title: 3D/BSA Sample 3

city: Minneapolis

first: Brenda

last: Ogle

state: MN

address: 312 Church St. SE, 7-130 Nils Hasselmo Hall

department: Department of Biomedical Engineering

institute: University of Minnesota

data_processing:
Gene expression was analyzed using the Galaxy software (Minnesota Supercomputing Institute (MSI), University of Minnesota, MN).
RNA sequencing reads were aligned to the human genome (hg19.fa and hg19_genes_2012-03-09.gtf) using the TopHat software (version 2.0.09, open source software, http://ccb.jhu.edu/software/tophat/index.shtml).
TopHat results were further analyzed using Cufflinks (version 2.2.1, open source software, http://cole-trapnell-lab.github.io/cufflinks/) software to assemble the gene transcripts and estimate gene abundance. Read counts were normalized to obtain FPKM (fragment per kilobase of transcript per million mapped reads).
Differential gene expression was determined using the Single Cell Differential Expression (SCDE) toolset. Genes with a q-value less than 0.05 were considered differentially expressed.
Gene-annotation enrichment analysis was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) informatics resources 6.7 of the National Institute of Allergy and Infectious Diseases (NIAID) and of the National Institutes of Health (NIH).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx

source_name: Mesenchymal stem cell

growth_protocol: Embryonic stem cell derived mesenchymal stem cells were cultured in αMEM, 10% fetal bovine serum, 1% L-glutamine, 1% non-essential amino acid, 1% penicillin/streptomyocin. MSCs were plated at 10,000 cells/mm2 with daily media changes for 28 days.

extract_protocol:
MSCs specifically within the structures were excised and RNA extracted according to the RNeasy Mini Kit (Qiagen, Germantown, MD).
mRNA library was produced according to the Illumina Nextera XT preparation kit’s manufacture protocol (Illumina, San Diego, CA).
RNA was sequenced using the Illumina MiSeq sequencher with paired end reads, a length of 75bp, and a depth 20 million reads.

treatment_protocol: ES-hMSCs were cultured for 28 days in five different environments: 2D tissue culture glass, 3D/BSA, 3D/FN, 3D/Col1, or 3D/LN

value: ES-derived MSC

tag: cell passage

tag: experimental group


title: 3D/BSA Sample 4

status: Public on Jan 01 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: 3D/BSA Sample 1


title: 3D/BSA Sample 5


title: 3D/BSA Sample 2


title: 107 salt-stress rep1

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: RDP1: NSFTV_107

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each gene with  htseq-count
Genome_build: Oryza sativa japonica reference genome v 6
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

organism: Oryza sativa

source_name: shoot

growth_protocol: Briefly, plants were grown in a controlled environment growth chamber. Seedlings were transplanted into the pots filled with Turface (Profile Products, LLC) and were grown in tap water for two days after transplanting. For the remainder of the experiment the plants were supplemented with half strength Yoshida solution (pH 5.8). Temperatures were maintained at 28 °C and 25 °C in day and night respectively, relative humidity was maintained at 60% in both day and night. Lighting was maintained at 800 μmoles·m−2·s−1 using high pressure sodium lights.

extract_protocol:
The samples were ground with Tissuelyser II (Invitrogen) and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
96 libraries were prepared using TruSeq RNA v2 library preparation reagents. Eighteen samples were sequenced per lane.

treatment_protocol: Salinity stress (6:1 molar ratio, NaCl:CaCl2) was increased to 6 dS·m-1 gradually in two 3 dS·m-1 intervals over a period of 24h. After 24h of 6 dS·m-1, aerial parts of the seedlings were excised from the roots and frozen immediately in liquid nitrogen.

tag: tissue

value: shoot

tag: genotype

tag: age

value: 8 days old


title: 3D/COL1 Sample 2


title: 107 control rep1

description: RDP1: NSFTV_107


title: 3D/COL1 Sample 3


title: 3D/COL1 Sample 1


title: 3D/BSA Sample 6


title: 107 control rep2

description: RDP1: NSFTV_107


title: 117 salt-stress rep2

description: RDP1: NSFTV_117


title: 105 salt-stress rep2

description: RDP1: NSFTV_105


title: 3D/COL1 Sample 4


title: 3D/COL1 Sample 5


title: 3D/LN Sample 1


title: 105 control rep2

description: RDP1: NSFTV_105


title: 105 control rep1

description: RDP1: NSFTV_105


title: 3D/LN Sample 4


title: 3D/FN Sample 6


title: 3D/LN Sample 5


title: 3D/FN Sample 5


title: 3D/FN Sample 4


title: 3D/FN Sample 2


title: 101 salt-stress rep1

description: RDP1: NSFTV_101


title: 3D/FN Sample 1


title: 120 control rep2

description: RDP1: NSFTV_120


title: 101 control rep2

description: RDP1: NSFTV_101


title: 101 control rep1

description: RDP1: NSFTV_101


title: 2D/D0 Sample 2


title: 2D/D0 Sample 1


title: 3D/LN Sample 2


title: 3D/LN Sample 3


title: 2D/D28 Sample 1


title: 2D/D28 Sample 2


title: KO-3 m6A-seq

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Low-quality reads were filetered. A read was defined as low-quality if it 1) carried adapter sequence; and/or 2) carried >10% unknown bases; and or 3) carried > 50% bases the base quality of which <15.
Clean reads were aligned to mm10 transcripts by Bowtie2(2.2.9) with such parameters: 1) -q; 2) --phred33; 3) -p 8; 4) -k 200.
FPKM values of each gene was calculated by RSEM(1.2.15) with default parameters.
Raw counts values of each gene was calculated by a function named "featureCounts" from a R package "Rsubread" with default parameters.
For m6A peak calling, the longest isoform was used if multiple isoforms were detected. Aligned reads were extended to 100 nt (average fragment size) and converted from genome-based coordinates to isoform-based coordinates to eliminate interference from introns in peak calling. The longest isoform of each mouse gene was scanned using a 100 nt sliding window with 10 nt steps. To reduce bias from potentially inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded.
For each gene, the reads count in each window was normalized by the median count of all windows of that gene. The window was called positive if FDR < 1% and log2(enrichment score) >= 1. Overlapping positive windows were merged.
The following four numbers were calculated to obtain the enrichment score of each peak (or window): read count of the IP sample in the current peak/window (a), median read count of the IP sample in all 100 nt windows on the current mRNA (b), read count of the input sample in the current peak/window (c), and median read count of the input sample in all 100 nt windows on the current mRNA (d). The enrichment score of each window was calculated as (a × d)/(b × c). Common peaks shared in the triplicates of a sample were kept with the peak annotation from replicate 1.
Genome_build: mm10
Supplementary_files_format_and_content: [RNA-Seq] The two columns of raw counts files are gene symbols and raw counts of reads mapped to these genes, respectively. The contents of FPKM files has been marked clearly by the header. For further information of such columns, you may access to this paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323.
Supplementary_files_format_and_content: [m6A-seq] m6Apeaklist_with_readcounts.xlsx

organism: Mus musculus

source_name: E14.5-derived neural stem/progenitor cells

growth_protocol: NSPCs were generated from E14.5 embryo brains and cultured in DMEM/F12 (GIBCO) supplemented with 20 ng/ml EGF (R&D systems, 236-EG-200), 10 ng/ml bFGF (R&D systems, 234-FSE 025), N2 supplement (Life, 17502-048), B27 supplement witout vitamin A (Thermo, 12587010)

extract_protocol:
mRNAs were isolated from total RNAs of NSPCs and fragmented into around 100nt length with sonication at 10 ng/ul in 100 ul RNase-free water with Bioruptor Pico (Diagenode) with 30 cycles of 30 sec on followed by 30 sec off.
libraries were prepared with Truseq Stranded mRNA library Prep Kit with the RFP incubation step shorten from 8 min to 20 sec.

value: NSPCs

tag: strain

tag: passage

value: Ythdf2 -/-

tag: rip antibody

value: m6A antibody (EpiMark® N6-Methyladenosine Enrichment Kit, NEB, E1610S)


title: 2D/D28 Sample 4


title: 2D/D28 Sample 3


title: 2D/D28 Sample 5


title: 2D/D28 Sample 6


title: KO-1 m6A-seq


title: 105 salt-stress rep1

description: RDP1: NSFTV_105


title: WT-3 m6A-seq

value: wild type


title: KO-2 m6A-seq


title: 101 salt-stress rep2

description: RDP1: NSFTV_101


title: 2D/D28 Sample 7


title: WT-2 m6A-seq


title: 2D/D0 Sample 3


title: 3D/FN Sample 3


title: sertoli_zika3

city: Edmonton

first: Juan

last: Jovel

state: Alberta

address: 7-142 KATZ Group Centre for Pharmacy & Health Research

country: Canada

institute: University of Alberta

data_processing: Raw counts and differential expression analysis results

growth_protocol: sertoli cells were grown in RPMI media supplemented with 10% BS

extract_protocol:
Total RNA was extracted with TRIzol
Libraries were constructed with illumina TrueSeq V2 kit according to manufacturerâ€™s protocols

treatment_protocol: Cells were either mock-inoculated or inoculated with 1 moi of purified zika virus

value: sertoli cells


title: sertoli_mock3

source_name: sertoli cells_mock3


title: sertoli_zika1


title: sertoli_mock2

source_name: sertoli cells_mock2


title: KO-3 input-seq


title: KO-2 input-seq


title: WT-1 m6A-seq


title: sertoli_mock1

source_name: sertoli cells_mock1


title: WT-3 input-seq


title: WT-2 input-seq


title: KO-1 input-seq


title: 1PPMHg3

city: Milwaukee

first: Francisco

middle: Xavier

last: Mora Zamorano

state: WI

address: 600 E Greenfield Ave

department: School of Freshwater Sciences

institute: University of Wisconsin - Milwaukee

data_processing:
Basecalling was performed using CASAVA 1.8.2.
Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt
FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer
The cleaned reads for each sample were independently aligned to the reference zebrafish genome (Zv9, UCSC) using TopHat
Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome
Genome_build: UCSC Zv9
Supplementary_files_format_and_content: Tab delimited matrix of gene counts and FPKM normalized counts

organism: Danio rerio

source_name: Embryo

growth_protocol: Zebrafish were exposed to MeHg diets  (0, 1, 3, and 10ppm) throughout their whole life cycle. Upon reaching adulthood, these fish were spawned and the newly acquired embryos were raised to 5 days post-fertilization for RNA extraction from whole embryo tissue.

extract_protocol:
High quality total RNA was extracted from pools of 5 whole embryos using the Direct-zol RNA MiniPrep kit (Zymo Research, Irving, CA)
Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin-Madison.
Each library was generated using a paired-end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA). Samples were run with 12 samples per lane, with 100 base pair, paired-end reads. Sequencing depth was 20-32 million reads per sample.

treatment_protocol: 5 day post-fertilization embryos were aquired from each of the parental dietary MeHg exposure groups. Then, RNA extractions were performed in pools of 5 embryos per MeHg exposure, in triplicate.

tag: generation

value: EK

tag: agent

value: 1ppm MeHg


title: 3PPMHg3

value: 3ppm MeHg


title: 10PPMHg1

value: 10ppm MeHg


title: 3PPMHg2


title: 1PPMHg2


title: 10PPMHg3


title: 3PPMHg1


title: WT-1 input-seq


title: 1PPMHg1


title: 10PPMHg2


title: sertoli_zika2


title: MouseLiver_(-MET)_RNAseq_Rep6

city: Durham

first: Jason

middle: W

last: Locasale

state: NC

address: Levine Science Research Center C270

department: Pharmacology and Cancer Biology

institute: Duke University

data_processing:
HCT116 ChIP-seq: Reads were aligned to a combinational genome consisting of the human reference genome hg19 and the Drosophila reference genome dm6 using Bowtie2. Alignment files were then filtered according to their alignment scores and down-sampled to ensure each file contains the same amount of unique Drosophila reads. Finally, reads mapped to hg19 in the normalized alignment files were kept for peak-calling and other following analyses. Processing of alignment files was done using SAMtools. Peaks were called using the --broad mode of MACS2 and filtered with the criterion that enrichment q-value is smaller than 1e-5.
Mouse liver ChIP-seq: Reads were aligned to a the reference genome mm8 using Bowtie2. Alignment files were then filtered according to their alignment scores and normalized by sequencing depth. Processing of alignment files was done using SAMtools. Peaks were called using the --broad mode of MACS2 and filtered with the criterion that enrichment q-value is smaller than 1e-5.
HCT116 RNA-seq: Raw reads were aligned to the human reference genome hg19 using TopHat2. Number of reads mapped to each gene feature was first quantified using HTSeq with the input of GTF files obtained from the UCSC Table Browser and then normalized using DESeq2. Differential expression analysis was done with DESeq2. P-values were adjusted using the Benjamini-Hochberg procedure.
Mouse liver RNA-seq: Raw reads were aligned to the mouse reference genome mm8 using TopHat2. Number of reads mapped to each gene feature was first quantified using HTSeq with the input of GTF files obtained from the UCSC Table Browser and then normalized using DESeq2. Differential expression analysis was done with DESeq2. P-values were adjusted using the Benjamini-Hochberg procedure.
Genome_build: hg19 (HCT116), mm8 (mouse liver)

molecule: polyA RNA

source_name: liver

extract_protocol:
Total RNA was extracted using the PARIS kit.
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: C57BL/6J mice were fed with either 0.86% (Kcal) methionine control diet or 0.12% (Kcal) methionine MR diet for 12 weeks and fasted before being sacrificed.

value: liver


title: CTRL3

value: 0ppm MeHg


title: CTRL1


title: T5R

first: Michael

middle: J

last: Carvan III

address: 600 E. Greenfield Ave.

institute: University of Wisconsin-Milwaukee

source_name: Retina

growth_protocol: Eggs of EK strain zebrafish were exposed to methylmercury (0.0 and 0.03μM with ethanol as the vehicle) for 24 hours, then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg.

extract_protocol:
High quality total RNA was extracted from the retina using RNeasy Micro Kit (QIAGEN, Valencia, CA, USA).
Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin-Madison.
Each library was generated using a paired-end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA). Samples were run with 12 samples per lane, with 100 base pair, paired-end reads. Sequencing depth was 14-32 million reads per sample.

treatment_protocol: The F1 generation embryos were exposed to MeHg. Retina of F3 generation was used for isolating RNA.

value: Retina

tag: mehg conc

value: 0.03µM MeHg


title: MouseLiver_(-MET)_RNAseq_Rep4


title: T4R


title: T6R


title: T2R


title: T3R


title: C7R

value: 0µM MeHg


title: MouseLiver_(-MET)_RNAseq_Rep2


title: T7R


title: MouseLiver_(-MET)_RNAseq_Rep1


title: C4R


title: C8R


title: C5R


title: C3R


title: MouseLiver_(+MET)_RNAseq_Rep6


title: CTRL2


title: T5B

source_name: Brain

extract_protocol:
High quality total RNA was extracted from the brain using RNeasy Micro Kit (QIAGEN, Valencia, CA, USA).
Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin-Madison.
Each library was generated using a paired-end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA). Samples were run with 12 samples per lane, with 100 base pair, paired-end reads. Sequencing depth was 14-32 million reads per sample.

treatment_protocol: The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.

value: Brain


title: MouseLiver_(+MET)_RNAseq_Rep5


title: T4B


title: C1R


title: T8B


title: MouseLiver_(+MET)_RNAseq_Rep3


title: T1B


title: T7B


title: MouseLiver_(+MET)_RNAseq_Rep4


title: T2B


title: C8B


title: MouseLiver_(+MET)_RNAseq_Rep2


title: MouseLiver_(-MET)_RNAseq_Rep3


title: MouseLiver_(+MET)_RNAseq_Rep1


title: C5B


title: C6B


title: C4B


title: C2B


title: C1B


title: Fra2_4

city: San Francisco

first: Kazuyuki

last: Tsujino

state: CA

address: 1550-4th Street

department: Medicine

institute: University of California, San Francisco

data_processing:
Sequencing yielded ~398 million reads with an average read depth of 49.8 million reads/sample.
Reads were then aligned to the murine genome and those that mapped uniquely to known mRNAs were used to assess differential expression.
No filtering was applied to the data set.
Genome_build: Ensembl Mouse GRCh38.78
Supplementary_files_format_and_content: tab delimited text file containing samples and their raw (unnormalized) read counts per gene.

source_name: Fra-2_control_lung cells

extract_protocol:
Total RNA was extracted from lysates using RNeasy Plus Micro kits (Qiagen) according to the manufacturer’s instructions. mRNA was isolated from 50 ng total RNA using Dynabeads mRNA Purification Kit (Ambion). Ovation® RNA-Seq System V2 (NuGEN Technologies, San Carlos, CA) was used for cDNA amplification from selected mRNA
cDNA libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA).

tag: strain background

tag: genotype/variation

value: Fra-2 transgenic; constituatively expressing Fra-2

value: post natal day 7

value: Lung myofibroblasts


title: Fra2_3


title: zfish_10ppm_R3

last: Carvan

address: 600 E. Greenfield

data_processing:
Basecalling was performed using CASAVA 1.8.2.
Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt
The cleaned reads for each sample were independently aligned to the reference zebrafish genome (Zv9, UCSC) using TopHat
The alignment output from TopHat was converted into a transcriptome using Cufflinks (v. 2.2.1), and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish
Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon
Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge
Differential expression was conducted with Cuffdiff using pooled dispersion, geometric normalization, and the merged ovary transcriptome.
Genome_build: UCSC Zv9
Supplementary_files_format_and_content: Cuffdiff outputs FPKM files, which show expression values. Included in ovary.zip

source_name: ovary

growth_protocol: Adult EK female zebrafish were exposed to MeHg (0, 1, 3, or 10 ppm with ethanol as the vehicle) for an entire life cycle, starting with maternal exposure. Fish were exposed until euthanized.

extract_protocol:
High quality total RNA was extracted from the ovary using Direct-zol* RNA MiniPrep kit (Zymo Research). Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance.
Each library was generated using a paired-end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA). Samples were run with 12 samples per lane, with 100 base pair, paired-end reads.

treatment_protocol: Ovaries were flash frozen in RNA-later and placed on dry ice immediately after dissection until proper storage at -80C.

value: ovary

tag: mehg exposure

value: 10 ppm


title: Fra2_2


title: zfish_10ppm_R1


title: zfish_10ppm_R2


title: zfish_3ppm_R3

value: 3 ppm


title: zfish_3ppm_R1


title: zfish_0ppm_R2

value: 0 ppm


title: zfish_0ppm_R3

value: EK


title: zfish_1ppm_R1

value: 1 ppm


title: Cntrl_3

source_name: control_lung cells

value: wildtype


title: zfish_0ppm_R1


title: Cntrl_2


title: LY10-RNASEQ-shSTAT3#10

city: Madison

first: Lixin

last: Rui

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

data_processing:
Sequence reads were filtered for average QC score>30. Reads were mapped  with Bowtie2 to the hg19 genome, with default parameters. Reads mapping to identical positions in the genome  were collapsed into one read.
RNAseq fpkm were generated by tophat and cufflink by following Trapnell et al.(2012).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq (bigwig file); RNA-seq (txt file: gene fpkm)

source_name: ABC DLBCL cell line (LY10)

growth_protocol: DLBCL cells were grown in RPMI1640 media plus 20%FBS,1%  penicillin, 1% streptomycin.

extract_protocol:
ChIP experiments are followed by Rui et al., 2016, PNAS 113(46): E7260-E7267; Total mRNA was extracted by Rneasy plus mini kit (Qiagen) following the manufacturer’s instructions.
ChIP library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330); cDNA library was construbuted by using Illumina Truseq RNA Library Prep Kit (RS-122-2002).

treatment_protocol: For ChIPseq experiments, cells were treated by eithor DMSO or AZD1480(JAK inhibitor) for 4hrs; For RNAseq experiments, shRNA was induced by Doxycycline for 48hrs.

tag: treatment

value: transduced with STAT3 shRNA#10 that was induced for expresion with 20 ng/ml doxycycline for 2 days


title: zfish_1ppm_R3


title: LY10-RNASEQ-shSTAT3#16

value: transduced with STAT3 shRNA#16 that was induced for expresion with 20 ng/ml doxycycline for 2 days


title: zfish_1ppm_R2


title: TMD8-RNASEQ-shSTAT3#16

source_name: ABC DLBCL cell line (TMD8)


title: LY10-RNASESQ-shSC4

value: transduced with control shRNA that was induced for expresion with 20 ng/ml doxycycline for 2 days


title: mm1179_hs1586_DKO_replicate_03_RNA-seq

city: Berkeley

first: Diane

last: Dickel

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description: Gene expression profiling in embryonic forelimb handplates

data_processing:
Basecalls performed using CASAVA bcl2fastq_v2.17
Reads were filtered cutadapt v1.1 with parameter "-m 25 -q 25" and aligned to the mm9 genome assembly using tophat _v2.0.6
Genome_build: mm9
Supplementary_files_format_and_content: fpkm values of genes calculated by cufflinks

source_name: pooled forelimbs from mm1179; hs1586 enhancer-null mouse embryos at e11.5

growth_protocol: Mice were maintained in an animal facilty under standard conditions.

extract_protocol:
Total RNA was extracted with Ambion RNAqueous Total RNA Isolation Kit
RNase-free DNase (Promega) treatment, Illumina TruSeq Stranded mRNA Sample Prep (according to manuf. protocol)

treatment_protocol: None.  WT, KO and DKO mice were not subjected to any treatment.

value: FVB

value: Forelimb handplate

tag: developmental stage

value: embryonic day 11.5


title: mm1179_hs1586_DKO_replicate_04_RNA-seq


title: TMD8-RNASEQ-shSTAT3#10


title: Cntrl_1


title: hs1586KO_replicate_04_RNA-seq

source_name: pooled forelimbs from hs1586 enhancer-null mouse embryos at e11.5

value: hs1586 KO


title: hs1586KO_replicate_03_RNA-seq


title: MouseLiver_(-MET)_RNAseq_Rep5

value: liver


title: M82 rep4

city: Davis

first: Siobhan

middle: M

last: Brady

address: 1 Shields Ave

department: Plant Biology

institute: UC Davis

data_processing:
Each pool was sequenced in 50 bp single-end format on a total of 5 lanes of a HiSeq 2000 platform (Illumina Inc. San Diego, CA, USA).  Two replicates were lost during library creation, S. pennellii #3 and IL7-5 #3.
Demultiplexed data and filtered and trimmed bad base calls.  Note that FASTQ files provided to GEO have been demultiplexed but not trimmed.
A chimeric reference was created for each IL by combining parental matched references (SlCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa and SpCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa) using the latter pennellii reference in the introgression region obtained from (Chitwood et al. 2013) or if not there then using introgression coordinates obtained by using the sequence data to locate the introgression.
Reads were mapped to chimeric references using BWA with parameters “aln -t 4 -k 1 -l 25 -n 0.1 -e 15 -i 10” and mapped read counts extracted with samtools.
Custom R code was used to combine count files, normalized using R edgeR package function calcNormFactors() method TMM, differentially expressed genes (DEG) called using edgeR.  Custom R code tested DEG for GO and other biological category enrichments and special gene set enrichments and looked for common enrichments in ILs exhibiting QTLs for various root traits.  Gene-gene and gene-trait correlations were done. Co-expression networks were built using partial correlation R package SPACE and using a probabilistic graphical model with bootstrap aggregation with R package DAGBAG.
Genome_build: Matched references from (Koenig et al. 2013) and chimeric references described above, based on International Tomato Annotation Group SL2.40 ITAG 2.3 genome at SolGenomics.net.

organism: Solanum lycopersicum

source_name: Root

growth_protocol: Seedlings of S. lycopersicum (cv. M82), S. pennellii (LA0716), and 75 introgression lines between those parents were grown according to (Ron et al., 2013). Plates were placed vertically in a rack in a randomized block design.

extract_protocol:
The  germination date was monitored for each seed. Immediately prior to harvesting root tissue for RNA-seq, each replicate of each genotype had between 2 and 5 plates, all of which were scanned with a Epson Perfection V700 photo flatbed scanner into 24-bit RGB TIF image files at 300 dpi. Images were analyzed with the imageJ program (Rasband 1997-2014) and custom macros. Based on germination date and scan date, seedling age in days after germination was determined, and primary roots of seedlings that were 3 or 4 days post-germination were traced with the imageJ polyline tool, following the root centerline from the top of the root (at start of hairs and change from green to white) to the tip. The coordinates of the polylines were recorded by the macros in data tables saved as files, along with metadata including genotype, plate ID, plating date, germination day of each seedling, plate harvest date, measurer, and two flags for each root: “collide” was true if the root contacted or crossed another root, and “along” was true if the root contacted another root and grew along it for any distance. The polylines in the vetted data were analyzed to measure root length and angle using multiple traits (Figure 1A). Additional data was calculated from the metadata: root age (days from germination to harvest), “germination age” (days from plating to germination), “plating age” (days from plating to harvest), and biological replicate number (based on plating date; replicates were named REP2 through REP5, and later replicates for fixing genotype errors were named REPN2 through REPN5 and REPX1 through REPX6). Four replicates of each of the 77 genotypes were grown. Plates were opened only once, at harvest time, to ensure the same growth conditions for all seedlings. Sampling occurred mid-afternoon. Between 7 and 14 root tips (1 cm), 3 to 4 days post-germination, from each genotype replicate were cut and immediately placed into a labeled 2ml tube containing silica beads and immersed in liquid nitrogen. Samples were stored at −80ºC until library preparation.
Libraries were created using a modified Kumar et. al. protocol. Library enrichment was done using 12 cycles. Each library was barcoded, using a unique bar code for each IL, but the same barcode for all replicates of an IL.  The libraries of each replicate were pooled, and the four pools were purified with Ampure beads. The library pooling was tested using a Bioanalyzer.

treatment_protocol: The experiments were carried out in a growth chamber with a 16:8 light:dark cycle at 22ºC and 50-75% humidity with a light intensity of 100μE.

value: Root

tag: solanum lycopersicum cultivar


title: M82 rep3


title: zfish_3ppm_R2


title: Cntrl_4

value: post natal day 7

value: Lung myofibroblasts


title: Fra2_1

value: Fra-2 transgenic; constituatively expressing Fra-2


title: STAT3CHIP-LY10-AZD1480

library_source: genomic

molecule: genomic DNA

value: AZD1480(JAK inhibitor) for 4hrs

tag: antibody

tag: antibody vendor/catalog#

value: sc-482X, Santa Cruz Biotechnology


title: M82 rep2

tag: tissue


title: mm1179KO_replicate_04_RNA-seq

source_name: pooled forelimbs from mm1179 enhancer-null mouse embryos at e11.5

tag: genotype

value: mm1179 KO


title: TMD8-RNASESQ-shSC4

tag: cell type


title: STAT3CHIP-TMD8-AZD1480


title: Wt_replicate_04_RNA-seq

source_name: pooled forelimbs from wild-type mouse embryos at e11.5

tag: strain

value: wild-type


title: STAT3CHIP-TMD8-DMSO

value: DMSO


title: mm1179_hs1586_DKO_replicate_02_RNA-seq


title: mm1179KO_replicate_03_RNA-seq


title: mm1179_hs1586_DKO_replicate_01_RNA-seq


title: M82 rep1


title: hs1586KO_replicate_01_RNA-seq


title: MM415-RM

first: Susana

last: Ortiz-Urda

address: 2340 Sutter Street, N461

department: Dermatology

description:
NRAS mutant cell line; treated with Trametinib for at least 6 months
Aggregated_Tables_FPKM.txt

data_processing:
Samples were processed by Centrillion Biosciencies Inc. (CA, US). Basecalling was performed with Casava 1.8
Processed reads were aligned to the human genome (hg19) with TopHat (version 2.0.11). Cufflinks (version 2.1.1) and Scripture (scripture-beta2.jar) were then used to perform de novo transcriptome assembly on the aligned reads.
To remove artifactual transcripts, we only considered: 1) transcripts called by both assembly programs (merging duplicate isoforms using Cuffcompare with parameters “c”, “=”, “j”), and 2) transcripts called in multiple samples.
Next, we identified putative novel lncRNAs with the following criteria: a) transcript length greater than 200bp, b) multi-exonic transcripts, and c) transcripts not overlapping RefSeq (v57) and GENCODE (lncRNA v19). The coding potential of these transcripts were assessed using CPAT (Coding Potential Assessment Tool), and Pfam/HMMER3 (protein domain database query). Transcripts were categorized as TUCPs (Transcripts of Unknown Coding Potential) if they had a CPAT/Pfam match, or as novel lncRNAs. We then used Cuffcompare to resolve duplicate transcripts across all samples, resulting in a final catalog of novel lncRNAs. TUCPs and novel lncRNAs were concatenated with RefSeq and GENCODE (annotated lncRNA) transcripts to create a reference for differential expression.
Using Cuffdiff, we identified significantly differentially expressed genes (comparing acute/resistant conditions to their naïve conditions) and calculated FPKM expression values (fragments per kilobase of transcript per million mapped reads) for each gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample and gene.

source_name: Malignant melanoma

growth_protocol: Human NRAS mutant DO4 and MM415 were maintained in RPMI 1640 media supplemented with 10% (vol/vol) heat inactivated fetal bovine serum; Primary avatar cell lines (AV1, AV4, AV5) were obtained from metastases of BRAF mutant patients and were maintained in IMDM media supplemented with 10% (vol/vol) heat inactivated fetal bovine serum. All cell lines were incubated at 37 °C under 5% CO2

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany). RNA-Seq was performed for 12 cell lines and conditions: DO4, MM415, AV1, AV4, AV5 parental cell lines; DO4 and MM415 cells after short-term (6 hours) treatment with GSK1120212; DO4-RM, MM415-RM, AV1-RM, AV4-RM, and AV5 ChrExp. cDNA sequencing libraries were prepared using the Illumina TruSeq Total RNA Sample kit, which uses Ribo-Zero to deplete rRNA, leaving ncRNAs intact.
Standard Immumina protocols were used. Paired-end, 101-bp sequencing was performed by Centrillion Biosciencies Inc. (CA, US) on an Illumina HiSeq 2000.  Sequence reads are aligned to the human genome (hg19) using TopHat.

treatment_protocol: To establish resistant cell lines, NRAS and BRAF mutant cell lines were continuously exposed to increasing concentrations of respectively MEK inhibitor (GSK1120212) (Selleckchem) and BRAF inhibitor PLX-4720 (Selleckchem). Resistant clones were selected, maintained and propagated in a complete medium supplemented with drugs for 6 months. Resistant clones were termed RM (Resistant to MAPKi): DO4-RM, MM415-RM, AV1-RM, and AV4-RM. AV5 cells did not acquire resistant, therefore the resulting clone after 6 months’ exposure to PLX-4720 was termed ChrExp (Chronical Exposed)

tag: cell line

value: Malignant melanoma derived cell line

tag: passages

tag: driver mutation

value: NRAS

tag: resistance

value: Resistant to MEK inhibitor Trametinib


title: MM415-6h

description:
NRAS mutant cell line; treated with Trametinib for 6h
Aggregated_Tables_FPKM.txt

value: Sensitive to MEK inhibitor Trametinib


title: mm1179KO_replicate_02_RNA-seq

value: FVB

value: Forelimb handplate


title: MM415

description:
NRAS mutant cell line
Aggregated_Tables_FPKM.txt


title: D04-6h


title: D04-RM


title: mm1179KO_replicate_01_RNA-seq

value: embryonic day 11.5


title: AV5-ChrExp

description:
Cell line obtained from metastases of BRAF mutant patients; treated with PLX-4720 for at least 6 months, without acquiring resistance
Aggregated_Tables_FPKM.txt

value: BRAF

value: Sensitive to BRAF inhibitor PLX-4720


title: S21_sham_input_2

first: John

last: Svaren

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Illumina Pipeline Casava 1.8.2
Reads were mapped to the Rattus norvegicus genome Rn5 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.
Hypergeometric optimization of motif enrichment (HOMER) (Heinz et al., 2010) was used to determine enriched binding regions for H3K27me3-ChIP
Genome_build: Rn5
Supplementary_files_format_and_content: bedgraph files provide tracks for uploading into genome browser. Text file is a combined peak file from the Homer analysis, which can also be used in genome browser.

organism: Rattus norvegicus

source_name: sciatic nerve

growth_protocol: Male Sprague Dawley rats (Harlan Laboratory) were housed with a normal light/dark cycles and ad libitum access to rat chow and water.

extract_protocol:
Sciatic nerves were subjected to MNase-ChIP with anti-H3K27me3 antibody from Active Motif (AM39155) as described previously with minor modification (Ma et al., 2015). After incubation with Dynabeads Protein G (Invitrogen, 10004D), ChIP samples were washed with washing buffer 1 (WB1, 50 mM Tris-HCl, pH7.5; 10 mM EDTA; 125 mM NaCl) once, WB2 (50 mM Tris-HCl, pH7.5; 10 mM EDTA; 250 mM NaCl) once, and WB3 (50 mM Tris-HCl, pH7.5; 10 mM EDTA; 500 mM NaCl) twice. The samples then eluted at 65°C with elution buffer (50 mM NaCl; 50 mM Tris-HCl, pH 7.5; 5mM EDTA; 1% SDS) for 15 min.
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

treatment_protocol: Sciatic nerves of adult Sprague-Dawley rats were cut by following the surgery protocol described previously (Hung et al., 2015).  As a control, the contralateral limb also received a sham operation consisting of only a skin incision. The nerve tissue distal to the transection and contralateral (sham) nerves were isolated at 1 d post-transection.

value: Sprague Dawley

tag: age

tag: gender

value: male

value: sciatic nerve


title: hs1586KO_replicate_02_RNA-seq

value: hs1586 KO


title: D04


title: S11_sham_input_1


title: S22_H3K27me3_Sham_2


title: STAT3CHIP-LY10-DMSO

value: sc-482X, Santa Cruz Biotechnology


title: S12_H3K27me3_Sham_1


title: Wt_replicate_02_RNA-seq


title: AV5

description:
Cell line obtained from metastases of BRAF mutant patients
Aggregated_Tables_FPKM.txt


title: hs1603KO_replicate_02_input

description: H3K27ac profiling in mouse embryonic limbs

data_processing:
Basecalls performed using CASAVA bcl2fastq_v2.17
Reads were filtered cutadapt v1.1 with parameter "-m 25 -q 25" and aligned to the mm9 genome assembly using bowtie v0.12.8, then peaks were called by MACS v1.4.2 with parameter "--mfold=10,30 -nomodel -p 0.0001"
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: pooled forelimbs from hs1603 enhancer-null mouse embryos at e11.5

extract_protocol:
Forelimbs from embryos at E11.5 were dissected and cells were disaggregated using a 2ml glass douncer. Nuclei were crosslinked with 1% formaldehyde for 5 minutes and quenched with Glycine (1mM final). Nuclear pellets were sonicated to a fragment range of 200-400bp using a Diagenode Bioruptor Sonicator. Sonicated extracts were precleared for 1 hour at 4˚C and incubated with anti-H3K27ac antibodies for 2 hours at 4˚C. Dynabeads (1:1 mixture of Protein A and G) were then incubated with the antibody-chromatin complexes for 30 minutes at 4˚C and ChIP-immune complexes were pulled down using a magnet.
Illumina Truseq DNA sample prep kit

treatment_protocol: None.  WT and KO mice were not subjected to any treatment.

value: Forelimb

value: hs1603 KO

tag: chip antibody

value: Input


title: Wt_replicate_03_RNA-seq

value: wild-type


title: Wt_replicate_01_RNA-seq


title: 8-cell_embryo3_8b

city: Beijing

first: YangLu

last: Yang

state: Beijing

address: Beijing Xicheng District Yongan Road NO.95

country: China

institute: Beijing Friendship Hospital, Capital Medical University

description:
Sequenced on Thermo Fisher Proton
Sample 156

data_processing:
library strategy: MAST-seq (Measure a single cell twice by RNA-Seq)
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling. For data from Ion Proton, base calls were collected using Ion Torrent Suite v4.3 software.
Adaptor contamination and low-quality reads were discarded from the raw data.
For Illumina paired-end reads, TopHat (version 2.0.10) were used for sequence alignment, and FPKM values were generated by Cufflinks (version 2.1.1). For Ion Proton RNA-Seq reads, 2-step alignment method which combined STAR (version 2.3.0) and bowtie2 (version 2.1.0) was applied. Unmapped reads produced by STAR were re-mapped with bowtie2 in the “very-sensitive-local” mode, and merged bam files were taken as input by Cufflinks.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly mm10.
Supplementary_files_format_and_content: FPKM table generated by cufflinks

growth_protocol: Isolation of zygotes, 2-cell, 4-cell, 8-cell embryos, inner cell mass (ICM) and trophectoderm (TE). 6- to 8-weeks old ICR female mice were injected with 7.5IU human chorionic gonadotropin (hCG) 46~48h after injection of 7.5IU pregnant mare serum gonadotrophin (PMSG). 2-cell, 4-cell and 8-cell stage embryos were collected from the oviduct of mated mice at 48, 56 and 70h post-hCG, respectively. The embryos were treated with Acid Tyrode’s solution to remove the zona pellucida and then were transferred to trypsin-EDTA and incubated at 37°C for 5 minutes. Then the embryos were washed with PBS-BSA buffer gently to dissociate the embryos into individual blastomeres. ICM and TE were isolated from mouse E3.5 blastocysts (Yan et al. 2013). The trophectoderm was isolated from the blastocysts with zona pellucida removed under a microscope by mechanically cut using a 30G needle. The exposed ICM was gently scraped from the trophectoderm. These two types of cells were then treated with Accutase or 0.005% trypsin at 37 °C for dissociated into single cell. Cell lines. Mouse embryonic fibroblast (MEF) was derived from E13.5 embryos of ICR strain. Mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatinized tissue culture plates and were passaged every two days.

extract_protocol:
The RNA of single mESC was extracted by the MAST-Seq protocol which was developed from the single cell RNA-Seq technique we previously developed (Tang et al. 2010b).
For the library constructed for Illumina sequencing platform, 10-100ng amplified cDNA was fragmentized to about 200bp fragments by Covaris S2, and purified with DNA Clean & Concentrator™-5. Then NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, Catalog #E7370L) was used to construct the cDNA library. The cDNA libraries were sequenced on Illumina HiSeq 2000 and 2500 instrument with 100bp reads and pair-end parameter. For the libraries constructed for Thermo Fisher Proton sequence platform, First, 10-100ng amplified cDNA was fragmentized to about 250bp fragments by Covaris S2, and purified with DNA Clean & Concentrator™-5. The Ion XpressTM Plus Fragment Library Kit (ThermoFisher, cat. no. 4471269) and Ion XpressTM Barcode Adapters 1-16 Kit (Thermo Fisher, cat. No. 4471250) were used to construct the library. Then, sequencing was performed using PI chips with the Ion PI Sequencing 200 kit v3 on Ion PI Proton system.

value: ICR

tag: tissue/cell type

value: mouse 8-cell embryo


title: hs1467KO_replicate_02_input

source_name: pooled forelimbs from hs1467 enhancer-null mouse embryos at e11.5

value: hs1467 KO


title: AV4

value: Malignant melanoma derived cell line


title: 8-cell_embryo3_7b

description:
Sequenced on Thermo Fisher Proton
Sample 154


title: 8-cell_embryo3_8a

description:
Sequenced on Thermo Fisher Proton
Sample 155


title: hs1262KO_replicate_02_input

source_name: pooled forelimbs from hs1262 enhancer-null mouse embryos at e11.5

value: FVB

value: hs1262 KO


title: 8-cell_embryo3_7a

description:
Sequenced on Thermo Fisher Proton
Sample 153


title: AV1-RM

description:
Cell line obtained from metastases of BRAF mutant patients; treated with PLX-4720 for at least 6 months
Aggregated_Tables_FPKM.txt

value: BRAF

value: Resistant to BRAF inhibitor PLX-4720


title: 8-cell_embryo3_6a

description:
Sequenced on Thermo Fisher Proton
Sample 151


title: hs1586KO_replicate_02_input

value: embryonic day 11.5


title: 8-cell_embryo3_6b

description:
Sequenced on Thermo Fisher Proton
Sample 152


title: 8-cell_embryo3_5b

description:
Sequenced on Thermo Fisher Proton
Sample 150


title: AV1

value: Sensitive to BRAF inhibitor PLX-4720


title: Neun DLPFC_Total_RNAseq_40

city: New York

first: Efrain

middle: A

last: Ribeiro

state: New York

address: 1425 Madison Ave, Icahn bldg. Rm 10-24

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: Sample name: 40

data_processing:
STAR
featureCounts
Filtered transcripts with <1CPM in more than 10 samples
Transformed to variance stabilized log-CPM
Voom differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet of normalized logCPM per sample with p-value

source_name: Neurons isolated from post-mortem dlPFC

extract_protocol:
~100mg of flash frozen tissue was pulverized prior to FACs using NeuN-antibody.
Clontech SMARTer Standed RNA-seq kit (634839): No ribosomal depletion was performed as nuclear RNA was sequenced, which contains low abundance of rRNA

treatment_protocol: Medicolegal investigations were performed to validate cocaine use dependence in control subjects

value: prefrontal cortex

tag: case/control

value: Cocaine Dependence

tag: race

value: Black

tag: ethnicity

value: Not Hispanic or Latino

tag: Cause of death

value: cocaine intoxication

tag: cocaine in blood (mg/l)

tag: cocaine in brain (mg/kg)

tag: be in blood (mg/l)

tag: be in brain (mg/kg)

tag: pmi (hours)

tag: ph


title: 8-cell_embryo3_5a

description:
Sequenced on Thermo Fisher Proton
Sample 149

tag: strain


title: hs1467KO_replicate_02_ChIP_H3K27ac

tag: tissue

value: Forelimb

tag: developmental stage

tag: genotype

value: anti-H3K27ac (Active Motif cat no. 39133)


title: 8-cell_embryo3_4b

description:
Sequenced on Thermo Fisher Proton
Sample 148

value: ICR


title: AV4-RM

tag: cell line

tag: passages

tag: driver mutation

tag: resistance


title: 8-cell_embryo3_4a

description:
Sequenced on Thermo Fisher Proton
Sample 147

tag: tissue/cell type

value: mouse 8-cell embryo


title: Neun DLPFC_Total_RNAseq_39

description: Sample name: 39

tag: case/control

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

value: cocaine toxicity


title: 8-cell_embryo3_3b

description:
Sequenced on Thermo Fisher Proton
Sample 146


title: 8-cell_embryo3_3a

description:
Sequenced on Thermo Fisher Proton
Sample 145


title: 8-cell_embryo3_2b

description:
Sequenced on Thermo Fisher Proton
Sample 144


title: hs1262KO_replicate_02_ChIP_H3K27ac

value: FVB

value: hs1262 KO

tag: chip antibody


title: hs1586KO_replicate_02_ChIP_H3K27ac

value: hs1586 KO


title: 8-cell_embryo3_2a

description:
Sequenced on Thermo Fisher Proton
Sample 143


title: hs1603KO_replicate_01_input

value: embryonic day 11.5

value: hs1603 KO

value: Input


title: Neun DLPFC_Total_RNAseq_36

description: Sample name: 36

value: prefrontal cortex

value: Cocaine Dependence

tag: Cause of death

value: acute cocaine overdose; hypertensive cardiac disease

tag: cocaine in blood (mg/l)

tag: cocaine in brain (mg/kg)

tag: be in blood (mg/l)

value: positive/no quant

tag: be in brain (mg/kg)


title: Neun DLPFC_Total_RNAseq_37

description: Sample name: 37

tag: tissue

value: Cocaine Use Disorder

value: Not Hispanic or Latino

value: cocaine intoxication

tag: pmi (hours)

tag: ph


title: hs1467KO_replicate_01_input

tag: strain

value: Forelimb

tag: developmental stage

tag: genotype

value: hs1467 KO


title: 8-cell_embryo2_7b

description:
Sequenced on Thermo Fisher Proton
Sample 138

value: ICR

tag: tissue/cell type

value: mouse 8-cell embryo


title: 8-cell_embryo2_8a

description:
Sequenced on Thermo Fisher Proton
Sample 139


title: Neun DLPFC_Total_RNAseq_34

description: Sample name: 34

tag: case/control

value: Black

value: cocaine toxicity; cerebrovascular accident


title: hs1262KO_replicate_01_input

description: H3K27ac profiling in mouse embryonic limbs

value: FVB

value: hs1262 KO


title: 8-cell_embryo2_6b

description:
Sequenced on Thermo Fisher Proton
Sample 136


title: 8-cell_embryo2_7a

description:
Sequenced on Thermo Fisher Proton
Sample 137


title: 8-cell_embryo2_6a

description:
Sequenced on Thermo Fisher Proton
Sample 135


title: hs1586KO_replicate_01_input

value: embryonic day 11.5

value: hs1586 KO


title: hs1603KO_replicate_01_ChIP_H3K27ac

value: hs1603 KO

value: anti-H3K27ac (Active Motif cat no. 39133)


title: 8-cell_embryo2_5b

description:
Sequenced on Thermo Fisher Proton
Sample 134


title: Neun DLPFC_Total_RNAseq_38

description: Sample name: 38

value: prefrontal cortex

value: Cocaine Dependence

tag: age

value: White

value: Hispanic or Latino

value: acute cocaine toxicity


title: 8-cell_embryo2_5a

description:
Sequenced on Thermo Fisher Proton
Sample 133


title: Neun DLPFC_Total_RNAseq_31

description: Sample name: 31

tag: race

value: Not Hispanic or Latino

value: cocaine intoxication


title: 8-cell_embryo2_4b

description:
Sequenced on Thermo Fisher Proton
Sample 132

value: ICR


title: Neun DLPFC_Total_RNAseq_30

description: Sample name: 30

tag: ethnicity


title: 8-cell_embryo3_1a

description:
Sequenced on Thermo Fisher Proton
Sample 141

value: mouse 8-cell embryo


title: hs1467KO_replicate_01_ChIP_H3K27ac

value: Forelimb

value: hs1467 KO

tag: chip antibody


title: 8-cell_embryo2_4a

description:
Sequenced on Thermo Fisher Proton
Sample 131


title: 8-cell_embryo2_8b

description:
Sequenced on Thermo Fisher Proton
Sample 140


title: 8-cell_embryo3_1b

description:
Sequenced on Thermo Fisher Proton
Sample 142


title: hs1603KO_replicate_02_ChIP_H3K27ac

value: FVB


title: hs1262KO_replicate_01_ChIP_H3K27ac

value: hs1262 KO


title: Neun DLPFC_Total_RNAseq_29

description: Sample name: 29

tag: Cause of death


title: hs1586KO_replicate_01_ChIP_H3K27ac

value: embryonic day 11.5


title: 8-cell_embryo2_3b

description:
Sequenced on Thermo Fisher Proton
Sample 130


title: 8-cell_embryo2_3a

description:
Sequenced on Thermo Fisher Proton
Sample 129


title: 8-cell_embryo2_2b

description:
Sequenced on Thermo Fisher Proton
Sample 128


title: Neun DLPFC_Total_RNAseq_33

description: Sample name: 33

tag: cocaine in blood (mg/l)


title: Neun DLPFC_Total_RNAseq_28

description: Sample name: 28

value: Black

value: concentric left ventricular hypertrophy;chronic cocaine abuse

value: Not Reported

tag: cocaine in brain (mg/kg)

value: Not reported


title: 8-cell_embryo2_2a

description:
Sequenced on Thermo Fisher Proton
Sample 127


title: 8-cell_embryo2_1a

description:
Sequenced on Thermo Fisher Proton
Sample 125


title: 8-cell_embryo2_1b

description:
Sequenced on Thermo Fisher Proton
Sample 126


title: Neun DLPFC_Total_RNAseq_32

description: Sample name: 32

value: prefrontal cortex

value: Cocaine Dependence

value: Massive pulmonary emboli;chronic cocaine abuse

tag: be in blood (mg/l)


title: Neun DLPFC_Total_RNAseq_27

description: Sample name: 27

value: White

value: atherosclerotic coronary artery disease; chronic cocaine abuse

tag: be in brain (mg/kg)


title: 8-cell_embryo1_8b

description:
Sequenced on Thermo Fisher Proton
Sample 124


title: 8-cell_embryo1_8a

description:
Sequenced on Thermo Fisher Proton
Sample 123


title: Neun DLPFC_Total_RNAseq_26

description: Sample name: 26

tag: tissue

value: Hispanic or Latino

value: acute cocaine toxicity


title: 8-cell_embryo1_7b

description:
Sequenced on Thermo Fisher Proton
Sample 122

value: ICR

value: mouse 8-cell embryo


title: Neun DLPFC_Total_RNAseq_25

description: Sample name: 25

value: cocaine intoxication

tag: pmi (hours)


title: 8-cell_embryo1_7a

description:
Sequenced on Thermo Fisher Proton
Sample 121


title: 8-cell_embryo1_6b

description:
Sequenced on Thermo Fisher Proton
Sample 120


title: 8-cell_embryo1_6a

description:
Sequenced on Thermo Fisher Proton
Sample 119


title: 8-cell_embryo1_5b

description:
Sequenced on Thermo Fisher Proton
Sample 118


title: 8-cell_embryo1_5a

description:
Sequenced on Thermo Fisher Proton
Sample 117


title: Neun DLPFC_Total_RNAseq_23

description: Sample name: 23

value: Not Hispanic or Latino

tag: ph


title: 8-cell_embryo1_4b

description:
Sequenced on Thermo Fisher Proton
Sample 116

tag: strain


title: 8-cell_embryo1_4a

description:
Sequenced on Thermo Fisher Proton
Sample 115


title: Neun DLPFC_Total_RNAseq_22

description: Sample name: 22


title: 8-cell_embryo1_3a

description:
Sequenced on Thermo Fisher Proton
Sample 113


title: 8-cell_embryo1_2a

description:
Sequenced on Thermo Fisher Proton
Sample 111


title: 8-cell_embryo1_3b

description:
Sequenced on Thermo Fisher Proton
Sample 114


title: 8-cell_embryo1_2b

description:
Sequenced on Thermo Fisher Proton
Sample 112


title: 8-cell_embryo1_1a

description:
Sequenced on Thermo Fisher Proton
Sample 109


title: 8-cell_embryo1_1b

description:
Sequenced on Thermo Fisher Proton
Sample 110


title: ISL1

city: Guangzhou

first: Minghui

last: He

address: International Biotech Island

department: Bioinformatics Department

institute: Forevergen Biosciences Co., Ltd

description: human mesenchymal stem cells

data_processing:
Base calling was performed using CASAVA version 1.8.2 (illumina)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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 RPKM value

source_name: ISL1-transduced hMSCs

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human mesenchymal stem cells


title: 4-cell_embryo3_4b

description:
Sequenced on Thermo Fisher Proton
Sample 108

value: mouse 4-cell embryo


title: FNSC

description: human mesenchymal stem cells

source_name: Control hMSCs


title: ET

city: Changsha City

first: Tian-Yin

last: Cheng

state: Hunan province

address: Furong District

department: College of Veterinary Medicine

institute: Hunan Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
When there is a reference genome, pair-end reads were always mapped using TopHat, following Cufflinks. However, in de novo analysis, pair-end reads were first used in the assembly process (We used CLC Genomics Workbench here). Then, to obtain gene expression value, "Map Reads to Reference" module of CLC calculates the reads coverage of each contig. And during this mapping step, all of the mappble reads (either reads in pairs or broken paired reads) were considered. That is because the expression value will be underestimated, if we discard broken paired reads.

Based on the above considerations, RPKM was used to perform the gene abundance measurements in our de novo analysis.
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values and raw fragment counts for each Sample

organism: Haemaphysalis flava

source_name: salivary gland

extract_protocol:
Total RNA was extracted with Trizol Reagent (Invitrogen, Carlsbad, CA, USA).
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: SGs were dissected and stored in liquid nitrogen until RNA extraction

value: salivary gland

tag: Stage

value: engorged Haemaphysalis flava ticks


title: Neun DLPFC_Total_RNAseq_17

description: Sample name: 17

value: Unaffected Control

value: Black

value: pulmonary thromboembolus, deep vein phlebothrombosis, arteriosclerotic cardiovascular disease

tag: manner of death

value: natural


title: Neun DLPFC_Total_RNAseq_15

description: Sample name: 15

value: prefrontal cortex

value: Atherosclerotic and hypertensive heart disease


title: SET

data_processing:
When there is a reference genome, pair-end reads were always mapped using TopHat, following Cufflinks. However, in de novo analysis, pair-end reads were first used in the assembly process (We used CLC Genomics Workbench here). Then, to obtain gene expression value, "Map Reads to Reference" module of CLC calculates the reads coverage of each contig. And during this mapping step, all of the mappble reads (either reads in pairs or broken paired reads) were considered. That is because the expression value will be underestimated, if we discard broken paired reads.

Based on the above considerations, RPKM was used to perform the gene abundance measurements in our de novo analysis.
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values and raw fragment counts for each Sample

value: semi-engorged Haemaphysalis flava ticks


title: 4-cell_embryo3_3b

description:
Sequenced on Thermo Fisher Proton
Sample 106

tag: tissue/cell type


title: Neun DLPFC_Total_RNAseq_24

description: Sample name: 24

tag: case/control

value: Cocaine Dependence

value: White

value: Hispanic or Latino


title: Neun DLPFC_Total_RNAseq_14

description: Sample name: 14

tag: age

value: cardiomegaly with left ventricular hypertrophy


title: 4-cell_embryo3_4a

description:
Sequenced on Thermo Fisher Proton
Sample 107

value: ICR


title: DMSO control_plusTEX, replicate 2

city: Garching

first: Jan

last: Vomacka

address: Lichtenbergstraße 4

department: Department of Chemistry

country: Germany

institute: Technische Universität München

data_processing:
Demultiplexing
Fastq quality trimming using a cut-off value of 20 (via FastX toolkit)
Fastq to fasta conversion (via READemption)
Read mapping using segemehl (via READemption)
Coverage calculation and normalisation (via READemption)
Gene-wise quantification (via READemption)
Differential gene expression analysis (via READemption)
Genome_build: NC_007795.1
Supplementary_files_format_and_content: The pairwise expression comparision based on these gene quantifications was done with READemption's subcommand "deseq" with relies on DESeq version 1.12.1.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus whole cells_DMSO

growth_protocol: 5 mL of B medium were inoculated with 50 µL ON culture (1:100). After 1-3 h the culture reached an OD600 between 0.38 and 0.59. Bacteria were then diluted in B medium in 4 steps to get a concentration of 3.4x10^4 bacteria per mL. Bacterial cultures were grown at 200 rpm for 20 h at 37°C.

extract_protocol:
Isolation of the RNA from 1x109 bacteria/sample was done with Precellys Bacterial/Fungal RNA Kit (12-7611-01) including a DNAse I digest. RNA was eluted with 43 µL RNAse free ddH2O.
Library construction was done according to Dugar et al. (Dugar, G., et al., High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet, 2013. 9(5): p. e1003495.)

treatment_protocol: 100 µM compound 3 dissolved in DMSO or just DMSO as a control were added before the 20 h growth period in a 1:100 volume ratio.

value: NCTC 8325


title: Neun DLPFC_Total_RNAseq_13

description: Sample name: 13

tag: race

value: atherosclerotic heart disease


title: 4-cell_embryo3_3a

description:
Sequenced on Thermo Fisher Proton
Sample 105

value: mouse 4-cell embryo


title: DMSO control_minusTEX, replicate 2


title: DMSO control_plusTEX, replicate 1


title: 4-cell_embryo3_2a

description:
Sequenced on Thermo Fisher Proton
Sample 103


title: 4-cell_embryo3_1a

description:
Sequenced on Thermo Fisher Proton
Sample 101


title: 4-cell_embryo2_4b

description:
Sequenced on Thermo Fisher Proton
Sample 100


title: Neun DLPFC_Total_RNAseq_21

description: Sample name: 21

tag: ethnicity

value: cocaine intoxication


title: Neun DLPFC_Total_RNAseq_19

description: Sample name: 19

value: Not Hispanic or Latino

value: atherosclerotic and hypertensive heart disease


title: Neun DLPFC_Total_RNAseq_12

description: Sample name: 12

value: Unaffected Control

value: blunt force craniocerebral trauma

value: MVA; accidental


title: Neun DLPFC_Total_RNAseq_11

description: Sample name: 11

value: prefrontal cortex

value: Black

value: gunshot wound to chest

value: homicide


title: DMSO control_minusTEX, replicate 1


title: 4-cell_embryo2_2b

description:
Sequenced on Thermo Fisher Proton
Sample 96


title: Neun DLPFC_Total_RNAseq_10

description: Sample name: 10

value: White

value: athrosclerotic coronary artery disease, cardiomegaly

value: natural


title: 4-cell_embryo2_2a

description:
Sequenced on Thermo Fisher Proton
Sample 95

value: ICR


title: compound treated_plusTEX, replicate 2

source_name: Staphylococcus aureus whole cells_treated with compound

value: NCTC 8325


title: 4-cell_embryo2_3b

description:
Sequenced on Thermo Fisher Proton
Sample 98


title: 4-cell_embryo3_2b

description:
Sequenced on Thermo Fisher Proton
Sample 104


title: 4-cell_embryo2_1b

description:
Sequenced on Thermo Fisher Proton
Sample 94


title: 4-cell_embryo2_1a

description:
Sequenced on Thermo Fisher Proton
Sample 93


title: Neun DLPFC_Total_RNAseq_8

description: Sample name: 8

value: Hispanic or Latino

value: idiopathic dilated cardiomyopathy


title: compound treated_plusTEX, replicate 1


title: 4-cell_embryo3_1b

description:
Sequenced on Thermo Fisher Proton
Sample 102

value: mouse 4-cell embryo


title: 4-cell_embryo1_4b

description:
Sequenced on Thermo Fisher Proton
Sample 92


title: compound treated_minusTEX, replicate 2


title: 4-cell_embryo2_3a

description:
Sequenced on Thermo Fisher Proton
Sample 97


title: 4-cell_embryo1_4a

description:
Sequenced on Thermo Fisher Proton
Sample 91


title: 4-cell_embryo1_3a

description:
Sequenced on Thermo Fisher Proton
Sample 89


title: Neun DLPFC_Total_RNAseq_7

description: Sample name: 7

value: Not Hispanic or Latino

value: gunshot wounds of chest


title: 4-cell_embryo1_3b

description:
Sequenced on Thermo Fisher Proton
Sample 90


title: Neun DLPFC_Total_RNAseq_6

description: Sample name: 6

value: Unaffected Control


title: 4-cell_embryo1_2a

description:
Sequenced on Thermo Fisher Proton
Sample 87


title: Neun DLPFC_Total_RNAseq_5

description: Sample name: 5

value: acute coronary thrombosis, atherosclerotic heart disease


title: 4-cell_embryo1_2b

description:
Sequenced on Thermo Fisher Proton
Sample 88


title: 4-cell_embryo1_1b

description:
Sequenced on Thermo Fisher Proton
Sample 86


title: 2-cell_embryo3_2b

description:
Sequenced on Thermo Fisher Proton
Sample 84

value: mouse 2-cell embryo


title: 2-cell_embryo3_2a

description:
Sequenced on Thermo Fisher Proton
Sample 83


title: Neun DLPFC_Total_RNAseq_3

description: Sample name: 3

value: prefrontal cortex

value: acute coronary thrombosis - LAD:coronary atherosclerosis


title: 2-cell_embryo3_1a

description:
Sequenced on Thermo Fisher Proton
Sample 81


title: Neun DLPFC_Total_RNAseq_2

description: Sample name: 2

value: Black

value: multiple gunshot wounds


title: 2-cell_embryo2_2b

description:
Sequenced on Thermo Fisher Proton
Sample 80


title: 2-cell_embryo2_2a

description:
Sequenced on Thermo Fisher Proton
Sample 79


title: Neun DLPFC_Total_RNAseq_4

description: Sample name: 4

value: gunshot wound to chest

value: homicide


title: 2-cell_embryo2_1a

description:
Sequenced on Thermo Fisher Proton
Sample 77


title: HepG2_siNC-3

city: Wuhan

first: Xiong

last: Qian

state: Hubei

address: Donghu South Road 7, Wuhan 430072, People’s Republic of China

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

data_processing:
HTSeq (version 0.6.1) (Anders et al., 2015) was utilized to calculate the number of aligned reads per gene. DEGs between two groups were identified using DEseq2
Clean reads were mapped to the human reference genome (hg19)
Genome_build: hg19
Supplementary_files_format_and_content:
siHOTAIR-vs-siNC.diff.txt:  unfiltered data generated by DESeq
siHOTAIR-vs-siNC.DESeq.diff.txt: filtered "siHOTAIR-vs-siNC.diff.txt" data, according to q value and log2fold
siHOTAIR-vs-siNC.DESeq.diffFilter.txt: filtered "siHOTAIR-vs-siNC.DESeq.diff.txt" which only retain the information of differentially expressed genes.

growth_protocol: Cells were cultured and maintained in Dulbecco’s modified Eagle’s high glucose medium (Gibco, Gaithersburg, MD) supplemented with 10% fetal bovine serum (Gibco), 50 U/ml penicillin and 50 mg/ml streptomycin at 37 °C in a humidified incubator in the presence of 5% CO2.

extract_protocol:
Total RNAs were extracted with Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacturer’s instructions. rRNA was subsequently eliminated with RiboMinusTM Transcriptome Isolation Kits for human (Thermo).
Sequencing libraries were generated using the a TruSeq Stranded total RNA sample preparation kit (Illumina, San Diego, CA) following the guidelines of the manufacturers.

treatment_protocol: For siRNA-mediated gene knockdown, cells were transfected with siRNA targeting HOTAIR (siHOTAIR) or negtive control siRNA(siNC)

tag: cell line

tag: cell type

value: Hepatocellular carcinoma (HCC)

tag: transfected with

value: negtive control siRNA(siNC)


title: 2-cell_embryo1_1b

description:
Sequenced on Thermo Fisher Proton
Sample 74

value: ICR


title: Neun DLPFC_Total_RNAseq_9

description: Sample name: 9

value: White

tag: Cause of death

value: cardiac arrest

value: natural

tag: cocaine in blood (mg/l)

tag: cocaine in brain (mg/kg)


title: zygote_embryo1_2a

description:
Sequenced on Thermo Fisher Proton
Sample 71

value: mouse zygote


title: HepG2_siNC-1


title: HepG2_siHOTAIR-3

value: siRNA targeting HOTAIR (siHOTAIR)


title: zygote_embryo1_1a

description:
Sequenced on Thermo Fisher Proton
Sample 69


title: 4-cell_embryo2_4a

description:
Sequenced on Thermo Fisher Proton
Sample 99

value: mouse 4-cell embryo


title: 2-cell_embryo2_1b

description:
Sequenced on Thermo Fisher Proton
Sample 78


title: Neun DLPFC_Total_RNAseq_1

description: Sample name: 1

tag: tissue

value: Unaffected Control

value: Not Hispanic or Latino

tag: be in blood (mg/l)

tag: be in brain (mg/kg)


title: 4-cell_embryo1_1a

description:
Sequenced on Thermo Fisher Proton
Sample 85

tag: strain


title: zygote_embryo1_2b

description:
Sequenced on Thermo Fisher Proton
Sample 72


title: 2-cell_embryo1_2b

description:
Sequenced on Thermo Fisher Proton
Sample 76

value: mouse 2-cell embryo


title: zygote_embryo1_1b

description:
Sequenced on Thermo Fisher Proton
Sample 70


title: HepG2_siHOTAIR-2


title: HepG2_siHOTAIR-1


title: 2-cell_embryo3_1b

description:
Sequenced on Thermo Fisher Proton
Sample 82


title: PENN rep3

organism: Solanum pennellii

value: Root

tag: solanum lycopersicum cultivar


title: PENN rep4


title: PENN rep1


title: IL12-4-1 rep3

organism: Solanum lycopersicum x Solanum pennellii

tag: solanum pennellii introgression line


title: 2-cell_embryo1_2a

description:
Sequenced on Thermo Fisher Proton
Sample 75

tag: tissue/cell type


title: IL12-4-1 rep4


title: IL12-3-1 rep4


title: IL12-4-1 rep2


title: IL12-4 rep2


title: IL12-3-1 rep3


title: IL12-4 rep4


title: IL12-4-1 rep1


title: IL12-4 rep3


title: WT-rep2

first: Sapna

last: Puri

address: 513 Parnassus avenue

institute: UCSF

data_processing:
RNA-seq data was analyzed under the Aroma framework (http://CRAN.R-project.org/package=aroma.core) in R/Bioconductor (http://www.R-project.org/).
The data were annotated with ENSEMBL Genome Reference Consortium Mouse Reference 38 release 79 (GRCm38.79) assembly, identifying each feature (tag) by its ENSEMBL gene ID.
The alignment for each sample was read using the TopHat v2 aligner in aroma.seq package (https://github.com/HenrikBengtsson/aroma.seq).
Groups were compared by performing exact test for negative-binomially distributed count data using edgeR package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: pancreatic islet

extract_protocol:
Islets were removed from pancreata using Collagenase treatment, purified from other pancreatic cells using a Histopaque density gradient and handpicked after washing.
RNA-Seq libraries were prepared as per manufacturer's instructions using the KAPA Stranded mRNA-Seq Kit Illumina platform

value: Mixed

value: pancreatic islet

value: 12 weeks

tag: genotype/variation

value: Wild type


title: IL12-3-1 rep1


title: IL12-3-1 rep2


title: WT-rep1

tag: age


title: IL12-3 rep4


title: IL12-3 rep3


title: IL12-3 rep2


title: R836A_eRRBS, biological replicate 3

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

description: TKO ES cells re-expressing R836A DNMT3A

data_processing:
Sequence reads from bisulfite-treated libraries were identified using standard Illumina base-calling software.
Residual cytosines (Cs) in each read were first converted to thymines (Ts), with each such conversion noted for subsequent analysis. A reference sequence database was constructed from the 50-bp ends of each computationally predicted MspI-TaqI fragment in the 40–350 bp size range.
All Cs in each fragment end were then converted to Ts; the converted reads were aligned to the converted reference by Bismark with Bowtie in the non-directional mode. The number of mismatches in the induced alignment was then counted between the unconverted read and reference, ignoring cases in which a T in the unconverted read is matched to a C in the unconverted reference. For a given read, the best alignment was kept. If there was more than one best alignment, the read was discarded as non-unique.
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.
Genome_build: mm9
Supplementary_files_format_and_content: bed files contain all mapped Cs with chr, start, end,  and methylated reads/total reads (percentage) listed.

source_name: DNMT TKO ES Cells

growth_protocol: Dnmt3a, Dnmt3b and Dnmt1 triple knockout (TKO) mouse ES cells were cultivated on gelatin-coated dishes in the high-glucose DMEM base medium (Invitrogen) supplemented with 15% of fetal bovine serum (FBS, Invitrogen), 1 x nonessential amino acids (Invitrogen), 0.1 mM 2-mercaptoethanol, and 1000 U/ml leukemia inhibitory factor (ESGRO).

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen).
eRRBS was carried out with a previously described protocol with slight modification (Garrett-Bakelman et al., 2015). Briefly, ~300 ng of genomic DNA were digested with three different enzymes (~80 units of MspI, 40 units of BfaI and 40 units of MseI) to enhance genomic fragmentation and coverage. The produced fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine, followed by overhang fill-in, 3’-terminal-A extension and purification. Bisulfite treatment of the fragments was done using the EZ DNA Methylation–Lightning kit (Zymo Research). Amplified eRRBS libraries was quality checked with Agilent 2200 TapeStation, followed by deep sequencing on the Illumina HiSeq-2000 genome analyzer with 50 bp PE parameters.

treatment_protocol: TKO ES cells were transfected by Lipofectamine 2000 (Invitrogen) with the pPyCAGIZ empty vector (EV) or that carrying wild-type (WT) or mutant DNMT3A. At 48 hours following transfection, the transduced ES cells were selected out in 50 µg/ml Zeocin (Invitrogen) for 10 days and continuously maintained in the medium with 25 µg/ml Zeocin.

value: ES Cells

tag: genotype

value: Dnmt1, Dnmt3a and Dnmt3b triple knockout stably expressing DNMT3A R836A


title: MYC-rep3

value: Transgenic


title: IL12-4 rep1


title: MYC-rep2


title: R836A_eRRBS, biological replicate 2

description: TKO ES cells re-expressing R836A DNMT3A


title: MYC-rep1


title: MYC-rep4


title: WT_eRRBS, biological replicate 3

description: TKO ES cells re-expressing WT DNMT3A

value: Dnmt1, Dnmt3a and Dnmt3b triple knockout stably expressing DNMT3A WT


title: R836A_eRRBS, biological replicate 1

description: TKO ES cells re-expressing R836A DNMT3A


title: HeLa-Thymidine-20hr

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing: All small RNA sequences except low-quality reads are provided with the number of reads for each unique sequence. Illumina SRA v1.5 3' adapter sequences are trimmed using half-open Smith-Waterman algorithm (score parameters: 2 for match, -2 for mismatch, -3 for linear gap penalty).

source_name: HeLa_thymidine double block_20 hr after the release

growth_protocol: HeLa cells were grown in RPMI supplemented with 10% FBS.

extract_protocol: To prepare small RNA cDNA libraries, total RNAs were separated on 15% urea-PAGE and 17~26nt RNAs were gel-purified. Size fractionized RNAs were ligated with 3' adapter using T4 RNA ligase2 trucated form (NEB). After gel purification, 3' adapter-ligated RNAs were ligated with 5' adapter using T4 RNA ligase1 (NEB). The gel-purified ligation products were reverse transcribed using superscript II (Invitrogen) and the cDNA was PCR-amplified with Phusion DNA polymerase (NEB).

treatment_protocol: Cells were synchronized in early S phase by a double thymidine block (Petersen 1999). Cells were treated with 2mM thymidine for 18hr and released into fresh media containing 10% FBS for 9hr, and 2mM thymidine was added for an additional 17hr. Entry into S phase was monitored by cell cycle profiles and FACS analysis. After second block, thymidine was removed by washing with 1X PBS two times and cells were released with fresh 10% FBS containing media. And then released cells prepared at the indicated time.

value: HeLa

value: Cervical cancer cells

tag: phase

value: S/G2 phase


title: WT_eRRBS, biological replicate 2

description: TKO ES cells re-expressing WT DNMT3A


title: KC-p120NULL #3

city: Worcester

first: Jason

middle: R

last: Pitarresi

state: MA

address: 364 Plantation Street

institute: University of Massachusetts Chan Medical School

description: KrasG12D;p120NULL in vitro recombined pancreatic ductal cells replicate #3

data_processing:
The FastQC software was applied on raw fastq files to examine the sequence quality.
Paired-end reads were aligned to the mouse genome NCBIM37 using Tophat software using default parameters.
Transcript expression quantification was performed using cufflinks.
Differential gene expression analysis was performed using cuffdiff 6.
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Pancreatic ductal cells

growth_protocol: Cells were grown on plastic in pancreatic ductal cell media

extract_protocol:
Qiagen RNAeasy kit following manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transduced with lentiviral Cre recombinase to activate KrasG12D and excise p120ctnLoxP alleles

value: pancreas

value: ductal cell

value: p120-homozygous deletion


title: WT_eRRBS, biological replicate 1

description: TKO ES cells re-expressing WT DNMT3A


title: IL12-2 rep1

source_name: Root


title: IL12-2 rep3


title: IL12-2 rep2


title: IL12-2 rep4


title: IL12-1-1 rep4


title: KC-p120NULL #2

description: KrasG12D;p120NULL in vitro recombined pancreatic ductal cells replicate #2


title: HeLa-Thymidine-14hr

source_name: HeLa_thymidine double block_14 hr after the release

tag: cell line

value: G1 phase


title: IL12-1-1 rep3


title: IL12-3 rep1


title: HeLa-Thymidine-18hr

source_name: HeLa_thymidine double block_18 hr after the release

tag: cell type

value: S phase


title: HeLa-Thymidine-16hr

source_name: HeLa_thymidine double block_16 hr after the release


title: HeLa-Thymidine-8hr

source_name: HeLa_thymidine double block_8 hr after the release

value: G2/M phase


title: KC-p120HET #2

description: KrasG12D;p120HET in vitro recombined pancreatic ductal cells replicate #2

value: p120-heterozygous deletion


title: IL12-1-1 rep2

value: Root


title: IL12-1-1 rep1


title: HeLa-Thymidine-10hr

source_name: HeLa_thymidine double block_10 hr after the release


title: KC-p120HET #1

description: KrasG12D;p120HET in vitro recombined pancreatic ductal cells replicate #1


title: IL12-1 rep4


title: KC-p120HET #3

description: KrasG12D;p120HET in vitro recombined pancreatic ductal cells replicate #3


title: KC-p120WT #3

description: KrasG12D;p120WT in vitro recombined pancreatic ductal cells replicate #3


title: IL12-1 rep3


title: KC-p120WT #2

description: KrasG12D;p120WT in vitro recombined pancreatic ductal cells replicate #2


title: KC-p120WT #1

description: KrasG12D;p120WT in vitro recombined pancreatic ductal cells replicate #1


title: IL12-1 rep1


title: IL11-4-1 rep4


title: IL11-4-1 rep2


title: Sm_Vh_46_2

city: Albuquerque

first: Charles

last: Cunningham

state: New Mexico

address: 1 University of New Mexico

department: Biology

institute: University of New Mexico

data_processing:
Raw read data was demultiplexed (segregated by library index) using Illumina CASAVA version 1.8.2.
Thereafter, NCGR's custom contaminant filtering pipeline removed anomalous sequences. These aberrant sequences include Illumina Phix control, library adapters, primer dimers and library indexes not part of the experiment.  NCGR's contaminant filtering pipeline ensures only the highest quality data goes into downstream analyses.
Sequenced reads were mapped to Ensembl Mouse release 75 (GRCm38) whole genome using Tophat2 v.2.0.12 using default settings.
Genome_build: Ensembl Mouse release 75 (GRCm38)
Supplementary_files_format_and_content: A matrix of the samples in a tab-delimited text file with the FPKM values.
Supplementary_files_format_and_content: A matrix of the samples in a tab-delimited text file with the raw count of the sequence reads.

source_name: Liver

extract_protocol:
Livers were removed, placed in RNA at 4°, and RNA was harvested using RNA Maxi Kit (Qiagen #75162).  RNA was tested on nanodrop and Bioanalzer. Illumina TruSeq RNA Library Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
TRUSEQ RNA Library Preparation on the Sciclone NGS Liquid Handler

treatment_protocol: Mice were gavaged at 32-35 days post infection with either Vehicle (Cremophor EL(250 mg/kg)) or Praziquantel (250 mg/kg).

value: Swiss Webster (CFW)

value: liver

tag: days post infection

value: 46 days

tag: treatment

value: Vehicle (Cremophor EL)


title: Sm_Vh_46_3


title: IL11-4-1 rep1


title: Sm_PZQ_46_1

value: Praziquantel (250 mg/kg)


title: IL11-4 rep4


title: Sm_PZQ_46_2


title: IL11-4 rep2


title: ui_Vh_46_3


title: IL11-4 rep1


title: Sm_Vh_46_1


title: IL11-3 rep4


title: IL11-4 rep3


title: ui_Vh_46_2


title: Sm_PZQ_39_3

value: 39 days


title: ui_Vh_46_1


title: IL11-3 rep3


title: KC-p120NULL #1

description: KrasG12D;p120NULL in vitro recombined pancreatic ductal cells replicate #1


title: IL12-1 rep2


title: Sm_PZQ_39_2


title: IL11-3 rep2


title: Sm_PZQ_39_1


title: IL11-3 rep1


title: Sm_Vh_39_3


title: IL11-2 rep4


title: Sm_Vh_39_2


title: ui_Vh_39_3


title: ui_Vh_39_1


title: ui_Vh_39_2


title: IL11-1 rep3


title: Sm_PZQ_35_3

value: 35 days


title: IL11-2 rep2


title: IL11-2 rep1


title: IL11-1 rep4


title: IL11-1 rep2


title: Sm_PZQ_35_2


title: Sm_Vh_35_3


title: IL10-3 rep3


title: Sm_Vh_35_2


title: Sm_PZQ_35_1


title: IL11-1 rep1


title: HepG2_siNC-2

value: Hepatocellular carcinoma (HCC)

tag: transfected with

value: negtive control siRNA(siNC)


title: Sm_Vh_35_1


title: IL10-3 rep2


title: IL10-3 rep1


title: ui_Vh_35_3


title: IL11-2 rep3


title: ui_Vh_35_2


title: Sm_Vh_39_1


title: IL10-2-2 rep4


title: IL10-2-2 rep3


title: IL10-2-2 rep2


title: compound treated_minusTEX, replicate 1

value: NCTC 8325


title: ui_Vh_35_1


title: Sm_PZQ_32_1

value: 32 days


title: Sm_PZQ_32_3


title: IL10-2 rep4


title: Sm_PZQ_32_2


title: IL10-2-2 rep1


title: IL10-3 rep4


title: Sm_Vh_32_3


title: Sm_Vh_32_2


title: IL10-2 rep3


title: IL10-2 rep2


title: ui_Vh_32_2


title: ui_Vh_32_1


title: ui_Vh_32_3


title: IL10-1-1 rep4


title: Sm_Vh_32_1


title: 2-cell_embryo1_1a

description:
Sequenced on Thermo Fisher Proton
Sample 73

value: ICR

value: mouse 2-cell embryo


title: IL10-1-1 rep2


title: IL10-2 rep1


title: IL10-1 rep3


title: NTC_R1

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: IUE: Plasmids containing NTC control or Nat14 shRNA were injected into the lateral ventricle of E14.5 mouse brains, which were given an electrical stimulation (34 V with 950 mA). Four days later, mice were sacrificed and embryonic brains were subjected to FAC-sorting.

data_processing:
The FASTQ files were aligned human genome (hg19) using TopHat v2.0.8
Samtools v0.1.19 was used for File format conversions (bam to sam)
Reads at transcripts were counted using HTSeq (v0.5.4p1)
Normalization (for library size) was done using DESeq
Differential expression analysis was done using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing normalized logFC

source_name: cortical cells

extract_protocol:
RNA was isolated using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using Nextera Illumina protocols

treatment_protocol: Electroporated E 18.5 embryonic brains were isolated, and downstream processing was done in cold HBSS. The cortical region of the brains was micro-dissected and processed for single cell dissociation using Neural Tissue Dissociation Kit (P) (130-092-628) following the manufacturer's instructions. GFP positive live cells were FACS sorted directly into RLT lysis buffer.

value: cortical cell

tag: source

value: Cells isolated from mouse cortex


title: NTC_R3


title: NTC_R2


title: IL10-1 rep2

data_processing:
Each pool was sequenced in 50 bp single-end format on a total of 5 lanes of a HiSeq 2000 platform (Illumina Inc. San Diego, CA, USA).  Two replicates were lost during library creation, S. pennellii #3 and IL7-5 #3.
Demultiplexed data and filtered and trimmed bad base calls.  Note that FASTQ files provided to GEO have been demultiplexed but not trimmed.
A chimeric reference was created for each IL by combining parental matched references (SlCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa and SpCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa) using the latter pennellii reference in the introgression region obtained from (Chitwood et al. 2013) or if not there then using introgression coordinates obtained by using the sequence data to locate the introgression.
Reads were mapped to chimeric references using BWA with parameters “aln -t 4 -k 1 -l 25 -n 0.1 -e 15 -i 10” and mapped read counts extracted with samtools.
Custom R code was used to combine count files, normalized using R edgeR package function calcNormFactors() method TMM, differentially expressed genes (DEG) called using edgeR.  Custom R code tested DEG for GO and other biological category enrichments and special gene set enrichments and looked for common enrichments in ILs exhibiting QTLs for various root traits.  Gene-gene and gene-trait correlations were done. Co-expression networks were built using partial correlation R package SPACE and using a probabilistic graphical model with bootstrap aggregation with R package DAGBAG.
Genome_build: Matched references from (Koenig et al. 2013) and chimeric references described above, based on International Tomato Annotation Group SL2.40 ITAG 2.3 genome at SolGenomics.net.

tag: tissue


title: IL10-1 rep1


title: shNat14_R3


title: IL10-1-1 rep3


title: shNat14_R1


title: IL9-3-2 rep4


title: IL9-3-2 rep3


title: IL9-3-2 rep1


title: IL9-3-2 rep2


title: IL9-3-1 rep3


title: Mll2_KO_RNA-Seq_rep4

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: RNAseq_groups_oocyte_mRNA_norep_RPKM_corrDNAcont.txt

data_processing:
Raw FastQ sequence files were initially quality and adapter trimmed using Trim Galore v0.4.2 using default parameters (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Mapping of ChIP-Seq data was performed using Bowtie 2 v2.2.9 against the mouse GRCm38 genome assembly. The resulting hits were filtered to remove mappings with a MAPQ scores of < 20. Mapping of RNA-Seq data was performed using HISAT2 v2.0.5 against the mouse GRCm38 genome guided by known splice sites taken from Ensembl v68. Hits were again filtered to remove mappings with MAPQ scores of <20.
For PBAT data, reads were trimmed with Trim Galore using --clip_r1 9 and --clip_r2 9. Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.16.3 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output, and methylation from single-end and paired-end mapping were merged into a single Bismark coverage report.
genome build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
processed data files format and content : "10_5_Domains_75_25_NoOverlap_NoGaps_NoInterm_NoSmall_NoGaps" file contains the GV methylated and unmethylated domains used for analyses in this study.
processed data files format and content : "RNAseq_groups_oocytemRNA_norep_RPKM_corrDNAcont" file contains RNA-seq quantitation for two groups: Mll2 WT oocytes and Mll2 cKO oocytes (each a replicate set of 4 single cell RNA-seq libraries).  RPKM was quantitated in SeqMonk for oocyte transcriptome mRNA annotation (Veselovska et al. 2014) excluding repetitive elements, correcting for DNA contamination
processed data files format and content : "ESC_oocyte_technicaloptimisation_2kbrunning_RPM_nofilters" file contains ChIP-seq quantitation for individual replicates for H3K4me3 in 1000 ESCs and 500 ESCs used for validation of the ULI-nChIP-seq method and the antibody titration for 125ng,and 62.5ng of antibody for H3K27ac and 125ng, 250ng and 500ng of H3K27me3 in GV oocytes (25-day old mice).  Reads per million was quantitated in SeqMonk for 2kb running window probes, with no filters applied.
processed data files format and content : "Dnmt3DKO.WT_H3K4me3_Me.Unme.domains_RPM" file contains ChIP-seq quantitation for H3K4me4 in GV oocytes (25-day old mice) from grouped Dnmt3a/b cDKO (N=4) and Dnmt3a/b WT controls (N=4).  Reads per million was quantitated in SeqMonk for GV methylated and unmethylated domains.
processed data files format and content : "GO_and_Mll2_peaks" file contains peak and seedpeak calls for H3K4me3 in non-growing oocytes (NGO) (5-day old mice), growing oocytes (GO) (10-day old mice), germinal vesicle (GV) oocytes (15-day old mice) and GV oocytes (25-day old mice), Mll2 WT GV oocytes (25-day old mice), and Mll2 KO GV oocytes (25-day old mice) using Chromstar peak calling program.  Temporal peak calling was done using a joint multivariate analysis (parameters: binsize = 1000bp, stepsize = 200bp, mode = differential). A cutoff of 1-10-4 was applied on the peak score (which is defined as the maximum posterior probability anywhere within a peak), to divide the resulting peak set into peaks with high H3K4me3 enrichment and seed-peaks with low H3K4me3 enrichment.
processed data files format and content : "bed_files_combinations_GV" file contains combinatorial peak for H3K4me3, H3K27ac, and H3K27me3 in germinal vesicle (GV) oocytes (25-day old mice) using Chromstar peak calling program.  Combinatorial chromatin states were called using a combined multivariate analysis. A cutoff of 1-10-4 was applied on the posterior probability in each bin to yield a stringent set of peaks.
processed data files format and content : "Epiblast_combinations_and_peaks" file contains combinatorial peak for H3K4me3, H3K27ac, and H3K27me3 in E6.5 epiblast using Chromstar peak calling program.   Combinatorial chromatin states were called using a combined multivariate analysis. A cutoff of 1-10-4 was applied on the posterior probability in each bin to yield a stringent set of peaks.
processed data files format and content : "bivalency_PGC_d05_d25_domains" file contains combinatorial peak for combined replicates for H3K4me3, H3K27me3 in non-growing oocytes (NGO) (5-day old mice), GV oocytes (25-day old mice), E11.5 primordial germ cells (Sachs et al. 2013).  Combinatorial chromatin states were called using a joint multivariate analysis (parameters: binsize = 1000bp, stepsize = 200bp, mode=differential).  A cutoff of 1-10-4 was applied on the peak score to select broad bivalent domains and subsequently only those domains were retained which contained clear enrichment, by applying a cutoff on the posterior probability of 1-10-4.
processed data files format and content : "OocyteH3K27ac_H3K27acGVpeaks_RPMcorrlength" file contains H3K27ac enrichment in grouped d5 NGOs and d25 GV oocytes for H3K27ac peaks called in GV oocytes using Chromstar.  Enrichment was quantitated as reads per million, corrected for probe length.
processed data files format and content : "Oocyte_H3K27ac_5kbrunning_RPM_nofilters" file contains H3K27ac enrichment in grouped d5 NGOs and d25 GV oocytes for running 5kb windows.  Enrichment was quantitated as reads per million.

source_name: Germinal vesicle oocytes

growth_protocol: Ovaries were collected from 5, 10, 15, and 25 day-old C57BL/6Babr or 21 or 25-day-old Mll2Gdf9cKO or 25-day-old Dnmt3a/bZp3cDKO mice and digested using 2mg/mL collagenase and 0.02% trypsin solution, gently agitating at 37°C for 20-30 minutes. Oocytes were hand collected and washed in M2 medium (Sigma), followed by 2 consecutive washes in PBS.

extract_protocol:
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Cells for ChIP-seq were flash frozen in nuclear lysis buffer, cells for PBAT were flash frozen in PBS
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Post-bisulfite adaptor tagging (PBAT) was used to generate whole-genome bisulfite sequencing libraries using 100 collected oocytes. Briefly, cells are lysed with 0.5% SDS in EB buffer and bisulfite-treated with one-step modification procedure using the Sigma Imprint DNA Modification kit. The resulting DNA are purified using columns from Zymo EZ DNA Methylation Direct kit. First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
ChIP-bisulfite-seq was done on MNase-digested 10% input samples from the ChIP protocol, detailed in the corresponding ChIP-seq samples.  Following DNA purification from chromatin using spri purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads, samples were bisulfite converted using the Zymo EZ DNA Methylation Direct kit.  First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 16-20 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.

tag: background strain

tag: time-point in reprogramming

value: postnatal day 21

tag: cell number

value: Germinal vesicle oocytes

tag: antibody amount

value: Mll2 floxed/floxed, Gdf9 +ve


title: IL9-3-1 rep4

extract_protocol:
The  germination date was monitored for each seed. Immediately prior to harvesting root tissue for RNA-seq, each replicate of each genotype had between 2 and 5 plates, all of which were scanned with a Epson Perfection V700 photo flatbed scanner into 24-bit RGB TIF image files at 300 dpi. Images were analyzed with the imageJ program (Rasband 1997-2014) and custom macros. Based on germination date and scan date, seedling age in days after germination was determined, and primary roots of seedlings that were 3 or 4 days post-germination were traced with the imageJ polyline tool, following the root centerline from the top of the root (at start of hairs and change from green to white) to the tip. The coordinates of the polylines were recorded by the macros in data tables saved as files, along with metadata including genotype, plate ID, plating date, germination day of each seedling, plate harvest date, measurer, and two flags for each root: “collide” was true if the root contacted or crossed another root, and “along” was true if the root contacted another root and grew along it for any distance. The polylines in the vetted data were analyzed to measure root length and angle using multiple traits (Figure 1A). Additional data was calculated from the metadata: root age (days from germination to harvest), “germination age” (days from plating to germination), “plating age” (days from plating to harvest), and biological replicate number (based on plating date; replicates were named REP2 through REP5, and later replicates for fixing genotype errors were named REPN2 through REPN5 and REPX1 through REPX6). Four replicates of each of the 77 genotypes were grown. Plates were opened only once, at harvest time, to ensure the same growth conditions for all seedlings. Sampling occurred mid-afternoon. Between 7 and 14 root tips (1 cm), 3 to 4 days post-germination, from each genotype replicate were cut and immediately placed into a labeled 2ml tube containing silica beads and immersed in liquid nitrogen. Samples were stored at −80ºC until library preparation.
Libraries were created using a modified Kumar et. al. protocol. Library enrichment was done using 12 cycles. Each library was barcoded, using a unique bar code for each IL, but the same barcode for all replicates of an IL.  The libraries of each replicate were pooled, and the four pools were purified with Ampure beads. The library pooling was tested using a Bioanalyzer.

tag: solanum pennellii introgression line

value: Root

tag: solanum lycopersicum cultivar


title: Mll2_KO_RNA-Seq_rep3


title: Mll2_ff_RNA-Seq_rep4

value: Mll2 floxed/floxed, Gdf9 -ve


title: Mll2_KO_RNA-Seq_rep2


title: Mll2_ff_RNA-Seq_rep3


title: IL10-1 rep4


title: Mll2_ff_RNA-Seq_rep2


title: Mll2_ff_RNA-Seq_rep1


title: IL9-3 rep2