGCT.PL1

description: Tissue captured from ear of cross Oh43_TIL11

source_name: ear tissue from cross Oh43_TIL11,biological replicate 2


title: Oh43_TIL11_CGATT.PL1_1

source_name: ear tissue from cross Oh43_TIL11,biological replicate 1


title: Oh43_TIL15_TCCTC.PL3


title: Oh43_TIL11_CGATT.PL1


title: W22_TIL14_CGATT.PL3_1


title: Oh43_TIL10_GCATG.PL6

description: Tissue captured from ear of cross Oh43_TIL10

source_name: ear tissue from cross Oh43_TIL10,biological replicate 1


title: Oh43_TIL15_GCTAT.PL1_1


title: Oh43_TIL10_GCATG.PL6_1


title: Oh43_TIL10_GCATG.PL3


title: Oh43_TIL11_TAGCT.PL1_1


title: Oh43_TIL09_TAGCT.PL4

description: Tissue captured from ear of cross Oh43_TIL09

source_name: ear tissue from cross Oh43_TIL09,biological replicate 2


title: Oh43_TIL09_ATGCT.PL3

source_name: ear tissue from cross Oh43_TIL09,biological replicate 1


title: Oh43_TIL25_TAGCT.PL2_1


title: Oh43_TIL03_TCCTC.PL4

description: Tissue captured from ear of cross Oh43_TIL03

source_name: ear tissue from cross Oh43_TIL03,biological replicate 1


title: Oh43_TIL09_ATGCT.PL3_1


title: Oh43_TIL09_TAGCT.PL4_1


title: Oh43_TIL10_GCATG.PL3_1


title: B73_TIL09_TAGCT.PL7_1

description: Tissue captured from leaf of cross B73_TIL09

source_name: leaf tissue from cross B73_TIL09,biological replicate 2


title: Oh43_TIL03_TCCTC.PL4_1


title: Oh43_TIL01_GTTCT.PL3_1

description: Tissue captured from ear of cross Oh43_TIL01

source_name: ear tissue from cross Oh43_TIL01,biological replicate 1


title: Oh43_TIL01_AGTCA.PL6_1

source_name: ear tissue from cross Oh43_TIL01,biological replicate 2


title: Mo17_TIL09_TGGAT.PL4

description: Tissue captured from ear of cross Mo17_TIL09

source_name: ear tissue from cross Mo17_TIL09,biological replicate 3


title: Mo17_TIL14_TCCAT.PL4_1

description: Tissue captured from ear of cross Mo17_TIL14

source_name: ear tissue from cross Mo17_TIL14,biological replicate 2


title: Oh43_TIL01_GTTCT.PL3


title: Oh43_TIL01_AGTCA.PL6


title: Mo17_TIL14_TCCAT.PL4


title: Mo17_TIL09_TGGAT.PL1

source_name: ear tissue from cross Mo17_TIL09,biological replicate 2


title: Mo17_TIL14_TCCAT.PL2_1

source_name: ear tissue from cross Mo17_TIL14,biological replicate 1


title: Mo17_TIL14_TCCAT.PL2


title: Mo17_TIL09_TGGAT.PL1_1


title: Mo17_TIL09_TCCTC.PL1

source_name: ear tissue from cross Mo17_TIL09,biological replicate 1


title: Ki3_TIL14_ATCGT.PL3

description: Tissue captured from ear of cross Ki3_TIL14

source_name: ear tissue from cross Ki3_TIL14,biological replicate 2


title: Mix_exvivo_rep3

description: PA14+Vpa co-culture extracted from murine tumors, sample 3

source_name: Murine tumor cells

growth_protocol: Eight to ten-week-old female BALB/c mice were subcutaneously (s.c.) inoculated at the abdomen with 5 x 105 CT26 cells. Mice bearing tumors of 4-7 mm diameter were i.v. infected with 5 x 106 colony-forming units (CFU) of P. aeruginosa PA14 and/or 2 x 108 CFU of V. parvula suspended in phosphate-buffered saline (PBS).

treatment_protocol: Two days post infection, mice were sacrificed and tumors were removed and adherent fatty tissue and fur was cleared. Immediately after tumor removal, the tissue was cut into small pieces and squeezed with a sterile syringe through a nylon filter with 70 µm pore size into a 6 well plate, prefilled with 2.5 ml pre-chilled RNAproctect Bacteria Reagent (Qiagen). The resulting mixture was used to rinse the filter again. Afterwards, the mixture was filtered through a nylon filter with 50 µm pore size. The filtered mix was collected in a sterile 2 ml reaction tube and centrifuged at 4°C for 2 min / 3000g. The supernatant was transferred in a sterile reaction tube and centrifuged at 4°C for 5 min / 17.000g. The pellet was stored at ‑70°C and Enrichment for bacterial RNA was achieved by using the MicrobEnrich Kit (Ambion).

value: Pseudomonas aeruginosa PA14,Veillonella Parvula DSM 2008

tag: strain

value: BALB/c


title: Ki3_TIL14_ATCGT.PL3_1

source_name: ear tissue from cross Ki3_TIL14, biological replicate 2


title: Mo17_TIL09_TCCTC.PL1_1


title: Ki3_TIL11_TCCAT.PL3_1

description: Tissue captured from ear of cross Ki3_TIL11

source_name: ear tissue from cross Ki3_TIL11,biological replicate 2


title: Ki3_TIL14_AGTCA.PL2

source_name: ear tissue from cross Ki3_TIL14,biological replicate 1


title: Mix_exvivo_rep2

description: PA14+Vpa co-culture extracted from murine tumors, sample 2


title: Ki3_TIL11_GTTCT.PL2

source_name: ear tissue from cross Ki3_TIL11,biological replicate 1


title: Ki3_TIL11_TCCAT.PL3


title: Ki3_TIL11_GTTCT.PL2_1


title: Ki3_TIL03_CGATT.PL2

description: Tissue captured from ear of cross Ki3_TIL03

source_name: ear tissue from cross Ki3_TIL03,biological replicate 1


title: Mix_exvivo_rep1

description: PA14+Vpa co-culture extracted from murine tumors, sample 1


title: Ki3_TIL09_CAGGT.PL4_1

description: Tissue captured from ear of cross Ki3_TIL09

source_name: ear tissue from cross Ki3_TIL09,biological replicate 2


title: Ki3_TIL03_CGATT.PL2_1


title: Ki3_TIL09_CAGGT.PL4


title: Pure_exvivo_Vpa_rep3

description: Vpa extracted from murine tumours, sample 3

value: Veillonella parvula DSM 2008


title: CML103_TIL11_TGGAT.PL3

description: Tissue captured from ear of cross CML103_TIL11

source_name: ear tissue from cross CML103_TIL11,biological replicate 2


title: Ki3_TIL09_ATGCT.PL2_1

source_name: ear tissue from cross Ki3_TIL09,biological replicate 1


title: Pure_exvivo_Vpa_rep1

description: Vpa extracted from murine tumours, sample 1


title: Mo17_TIL09_TGGAT.PL4_1


title: Pure_exvivo_Vpa_rep2

description: Vpa extracted from murine tumours, sample 2


title: CML103_TIL14_GCTAT.PL4

description: Tissue captured from ear of cross CML103_TIL14

source_name: ear tissue from cross CML103_TIL14,biological replicate 2


title: Ki3_TIL14_AGTCA.PL2_1


title: CML103_TIL11_ATCGT.PL4

source_name: ear tissue from cross CML103_TIL11,biological replicate 1


title: CML103_TIL14_GCTAT.PL4_1


title: Pure_exvivo_PA14_rep2

description: PA14 extracted from murine tumours, sample 2

value: Pseudomonas aeruginosa PA14


title: CML103_TIL14_CAGGT.PL1

source_name: ear tissue from cross CML103_TIL14,biological replicate 1


title: CML103_TIL14_CAGGT.PL1_1


title: CML103_TIL03_TGTGC.PL1_1

description: Tissue captured from ear of cross CML103_TIL03

source_name: ear tissue from cross CML103_TIL03,biological replicate 2


title: Ki3_TIL09_ATGCT.PL2


title: CML103_TIL03_GTTCT.PL4

source_name: ear tissue from cross CML103_TIL03,biological replicate 1


title: CML103_TIL11_ATCGT.PL4_1


title: CML103_TIL11_TGGAT.PL3_1


title: CML103_TIL03_TGTGC.PL1


title: CML103_TIL03_GTTCT.PL4_1


title: B73_TIL25_GTAAG.PL1_1

description: Tissue captured from ear of cross B73_TIL25

source_name: ear tissue from cross B73_TIL25,biological replicate 4


title: B73_TIL25_CGATT.PL4_1

source_name: ear tissue from cross B73_TIL25,biological replicate 3


title: B73_TIL25_ATCGT.PL2_1

source_name: ear tissue from cross B73_TIL25,biological replicate 1


title: Pure_exvivo_PA14_rep3

description: PA14 extracted from murine tumours, sample 3

source_name: Murine tumor cells


title: B73_TIL25_ATGCT.PL1_1

source_name: ear tissue from cross B73_TIL25,biological replicate 2


title: B73_TIL14_GTTCT.PL1

description: Tissue captured from ear of cross B73_TIL14

source_name: ear tissue from cross B73_TIL14, biological replicate 3


title: B73_TIL14_GTTCT.PL1_1


title: B73_TIL14_TCCAT.PL1_1

source_name: ear tissue from cross B73_TIL14, biological replicate 4


title: B73_TIL14_AGTCA.PL1_1

source_name: ear tissue from cross B73_TIL14, biological replicate 1


title: B73_TIL14_ATCGT.PL1_1

source_name: ear tissue from cross B73_TIL14, biological replicate 2


title: B73_TIL11_GTAAG.PL4_1

description: Tissue captured from ear of cross B73_TIL11

source_name: ear tissue from cross B73_TIL11, biological replicate 2


title: Pure_exvivo_PA14_rep1

description: PA14 extracted from murine tumours, sample 1


title: B73_TIL14_AGTCA.PL1


title: B73_TIL11_GTAAG.PL4


title: B73_TIL14_ATCGT.PL1


title: B73_TIL11_CAGGT.PL3

source_name: ear tissue from cross B73_TIL11, biological replicate 1


title: B73_TIL05_TCCTC.PL6

description: Tissue captured from ear of cross B73_TIL05

source_name: ear tissue from cross B73_TIL05, biological replicate 2


title: B73_TIL09_GCATG.PL1

description: Tissue captured from ear of cross B73_TIL09

source_name: ear tissue from cross B73_TIL09, biological replicate 1


title: B73_TIL25_GTAAG.PL1


title: B73_TIL09_GCATG.PL1_1

source_name: ear tissue from cross B73_TIL09,biological replicate 1


title: B73_TIL25_CGATT.PL4


title: B73_TIL25_ATGCT.PL1


title: B73_TIL09_TAGCT.PL3

source_name: ear tissue from cross B73_TIL09, biological replicate 2


title: B73_TIL05_TCCTC.PL6_1


title: B73_TIL11_CAGGT.PL3_1


title: B73_TIL03_GTAAG.PL6

description: Tissue captured from ear of cross B73_TIL03

source_name: ear tissue from cross B73_TIL03, biological replicate 2


title: B73_TIL05_GCTAT.PL3_1

source_name: ear tissue from cross B73_TIL05, biological replicate 1


title: B73_TIL25_ATCGT.PL2


title: B73_TIL14_TCCAT.PL1


title: B73_TIL03_GTAAG.PL6_1


title: B73_TIL05_GCTAT.PL3


title: B73_TIL03_GCATG.PL4

source_name: ear tissue from cross B73_TIL03, biological replicate 1


title: B73_TIL03_GCATG.PL4_1


title: B73_TIL01_TGTGC.PL6

description: Tissue captured from ear of cross B73_TIL01

source_name: ear tissue from cross B73_TIL01, biological replicate 2


title: B73_TIL01_TGTGC.PL6_1


title: B73_TIL01_AGTCA.PL4

source_name: ear tissue from cross B73_TIL01, biological replicate 1


title: B73_TIL09_TAGCT.PL3_1

source_name: ear tissue from cross B73_TIL09,biological replicate 2


title: MRC_5_PD32_3

source_name: total RNA extracted from MRC-5 fibroblasts

tag: cell type

tag: treatment

value: control


title: MRC_5_PD32_2


title: Coilin_ChIPseq

city: New Haven

first: Karla

last: Neugebauer

state: CT

address: 333 Cedar Street

department: Molecular Biophysics & Biochemistry

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Remaining adaptor sequences were trimmed from reads using cutadapt -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCCATATCTCGTATGCCGTCTTCTGCTT -m 25 -O 9 --match-read-wildcards
ChIP-seq reads were aligned to hg19 using Bowtie2 v2.0.4 -N1
Peaks were called using MACS v1.4.2 using input file as a control
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file include genomic position of identified ChIP peaks

source_name: HeLa Kyoto

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol:
After cell lysis, DNA was sheared to fragments of ~200bp and lysate was cleared by centrifugation. 25% of the supernatant was used as input and the remaiining part was used to precipitate coilin with Dynabeads Protein G coupled to goat anti-EGFP antibody. After stringent washing, the DNA was eluted and de-crosslinked by Proteinase K treatment. DNA fragments were purified by phenol-chlorophorm extraction.
Chipped DNA was end repaired with End Repair Module and A-Tailed with dA-Tailing Module (NEB). Universal Illumina adaptors were ligated to DNA ends and amplified using PCR Enrich Adaptor Ligated cDNA Library module (NEB). Products were purified and size selected on 2% Agarose gel.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.

value: coilin-LAP HeLa

tag: chip antibody

value: polyclonal goat anti-EGFP


title: Input


title: Coilin_iCLIP_Mm_rep1

description:
Sample 4
processed data file: peaks_mCoilin-all-sum_sum_S_mm9--ensembl59_from_1406-2365-2367-2368-2369_bedGraph.bed

data_processing:
Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: mm9 (mouse samples); hg19 (human samples)
Supplementary_files_format_and_content: .bed files describing significant crosslink sites for individual replicates, combined samples from 5 mouse replicates and 2 human replicates.

extract_protocol:
Cells were lysed and treated with RNase I. Coilin-GFP was immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to 3' linker. Protein-RNA complexes were resolved on denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the protein expected size was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was separated into 3 size fractions by denaturing gel electrophoresis and circularized by ssDNA circligase. Specific oligo was annealed to create restriction site and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied to create final library. For more details see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

value: coilin-GFP expressing P19

value: coilin-LAP

value: anti-EGFP

tag: antibody ref.

tag: barcode sequence

value: NNTGNNGGC


title: Mix_invitro

description: PA14+Vpa co-culture anaerobic in vitro growth

organism:
Veillonella parvula DSM 2008
Pseudomonas aeruginosa PA14

source_name: mixed planktonic culture


title: Coilin_iCLIP_Mm_rep3

description:
Sample 5
processed data file: peaks_mCoilin-all-sum_sum_S_mm9--ensembl59_from_1406-2365-2367-2368-2369_bedGraph.bed

value: NNCGNNCGA


title: Coilin_iCLIP_Hs_rep2

description:
Sample 7
processed data file: peaks_hCoilin-all-sum_sum_S_hg19--ensembl59_from_1407-2370_bedGraph.bed

value: coilin-GFP expressing HeLa

value: NNTGNNTAC


title: Pure_invitro_Vpa

description: Vpa anaerobic in vitro growth

organism: Veillonella parvula DSM 2008

source_name: Vpa planktonic culture


title: Coilin_iCLIP_Mm_rep5

description:
Sample 2
processed data file: peaks_mCoilin-all-sum_sum_S_mm9--ensembl59_from_1406-2365-2367-2368-2369_bedGraph.bed

value: NNTCNNTGG


title: B73_TIL01_AGTCA.PL4_1

tag: genotype

tag: tissue

value: ear


title: Coilin_iCLIP_Hs_rep1

description:
Sample 6
processed data file: peaks_hCoilin-all-sum_sum_S_hg19--ensembl59_from_1407-2370_bedGraph.bed

value: NNCCNNACC


title: Coilin_iCLIP_Mm_rep4

description:
Sample 1
processed data file: peaks_mCoilin-all-sum_sum_S_mm9--ensembl59_from_1406-2365-2367-2368-2369_bedGraph.bed


title: PolyA- RNAseq

data_processing:
Basecalls performed using CASAVA version 1.8.2
Remaining adaptor sequences were trimmed from reads using cutadapt -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATCTCGTATGC -m 15 -O 9 --match-read-wildcards
RNA-seq reads were aligned to hg19 using Tophat v2.0.0 coupled with Bowtie v1.0.0
RPKM was calculated using Cufflinks v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: Tab-dedlimited text file containing RPKM values for snoRNA and snRNA genes

source_name: HeLa

extract_protocol:
Total HeLa RNA was isolated using TRIzol. PolyA+ and rRNA was depleted with MicroPoly(A)Purist Kit (Ambion) and Ribo-Zero rRNA removal Kit (Epicentre).
Library was prepared using NEBNext mRNA Sample Prep Master Mix Set kit (NEB).

value: HeLa


title: KD_rep1 [do1557_PolIII_skin_1900_mmudo1411do1411_kd_CRI01]

city: Cambridge

first: Patrick

last: Lombard

state: Cambridgeshire

address: Tennis Court Road, Cambridge

country: United Kingdom

institute: University of Cambridge

description: polIII.counts.dat

data_processing:
RNA Methylation profiling by high throughput sequencing
Reads were aligned to the  mouse reference genome (GRCm38/mm9) using Bismark (version 0.7.6). Only the reads uniquely aligning to the genome and aligning without mismatch were considered for further analysis.
small non-coding RNA profiling by high throughput sequencing
Adapters were removed, and the 20-200 nt reads were aligned to the mouse and human reference genomes (UCSC mm9 and GRCh37/hg19) with options m 500 -v2 -best -strataas decribed for PolII ChIP-seq reads. To account for the addition of CCA 3'-ends to mature tRNAs, unaligned reads were trimmed of CCA[CCA] ends and realigned using the same options. Annotations were conducted based on the gene loci predicted by tRNAscan-SE in the mouse and based on predicted tRNA genes from GtRNAdB (http://lowelab.ucsc.edu/GtRNAdb) in human. Fragments that matched at multiple tRNA genes were distributed proportionally to the fraction of uniquely matching fragments at these regions as described (Kutter et al. 2011/2?). Reads with CCA[CCA] ends that covered at least 90% of the tRNA gene were considered mature tRNAs. For fragment aligning at tRNA genes, reads that exceeded the gene start or end by more than 10 % were discarded.  For all mature tRNAs and fragments aligning at tRNA genes, counts were normalized and differential abundance of the fragments was evaluated with the Bioconductor/R package DESeq (Anders and Huber, 2010).
Pol III Chromatin-IP profiling by high throughput sequencing
In the mouse reference genome (UCSC NCBI37/mm9), 3,282 candidate tRNA genes were predicted with tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE) including genes with an 'undetermined' isoacceptor family; loci marked as pseudogenes were discarded. PolIII ChIP-seq reads were aligned to the reference genome using Bowtie (Langmead et al, 2009). Two mismatches and at most 500 multiple matches were tolerated, i.e. specifically the Bowtie options m 500 -v2 -best -strata
Genome_build: mm9
Supplementary_files_format_and_content: GSM1090034..GSM1090041: Tabdeliminated text file methylation report. Columns contain chromosome, start, end, percentage methylation, methylated calls, unmethylated calls.
Supplementary_files_format_and_content: GSM1090042..GSM1090049: Tab deliminated text file containing counts for the tRNA's
Supplementary_files_format_and_content: GSM1090050..GSM1090054: Tab deliminated text file containing counts for the tRNA's

source_name: total mouse skin

growth_protocol: Total mouse back skin from wild-type and NSun2 -/- males in anagen (postnatal day 25) were used. NSun2 -/- mice (GGTC-clone ID: D014D11) were generated by the German Gene Trap Consortium, and bred under a C57Bl6/J CBA F1 background. Wild-type mice were coming from the same breedings as NSun2 -/- mice.

extract_protocol:
Fixed material was lysed, sonicated and then incubated with antibodies recognizing antigen POLR3A, the RPC1/155 subunit of Pol III as indicated in (Kutter, Brown et al. 2011). Input material was lysed, sonicated and but not incubated with antibodies.
The immunoprecipitated and input material was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size-selected (200-300 base pairs). Each experiment was done on skin material isolated from 3 3.5-weeks old male mice pooled together. At least two independent biological replicates from wild type and one for NSun2 -/- animals were carried out.
Pol III ChIP sequencing was performed from back skin from two wild-type independent biological replicates and one NSun2 -/- independent biological replicate. Input libraries were only from one wild-type independent biological replicate and one NSun2 -/- independent biological replicate. Each biological replicate were done from material from 3 mice pooled together. All libraries were sequenced on the Illumina Genome Analyzer II (single-ended and 100 pb read length) and post-processed using the standard GA pipeline software v1.4 (Illumina).

treatment_protocol: Mouse back skin was collected at P25 (postnatal day 25), when hair follicles start the growing phase or anagen phase of the hair cycle. Skin was shaved before collection, and immediately fixed in 1% formaldehyde (v/v).

tag: background strain

value: C57Bl6/J CBA F1

tag: genotype/variation

value: NSun2 -/-


title: KD_Input [do1415_Input_skin_none_mmudo1411_kd_CRI01]

description: polIII.counts.dat

value: input


title: KO_rep4 [do1293_RNAseq_skin_mmuCBA_x_C57BL13_8_CRI01]

description: trna.counts.dat

extract_protocol:
Total RNA from mouse skin was prepared using Trizol reagent (Invitrogen) according to the manufacturer's instructions and then treated with DNase (Turbo DNase, Ambion).
Total RNA was extracted as described previously. Ribosomal RNA was depleted from total RNA using Ribo-zero (Epicentre, Illumina). The remaining RNA fraction was gel size-selected or with MirVana isolation kit (Invitrogen) for 20-200 base-paired RNAs. tRNAs were then de-aminoaclylated in 0.1M Tris-HCl pH9.0 and 1mM EDTA for 30 min at 37°C. tRNA libraries were performed according to TruSeq Small RNA preparation kit (Illumina). Briefly 3’ adenylated and 5’phosphorylated adapters suitable for Illumina RNA sequencing were ligated to 300 ng of RNA obtained after de-aminioacylation. RNA was reverse-transcribed at 50ºC for 1 hour (SuperScript III cDNA synthesis kit, Invitrogen), followed by 16 cycle-PCR amplification with Phusion DNA polymerase (Thermo scientific) and size-selected (~140-210 base pairs) before sequencing.
Small RNA sequencing of RNA from back skin from four wild-type independent biological replicates and four NSun2 -/- independent biological replicates were used. All libraries were sequenced on the Illumina Genome Analyzer II (single-ended and 100 pb read length) and post-processed using the standard GA pipeline software v1.4 (Illumina).

treatment_protocol: Mouse back skin was collected at P25 (postnatal day 25), when hair follicles start the growing phase or anagen phase of the hair cycle. Skin was shaved before collection, and immediately snap-frozen in liquid N2.


title: Coilin_iCLIP_Mm_rep2

description:
Sample 3
processed data file: peaks_mCoilin-all-sum_sum_S_mm9--ensembl59_from_1406-2365-2367-2368-2369_bedGraph.bed

tag: cell line

value: NNCGNNCCG


title: WT-Input [do1414_Input_skin_none_mmudo1411_wt_CRI01]

description: polIII.counts.dat

value: WT


title: Wt_rep1 [do1411_PolII_skin_1900_mmudo1411_CRI01]

description: polIII.counts.dat

value: antibodies recognizing antigen POLR3A, the RPC1/155 subunit of Pol III as indicated in (Kutter, Brown et al. 2011)


title: Wt_rep2 [do1556_PolIII_skin_1900_mmudo1411do1411_wt_CRI01]

description: polIII.counts.dat


title: Wt_rep4 [do1289_RNAseq_skin_mmuCBA_x_C57BL9_4_CRI01]

description: trna.counts.dat


title: KO_rep2 [do1291_RNAseq_skin_mmuCBA_x_C57BL11_6_CRI01]

description: trna.counts.dat


title: KO_rep1 [do1290_RNAseq_skin_mmuCBA_x_C57BL10_5_CRI01]

description: trna.counts.dat


title: KO_rep3 [do1292_RNAseq_skin_mmuCBA_x_C57BL12_7_CRI01]

description: trna.counts.dat


title: Wt_rep2 [do1287_RNAseq_skin_mmuCBA_x_C57BL7_2_CRI01]

description: trna.counts.dat


title: Wt_rep1 [do1286_RNAseq_skin_mmuCBA_x_C57BL6_1_CRI01]

description: trna.counts.dat


title: Wt_rep3 [do1288_RNAseq_skin_mmuCBA_x_C57BL8_3_CRI01]

description: trna.counts.dat


title: MRC_5_PD32_1

tag: population doublings

value: MRC-5 fibroblasts

value: control


title: Nsun_rep4 [do1668_unk_skin_unk_mmuNSUN2#4_CRI01]

extract_protocol:
Total RNA from mouse skin was prepared using Trizol reagent (Invitrogen) according to the manufacturer's instructions and then treated with DNase (Turbo DNase, Ambion).
Total RNA was extracted as described previously, DNase and Ribo-zero treated. The remaining RNA fraction was bisulfite-converted as followed; about 2 μg of RNA was mixed in 70μl of 40% sodium bisulfite pH 5.0 and DNA protection buffer (EpiTect Bisulfite Kit, Qiagen). The reaction mixture was incubated for four cycles of 5 min at 70ºC followed by 1 hour at 60ºC and then desalted with Micro Bio-spin 6 chromatography columns (Bio-Rad). RNA was desulfonated by adding an equal volume of 1M Tris (pH 9.0) to the reaction mixture and incubated for 1h at 37°C, followed by ethanol precipitation.The bisulfite-converted RNA quality and concentration was then assessed on a Bioanalyzer 2100 RNA nano-chip (Agilent). About 120 ng of bisulfite-converted RNA was used to generate Bisulfite-seq libraries. Bs-Seq libraries were performed according to TruSeq Small RNA preparation kit (Illumina). Since the sample was already sufficiently fragmented by the bisulfite-conversion reaction (about 50-120nt), the size selection step prior to adaptor hybridization and ligation was not performed. First 2’,3’-cyclic phosphate and 5’-hydroxyl termini produced during the bisulfite/desulfonation reaction were end-repaired with T4 PNK and Spermidine (New England Biolabs). RNA adapters suitable for Illumina sequencing were then ligated, reverse-transcribed at 50ºC for 1 hour with SuperScript III and 1mM of each dNTP (SuperScript III cDNA synthesis kit, Invitrogen) followed by 18 cycle-PCR amplification. The amplified product was not size-selected before sequencing.
RNA bisulfite sequencing of RNA from back skin from four wild-type independent biological replicates and four NSun2 -/- independent biological replicates were used. All libraries were sequenced on the Illumina Genome Analyzer II (single-ended and 100 pb read length) and post-processed using the standard GA pipeline software v1.4 (Illumina).


title: Nsun_rep3 [do1667_unk_skin_unk_mmuNSUN2#3_CRI01]


title: Nsun_rep2 [do1666_unk_skin_unk_mmuNSUN2#2_CRI01]


title: Wt_rep3 [do1663_unk_skin_unk_mmuWT#3_CRI01]


title: Wt_rep2 [do1662_unk_skin_unk_mmuWT#2_CRI01]


title: Wt_rep1 [do1661_unk_skin_unk_mmuWT#1_CRI01]


title: Wt_rep4 [do1664_unk_skin_unk_mmuWT#4_CRI01]


title: NT2D1 OCT4

status: Public on Nov 05 2014

city: New York

first: Raju

middle: S

last: Chaganti

state: NY

address: 430 East, 67 Street, RRL-337,New York

department: Cell Biology

institute: MSKCC

description: OCT4 ChIPseq

data_processing:
Sequences were mapped to the human genome hg19 using ABI’s Corona Lite Plus genome mapping utility, allowing for up to four mismatches and retaining only unique matches.
We called peaks with MACS (Zhang, et al. 2008), using a band width of 200, model fold 5, and p-value cutoff of 1E-03 against IgG control
MACS identifies peaks on a per-window basis by comparing the number of tags in each genome window to the number of expected tags as calculated by a Poisson distribution and to the distribution of normalized per-window counts in IgG control
Candidate transcription-factor targets were identified based on transcription start site proximity (10Kb, 5Kb and 2Kb) to predicted peaks
Genome_build: HG19
Supplementary_files_format_and_content: text files contain macs output format

source_name: Human Germ Cell Tumour_NANOG

extract_protocol:
Cells were sonicated using Covaris and then the TF-chromatin comples were isolated using magnetic beads linked to specific antibody
SOLiD System 2.0. Fragment Library Preparation protocol was based on size and concentration of ChIP-DNA

value: Embryonic Carcinoma Cells


title: NT2D1 SOX2

description: SOX2 ChIPseq

source_name: Human Germ Cell Tumour_SOX2