title: 24 h DENV2 infection Total cell lysate mRNA-seq (rep 2)

first: David

last: Reid

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

description: processed data file: DENVExpression-wholecell.xlsx

data_processing:
Read trimming with cutadapt
Map reads to transcriptome with Bowtie (no mismatches)
Quantify translation as RPKM
Genome_build: hg19 (transcripts selected using Tophat/Cufflinks) + EU081177.1 + EU081230.1 + M29095.1
Supplementary_files_format_and_content: Excel spreadsheet indicating RPKM values

source_name: Huh7 cells

growth_protocol: Cultured in DMEM + 10% FBS, 37C, 5% CO2

extract_protocol:
Pre-treatment with 180 uM cycloheximide for 30s. PBS wash. For fractionated cells, release cytosol with digitonin. Extract remaining sample with dodecyl maltoside.
NEB Directional Small RNA kit
PNK end polishing, linker ligation, reverse transcription, PCR amplification

treatment_protocol: Infection with DENV or treatment with interferon

value: Huh7 cells

tag: protocol

value: 24 h DENV2 infection

tag: compartment

value: Total cell lysate

tag: analysis

value: mRNA-seq

tag: replicate

value: rep 2


title: 48 h DENV2 infection Total cell lysate mRNA-seq (rep 2)

status: Public on Sep 01 2016

type: SRA

city: Durham

state: NC

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: 48 h DENV2 infection

tag: strain


title: 12 h DENV2 infection Total cell lysate mRNA-seq (rep 2)

value: 12 h DENV2 infection


title: gd7_wce_2

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

library_source: genomic

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: gd7 embryos

growth_protocol: Fly stocks Toll10b (Meso) and gd7 (Ecto) were kind gifts from Mike Levine (UC Berkeley). gd7/gd7 females were crossed to gd7/+ males, and Toll10b, e /TM3, Sb, Ser, e females were crossed to Toll10b, e/TM3, Sb, Ser, e males. Offspring of these crosses were used for embryo collections. For Trl, Sna, Pc ChIPs wild type embryos (Oregon-R) were used. Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).

extract_protocol: ChIP-seq was performed according to He et al. (2011) with whole cell extract (WCE) derived from 100 mg embryos per ChIP

treatment_protocol: Embryos were dechorionated in 100% bleach for ~1 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.

tag: developmental stage

value: 2-4 hr after egg deposition

tag: genotype/variation

tag: chip antibody

tag: barcode kit

value: custom

tag: library kit

value: NEB-next-DNA


title: 6 h DENV2 infection Total cell lysate mRNA-seq (rep 1)

value: 6 h DENV2 infection

value: rep 1


title: gd7_wce_1


title: gd7_h3k4me1_1

value: H3K4me1 (Active Motif Carlsbad, CA, catalog #39635)


title: 72 h DENV2 infection Total cell lysate mRNA-seq (rep 1)

value: 72 h DENV2 infection


title: 48 h DENV2 infection Total cell lysate mRNA-seq (rep 1)


title: 24 h DENV2 infection Total cell lysate mRNA-seq (rep 1)


title: 12 h DENV2 infection Total cell lysate mRNA-seq (rep 1)


title: gd7_h3k27ac_1

value: H3K27ac (Active Motif Carlsbad, CA, catalog #39133)


title: 6 h DENV2 infection Total cell lysate mRNA-seq (rep 2)


title: 72 h DENV1 infection Total cell lysate mRNA-seq (rep 2)

value: 72 h DENV1 infection


title: Uninfected Total cell lysate mRNA-seq (rep 2)

value: Uninfected


title: aTh17plusDMAT

city: Mainz

first: Tobias

last: Bopp

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Illumina CASAVA 1.8.2 software were used for basecalling
Sequence reads were trimmed for adapter sequence on the Miseq-system and further processed using the software CLC genomics workbench (5.1; using CLC's default settings for RNA-Seq analysis). Reads were aligned to mm9 genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated employing CLC Genomics Workbench (5.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Mus musculus

source_name: aTh17_CK2 inhibitor

extract_protocol:
naive CD4+ T cells were stimulated as described above and total RNA was isolated using Trizol. TruSeq RNA Sample Prep Kit V2 was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNAv2 protocol

treatment_protocol: naive CD4+ T cells were stimulated by platebound anti-CD3 and anti-CD28 under Th17 cell polarizing conditions as follows: aTh17 cells were differentiated by addition of 10ng/ml IL-1β, 10ng/ml mrIL-6, 20ng/ml mrIL-23, 10µg/ml anti-IL-4 (clone 11B11) and 10µg/ml anti-IFN-γ (XMG1.2). cTh17 ("TGF-β + IL-6") cell differentiation was carried out by addition of 1ng/ml TGF-β, 5ng/ml mrIL-6, 10µg/ml anti-IL-4 (clone 11B11) and 10µg/ml anti-IFN-γ (XMG1.2). Additionally CK2 activity was inhibited during differentiation by addition of either CK2 inhibitor DMAT (1.5µM) or CX4945 (1µM) for 24 hours.

tag: tissue

value: spleen

tag: cell type source

value: naive CD4+ T cells

tag: cell type

value: developing Th17  cells

tag: treated with

value: CK2 inhibitor DMAT (1.5µM) for 24 h


title: aTh17withoutDMAT


title: aTh17plusCX4945

value: CK2 inhibitor CX4945 (1µM) for 24 h


title: 48 h DENV1 infection Total cell lysate mRNA-seq (rep 2)

value: Huh7 cells

value: 48 h DENV1 infection

value: Total cell lysate

value: mRNA-seq

value: rep 2


title: 72 h DENV2 infection Total cell lysate mRNA-seq (rep 2)


title: 24 h DENV1 infection Total cell lysate mRNA-seq (rep 2)

value: 24 h DENV1 infection


title: tl10b_h3k4me1_1

source_name: tl10b embryos

value: 2-4 hr after egg deposition

value: Biooscientific

value: Millipore


title: 6 h DENV1 infection Total cell lysate mRNA-seq (rep 2)

value: 6 h DENV1 infection


title: 12 h DENV1 infection Total cell lysate mRNA-seq (rep 2)

value: 12 h DENV1 infection


title: Uninfected Total cell lysate mRNA-seq (rep 1)

value: Uninfected

value: rep 1


title: 72 h DENV1 infection Total cell lysate mRNA-seq (rep 1)

value: 72 h DENV1 infection


title: 48 h DENV1 infection Total cell lysate mRNA-seq (rep 1)


title: 6 h DENV1 infection Total cell lysate mRNA-seq (rep 1)


title: 24 h DENV1 infection Total cell lysate mRNA-seq (rep 1)


title: 12 h DENV1 infection Total cell lysate mRNA-seq (rep 1)


title: gd7_zld_2

description: ChIP-seq for Zelda in gd7 (replicate 2)

data_processing:
RNA-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to FlyBase r5.57 genome and gene annotations using Tophat v2.0.14.
Differential gene expression was determined using cuffdiff (Cufflinks v2.2.1) between the three mutant genotypes (Toll10b, Toll rm9/rm10, gd7)
----------------------------------------------
ATAC-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 25 bp each and aligned to the UCSC Drosophila melanogaster dm3 genome with Bowtie 1.1.2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
Genome_build: UCSC dm3
BigWig files contain per-base coverage of all aligned read pairs
----------------------------------------------
ChIP-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

growth_protocol: Adult flies were used in population cages for embryo collections and embryos were collected on apple juice plates for 2 h at 25°C in cages and then matured at 25°C for another 2 h (2-4 h after egg deposition (AED)).

extract_protocol:
ChIP-seq experiments were performed as described (He et al 2011, Nature Genet, He et al 2015, Nature Biotech) with the following differences: ~100 mg embryos were used per IP. After incubation of magnetic beads with antibodies, H3K27ac IP samples were washed 3 times by rotating tubes for 3 min at 4°C to reduce background.
Several different methods were used for library construction, please refer to the supplemental material of Koenecke et al 2016, Genome Research or Koenecke and Johnston, 2016, Genome Biol

treatment_protocol: Embryos were dechorionated for 1 min with 100% bleach and then cross-linked for 15 min with 1.8% formaldehyde (final concentration in water phase).

tag: barcode-kit

value: Custom GenScript Zld (aa 1117-1327)

tag: library-kit

value: NEB-next-ChIP


title: 24 h DENV2 infection Total cell lysate ribosome profiling (rep 2)

description:
Library strategy: Ribo-Seq
processed data file: DENVExpression-wholecell.xlsx

tag: protocol

value: 24 h DENV2 infection

value: ribosome profiling


title: 48 h DENV2 infection Total cell lysate ribosome profiling (rep 2)

value: Huh7 cells

value: 48 h DENV2 infection

tag: compartment


title: aTh17withoutCX4945

value: spleen

value: naive CD4+ T cells

value: developing Th17  cells


title: 12 h DENV2 infection Total cell lysate ribosome profiling (rep 2)

value: 12 h DENV2 infection

value: Total cell lysate

tag: analysis

value: rep 2


title: gd7_zld_1

description: ChIP-seq for Zelda in gd7 (replicate 1)

value: 2-4 hr after egg deposition


title: 72 h DENV2 infection Total cell lysate ribosome profiling (rep 1)

value: 72 h DENV2 infection

tag: replicate


title: 6 h DENV2 infection Total cell lysate ribosome profiling (rep 1)

tag: cell line

value: 6 h DENV2 infection


title: 48 h DENV2 infection Total cell lysate ribosome profiling (rep 1)

value: rep 1

tag: strain


title: zm_4n_3

first: Chris

middle: W

last: Seidel

department: Genomics

institute: Stowers Institute

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned to hg19 using tophat2 with the option -g 1 and gene models from Ensembl 75.
RPKM values on gene models from Ensembl 75 were tallied using the GenomicRanges and edgeR packages in R.
Genome_build: hg19
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.

molecule: polyA RNA

growth_protocol: Cells were grown at 37°C in 5% CO2 in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA isolation was performed using Maxwell 16 LEV simplyRNA Tissue kit on a Maxwell 16 Research Instrument (Promega).
Poly-A non-stranded RNA Seq libraries were prepared using TruSeq RNA Sample Prep Kit v2 (RS-122-2002).

treatment_protocol: Cells were treated with 2.5uM ZM447439 for 24 hours, labeled  with 2 μg/mL Hoechst 33342 for 60 minutes at 37˚C and FACS-sorted into 2N and 4N populations.

tag: ploidy

tag: drug


title: 24 h DENV2 infection Total cell lysate ribosome profiling (rep 1)


title: Zfatf/f-LckCre_thymocytes_H3K9ac/K27ac_ChIPseq

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

data_processing:
Paired-end sequencing (101bp x2) was performed on the HiSeq1500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Reads from each sample were first trimmed by removing adapters and low quality bases at ends using Trimmomatic 0.22.
Approximately the same number of reads (30 ~ 60 million reads) for a pair of ChIP and corresponding input libraries were aligned to the mouse reference genome (mm9) using the Burrows-Wheeler Aligner 0.6.2.
Uniquely mapped reads were selected by a custom script, converted from sam to bam using SAMtools 0.1.18. Reads with mapping quality < 20 were removed using SAMtools 0.1.18.
The resultant bam files were visualized using the Integrative Genomics Viewer (IGV). The uniquely mapped reads were analysed using the MACS algorithm implemented in the Avadis NGS softwere (Agilent) to identify ChIPseq peaks using the matched input DNA reads as a control.
Genome_build: mm9
Supplementary_files_format_and_content: text files with MACS called peaks.

source_name: Thymocytes

extract_protocol:
Thymocytes (1.5 × 10^8 cells) from 4 to 5-weeks-old Zfatf/f or Zfatf/f-LckCre mice were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking reaction was quenched with 125 mM glycine for 5 min. The cells were rinsed with PBS twice and incubated in 600 µl of MNase treated buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% NP-40, 5 mM CaCl2) containing 375 unit MNase (Roche) for 0.5 h at 37°C. The MNase reaction was stopped by adding 600 µl of lysis buffer  (100 mM Tris-HCl, pH 8.0, 20 mM EDTA, 2% SDS, protease inhibitor cocktail (Roche)), and the lysate was sonicated using a Bioruptor (Cosmo Bio, Tokyo, Japan) for two cycles of one minute with 30 seconds on/off. The sonicated lysate was subjected to immunoprecipitation with a monoclonal antibody against ZFAT (prepared in Dr. Shirasawa's lab), H3K9me3 (MBL), or H3K9ac/K27ac (MBL).
The immunoprecipitated DNA was purified using MinElute Reaction Cleanup kit (Qiagen) according to the manufacturer’s instructions. ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set and Multiplex Oligos for Illumina (New England Biolabs) according to manufacturer's instructions. ChIP or input DNA (0.1 ~ 1 ng) was subjected to end repair, dA-tailing, and adaptor-ligation, and amplified by 6-13 cycles of PCR.

value: Thymus


title: Zfatf/f-LckCre_thymocytes_input_2


title: Uninfected Total cell lysate ribosome profiling (rep 2)

value: Uninfected


title: zm_4n_2


title: 12 h DENV2 infection Total cell lysate ribosome profiling (rep 1)


title: zm_2n_3


title: Zfatf/f_thymocytes_input_2


title: Zfatf/f_thymocytes_H3K9ac/K27ac_ChIPseq


title: 72 h DENV1 infection Total cell lysate ribosome profiling (rep 2)

value: 72 h DENV1 infection


title: zm_2n_2


title: zm_4n_1


title: Zfatf/f_thymocytes_H3K9me3_ChIPseq


title: 72 h DENV2 infection Total cell lysate ribosome profiling (rep 2)


title: 6 h DENV2 infection Total cell lysate ribosome profiling (rep 2)


title: Zfatf/f-LckCre_thymocytes_input


title: zm_2n_1


title: 48 h DENV1 infection Total cell lysate ribosome profiling (rep 2)

value: 48 h DENV1 infection


title: ChIP_rabIgG_U2OS

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
Sequencing reads were mapped to the human genome (NCBI36)
peaks called with koli as described before
Genome_build: hg18
Supplementary_files_format_and_content: Chromosome, peak start and peak end refers to  to genome assembly NCBI36; Peak summit defined as the point of maximum height that is closest to the center of the peak; Peak height the maximum number of overlapping sequences; Fold change calculated from the areas of the peaks in the ChIP sample vs. IgG sample; p-value probability of observing the difference between the sequence counts in the ChIP sample and IgG control by chance estimated using Winflat program

growth_protocol: cells were cultured in media supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol:
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed according to Illuminas standard protocol.

value: osteosarcoma

tag: chip antibody

value: normal rabbit IgG (sc-2027, Santa Cruz Biotechnology)


title: tl10b_zld_2

description: ChIP-seq for Zelda in Toll10b (replicate 2)

tag: developmental stage

value: Custom GenScript Zld (aa 1117-1327)

value: NEB-next-ChIP


title: ChIP_NPAT_U2OS

value: NPAT (sc-67007, Santa Cruz Biotechnology)


title: ChIP_CASP8AP2_U2OS

value: CASP8AP2 (sc-9088, Santa Cruz Biotechnology)


title: cytD_4n_3

value: CytochalasinD


title: 6 h DENV1 infection Total cell lysate ribosome profiling (rep 2)

value: Huh7 cells

value: 6 h DENV1 infection

value: Total cell lysate

value: ribosome profiling


title: Zfatf/f-LckCre_thymocytes_ZFAT_ChIPseq


title: 24 h DENV1 infection Total cell lysate ribosome profiling (rep 2)

value: 24 h DENV1 infection

value: rep 2


title: Zfatf/f_thymocytes_input

value: Thymus


title: ChIP_E2F1_U2OS

value: E2F1 (sc-193, Santa Cruz Biotechnology)


title: cytD_4n_2


title: 12 h DENV1 infection Total cell lysate ribosome profiling (rep 2)

value: 12 h DENV1 infection


title: tl10b_zld_1

description: ChIP-seq for Zelda in Toll10b (replicate 1)

value: 2-4 hr after egg deposition


title: ChIP_NPAT_hTERT-RPE1

value: Epithelial cells immortalized with hTERT


title: cytD_2n_2


title: Zfatf/f_thymocytes_ZFAT_ChIPseq


title: TTT-B

city: Hangzhou

first: Liping

last: Chen

address: Yuhangtang road No.866

department: Vegetable science

country: China

institute: Zhejiang University

description: small RNA

data_processing:
The very basic figure from sequencing is converted into sequence data by the base calling step
remove the contaminant reads and low quality reads from the fq file and get the final clean reads
Supplementary_files_format_and_content: fa files

organism: Brassica juncea

source_name: leaf

extract_protocol:
Total RNAs of the fourth  leaves of eight samples were extracted using theTrizol kit (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: four-leaf stage

value: leaf

value: TTT


title: Uninfected Total cell lysate ribosome profiling (rep 1)

value: Uninfected

value: rep 1


title: cytD_4n_1

value: CytochalasinD


title: ChIP_CASP8AP2_hTERT-RPE1

value: CASP8AP2 (sc-9088, Santa Cruz Biotechnology)


title: ChIP_E2F1_hTERT-RPE1


title: TTT-A

description: small RNA


title: cytD_2n_1


title: unt_4n_3

value: untreated


title: miR-203_new mutants

city: El Paso

first: Haoquan

last: wu

state: Texas

address: 5001 El Paso Dr

department: Biomedical Scienes

institute: Texas Tech Health Sciences Center El Paso

data_processing:
Fastq quality filter by fastq_illumina_filter
Trimed the sequences missing 3' adaptor
Trimed the sequences missing 5' adaptor
Trimed the sequences that is shorter than 15bp
Trimed the sequences contains "N"
Merged reads
Removed the reads with <5 copies
Reads align to corresponding pri-miRNA
Genome_build: N/A
Supplementary_files_format_and_content: Generate a table contain the reads and sequences for each sample

source_name: 293FT cell

growth_protocol: 293 FT cell was cultured in DMEM with 10% FBS and 1X PS.

extract_protocol:
small RNA was prepared with miReasy Kit (QIAGEN)
The library construction follows Illumina’s TruSeq method. Briefly, 50ng of small RNA for cells transfected with each construct was ligated with 3’-linker (5rApp/TCGCTTGGCACCATCTATTC/3ddC) and 5’-linker (TCTACAGTCCGACGATCXXXXXXGCGA, where the X string denotes barcode sequence) respectively. Sequences for Illumina TruSeq chemistry were introduced during the PCR step. Libraries were multiplexed and sequenced on an Illumina MiSeq platform.
TruSeq

treatment_protocol: 293FT cells were transfected with constructs of pri-miRNAs


title: 24 h DENV1 infection Total cell lysate ribosome profiling (rep 1)

value: Huh7 cells

value: Total cell lysate


title: 48 h DENV1 infection Total cell lysate ribosome profiling (rep 1)

value: 48 h DENV1 infection

value: ribosome profiling


title: miR-203_old mutants


title: pre-miR-203_new mutants


title: 6 h DENV1 infection Total cell lysate ribosome profiling (rep 1)

value: 6 h DENV1 infection


title: 12 h DENV1 infection Total cell lysate ribosome profiling (rep 1)


title: unt_2n_3


title: Uninfected ER mRNA-seq (Rep 2)

description: processed data file: dengueExpression-fractionated.xlsx

value: ER

value: mRNA-seq

value: Rep 2


title: cytD_2n_3


title: pre-miR-203_old mutants


title: ChIP_rabIgG_hTERT-RPE1

value: Epithelial cells immortalized with hTERT

value: normal rabbit IgG (sc-2027, Santa Cruz Biotechnology)


title: unt_2n_2


title: unt_4n_1


title: unt_2n_1


title: Uninfected cytosol mRNA-seq (Rep 2)

value: cytosol


title: Interferon treatment ER mRNA-seq (Rep 2)

value: Interferon treatment


title: Metformin

city: Farmington

first: Tingting

last: Geng

state: CT

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

data_processing:
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary analysis pipeline, which is written in Python and used Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) to perform the alignment. Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off when doing methylation calling. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. Fisher’s exact test or t-test was performed for each CpG site which has at least five reads coverage, and promoter, gene body and CpG island annotations were added for each CpG included in the comparison.
Genome_build: hg19
Supplementary_files_format_and_content: excle file

source_name: human endometrial cancer ARK2 cells

growth_protocol: The cells were cultured in RPMI1640 (Gibco, 11965-092) supplemented with 10% fetal bovine serum, heat inactivated, 1% amphotericin B, 1% penicillin/streptomycin, and 1% L-glutamine.

extract_protocol:
Genomic DNA was extracted from ARK2 in one well of 6-well plates using Quick-gDNA MicroPrep.
Libraries were prepared from 200-500 ng of genomic DNA digested with 60 units of Taq?I and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator™-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR, Cat#D4005) for sequencing on an Illumina HiSeq.
RRHP library

treatment_protocol: ARK2 cells were incubated with metformin for 48 h, and metformin was used at final concentrations of 2 mM.

tag: treatment

value: Metformin


title: Interferon treatment cytosol mRNA-seq (Rep 2)


title: 40 h infection ER mRNA-seq (Rep 2)

value: 40 h infection


title: Control

value: control


title: 72 h DENV1 infection Total cell lysate ribosome profiling (rep 1)

value: 72 h DENV1 infection

value: rep 1


title: RiboMinusRNAseq MCF7 hypoxia, exp 3

city: Heverlee

first: Bernard

last: thienpont

address: Herestraat 49

department: Vesalius Research Center

country: Belgium

institute: VIB

description:
rRNA-depleted RNA
RNAseq_raw_reads.txt
RNAseq_EdgeR_DE.txt

data_processing:
alignment was done using Bowtie 0.12.8 (-v 2 -m 1 --best -S)
SeqMonk 0.29.0 was used to determine read counts at genes  as described in ensembl release grch37.
Genome_build: hg19
Supplementary_files_format_and_content: raw read .txt files contain the numer of reads in each experiment at the gene. These are normalized to the total read count, and averages per condition directly compared and reported as log2(hypoxia/normoxia).

source_name: MCF7 cells

growth_protocol: MCF7cells were cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM

extract_protocol:
RNA was extracted using TriZOL according to manufacturers instructions, treated with Turbo DNase (Ambion) and repurified using RNeasy Mini Kits (Qiagen). Ribosomal RNA  was depleted from 5ug of total RNA using the RiboMinus Eukaryote System (Life technologies).
cDNA synthesis was performed using SuperScript® III Reverse Transcriptase kit (Invitrogen). 3 µg of Random Primers (Invitrogen), 8 µL of 5× First-Strand Buffer and 10 µL of RNA mix was incubated at 94°C for 3 min and then at 4°C for 1 min. Then, 2 µL of 10 mM dNTP Mix (Invitrogen), 4 µL of 0.1 M DTT, 2 µL of SUPERase• In™ RNase Inhibitor 20U/ µL (Ambion), 2 µL of SuperScript™ III RT (200 units/µL) and 8 µL of Actinomycin D (1µg/µL) were added and the mix were incubated 5 min at 25°C, 60 min at 50°C and 15 min at 70°C to heat inactivating the reaction. The cDNA was purified by using 80 µL (2× volume) of Agencourt AMPure XP and eluted in 50 µL of the following mix: 5 µL of 10X NEBuffer 2, 1.5 µL of 10 mM dNTP mix (10mM dATP, dCTP, dGTP, dUTP, Sigma), 0.1µL of RNaseH (10 U/µL, Ambion), 2.5 µL of DNA Polymerase I Klenov (10U/µL, NEB) and water until 50 µL. The eluted cDNA was incubated for 30 min at 16°C, purified by Agencourt AMPure XP and eluted in 30 µL of dA-Tailing mix (2 µL of Klenow Fragment, 3 µL of 10X NEBNext dA-Tailing Reaction Buffer and 25 µL of water). After 30 min incubation at 37°C, the DNA was purified by Agencourt AMPure XP, eluted in TE buffer and quantified on NanoDrop. Libraries were subsequently prepared using the NextNEB Ultra library prep kit (NEB).

treatment_protocol: cells were grown for 24 hours at normoxic or hypoxic oxygen tensions

tag: oxygen concentration

value: 0.5% oxygen

tag: experiment

value: A


title: RiboMinusRNAseq MCF7 normoxia, exp 3

value: 21% oxygen


title: 24 h infection ER mRNA-seq (Rep 2)

value: Huh7 cells

value: 24 h infection


title: RiboMinusRNAseq MCF7 hypoxia, exp 2

value: B


title: 24 h infection cytosol mRNA-seq (Rep 2)

value: mRNA-seq


title: 12 h infection cytosol mRNA-seq (Rep 2)

value: 12 h infection

value: Rep 2


title: 6 h infection ER mRNA-seq (Rep 2)

value: 6 h infection

value: ER


title: 12 h infection ER mRNA-seq (Rep 2)


title: RiboMinusRNAseq MCF7 normoxia, exp 2


title: input MCF7 normoxia exp 3

description:
raw read counts input and hmDIP.txt
differential hydroxymethylation

data_processing:
alignment was done using Bowtie 0.12.8 (-v 2 -m 1 --best -S), or BisMark
SeqMonk 0.29.0 was used to determine read counts at coding gene promoters (2000 bp upstream to 500 bp downstream of the gene start site) as described in ensembl release grch37.
differential methylation or hydroxymethylation was determined using EdgeR version 3.6.8, correcting for experiment variable, and this for pairwise comparisons between experiments and comparisons within single experiments. for hmDIPseq, library sizes were corrected to reflect the ratio at input
Genome_build: Hg19
Supplementary_files_format_and_content: raw read .txt files contain the numer of reads in each experiment at the promoter. These are compared using EdgeR, generating result files with logCPM (log2 counts per million), logFC (log fold change) and P-values of change.

extract_protocol:
Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, with all buffers supplemented with DFO (200 µM), dissolved in 80 µL PBS-DFO with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit (all buffers supplemented with DFO), eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing.
Library preparations and DNA immunoprecipitations were as described by Taiwo and colleagues (Nat Protoc 2012), using established antibodies targeting 5mC  and 5hmC.

tag: dip antibody


title: 6 h infection cytosol mRNA-seq (Rep 2)

value: cytosol


title: 40 h infection cytosol mRNA-seq (Rep 2)


title: RiboMinusRNAseq MCF7 normoxia, exp 1


title: unt_4n_2

value: untreated


title: Uninfected cytosol mRNA-seq (Rep 1)

value: Uninfected

value: Rep 1


title: input MCF7 normoxia exp 1


title: input MCF7 normoxia exp 2


title: hmDIPseq MCF7 normoxia exp 3

value: anti 5hmC (Active Motif cat 39791)


title: input MCF7 hypoxia exp 3


title: 24 h infection cytosol mRNA-seq (Rep 1)


title: 40 h infection ER mRNA-seq (Rep 1)

value: 40 h infection


title: input MCF7 hypoxia exp 2

value: 0.5% oxygen


title: hmDIPseq MCF7 normoxia exp 2

value: A


title: input MCF7 hypoxia exp 1


title: RiboMinusRNAseq MCF7 hypoxia, exp1


title: 6 h infection ER mRNA-seq (Rep 1)


title: 24 h infection ER mRNA-seq (Rep 1)


title: Uninfected ER mRNA-seq (Rep 1)


title: 12 h infection cytosol mRNA-seq (Rep 1)


title: Interferon treatment ER mRNA-seq (Rep 1)

value: Interferon treatment


title: 40 h infection cytosol mRNA-seq (Rep 1)

value: Huh7 cells


title: 6 h infection cytosol mRNA-seq (Rep 1)


title: hmDIPseq MCF7 hypoxia exp 1


title: Uninfected ER ribosome profiling (Rep 4)

description:
Library strategy: Ribo-Seq
processed data file: dengueExpression-fractionated.xlsx

value: ribosome profiling

value: Rep 4


title: hmDIPseq MCF7 normoxia exp 1

value: 21% oxygen


title: Uninfected cytosol ribosome profiling (Rep 4)


title: 12 h infection ER mRNA-seq (Rep 1)

value: 12 h infection

value: mRNA-seq


title: hmDIPseq MCF7 hypoxia exp 3


title: SZ_BA24_17

city: Harbin

first: Jing

last: Hu

state: Heilongjiang

address: 157 Baojian Road

department: College of Bioinformatics Science and Technology

institute: Harbin medical university

data_processing:
RNA-seq reads were mapped to the human reference genome (version hg19) using Tophat (version 2.0.13) with default parameters. Only uniquely mapped reads with no more than two mismatches were retained.
Read counts for each lincRNA and protein-coding gene (PCG) were computed using HTSeq.
Fragments per kilobase of transcript per million fragments mapped (FPKM) value was calculated for each lincRNA and PCG. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count and FPKM values for each Sample ...

source_name: Brain

extract_protocol:
the tissue samples were homogenized in TRIzol solvent (Invitrogen, Carlsbad, CA, USA), and the total RNA was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen # 74804) and QIAzol Lysis Reagent (Qiagen # 79306). Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from all samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease stage

value: Schizophrenia

tag: brain region

value: Brodmann's Area 24

tag: tissue

value: brain


title: SZ_BA24_18


title: hmDIPseq MCF7 hypoxia exp 2


title: Interferon treatment ER ribosome profiling (Rep 4)

tag: protocol

value: ER


title: Interferon treatment cytosol mRNA-seq (Rep 1)

tag: compartment

value: cytosol


title: SZ_BA24_16


title: Interferon treatment cytosol ribosome profiling (Rep 4)

tag: analysis


title: SZ_BA24_19


title: Control_BA24_12

value: Control


title: SZ_BA24_14


title: 40 h infection ER ribosome profiling (Rep 4)

tag: replicate


title: 40 h infection cytosol ribosome profiling (Rep 4)

tag: cell line


title: 24 h infection ER ribosome profiling (Rep 4)

value: 24 h infection

tag: strain


title: Control_BA24_13


title: Control_BA24_11


title: 12 h infection cytosol ribosome profiling (Rep 4)


title: Control_BA24_9


title: 6 h infection ER ribosome profiling (Rep 4)

value: 6 h infection


title: Control_BA24_8


title: Control_BA24_10


title: BD_BA24_7

value: Bipolar Disorder


title: BD_BA24_6


title: BD_BA24_5


title: Interferon treatment ER ribosome profiling (Rep 3)

value: Rep 3


title: Uninfected ER ribosome profiling (Rep 3)

value: Uninfected


title: Q Rep2

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
bam files with short reads aligned against the yeast genome were provided by the sequencing facility
read counts per gene and transcripts per million (TPM) were calculated with an in-house Perl script
values across biological replicates were merged using the mean
log2 ratios of Log vs Q were calculated based on the merged values
Genome_build: R64-1-1_20110208
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts and TPM values for each sample as well as averaged values for each growth phase and log2-ratios of the merged values

organism: Saccharomyces cerevisiae

source_name: Purified quiescent cells (day 7)

growth_protocol: All yeast cells (YCH406; MATa (hta1-htb1)∆::LEU2, (hta2-htb2)∆::TRP1, his3∆200 leu2∆1, ura3-52, trp1∆ RPB3-9Myc::hphNT1 <pSAB6 (HTA1-HTB1-URA3)> <pZS145 (HTA1-Flag-HTB1::HIS3)>) were cultured at 30oC in YPD + A medium (.04 mg/mL adenine and 50 mg/mL ampicillin) and grown to an OD600 of 0.8 – 1.0 for log phase samples.  Cells were grown through the diauxic shift into stationary phase and separated into quiescent and non-quiescent populations at 3, 5, 7 and 14 days after inoculation according to Allen et al., (2006). J. Cell Biol. 174. 89-100. 6.5 mL of cells were overlaid on a 10 mL PercollTM gradient after resuspension in 1/10 volume of 50 mM Tris-HCl, pH 7.5.   Quiescent and non-quiescent cell fractions were collected, and the quiescent cell fraction was further purified by centrifugation and collection on a fresh Percoll gradient.   Cells were washed in 5 volumes of Tris-HCl buffer and pelleted.

extract_protocol:
Total RNA was isolated by the hot phenol method (Aragon, A.D. et al., 2006, Genome Biol.) from 3 biological replicates using 10 OD600 units of log phase cells and 7-day Q cells (RNA-seq). 5 g of total RNA were treated with DNase (RQI DNase, Promega), and ERCC RNA Spike-In Control Mixes #1 and 2 were added before removal of the ribosomal RNA with the Ribo-ZeroTM Magnetic Gold Kit for yeast (Epicentre  #MRZY1324).
Libraries were prepared using the Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries (Ion Torrent #4476290) starting with 250 ng of rRNA-depleted RNA. Sequencing was performed on the Ion Proton System in the University of New Mexico Comprehensive Cancer Center’s ATG Shared Resource facility, and reads were mapped to the yeast genome.

tag: cell growth stage

value: Stationary Phase:Day 7 cells


title: BD_BA24_4


title: Q Rep3


title: Q Rep1


title: Interferon treatment cytosol ribosome profiling (Rep 3)

value: Huh7 cells

value: Interferon treatment

value: ribosome profiling


title: Log Rep3

source_name: Actively growing cells

value: Exponentially growing


title: BD_BA24_3


title: BD_BA24_2


title: Log Rep1


title: 40 h infection ER ribosome profiling (Rep 3)

value: 40 h infection


title: Log Rep2


title: 40 h infection cytosol ribosome profiling (Rep 3)


title: BD_BA24_1


title: 24 h infection cytosol ribosome profiling (Rep 3)


title: SZ_BA9_18

value: Schizophrenia

value: Brodmann's Area 9


title: 12 h infection ER ribosome profiling (Rep 4)

value: 12 h infection

value: Rep 4


title: 12 h infection ER ribosome profiling (Rep 3)

value: ER


title: SZ_BA9_17

value: brain


title: 12 h infection cytosol ribosome profiling (Rep 3)

value: cytosol


title: SZ_BA9_16


title: Uninfected cytosol ribosome profiling (Rep 3)


title: 24 h infection ER ribosome profiling (Rep 3)

value: 24 h infection


title: 6 h infection ER ribosome profiling (Rep 3)

value: 6 h infection


title: Control_BA9_13

value: Control


title: SZ_BA9_15


title: SZ_BA9_14


title: Interferon treatment ER ribosome profiling (Rep 2)

value: Rep 2


title: 6 h infection cytosol ribosome profiling (Rep 3)

value: Rep 3


title: Interferon treatment cytosol ribosome profiling (Rep 2)

value: Huh7 cells


title: BD_BA9_5

value: Bipolar Disorder


title: BD_BA9_7


title: 40 h infection cytosol ribosome profiling (Rep 2)

value: ribosome profiling


title: Uninfected ER ribosome profiling (Rep 2)

value: Uninfected


title: Uninfected cytosol ribosome profiling (Rep 2)


title: 24 h infection ER ribosome profiling (Rep 2)


title: 12 h infection ER ribosome profiling (Rep 2)


title: SZ_BA24_15

value: Brodmann's Area 24


title: 6 h infection cytosol ribosome profiling (Rep 2)


title: 24 h infection cytosol ribosome profiling (Rep 2)


title: BD_BA9_6


title: BD_BA9_2


title: Uninfected ER ribosome profiling (Rep 1)

value: Rep 1


title: Control_BA9_8

value: Brodmann's Area 9


title: Control_BA9_11


title: BD_BA9_1


title: Control_BA9_10


title: Control_BA9_9


title: 12 h infection cytosol ribosome profiling (Rep 2)

value: 12 h infection


title: 6 h infection ER ribosome profiling (Rep 2)


title: BD_BA9_4


title: BD_BA9_3


title: 24 h infection cytosol ribosome profiling (Rep 4)

value: Rep 4


title: Control_BA9_12


title: 40 h infection ER ribosome profiling (Rep 2)

value: 40 h infection

value: ER


title: Interferon treatment ER ribosome profiling (Rep 1)

value: Interferon treatment


title: Interferon treatment cytosol ribosome profiling (Rep 1)

value: cytosol


title: Uninfected cytosol ribosome profiling (Rep 1)


title: SZ_BA11_42

value: Schizophrenia

value: Brodmann's Area 11

value: brain


title: 6 h infection cytosol ribosome profiling (Rep 4)

value: 6 h infection


title: SZ_BA9_19


title: SZ_BA11_40


title: SZ_BA11_41


title: SZ_BA11_43


title: wt rspd rep2

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

description: wild type purified round spermatids

data_processing:
Torrent Suite
Cutadapt remove adaptor sequence
The reads were mapped to reference small RNA file though our house pipeline
The mapped reads were counted though featureCount
The counts were normalize though Deseq2
Genome_build: mm9
Supplementary_files_format_and_content: counts txt file

source_name: WT_round spermatids

growth_protocol: All animal work was performed following the protocol approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Nevada, Reno. Mice were housed and maintained under specific pathogen-free conditions with a temperature- and humidity-controlled animal facility in the University of Nevada, Reno. Global Miwi KO mouse line was recovered using cryopreserved sperm, purchased from the Mutant Mouse Resource & Research Center (MMRRC) (Item# 029995-MU-SPERM) in the Genetic Engineering Center of the University of Nevada, Reno.  All mice used in this study were on the C57BL/6J background.

extract_protocol:
Small RNA was isolated from round spermatids using the mirVana RNA isolation kit (Ambion) according to the manufacturer’s instructions. RNA quality and quantity were assessed using the Agilent 2100 Bioanalyzer.
Libraries were prepared using the Ion Total RNA-Seq Kit v2 (Invitrogen)

treatment_protocol: 6-8 week-old WT and Miwi KO female mice were each injected with 5IU of pregnant mare’s serum gonadotropin (PMSG), followed by injection of 5IU of human chorionic gonadotropin (hCG) 48h apart. Mature oocytes were collected from oviducts 14–16h after hCG injection and cumulus cells were removed by treatment with 0.1% bovine testicular hyaluronidase in HEPES-CZB at 37°C for 2–3 min. Cumulus-free oocytes were rinsed and kept in CZB at 37°C under 5% CO2 in air before ROSI.

tag: age

value: post natal day 21

tag: genotype

value: wild type

value: testes

value: round spermatids


title: 24 h infection ER ribosome profiling (Rep 1)

value: Huh7 cells

value: 24 h infection

value: ribosome profiling


title: wt rspd rep3

description: wild type purified round spermatids


title: SZ_BA11_39


title: SZ_BA11_44


title: 24 h infection cytosol ribosome profiling (Rep 1)

value: Rep 1


title: 12 h infection ER ribosome profiling (Rep 1)

value: 12 h infection


title: SZ_BA11_37


title: SZ_BA11_38


title: miwi ko rspd rep3

description: Miwi knockout purified round spermatids

source_name: KO_round spermatids

value: Miwi knockout


title: 12 h infection cytosol ribosome profiling (Rep 1)


title: 40 h infection ER ribosome profiling (Rep 1)

value: 40 h infection

value: ER


title: 40 h infection cytosol ribosome profiling (Rep 1)

value: cytosol


title: 6 h infection ER ribosome profiling (Rep 1)


title: miwi ko rspd rep1

description: Miwi knockout purified round spermatids


title: SZ_BA11_35

value: Schizophrenia


title: SZ_BA11_36

value: Brodmann's Area 11


title: miwi ko rspd rep2

description: Miwi knockout purified round spermatids


title: SZ_BA11_34

value: brain


title: SZ_BA11_33


title: SZ_BA11_31


title: 6 h infection cytosol ribosome profiling (Rep 1)

value: 6 h infection


title: wt rspd rep1

description: wild type purified round spermatids

value: post natal day 21


title: SZ_BA11_29


title: SZ_BA11_30


title: MNxMN_buds1_bisulfite

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Bisulfite-Seq

data_processing:
For all libraries: FastQC was used to examine read quality. Low quality reads were removed with trim_galore with parameters --clip_R1 8, --clip_R2 8, --stringency 3, -q 25, -r1 32, -r2 32 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, version from 16 July 2014).
For RNA-seq libraries: reads passing quality filters were mapped to lyrata genome using Tophat v2.0.13 (https://ccb.jhu.edu/software/tophat/).  Parameters used for 40x40bp libraries:  --segment_length 16, -r 220, --read-edit-dist 2, -N 2.  Parameters used for 80x80bp libraries:  --segment_length 25, -r 140, --read-edit-dist 4, -N 4. Parameters used for 100x100bp libraries:  --segment_length 25, -r 220, --read-edit-dist 5, -N 5.  For the 4 libraries prepared using the Illumina TruSeq RNA-seq kit, used --library-type fr-firststrand, all others --library-type fr-secondstrand.  For all libraries, used parameters -i 20 and -I 5000.  All other parameters default.  Uniquely mapped reads were obtained by removing all reads with MAPQ score < 5.  PCR duplicates were removed using picard-tools v.2.0.1 MarkDuplicates (http://broadinstitute.github.io/picard/) with REMOVE_DUPLICATES=true to obtain final set of alignments.
For bisulfite-seq libraries: reads passing quality filters were mapped to the bisulfite-converted lyrata genome using Bismark v0.13.0 (http://www.bioinformatics.babraham.ac.uk/projects/bismark/), except KAxMN libraries, which were mapped to a bisulfite-converted "pseudometagenome" consisting of the lyrata genome noted previously (from MN) appended to another copy of the lyrata genome with Kar SNP substitutions (alyr_MN_Kar_metagenome.fa) .  Parameters for the two 40x40 libraries: -n 1, -l 40.  For the two 100x100 libraries: -n 2, -l 80.  All other parameters default.  Uniquely mapping reads obtained from Bismark were then further filtered to remove PCR duplicates using a script provided with Bismark (deduplicate_bismark_alignment_output.pl), and methylation information was extracted using bismark_methylation_extractor.  Resulting data were processed into BED-like format (see "Supplementary_files_format_and_content" below) and saved with file format MNxMN_SS_BS_***.bed where SS = sample (b1,b2,N1 or E1), and *** is context (CpG, CHG or CHH).
htseq-count from the "HTSeq" framework v0.6.1p1 was used to generate total read counts for each annotated gene in alyr2_gene_annot.gtf from the mapped RNA-seq reads, with parameters  -m intersection-nonempty, with --stranded reverse for Illumina Truseq libraries, and --stranded yes for all other libraries.
Allele-specific read counts for each annotated gene for all RNA-seq libraries were generated by first assigning each read overlapping a SNP to MN or Kar based on the allele using a python script (if conflicting information from multiple SNPs, read was not assigned to either strain), then the number of reads assigned to each strain (Kar or MN) for each gene was counted using htseq-count with the same parameters as above for total counts.
FPKM values for all RNA-seq libraries were obtained using Cufflinks v2.2.1 (http://cole-trapnell-lab.github.io/cufflinks/), using --library-type fr-firststrand for all Truseq RNA-seq libraries and fr-secondstrand for all others.  All other parameters were left at default values.
Updated A. lyrata gene annotations were obtained by using Cufflinks and Trinity (genome-guided) in parallel to predict transcripts. Resulting transcripts were processed by PASA to update the previous annotations with 3 rounds of updating. Final annotations were compared to the published original set and more recent updated set (Rawat et al. 2015), and the model with the most support was kept.
Genome_build: Arabidopsis lyrata genome sequence assembly v.1.0 (phytozome.jgi.doe.gov/alyrata)
Supplementary_files_format_and_content: *_stats.txt = tab-delimited file containing RNA-seq data for each library, with one row per gene.  Contains gene ID (locus_name), gene coordinates (pos), number of RNA-seq reads aligned to gene (num_reads), FPKM (FPKM), number of reads assigned to MN47 (numRef, only if MNxKar or KarxMN cross), number of reads assigned to Kar (NumOth, only if MNxKar or KarxMN cross)
Supplementary_files_format_and_content: *_CpG.txt, *_CHG.txt and *_CHH.txt = contains per-cytosine methylation information for each library in each of these three contexts, in BED-like format.  For KAxMN libraries, additional files MN47_CpG.txt, etc. contain methylation data from reads that mapped preferentially to that strain.  First three fields represent the location of the CpG, CHG or CHH (BED-like format, 0-based indexing).  Fourth field is number of reads overlapping that position that were unmethylated at that position, fifth field is number of reads overlapping methylated reads, and sixth field is the percent of overlapping reads that were methylated at that position.

organism: Arabidopsis lyrata

source_name: buds

growth_protocol: Plants were grown in a greenhouse with 16 hr of light at 21 C or in a growth chamber with 16 hr of light (120 μMol), 20 C and 50% humidity , vernalized at 4C for a month after rosettes had formed, and returned to the greenhouse/growth chamber.  Seeds were dissected into embryo, endosperm and seedcoat at approximately the late torpedo to bent cotyledon stage (~15-19 DAP).

extract_protocol:
Epicentre EpiGnome Methyl-Seq kit protocol sequenced on 10/3/14 with barcode GCCAAT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.

value: MN47 female x MN47 male

tag: developmental stage

value: flowering adult

tag: read length


title: MNxMN_embryo_bisulfite

description: Bisulfite-Seq

source_name: embryo

extract_protocol:
Epicentre EpiGnome Methyl-Seq kit protocol sequenced on 4/2/15 with barcode CTTGTA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.

value: linear to bent cotelydon stage seed


title: KAxMN_embryo_bisulfite

description: bisulfite-treated genomic DNA

extract_protocol:
Epicentre EpiGnome Methyl-Seq kit protocol sequenced on 2/24/16 with barcode CAGATC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries and DNA-seq libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from leaves, dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated.

treatment_protocol: no treatment

value: Kar female x MN47 male


title: MNxMN_endosperm_bisulfite

description: Bisulfite-Seq

source_name: endosperm

extract_protocol:
Epicentre EpiGnome Methyl-Seq kit protocol sequenced on 4/2/15 with barcode GCCAAT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_28

value: Control


title: MNxMN_seedcoat2

description: RNA-seq

source_name: seed coat

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 10/17/14 with barcode TGACCA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_27


title: Control_BA11_26


title: Control_BA11_24


title: MNxMN_endo1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode GGCTAC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: MNxMN_endo3

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 8/8/14 with barcode TAGCTT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: MNxMN_seedcoat1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 8/8/14 with barcode CTTGTA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_25


title: KAxMN_endosperm_bisulfite

description: bisulfite-treated genomic DNA

extract_protocol:
Epicentre EpiGnome Methyl-Seq kit protocol sequenced on 2/24/16 with barcode ACTTGA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries and DNA-seq libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from leaves, dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated.


title: Control_BA11_21


title: MNxMN_emb2

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode ACTTGA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: MNxMN_emb1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode CAGATC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_20


title: SZ_BA11_32


title: MNxMN_emb3

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 8/8/14 with barcode GGCTAC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: MNxKar_endo3

description: RNA-seq

extract_protocol:
Illumina Truseq stranded mRNA sequenced on 12/19/14 with barcode TAGCTT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.

value: MN47 female x Kar male


title: MNxMN_buds2_bisulfite

description: Bisulfite-Seq

extract_protocol:
Epicentre EpiGnome Methyl-Seq kit protocol sequenced on 10/3/14 with barcode CTTGTA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: MNxKar_endo2

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 10/17/14 with barcode TTAGGC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_19

extract_protocol:
the tissue samples were homogenized in TRIzol solvent (Invitrogen, Carlsbad, CA, USA), and the total RNA was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen # 74804) and QIAzol Lysis Reagent (Qiagen # 79306). Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from all samples.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Control_BA11_18


title: MNxKar_endo1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode GCCAAT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_17


title: MNxKar_emb2

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 8/8/14 with barcode GATCAG
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: BD_BA11_16

value: Bipolar Disorder


title: BD_BA11_14


title: MNxKar_emb3

description: RNA-seq

extract_protocol:
Illumina Truseq stranded mRNA sequenced on 12/19/14 with barcode CTTGTA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: MNxMN_endo2

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode CTTGTA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: MNxKar_emb1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode TGACCA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: BD_BA11_13


title: KarxMN_buds1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode TTAGGC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: KarxMN_buds2

description: RNA-seq


title: BD_BA11_11


title: KarxMN_endo4

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 8/2/13 with barcode TGACCA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_22


title: BD_BA11_12


title: BD_BA11_10


title: KarxMN_endo3

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 8/2/13 with barcode TTAGGC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: KarxMN_endo1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode ATCACG
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: KarxMN_endo2

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode CGATGT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: BD_BA11_8


title: BD_BA11_7


title: KarxMN_emb2

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/19/14 with barcode CGATGT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: KarxMN_emb1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/19/14 with barcode ATCACG
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: BD_BA11_6


title: KarxKar_endo3

description: RNA-seq

extract_protocol:
Illumina Truseq stranded mRNA sequenced on 12/19/14 with barcode GATCAG
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.

value: Kar female x Kar male


title: KarxKar_endo2

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 4/29/14 with barcode CGATGT
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: Control_BA11_23


title: BD_BA11_15


title: KarxKar_emb3

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 4/9/14 with barcode CAGATC
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: BD_BA11_4


title: KarxKar_endo1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 4/9/14 with barcode ACTTGA
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.


title: BD_BA11_3

extract_protocol:
the tissue samples were homogenized in TRIzol solvent (Invitrogen, Carlsbad, CA, USA), and the total RNA was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen # 74804) and QIAzol Lysis Reagent (Qiagen # 79306). Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from all samples.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: BD_BA11_2


title: BD_BA11_1


title: BD_BA11_5


title: KarxKar_emb1

description: RNA-seq

extract_protocol:
Integenex PolyA prep protocol (Wafergen Biosystems) sequenced on 12/6/13 with barcode GATCAG
Seeds from crosses were hand-dissected into embryo, endosperm and seed coat, and total RNA was isolated using the RNAqueous Micro Kit (Ambion, Life Technologies Corp.). Input for mRNA-seq library construction varied from 120ng - 800ng. For bisulfite-sequencing libraries, genomic DNA was isolated from fresh flower bud tissue using the DNeasy Plant Mini Kit (Qiagen), or from dissected embryo or endosperm using CTAB. DNA was RNase treated.
Strand-specific mRNA-seq libraries were prepared by the Whitehead Institute Genome Technology Core using the Integenex PolyA prep protocol (Wafergen Biosystems, Fremont CA) or using the Illumina TruSeq Stranded mRNA Kit. Libraries were multiplexed and sequenced on an Illumina HiSeq 2000 machine as 40x40, 80x80 or 100x100 paired end reads. 500 ng of genomic DNA was used for bisulfite treatment with the MethylCode Bisulfite Conversion Kit (Invitrogen, Life Technologies Corporation), according to the manufacturer’s protocol. Bisulfite-sequencing libraries were constructed using the EpiGnome Methyl-seq Kit (Epicentre, Biotechnologies, Madison, WI) according to the manufacturer’s protocol. Library quality was evaluated using a bioanalyzer and then sequenced on an Illumina HiSeq2000 using a 40x40 or 100x100 paired end protocol at the Whitehead Institute Genome Technology Core. Barcodes and date sequenced are indicated above.