title: Df(2L)ED1473/+_female_rep1


title: Df(2L)ED1305/+_male_rep1

status: Public on Jan 31 2016

type: SRA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
RNA-Seq reads were aligned to the Drosophila genome assembly (Berkley Drosophila Genome Project Release 5, obtained from FlyBase. http://www.flybase.org) using TopHat 2.0.10 (Trapnell et al., 2009. Bioinformatics) with -g 1 and -G parameters. As a gene model for the -G parameter, we used an annotation file from FlyBase (5.57) where we removed genes from uncertain physical locations (e.g., chrU and chrUextra).
From the alignment result, abundance of transcripts were measured as read counts using HTseq (Anders et al., 2014. Bioinformatics) with default options (-m union -t exon).
From the alignment result, Fragments per Kilobase per Million mapped reads (FPKM) values were calculated using Cufflinks (Trapnell et al., 2010. Nature Biotechnology). We used -G, -b, and -u parameters in running Cufflinks.
Genome_build: Release 5
Supplementary_files_format_and_content: Tab-delimited text files that are generated from HTseq and Cufflink. Each contains read counts and FPKM values, respectively, at gene level.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Whole animal

growth_protocol: The Drosophila deletion stocks were generated by DrosDel (http://www.drosdel.org.uk) as described in (Ryder et al., 2007). Flies were maintained at 25oC on standard yeast/cornmeal medium (Fly Facility, University of Cambridge, UK). We crossed males from DrosDel lines to w1118 virgin females to generate hemizygotes without balancer chromosomes. The w1118 line we used is the parental line for the DroDel project, so all flies are isogenic other than for the deleted region they carry. We prepared duplicates of 15-25 sexed Df/+ progeny (mean 21.65, standard deviation 7.4) 5 days post eclosion for RNA extraction.

extract_protocol:
Flies were homogenized in 500 μl of RNAlater solution (Life Technologies, Grand Island, NY, USA) for 90 seconds in 96 deep well plates with 3 mm tungsten carbide beads (Qiagen, West Sussex, UK) using a Qiagen Tissue Lyser II (Qiagen, West Sussex, UK). Extraction of total RNA was performed using the RNeasy 96 kit (Qiagen, Valencia, CA, USA) based on the manufacturer's guide (Protocol for Isolation of Total RNA from animal cells using QIAvac96 vacuum manifold, Cat#19504). We made a minor modification to dilute the RNAlater solution, so instead of mixing 150 μl of RLT buffer (Qiagen, Cat#79216) and 150 μl of 70% ethanol, we mixed 150 μl of RLT buffer, 120 μl of 100% ethanol, and 30 μl of lysate in RNAlater and applied this to the extraction columns.
Libraries were prepared using Illumina's (San Diego, CA, USA) TruSeq RNA sample preparation kit v2 - set A and B (Cat # RS-122-200). RNA amount was quantified using RiboGreen kits (Life Technology, Grand Island, NY, USA). 100 ng of RNA was used as input to follow the 1/2 scaled protocol from the original manufacturer's High Sample Protocol (Illumina, Part# 15026495 Rev. C). We added 10 pg (353 samples) or 500 pg (43 samples) of external RNAs as spike-in during the 8 minute RNA fragmentation step. The constructed libraries were sequenced with a HiSeq 2000 (Illumina, San Diego, CA, USA).

tag: tissue

value: Whole animal

tag: gender

value: male

tag: genotype


title: Df(2L)ED1305/+_female_rep1

value: female


title: Df(2L)ED929/+_male_rep2


title: Df(2L)ED929/+_female_rep2


title: Df(2L)ED929/+_male_rep1


title: Df(2L)ED1305/+_female_rep2


title: Df(2L)ED1315/+_female_rep1


title: Df(2L)ED80/+_female_rep2


title: Df(2L)ED80/+_male_rep1


title: Df(2L)ED80/+_male_rep2


title: Df(2L)ED80/+_female_rep1


title: Df(2L)ED800/+_male_rep2


title: Df(2L)ED800/+_female_rep2


title: Df(2L)ED800/+_female_rep1


title: Df(2L)ED479/+_male_rep1


title: Df(2L)ED49/+_male_rep2


title: Df(2L)ED479/+_female_rep2


title: Df(2L)ED479/+_female_rep1


title: Df(2L)ED49/+_male_rep1


title: Df(2L)ED40/+_male_rep1


title: Df(2L)ED40/+_male_rep2


title: Df(2L)ED40/+_female_rep1


title: Df(2L)ED800/+_male_rep1


title: Df(2L)ED247/+_male_rep2


title: Df(2L)ED354/+_male_rep2


title: Df(2L)ED929/+_female_rep1


title: Df(2L)ED49/+_female_rep2


title: Df(2L)ED354/+_female_rep2


title: Df(2L)ED354/+_male_rep1


title: Df(2L)ED40/+_female_rep2


title: Df(2L)ED354/+_female_rep1


title: Df(2L)ED353/+_male_rep1


title: Df(2L)ED353/+_male_rep2


title: Df(2L)ED479/+_male_rep2


title: Df(2L)ED353/+_female_rep2


title: Df(2L)ED343/+_male_rep2


title: Df(2L)ED353/+_female_rep1


title: Df(2L)ED343/+_female_rep1


title: Df(2L)ED343/+_male_rep1


title: Df(2L)ED4559/+_male_rep2


title: Df(2L)ED343/+_female_rep2


title: Df(2L)ED33/+_male_rep1


title: Df(2L)ED33/+_female_rep1


title: Df(2L)ED299/+_male_rep1


title: Df(2L)ED292/+_male_rep2


title: Df(2L)ED299/+_male_rep2


title: Df(2L)ED299/+_female_rep1


title: Df(2L)ED299/+_female_rep2


title: Df(2L)ED49/+_female_rep1


title: Df(2L)ED292/+_female_rep2


title: Df(2L)ED292/+_male_rep1


title: RM2-1 rSomatic single cell 20 from testis

city: Beijing

first: Xiaolong

last: Cui

address: No.1 Beichen West Road

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: processed data in C1_RNAseq.txt

data_processing:
Illumina Casava1.8 software was used for basecalling.
Quality of sequencing reads were assessed using FastQC (version 0.10.1).
Low quality bases were trimmed with a cutoff of Phred quality score 20 using Fastq Quality Trimmer program in FASTX-Toolkit (version 0.0.13).
High quality reads were mapped to the reference genome (version mm10 and rn5) using TopHat (version 2.0.10).
Cufflinks (version 2.1.1) was used to charaterize the transcriptomes based on the RefSeq reference annotation.
Genome_build: mm10, rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism:
Mus musculus
Rattus norvegicus

source_name: somatic single cells derived from RM2-1 rat chimaera testis

extract_protocol:
Total RNAs were isolated using Trizol reagent.
Total RNAs were prepared for illumina mRNA-Seq libraries using the TruSeq RNA Sample Prep Kit according to the manufacture's instruction.

tag: cell type

value: somatic

tag: cell line


title: RM2-1 rSomatic single cell 17 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 18 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED292/+_female_rep1


title: RM2-1 rSomatic single cell 15 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 13 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 11 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED285/+_female_rep2


title: RM2-1 rSomatic single cell 10 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED285/+_female_rep1


title: Df(2L)ED280/+_male_rep2


title: RM2-1 rSomatic single cell 7 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 19 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 16 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 12 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 14 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED285/+_male_rep2


title: Df(2L)ED285/+_male_rep1


title: Df(2L)ED33/+_female_rep2


title: RM2-1 rSomatic single cell 4 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED280/+_female_rep1


title: RM2-1 rSomatic single cell 3 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED33/+_male_rep2


title: RM2-1 rLung single cell 2

description: processed data in C1_RNAseq.txt

source_name: lung single cells derived from RM2-1 rat chimaera

value: lung


title: Df(2L)ED280/+_female_rep2


title: Df(2L)ED21/+_male_rep2


title: RM2-1 rSomatic single cell 1 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rLung single cell 3

description: processed data in C1_RNAseq.txt


title: RM2-1 rLung single cell 4

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 2 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED21/+_male_rep1


title: RM2-1 rSomatic single cell 9 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 8 from testis

description: processed data in C1_RNAseq.txt


title: RM2-1 AdES single cell 6

description: processed data in C1_RNAseq.txt

source_name: embryonic stem cell line RM2-1

value: G0/G1 stage embryonic stem cell


title: RM2-1 rLung single cell 1

description: processed data in C1_RNAseq.txt


title: RM2-1 AdES single cell 5

description: processed data in C1_RNAseq.txt


title: Df(2L)ED21/+_female_rep2


title: RM2-1 AdES single cell 4

description: processed data in C1_RNAseq.txt


title: Df(2L)ED280/+_male_rep1


title: Df(2L)ED21/+_female_rep1


title: RM2-1 AdES single cell 2

description: processed data in C1_RNAseq.txt


title: RM2-1 AdES single cell 1

description: processed data in C1_RNAseq.txt


title: RM2-1 rSomatic single cell 5 from testis

description: processed data in C1_RNAseq.txt


title: RM1-1 mSomatic single cell 4 from testis

description: processed data in C1_RNAseq.txt

source_name: somatic single cells derived from RM1-1 mouse chimaera testis


title: RM1-1 mSomatic single cell 3 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED136/+_male_rep2


title: Df(2L)ED136/+_male_rep1


title: RM1-1 mNeuron single cell 8

description: processed data in C1_RNAseq.txt

source_name: neuron single cells derived from RM1-1 mouse chimaera

value: neuron


title: RM1-1 mNeuron single cell 7

description: processed data in C1_RNAseq.txt


title: RM1-1 mNeuron single cell 6

description: processed data in C1_RNAseq.txt


title: RM1-1 mNeuron single cell 4

description: processed data in C1_RNAseq.txt


title: RM1-1 mSomatic single cell 1 from testis

description: processed data in C1_RNAseq.txt


title: RM1-1 mNeuron single cell 5

description: processed data in C1_RNAseq.txt


title: Df(2L)ED136/+_female_rep1


title: RM1-1 mNeuron single cell 3

description: processed data in C1_RNAseq.txt


title: Df(2L)ED136/+_female_rep2


title: Df(2L)ED1317/+_male_rep2


title: RM1-1 mSomatic single cell 2 from testis

description: processed data in C1_RNAseq.txt


title: RM1-1 mNeuron single cell 2

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1317/+_male_rep1


title: RM1-1 AdES single cell 4

description: processed data in C1_RNAseq.txt

source_name: embryonic stem cell line RM1-1


title: Df(2L)ED1317/+_female_rep2


title: RM2-1 AdES single cell 3

description: processed data in C1_RNAseq.txt


title: RM1-1 AdES single cell 3

description: processed data in C1_RNAseq.txt


title: RM1-1 AdES single cell 2

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1317/+_female_rep1


title: Df(2L)ED1231/+_male_rep2


title: RM1-1 AdES single cell 1

description: processed data in C1_RNAseq.txt


title: RM1-1 EB single cell 3

description: processed data in C1_RNAseq.txt

source_name: EB single cells derived from RM1-1 AdESCs

value: EB


title: RM1-1 EB single cell 4

description: processed data in C1_RNAseq.txt


title: RM1-1 EB single cell 5

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1231/+_male_rep1


title: Df(2L)ED1231/+_female_rep2


title: RM1-1 EB single cell 1

description: processed data in C1_RNAseq.txt


title: MR2-1 AdES single cell 8

description: processed data in C1_RNAseq.txt

source_name: embryonic stem cell line MR2-1


title: MR2-1 AdES single cell 5

description: processed data in C1_RNAseq.txt


title: RM1-1 EB single cell 2

description: processed data in C1_RNAseq.txt


title: MR2-1 AdES single cell 7

description: processed data in C1_RNAseq.txt


title: MR2-1 AdES single cell 6

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1231/+_female_rep1


title: MR2-1 AdES single cell 2

description: processed data in C1_RNAseq.txt


title: MR2-1 AdES single cell 4

description: processed data in C1_RNAseq.txt


title: RM1-1 mNeuron single cell 1

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 12

description: processed data in C1_RNAseq.txt

source_name: EB single cells derived from MR2-1 AdESCs


title: Df(2L)ED1200/+_female_rep2


title: MR2-1 AdES single cell 3

description: processed data in C1_RNAseq.txt


title: MR2-1 AdES single cell 1

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 10

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 11

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 8

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 9

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1200/+_female_rep1


title: Df(2L)ED793/+_male_rep2


title: MR2-1 EB single cell 7

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 5

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 6

description: processed data in C1_RNAseq.txt


title: Df(2L)ED793/+_female_rep2


title: MR2-1 EB single cell 4

description: processed data in C1_RNAseq.txt


title: Df(2L)ED793/+_female_rep1


title: Df(2L)ED1200/+_male_rep1


title: MR1-1 mFibroblast single cell 10

description: processed data in C1_RNAseq.txt

source_name: fibroblast single cells derived from MR1-1 mouse chimaera

value: fibroblast


title: MR1-1 mFibroblast single cell 9

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 1

description: processed data in C1_RNAseq.txt


title: MR2-1 EB single cell 2

description: processed data in C1_RNAseq.txt


title: MR1-1 mFibroblast single cell 7

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1200/+_male_rep2


title: MR1-1 mFibroblast single cell 8

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1050/+_female_rep2


title: Df(2L)ED1050/+_female_rep1


title: MR1-1 mFibroblast single cell 6

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1050/+_male_rep1


title: Df(2L)ED793/+_male_rep1


title: MR2-1 EB single cell 3

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1109/+_male_rep2


title: MR1-1 mFibroblast single cell 4

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1109/+_female_rep2


title: MR1-1 mFibroblast single cell 3

description: processed data in C1_RNAseq.txt


title: Df(2L)ED508/+_male_rep2


title: MR1-1 mFibroblast single cell 2

description: processed data in C1_RNAseq.txt


title: MR1-1 mFibroblast single cell 1

description: processed data in C1_RNAseq.txt


title: MR1-1 AdES single cell 6

description: processed data in C1_RNAseq.txt

source_name: embryonic stem cell line MR1-1


title: Df(2L)ED508/+_male_rep1


title: Df(2L)ED1050/+_male_rep2


title: Df(2L)ED508/+_female_rep2


title: MR1-1 AdES single cell 5

description: processed data in C1_RNAseq.txt


title: MR1-1 AdES single cell 4

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1109/+_male_rep1


title: Df(2L)ED508/+_female_rep1


title: MR1-1 AdES single cell 3

description: processed data in C1_RNAseq.txt


title: Df(2L)ED123/+_male_rep1


title: MR1-1 mFibroblast single cell 5

description: processed data in C1_RNAseq.txt


title: MR1-1 AdESCs

description: processed data in Bulk_RNAseq.txt


title: Df(2L)ED123/+_male_rep2


title: MR2-1 AdESCs

description: processed data in Bulk_RNAseq.txt


title: MR1-1 AdES single cell 2

description: processed data in C1_RNAseq.txt


title: Df(2L)ED1109/+_female_rep1


title: Df(2L)ED6569/+_male_rep1


title: Df(2L)ED6569/+_female_rep2


title: RM2-1 AdESCs

description: processed data in Bulk_RNAseq.txt


title: MR1-1 AdES single cell 1

description: processed data in C1_RNAseq.txt


title: Df(2L)ED123/+_female_rep1


title: RM1-1 AdESCs

description: processed data in Bulk_RNAseq.txt


title: Df(2L)ED6569/+_male_rep2


title: Df(2L)ED62/+_male_rep1


title: Df(2L)ED6569/+_female_rep1


title: Df(2L)ED62/+_female_rep2


title: Df(2L)ED62/+_female_rep1


title: Df(2L)ED7007/+_male_rep2


title: Df(2L)ED7007/+_female_rep1


title: Df(2L)ED7007/+_male_rep1


title: Df(2L)ED7007/+_female_rep2


title: Df(2L)ED123/+_female_rep2


title: Df(2L)ED1203/+_male_rep1


title: Df(2L)ED1203/+_male_rep2


title: Df(2L)ED1203/+_female_rep2


title: Df(2L)ED1203/+_female_rep1


title: Df(2L)ED623/+_male_rep1


title: Df(2L)ED62/+_male_rep2


title: Df(2L)ED623/+_male_rep2


title: Df(2L)ED94/+_female_rep2


title: Df(2L)ED623/+_female_rep2


title: Df(2L)ED94/+_male_rep2


title: Df(2L)ED623/+_female_rep1


title: Df(2L)ED678/+_male_rep2


title: Df(2L)ED775/+_female_rep2


title: Df(2L)ED94/+_female_rep1


title: Df(2L)ED775/+_male_rep2


title: Df(2L)ED678/+_male_rep1


title: Df(2L)ED678/+_female_rep1


title: Df(2L)ED775/+_male_rep1


title: Df(2L)ED4651/+_male_rep2


title: Df(2L)ED678/+_female_rep2


title: Df(2L)ED4651/+_female_rep2


title: Df(2L)ED4651/+_female_rep1


title: Df(2L)ED369/+_male_rep1


title: Df(2L)ED369/+_male_rep2


title: Df(2L)ED369/+_female_rep2


title: Df(2L)ED369/+_female_rep1


title: Df(2L)ED94/+_male_rep1


title: Df(2L)ED775/+_female_rep1


title: Df(2L)ED320/+_female_rep1


title: Df(2L)ED320/+_male_rep2


title: Df(2L)ED19/+_male_rep1


title: Df(2L)ED320/+_female_rep2


title: RM2-1 rSomatic single cell 6 from testis

description: processed data in C1_RNAseq.txt


title: Df(2L)ED134/+_male_rep1


title: Df(2L)ED320/+_male_rep1


title: Df(2L)ED134/+_female_rep2


title: Df(2L)ED134/+_male_rep2


title: Df(2L)ED134/+_female_rep1


title: Df(2L)ED1303/+_male_rep1


title: Df(2L)ED19/+_male_rep2


title: Df(2L)ED19/+_female_rep1


title: Df(2L)ED647/+_male_rep2


title: Df(2L)ED647/+_male_rep1


title: Df(2L)ED1303/+_female_rep1


title: Df(2L)ED1303/+_male_rep2


title: Df(2L)ED1303/+_female_rep2


title: Df(2L)ED647/+_female_rep1


title: Df(2L)ED19/+_female_rep2


title: Df(2L)ED4651/+_male_rep1


title: Df(2L)ED647/+_female_rep2


title: Df(2L)ED87/+_male_rep2


title: Df(2L)ED87/+_male_rep1


title: Df(2L)ED87/+_female_rep2


title: Df(2L)ED87/+_female_rep1


title: Df(2L)ED746/+_male_rep2


title: Df(2L)ED746/+_male_rep1


title: Df(2L)ED746/+_female_rep2


title: Df(2L)ED746/+_female_rep1


title: Df(2L)ED700/+_male_rep1


title: Df(2L)ED700/+_female_rep1


title: Df(2L)ED700/+_female_rep2


title: Df(2L)ED695/+_male_rep2


title: Df(2L)ED695/+_male_rep1


title: Df(2L)ED284/+_female_rep2


title: Df(2L)ED284/+_male_rep1


title: Df(2L)ED270/+_male_rep2


title: Df(2L)ED270/+_female_rep2


title: Df(2L)ED695/+_female_rep1


title: Df(2L)ED206/+_male_rep1


title: Df(2L)ED206/+_male_rep2


title: Df(2L)ED206/+_female_rep2


title: Df(2L)ED695/+_female_rep2


title: Df(2L)ED206/+_female_rep1


title: Df(2L)ED270/+_male_rep1


title: Df(2L)ED784/+_male_rep1


title: Df(2L)ED284/+_female_rep1


title: Df(2L)ED270/+_female_rep1


title: Df(2L)ED784/+_female_rep2


title: Df(2L)ED700/+_male_rep2


title: Df(2L)ED784/+_male_rep2


title: Df(2L)ED784/+_female_rep1


title: Df(2L)ED778/+_male_rep1


title: Df(2L)ED778/+_male_rep2


title: Df(2L)ED778/+_female_rep1


title: Df(2L)ED778/+_female_rep2


title: Df(2L)ED777/+_male_rep2


title: Df(2L)ED777/+_male_rep1


title: Df(2L)ED777/+_female_rep2


title: Df(2L)ED776/+_male_rep1


title: Df(2L)ED776/+_male_rep2


title: Df(2L)ED776/+_female_rep1


title: Df(2L)ED774/+_male_rep2


title: Df(2L)ED774/+_male_rep1


title: Df(2L)ED774/+_female_rep2


title: F146 ESCs

description: processed data in Bulk_RNAseq.txt

organism: Mus musculus

source_name: embryonic stem cell line F146


title: Df(2L)ED774/+_female_rep1


title: F145 ESCs

description: processed data in Bulk_RNAseq.txt

source_name: embryonic stem cell line F145


title: Df(2L)ED773/+_female_rep2


title: Df(2L)ED773/+_male_rep1


title: Df(2L)ED3/+_female_rep1


title: Df(2L)ED3/+_male_rep1


title: mNPC_RNASeq

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description: FACS was performed by transgenic RFP

data_processing:
Base call by bcl2fastq v. 2.17
Fastq files were aligned using DNA Nexus or TopHat. Human data was aligned to hg19, and mouse data was aligned to mm10.
RPKM was calculated with Partek.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: wig profiles were generated using QuEST

source_name: Cited1+ cells from mouse embryonic kidney obtained by FACS

extract_protocol:
RNA was collected from FACS isolated cells using the Qiagen RNeasy Micro Kit
Libraries were constructed using KAPA Stranded mRNA-Seq Kit, with mRNA captured by KAPA mRNA Capture Beads, and subsequently sequenced by Illumina HiSeq 2000.

tag: developmental stage

value: 15.5 days

tag: strain

value: Swiss Webster/C57BL/6J


title: Df(2L)ED773/+_male_rep2


title: Df(2L)ED3/+_male_rep2


title: Df(2L)ED773/+_female_rep1


title: input_mDNA

library_source: genomic

data_processing:
Base call by bcl2fastq v. 2.17
Fastq files were aligned using Novoalign. Human data was aligned to hg19, and mouse data was aligned to mm9.
ChIP-Seq peaks were called using QuEST (Valouev et al., 2008).
peak files were generated by extracting the chromosome numbers coordinates and QuEST enrichment score from QuEST.out files
wig profiles were generated using QuEST
Genome_build: hg19/mm9
Supplementary_files_format_and_content: wiggle files represents ChIP-Seq tags; peak files

molecule: genomic DNA

source_name: mouse embryonic kidney

extract_protocol:
Cortex of human embryonic kidneys were micro-dissected and fixed in crosslinking buffer containing 1% PFA for 30 min, then homogenized, followed by chromatin extraction and sonication. Sonicated chromatin was then immuno-precipitated with the indicated antibodies. The precipitated DNA was subsequently collected with Qiagen PCR product purification kit. Mouse embryonic kidneys were processed in a similar way.
Libraries were constructed using ThruPLEX-FD Prep Kit (Rubicon Genomics), and subsequently sequenced by Illumina HiSeq 2000.

value: 16.5 days

value: Swiss Webster

tag: chip antibody


title: mH3K27me3_ChIPSeq

source_name: Cited1 expressing cells from mouse embryonic kidney

value: H3K27me3 antibody (Abcam, ab6002)


title: Asr1-RING mutant 1

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to sacCer2 using Tophat 2
FPKM were quantified by Cufflinks
Genome_build: sacCer2
Supplementary_files_format_and_content: FPKM Table

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were growth in enriched media to log phase (~0.8 O.D.).

extract_protocol:
RNA was extracted using the Hot Acid Phenol protocol and treated with Dnase to remove DNA contamination. Ribosomal reduction was performed to remove rRNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: Asr1-RING mutant 2


title: mH3K27ac_ChIPSeq

value: H3K27ac antibody (Abcam, ab4729)


title: mSix2_ChIPSeq

value: Six2 antibody (Proteintech,11562-1-AP)


title: Df(2L)ED776/+_female_rep2

source_name: Whole animal


title: hNPC_RNASeq

description: FACS was performed by ITGA8 Ab

organism: Homo sapiens

source_name: ITGA8+ cells from human embryonic kidney obtained by FACS

value: 17 weeks


title: WT 2

value: wild type


title: WT 1


title: Df(2L)ED777/+_female_rep1

value: Whole animal


title: hH3K27ac_ChIPSeq_1

source_name: human embryonic kidney cortex

value: 16 weeks


title: hH3K27ac_ChIPSeq_2


title: input_hDNA_2


title: Df(2L)ED3/+_female_rep2

value: female


title: SKNSH-pLX-GFP_RA_2

city: Amsterdam

first: Prashanth Kumar

last: Bajpe

address: Plesmanlaan 121

department: Molecular Carcinogenesis

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 51 bp reads) and were processed by the Illumina pipeline.
Reads were aligned to hg19 using TopHat v2.0.6
The genecounts were generated using HTseq-count. HTseq-count was used in default (union) mode.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes gene read count values for each Sample

source_name: Neuroblastoma SK-N-SH control cells, RA treated

growth_protocol: Cells were grown in DMEM supplemented with 8% serum, 1% penstrep and 1% glutamine

extract_protocol:
Cells were lysed in Trizol.
RNA-Seq libraries were prepared using the reagents provided in the Illumina TruSeq™ RNA Sample Preparation Kit, following the manufacturer’s protocol. Libraries were PCR amplified for 11 cycles and sequenced on an Illumina HiSeq 2000 System with TruSeq reagent kits and software, generating 51bp reads.

treatment_protocol: Cells were treated with either 1uM of Retinoic acid (RA) or vehicle control.

value: human neuroblastoma cells

value: SK-N-SH

tag: clone

value: control

tag: treatment

value: 1uM Retinoic acid


title: hSIX1_ChIPSeq_1

value: SIX1 antibidy (Cell Signaling; 12891S)


title: hSIX2_ChIPSeq_1

value: SIX2 antibody (MyBiosource, MBS610128)


title: SD3.23_RA_2

source_name: Neuroblastoma SK-N-SH MAML3 overexpressing cells, untreated


title: hSIX1_ChIPSeq_2


title: hSIX2_ChIPSeq_2


title: SD3.23_RA_1


title: SKNSH-pLX-GFP_RA_1


title: Df(2L)ED284/+_male_rep2

value: male


title: MAML3 ChIP-seq-RA-rep2

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 50bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters. DFilter was run with bs=50, ks=30, refine, nonzero for ChIP data.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using genomecov utility from bedtools; intersect.bed files contain peaks called by both peak calling algorithms

growth_protocol: Cells were grown in DMEM supplemented with 10% serum, 1% penstrep and 1% glutamine. 24 hours before RA treatment, the cells were grown in DMEM supplemented with 10% charcoal stripped serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were treated with either 1uM of retinoic acid (RA) or with vehicle control (UT).

value: MAML3, Bethyl Laboratories, Cat No. A300-684A

value: RA treated


title: MAML3 ChIP-seq-UT-rep2

source_name: Neuroblastoma SK-N-SH control cells, untreated

value: untreated


title: MAML3 ChIP-seq-RA-rep1


title: Input-RA


title: RAR alpha ChIP-seq-RA-rep2

value: RARα (C-20), Santa Cruz,Cat No. Sc551


title: input_hDNA_1


title: RAR alpha ChIP-seq-UT-rep2


title: SD3.23_UT_1

value: Untreated


title: Input-UT


title: RAR alpha ChIP-seq-RA-rep1


title: wild-type (sample contains 3 reps)

status: Public on Jan 30 2016

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

data_processing:
RNA-seq reads were aligned to the Arabidopsis thaliana genome (TAIR10) by Tophat (v2.0.11) with default parameters, and only uniquely mapped reads were retained for subsequent analysis.
Gene expression was measured as reads per kilobase of exon model per million mapped reads (RPKM), and differentially expressed genes (fold-change >1.5) were identified using the R package DEGseq with a p-value <0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: The tab-delimited text file include RPKM and fold-change (ago1/wt) values for each gene.

organism: Arabidopsis thaliana

source_name: flower buds

growth_protocol: Arabidopsis plants were germinated in the soil and grown under the standard long day conditions (16 hours light, 8 hours dark, at 20°C) . The open flower buds were collected for subsequent RNA-seq.

extract_protocol:
Total RNAs from wild type and ago1-27 flower buds were isolated using TRIzol (Invitrogen) following manufacturer’s instructions.
RNA-seq libraries were constructed using the TruSeq protocol (Illumina). 50-nt single-end non-strand-specific RNA-seq was conducted on an Illumina HiSeq 2000 platform.


title: ago1-27 (sample contains 3 reps)


title: SD3.23_UT_2


title: MAML3 ChIP-seq-UT-rep1


title: SKNSH-pLX-GFP_UT_2


title: cardiomyocyte MBD-seq R2_MBD

city: Duarte

first: Joshua

last: Tompkins

state: CA

address: 1500 E Duarte Road

department: DMRI

institute: City of Hope

description:
MBD
MBD

data_processing:
For MBD-seq, paired-end reads were aligned with bowtie and differential methylated regions (DMRs) were calculated with bioconductor package MEDIPS 1.12.0
100 bp windows and standard filters for P-values (p<0.01), minimal coverage (>0.25 rpm), and pair-wise comparison ratios (>1.25) merging biological replicates by mean values (Lienhard et al., 2014).
Hypergeometric Optimization of Motif EnRichment (HOMER v4.7; annotatePeaks.pl) was used for DMR annotation by gene proximity and functional region (Heinz et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited. DMR peak ID/read values, chromosome location, annotations, ensemble transcript ids, nearest promoter id and distance

source_name: differentiated from H7 hESCs Percoll purified

growth_protocol: H7 hESCs (p60) were enzymatically dissociated into single cells with Accutase (Millipore SCR005) and seeded at 1.2-2.0 x 104 cells/cm2 onto Synthemax II (Corning 3535XX1) coated plates in E8 medium (Life technologies A1517001) supplemented with 10 μM Y27632 (EMD Chemicals 688000). Cell cultures were grown at 37°C and 5% CO2 for 2-3 days with daily media changes. On D1 of cardiac induction, RPMI1640 (Life technologies 11875-119) supplemented with B27 minus insulin (A1895601) and 12 μM of CHIR99021 (Selleckchem S2924) was used to replace E8 media for 24 hours, followed by media replacement with RPMI1640 supplemented with B27 minus insulin with 5 μM of IWP4 (04-0036) for 2 days, and lastly, standard RPMI1640  12  with B27 supplement (17504-044) for the remainder of the differentiation course. Media was changed every 2-3 days until D31. D31 CMs were purified through Percoll density gradients as described by Xu et al. (2002).

extract_protocol:
genomic DNA was isolated using qiagen blood and tissue kit.
Methyl binding domain (MBD) reactions. MBD and control reactions were performed according to the manufacturers’ protocol (MethylMiner Methylated DNA Enrichment Kit; ME10025, Invitrogen). Isolated genomic DNA was sonicated and gel purified at a range of 100-300 bp. 3.5 ug was used for methyl enrichment using the single fraction elution protocol. Five to ten nanogram of MBD purified DNA was end-repaired, a single adenosine was added and ligated to Illumina adaptor oligonucleotides (TruSeq DNA sample prep Kit, Illumina). Sonicated  14  genomic DNA at 1% of MBD reaction input was used for input library preparation. 13 cycles of PCR was performed with universal primer P1.0 (5’AATGATACGGCGACCACCGAGATCTACACTCTTTCC CTACAC GACGCTCTTCCGATCT) and a barcoded index primer (5’CAAGCAGAAGACGGCATACG AGAT NNNNNNGTGACTGGAGTTC).Both RNA-seq and MBD-seq library templates were prepared for sequencing using cBot cluster generation system (Illumina) with TruSeq PE Cluster V3 Kit. The sequencing run was performed with paired end mode of 100 cycles of read 1, 7 cycles of index read, and 100 cycles of read 2 using Illumina HiSeq 2500 platform with TruSeq SBS V3 Kits. Sequencing library preparation and reactions were conducted at City of Hope’s integrative genomics core

treatment_protocol: On D1 of cardiac induction, RPMI1640 (Life technologies 11875-119) supplemented with B27 minus insulin (A1895601) and 12 μM of CHIR99021 (Selleckchem S2924) was used to replace E8 media for 24 hours, followed by media replacement with RPMI1640 supplemented with B27 minus insulin with 5 μM of IWP4 (04-0036) for 2 days, and lastly, standard RPMI1640  12  with B27 supplement (17504-044) for the remainder of the differentiation course. Media was changed every 2-3 days until D31. D31 CMs were purified through Percoll density gradients as described by Xu et al. (2002). PMESO and CMESO populations were isolated using ROR2 or ROR2/PDGRFa FACS sorts, respectively.

value: H7 derived


title: AdV-GFP replicate 2

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Libraries were run on an Illumina HiSeq 2000.
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using the RNAExpress application on BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing gene symbol and raw read numbers for each gene in each sample

source_name: HEK 293T cells

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: AdV-GFP


title: AdV-VP55 replicate 2


title: RAR alpha ChIP-seq-UT-rep1


title: SKNSH-pLX-GFP_UT_1


title: Mock

value: Mock


title: CMESO MBD-seq R2_MBD

description:
MBD
MBD

source_name: differentiated from H7 hESCs FACS sorted


title: cardiomyocyte MBD-seq R2_INPUT

description:
INPUT
INPUT


title: cardiomyocyte MBD-seq R1_MBD

description:
MBD
MBD


title: AdV-VP55 replicate 1


title: AdV-GFP replicate 1


title: CMESO MBD-seq R2_INPUT

description:
INPUT
INPUT


title: cardiomyocyte MBD-seq R1_INPUT

description:
INPUT
INPUT


title: HCC-C6-R-14P-6

city: Gaithersburg

first: Dong

last: Shen

address: MedImmune Way

department: Translational Science

institute: Medimmune

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human genome reference hg19  via Bowtie
Genome_build: hg19
Supplementary_files_format_and_content: The normalized readcount for each gene for each sample processed via Deseq

source_name: HCC-C6 Non-recurrent Tumor's Adjacent Normal

extract_protocol:
Tumor and normal samples  were removed, flash frozen on dry ice, and RNA was harvested.  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HCC Non-recurrent Tumor's Adjacent Normal

tag: individual

value: M

tag: age

tag: hbv (pre-olt)

value: Positive

tag: hbv (post-olt)

value: Negative

tag: primary tumor and nat rna

value: Yes

tag: primary tumor biopsy method

value: OLT

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

value: Ⅱ

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions

value: RFA=Radiofrequency ablation; VATS=Video-assisted thorascopic surgery; OLT=Orthotopic liver transplantation; AFP=Alpha-fetoprotein


title: HCC-C6-R-14T-6

source_name: HCC-C6 Non-recurrent Tumor

tag: tissue

value: HCC Non-recurrent Tumor

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade


title: CMESO MBD-seq R1_MBD

description:
MBD
MBD

tag: cell line


title: CMESO MBD-seq R1_INPUT

description:
INPUT
INPUT


title: HCC-C9-R-14P-9

source_name: HCC-C9 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: HCC-C8-R-14P-8

source_name: HCC-C8 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

value: Ⅰ

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade


title: HCC-C2-R-14P-2

source_name: HCC-C2 Non-recurrent Tumor's Adjacent Normal

tag: tissue

value: I-II

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

value: D

tag: definitions


title: HCC-C19-R-14T-19

source_name: HCC-C19 Non-recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

value: Ⅱ-Ⅲ

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

value: B


title: HCC-C2-R-14T-2

source_name: HCC-C2 Non-recurrent Tumor

tag: tissue

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: PMESO MBD-seq R2_INPUT

description:
INPUT
INPUT

tag: cell line

value: H7 derived


title: PMESO MBD-seq R1_INPUT

description:
INPUT
INPUT


title: PMESO MBD-seq R1_MBD

description:
MBD
MBD


title: PMESO MBD-seq R2_MBD

description:
MBD
MBD


title: HCC-C19-R-14P-19

source_name: HCC-C19 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis


title: hESC MBD-seq R2_MBD

description:
MBD
MBD

source_name: H7 hESCs

tag: cell line


title: hESC MBD-seq R2_INPUT

description:
INPUT
INPUT


title: HCC-C18-R-14T-18

source_name: HCC-C18 Non-recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: hESC MBD-seq R1_INPUT

description:
INPUT
INPUT

tag: cell line


title: hESC MBD-seq R1_MBD

description:
MBD
MBD


title: D4 ROR2(+)/PDGFRa(-) RNA-seq R2

data_processing:
paired-end reads were aligned to hg19 with Bowtie (2.1.0.0) using TopHat (2.0.8b)
transcripts were assembled and identified as differentially expressed by Cufflinks (Trapnell et al., 2012)
Genome_build: hg19
Supplementary_files_format_and_content: For time course not FACS sorted: tab delimited. Mean FPKM values by time point for each official gene symbol. For FACS sorted: PMESO, D3 ROR2(-), CMESO, D4 ROR2(+)/PDGFRa(-). Tab delimited. Mean FPKM values for positive (p) and negative (n) sorts. Significance testing for differential expression.

growth_protocol: H7 hESCs (p60) were enzymatically dissociated into single cells with Accutase (Millipore SCR005) and seeded at 1.2-2.0 x 10^4 cells/cm2 onto Synthemax II (Corning 3535XX1) coated plates in E8 medium (Life technologies A1517001) supplemented with 10 μM Y27632 (EMD Chemicals 688000). Cell cultures were grown at 37°C and 5% CO2 for 2-3 days with daily media changes. On D1 of cardiac induction, RPMI1640 (Life technologies 11875-119) supplemented with B27 minus insulin (A1895601) and 12 μM of CHIR99021 (Selleckchem S2924) was used to replace E8 media for 24 hours, followed by media replacement with RPMI1640 supplemented with B27 minus insulin with 5 μM of IWP4 (04-0036) for 2 days, and lastly, standard RPMI1640  12  with B27 supplement (17504-044) for the remainder of the differentiation course. Media was changed every 2-3 days until D31. D31 CMs were purified through Percoll density gradients as described by Xu et al. (2002).

extract_protocol:
RNA was isolated using qiagen total RNA isolation kit.
500 ng of total RNA from each sample was used for ribosomal RNA removal follow RiboZero kit instructions. The resulting RNA was fragmented with divalent cations under elevated temperature. First-strand cDNA synthesis produced single-stranded DNA copies from the fragmented RNA by reverse transcription. After second-strand cDNA synthesis, the double-stranded DNA underwent end repair, and the 3′ ends were adenylated. Finally, universal adapters were ligated to the cDNA fragments, and 10 cycles of PCR was performed to produce the final sequencing library. Five to ten nanogram of MBD purified DNA was end-repaired, a single adenosine was added and ligated to Illumina adaptor oligonucleotides (TruSeq DNA sample prep Kit, Illumina). Both RNA-seq and MBD-seq library templates were prepared for sequencing using cBot cluster generation system (Illumina) with TruSeq PE Cluster V3 Kit. The sequencing run was performed with paired end mode of 100 cycles of read 1, 7 cycles of index read, and 100 cycles of read 2 using Illumina HiSeq 2500 platform with TruSeq SBS V3 Kits. Sequencing library preparation and reactions were conducted at City of Hope’s integrative genomics core


title: D4 ROR2(+)/PDGFRa(-) RNA-seq R1


title: HCC-C9-R-14T-9

source_name: HCC-C9 Non-recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis


title: HCC-C15-R-14P-15

source_name: HCC-C15 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: HCC-C8-R-14T-8

source_name: HCC-C8 Non-recurrent Tumor

tag: tissue

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis


title: CMESO RNA-seq R1

tag: cell line


title: HCC-C14-R-14P-14

source_name: HCC-C14 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: D3 ROR2(-) RNA-seq R1

tag: cell line


title: HCC-C13-R-14T-13

source_name: HCC-C13 Non-recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

value: C


title: PMESO RNA-seq R2

tag: cell line


title: HCC-C13-R-14P-13

source_name: HCC-C13 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: HCC-C12-R-14T-12

source_name: HCC-C12 Non-recurrent Tumor

tag: tissue

tag: individual

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis


title: PMESO RNA-seq R1

source_name: differentiated from H7 hESCs FACS sorted

tag: cell line


title: HCC-C18-R-14P-18

source_name: HCC-C18 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: cardiomyocyte RNA-seq R2

source_name: differentiated from H7 hESCs

tag: cell line


title: HCC-C11-R-14T-11

source_name: HCC-C11 Non-recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis


title: cardiomyocyte RNA-seq R1

tag: cell line


title: HCC-C11-R-14P-11

source_name: HCC-C11 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: HCC-C16-R-14T-16

source_name: HCC-C16 Non-recurrent Tumor

tag: tissue

tag: individual

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis


title: HCC-C16-R-14P-16

source_name: HCC-C16 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: gender

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: HCC-C12-R-14P-12

source_name: HCC-C12 Non-recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis


title: HCC-C15-R-14T-15

source_name: HCC-C15 Non-recurrent Tumor

tag: tissue

tag: gender

tag: glu

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: VP55+dsRNA replicate 2

description: 24 hr treatment with AdV then 8hr with dsRNA

data_processing:
Libraries were run on an Illumina MiSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using the RNAExpress application on BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing gene symbol and raw read numbers for each gene in each sample

source_name: BJ cells

tag: treatment


title: GFP+dsRNA replicate 2

value: GFP+dsRNA


title: CMESO RNA-seq R2

tag: cell line


title: D15 RNA-seq R2


title: VP55+dsRNA replicate 1


title: D15 RNA-seq R1


title: HCC8-R-13P-8

source_name: HCC8  Recurrent Tumor's Adjacent Normal

tag: tissue

value: HCC Recurrent Tumor's Adjacent Normal

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

value: III

tag: primary tumor cirrhosis

tag: recurrent tumor method

value: RFA

tag: recurrent tumor organ

value: liver

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu


title: D10 RNA-seq R2

tag: cell line


title: HCC8-R-13T-8

source_name: HCC8  Recurrent Tumor

tag: tissue

value: HCC Recurrent Tumor

tag: individual

tag: gender

value: M

tag: age

value: Positive

value: Negative

value: Yes

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: D3 ROR2(-) RNA-seq R2

tag: cell line


title: HCC-C14-R-14T-14

source_name: HCC-C14 Non-recurrent Tumor

tag: tissue

value: HCC Non-recurrent Tumor

tag: individual

tag: gender

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

value: OLT

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

value: Ⅱ

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu

value: RFA=Radiofrequency ablation; VATS=Video-assisted thorascopic surgery; OLT=Orthotopic liver transplantation; AFP=Alpha-fetoprotein


title: D10 RNA-seq R1

tag: cell line


title: VP55+IFN replicate 2

description: 24 hr treatment with AdV then 6hrs with IFN

tag: treatment


title: GFP+dsRNA replicate 1


title: VP55+IFN replicate 1


title: GFP+IFN replicate 2

value: GFP+IFN


title: HCC7-R-13T-18

source_name: HCC7  Recurrent Tumor

tag: tissue

tag: individual

tag: gender

value: not collected

tag: age

value: #N/A

tag: hbv (pre-olt)

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: D8 RNA-seq R2

tag: cell line

value: H7 derived


title: VP55 9 day replicate 1

tag: treatment

value: VP55 9 day


title: VP55 9 day replicate 2


title: HCC7-R-13P-18

source_name: HCC7  Recurrent Tumor's Adjacent Normal

tag: tissue

value: HCC Recurrent Tumor's Adjacent Normal

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu


title: HCC6-R-13T-6

source_name: HCC6  Recurrent Tumor

tag: tissue

tag: individual

tag: gender

value: III

value: VATS

value: lung

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

value: B

tag: definitions


title: GFP 9 day replicate 2

tag: treatment

value: GFP 9 day


title: HCC6-R-13P-6

source_name: HCC6  Recurrent Tumor's  Adjacent Normal

tag: tissue

value: HCC Recurrent Tumor's  Adjacent Normal

tag: individual

value: M

tag: age

tag: hbv (pre-olt)

value: Positive

tag: hbv (post-olt)

value: Negative

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu


title: GFP 9 day replicate 1

tag: treatment


title: D8 RNA-seq R1

tag: cell line


title: D6 RNA-seq R2


title: D6 RNA-seq R1


title: D5 RNA-seq R2


title: VP55 24hr replicate 2

value: VP55 24hr


title: VP55 24hr replicate 1


title: HCC5-R-13P-5

source_name: HCC5  Recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

value: Yes

value: OLT

value: II

value: RFA

value: liver

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions

value: RFA=Radiofrequency ablation; VATS=Video-assisted thorascopic surgery; OLT=Orthotopic liver transplantation; AFP=Alpha-fetoprotein


title: HCC4-R-13T-4

source_name: HCC4  Recurrent Tumor

tag: tissue

value: HCC Recurrent Tumor

tag: individual

tag: gender

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

value: No

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu


title: D5 RNA-seq R1

source_name: differentiated from H7 hESCs

tag: cell line

value: H7 derived


title: GFP+IFN replicate 1

tag: treatment

value: GFP+IFN


title: yeast_S288C_Ribo-seq rep2

city: University Park

first: Nabeel

last: Ahmed

state: PENNSYLVANIA

address: 407 Chemistry Building

department: The Huck Institutes of the Life Sciences

institute: Pennsylvania State University

data_processing:
The raw reads from the ribosome protected fragments were trimmed of the 3’ custom adapter CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG using cutadapt (v1.1).
The low quality reads were filtered using PRINSEQ (v0.20.4), and reads shorter than 20 nucleotides were discarded
The processed reads were first aligned to the ribosomal RNA sequences using Bowtie 2 (v2.2.3). The unaligned reads were then aligned to the S. cerevisae assembly R64-1-1 (UCSC: sacCer3) using Tophat (v2.0.13) with up to two mismatches allowed.
Gene annotations were obtained from Saccharomyces Genome Database (http://www.yeastgenome.org/) on October 30, 2014.
For downstream analysis, only reads with length 27 to 32 nucleotides were considered, as they are more likely to represent the ribosome-protected fragments. The ribosome profiles of individual genes were obtained by quantifying the coverage at a gene position by the 5’ end of the reads. The genes containing reads with multiple alignments were filtered. Since the active site of translation is around 15 nucleotides downstream of the 5’ end of the ribosome protected fragment, the ribosome profiles of genes were calculated from 5 codons upstream of the second codon(where the translation elongation starts) to 6 codons upstream of the stop codon (we also exclude the stop codon).
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files containing coverage at chromosome position determined from 5' end of the reads
Supplementary_files_format_and_content: tab delimited file with filtered gene names and corresponding Pearson correlation coefficient(r) values

growth_protocol: Yeast cells grown in YPD, at 30°C to an optical density (OD600) of 0.5

extract_protocol:
Frozen cells were mechanically lysed for 2 min at 30 Hz using a Retsch MM400 mixer mill and a lysis buffer composed of 20 mM Tris pH 8.0, 140 mM KCl, 6 mM MgCl2, 0.1% NP-40, 100 µg/ml cycloheximide, 200 µg/ml heparin, 1 mM PMSF, 20 µg/ml leupeptin, 20 µg/ml aprotinin, 1 mg/ml AEBSF, 1 µg/ml E-64, 40 µg/ml bestatin, 12.5 U DNase. Lysates were thawed and exposed parts of mRNAs were digested with 5 U/A260 RNaseI (Ambion) at 25°C, 650 rpm for 1 h. Digestion was stopped by adding 8 U/A260 SUPERase·In (Ambion) and the lysate was cleared of membranes, organelles and cell debris by centrifugation at 4°C and 30,000 g for 5 min. The supernatant was loaded on a 10-50% sucrose gradient (20 mM Tris pH 8.0, 140 mM KCl, 6 mM MgCl2, 100 µg/ml cycloheximide, 1x EDTA-free protease inhibitor tablets (Roche)) and monosome fractions were pooled. RNA was isolated from monosomes by hot-phenol extraction and directly precipitated using GlycoBlue as coprecipitant.
5 pmol of dephosphorylated mRNA footprints were linked to the 1 µg linker L1’ by incubation with 200 U T4 RNA Ligase 2, truncated (NEB) at 37°C for 2.5 h in buffer containing 20 mM Tris pH7, 20% PEG MW 8000, 10% DMSO, 20 U SUPERase·In. Linked footprints were size-selected by gel electrophoresis. Reverse transcription was carried out with 200 U SuperScript III (Invitrogen), 20 U SUPERase·In, 10 nmol dNTP, 25 pmol Linker L1’L2’, 100 nmol DTT in 20 µl of 1x FSB buffer (Invitrogen). Circularization by incubation with CircLigase (Epicentre) was performed two times for one hour each (a second aliquot of CircLigase was added after one hour) and the product was directly used for amplification by PCR.

treatment_protocol: Cells were harvested by fast filtration in the absence of antibiotics and immediately flash-frozen in liquid nitrogen. It took 40 sec from growth in YPD to being frozen in liquid nitrogen.

tag: strain

tag: genotype/variation

value: wild type


title: GFP 24hr replicate 2

value: GFP 24hr


title: HCC3-R-13T-3

source_name: HCC3  Recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

value: III

tag: alt

tag: ast

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

value: B

tag: definitions


title: GFP 24hr replicate 1

tag: treatment


title: D4 RNA-seq R1

tag: cell line


title: yeast_S288C_Ribo-seq rep1

tag: strain

tag: genotype/variation


title: D4 RNA-seq R2


title: HCC4-R-13P-4

source_name: HCC4  Recurrent Tumor's Adjacent Normal

tag: tissue

value: HCC Recurrent Tumor's Adjacent Normal

tag: individual

tag: gender

value: M

tag: age

tag: hbv (pre-olt)

value: Positive

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast


title: D3 RNA-seq R2

tag: cell line


title: Mock replicate 2

tag: treatment

value: Mock


title: HCC3-R-13P-3

source_name: HCC3  Recurrent Tumor's Adjacent Normal

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

value: Negative

tag: primary tumor and nat rna

value: Yes

value: OLT

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: D3 RNA-seq R1

tag: cell line


title: Mock replicate 1

tag: treatment


title: HCC2-R-13T-2

source_name: HCC2  Recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

value: II

tag: primary tumor cirrhosis

tag: recurrent tumor method

value: RFA

tag: recurrent tumor organ

value: liver

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast


title: D2 RNA-seq R2

tag: cell line


title: HCC2-R-13P-2

source_name: HCC2  Recurrent Tumor's  Adjacent Normal

tag: tissue

value: HCC Recurrent Tumor's  Adjacent Normal

tag: individual

tag: gender

tag: age

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions

value: RFA=Radiofrequency ablation; VATS=Video-assisted thorascopic surgery; OLT=Orthotopic liver transplantation; AFP=Alpha-fetoprotein


title: HCC5-R-13T-5

source_name: HCC5  Recurrent Tumor

tag: tissue

value: HCC Recurrent Tumor

tag: individual

tag: hbv (pre-olt)

tag: primary tumor biopsy method

tag: primary tumor content (%)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast


title: D2 RNA-seq R1

tag: cell line

value: H7 derived


title: Ctrl_2

city: Brussels

first: Andre

middle: M

last: GOFFINET

address: Avenue Mounier 73

department: Neuroscience

country: Belgium

institute: University of Louvain

data_processing:
Sequence quality: Expressed as Phred scores, calculated FastQC
Sequence mapping: Mapping was performed on the mouse genome reference sequence GRCm38 (annotated by Ensembl), using Tophat[3] version 2.0.9 in conjunction with Bowtie[4] version 1.0.0.
Expression analysis: Cufflinks v 2.1.1 was used to detect genes and transcripts that are expressed by comparing the Tophat2 read mapping with the Ensembl gene models for the grch37 release of the mouse genome.
Differential expression: Determined using the edgeR R Bioconductor 2.12 suite, using the the easyRNASeq package
Supplementary_files_format_and_content: One Excel comma separated values (CSV) file with 10 columns in counts per million for Fzd3_1, Fzd3_2, Fzd3_3, Celsr3_1, Celsr3_2, Celsr3_4, and gene_name

source_name: cerebral cortex E16.5

extract_protocol:
Embryonic cortices were microdissected on ice and RNA was harvested using Trizol reagent.  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared and sequencing was performed by Bekcman Coulter, using Illumina protocols (Illumina RNA Seq Tuxedo expression analysis)

tag: genotype

value: Control +/+

tag: tissue

value: embryonic cerebral cortex

tag: developmental stage

value: embryonic day (E) 16.5


title: Ctrl_3


title: HCC10-R-13T-10

source_name: HCC10  Recurrent Tumor

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: hbv (post-olt)

tag: primary tumor and nat rna

tag: primary tumor biopsy method

tag: primary tumor content (%)

value: III

value: No

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: HCC10-R-13P-10

source_name: HCC10  Recurrent Tumor's Adjacent Normal

tag: tissue

value: HCC Recurrent Tumor's Adjacent Normal

tag: individual

tag: gender

value: M

tag: age

tag: hbv (pre-olt)

value: Positive

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

tag: recurrent tumor organ

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast


title: Celsr3_4

tag: genotype

value: Celsr3 -/- mutant

tag: tissue

tag: developmental stage


title: Ctrl_1


title: HCC1-R-13P-1

source_name: HCC1 Recurrent Tumor's Adjacent Normal

tag: individual

tag: gender

tag: age

tag: hbv (post-olt)

value: Negative

tag: primary tumor and nat rna

value: Yes

tag: primary tumor biopsy method

value: OLT

tag: primary tumor content (%)

tag: ggt

tag: tb

tag: db

tag: alb

tag: hgb

tag: pt

tag: hbsag

tag: hbvdna

tag: afp

tag: cea

tag: bclc stage pre-ltx

tag: definitions


title: HCC1-R-13T-1

source_name: HCC1 Recurrent Tumor

tag: tissue

tag: individual

tag: gender

tag: age

tag: hbv (pre-olt)

tag: primary tumor size (cm)

tag: primary tumor grade

tag: primary tumor cirrhosis

tag: recurrent tumor method

value: RFA

tag: recurrent tumor organ

value: liver

tag: recurrent tumor size (cm)

tag: recurrent tumor content (%)

tag: recurrent tumor grade

tag: recurrent tumor cirrhosis

tag: glu

tag: alt

tag: ast


title: Female 2-rRNA

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description: This sample is of Plasmodium falciparum female gametocyte at stage V. It is the second of three biological replicates used in this experiment, each from separate cultures.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mapped to the P. falciparum genome sequence (Genedb v3.1) using TopHat (Trapnell et al., 2009). Output was filtered to retain only reads that were mapped with ≤ 2 mismatches in the 100-bp long reads.
The RNA-Seq data were converted to transcripts levels by by Kallisto followed by Deseq (Anders and Huber, 2010; Bray et al., 2015). 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: P. falciparum genome sequence (Genedb v3.1)
Supplementary_files_format_and_content: Excel files include values for each genes from each samples

organism: Plasmodium falciparum

source_name: Female gametocyte

growth_protocol:
P. falciparum parasites were maintained as described previously (Trager and Jensen, 1976)
Induction of gametocytogenesis was performed as described (Fivelman et al., 2007).  Ganetocytes were harvested at  Day 12 (stage V).

extract_protocol:
The male and female gametocytes were separated by cell-sorter based on GFP intensity. Total RNA was extracted using the Trizol reagent (invirtogen.com)
Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Total RNA with and without rRNA depletion were processed for generation libraries using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina Inc., San Diego, CA).

tag: strain

tag: tissue

value: Female

value: Day 12

value: gametocyte at stage V


title: Female 3-rRNA

description: This sample is of Plasmodium falciparum female gametocyte at stage V. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Fzd3_1

tag: genotype

value: Fzd3 -/- mutant

tag: developmental stage


title: D1 RNA-seq R1

tag: cell line

value: H7 derived


title: Celsr3_2

value: embryonic cerebral cortex

value: embryonic day (E) 16.5


title: Male 2-rRNA

description: This sample is of Plasmodium falciparum male gametocyte at stage V. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Male gametocyte

value: Male

tag: age


title: Female 1-rRNA

description: This sample is of Plasmodium falciparum female gametocyte at stage V. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Celsr3_1


title: D1 RNA-seq R2


title: Fzd3_3


title: Female 2-mRNA


title: Male 3-mRNA

description: This sample is of Plasmodium falciparum male gametocyte at stage V. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: hESC RNA-seq R1

source_name: H7 hESCs


title: Female 3-mRNA


title: Female 1-mRNA


title: Male 2-mRNA


title: Male 1-mRNA

description: This sample is of Plasmodium falciparum male gametocyte at stage V. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: hESC RNA-seq R2


title: Transcriptome sequencing analysis [PB-Lef1 P5]

status: Public on Jan 29 2016

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Illumina GA pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per kilobaseof exon per million fragments mapped (FPKM) were calculated using iIllumina  protocol from chinese BGI company.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: lef1-transfected 46C mouse ESCs

growth_protocol: 46C mouse ESCs were routinely cultured in serum/Lif condition  (typically 1× 105 cells into a T75 flask) on gelatin-coated tissue culture plate (BD Falcon,USA).

extract_protocol:
Standard illumina RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The empty vector-transfected ESCs were collected at passage 2 after empty vector was introduced into ESCs,  the lef1-transfected ESCs were collected at passage 2 and 5 respectively after lef1 was introduced into ESCs.

tag: cell type

value: embryonic stem cells (ESCs)

tag: transfected with

value: lef1 (PB-Lef1)

tag: passages


title: Ba/F3 + hCALR-del52 + IL-3, replicate 2

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

description: expression profile of Ba/F3 const. expressing hCALR-del52, replicate 2

data_processing:
Illumina Real Time Analysis (RTA) Software (1.17.21.3) was used for base-calling, BamIndexDecoder (1.12) for de-mutliplexing
Alignment to the reference genome and transcriptome (Ensgene annotation) was performed with the help of Bowtie2 (2.1.0) and Tophat2 (2.0.9), estimation of FPKM values and differential expression analysis with Cufflinks/Cuffdiff (2.1.1.).
Tophat was run with parameters --library-type fr-unstranded --no-coverage-search -g 100 --segment-length 25 --b2-L 15 --b2-n-ceil L,0,0.05 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2.
Cufflinks was run with parameters --GTF-guide and --frag-bias-correct; Cuffdiff with --library-norm-method geometric --dispersion-method pooled.
Further post-processing steps were performed as described in the processed data file.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with mean FPKM values per group and gene, and (FDR-corrected) p-values for differential expression (s.a. sheet 'Explanations' in hCALRwt+IL3_hCALRdel52+IL3_annotated_ess.xls)

source_name: Ba/F3 + hCALR-del52 + IL-3

growth_protocol: Ba/F3 cells were cultured in complete RPMI (10% FCS, Pen/Strep, L-glutamine) in the presence of 1 ng/ml of IL-3.

extract_protocol:
TRIzol (Life Technologies) from 10^7 cells per replicate
Illumina TruSeq RNA Sample Prep Kit v2 from 2µg RNA per library

value: pro-B cell line

tag: vector

value: pMSCV-IRES-GFP

tag: cytokine


title: Transcriptome sequencing analysis [PB]

source_name: empty vector-transfected 46C mouse ESCs

value: empty vector (PB)


title: Ba/F3 + hCALR-del52 + IL-3, replicate 3

description: expression profile of Ba/F3 const. expressing hCALR-del52, replicate 3


title: Ba/F3 + hCALR-del52 + IL-3, replicate 1

description: expression profile of Ba/F3 const. expressing hCALR-del52, replicate 1


title: Male 3-rRNA


title: Ba/F3 + hCALR + IL-3, replicate 3

description: expression profile of Ba/F3 const. expressing hCALR, replicate 3

source_name: Ba/F3 + hCALR + IL-3


title: Ba/F3 + hCALR + IL-3, replicate 1

description: expression profile of Ba/F3 const. expressing hCALR, replicate 1


title: Ba/F3 + hCALR + IL-3, replicate 2

description: expression profile of Ba/F3 const. expressing hCALR, replicate 2


title: Fzd3_2


title: Sample_N49

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

institute: Medical College of Wisconsin

description: exRNA seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to different RNA species using bowtie v1.1.1 with parameters -l 18, -v 1, -m 2, and --norc --best --strata
An iterative alignment strategy was ued: unmapped sequences from the previous alignment were used for the mapping of the next RNA reference species. The sequential alignment followed the order of mature miRNA, precursor miRNA, piwiRNA, siRNA, lncRNA, mRNA, pseudo genes, antisense RNA, rRNA, snRNA, snoRNA, misc-RNA, other transcribed RNA, FLJ human cDNA, and predicted RNA.
Reads per Megabase of library size (RPM) were calculated.
For detail, please see Yuan T et al. eRNA: A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. BMC Genomics, 2014, 15:176.  PMCID: PMC4029068
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: plasma microvesicles

extract_protocol:
microvesicles were isolated from 250 μL of plasma using the ExoQuick exosome precipitation solution (System Biosciences, Mountain View, CA, USA). Microvesicle RNA was prepared using a miRNeasy Micro Kit (QIAGEN, Valencia, CA, USA)
Libraries were prepared according to NEBNext multiplex small RNA library preparation kit (NEB, New England Biolab, Ipswich, MA, USA). For detail, see Huang X at al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics, 2013; 14:319. PMCID: PMC3653748

tag: Sex

tag: age (years)

tag: disease status

value: Normal

tag: disease type

value: Healthy Control


title: Sample_4S25

description: exRNA seq

value: Cancer

value: Colorectal Cancer


title: Sample_PC12

description: exRNA seq

value: Prostate Cancer


title: Sample_PC26

description: exRNA seq


title: Sample_4S19

description: exRNA seq

value: Female


title: Sample_4S22

description: exRNA seq


title: Sample_4S10

description: exRNA seq


title: Sample_Pan06

description: exRNA seq

value: Pancreatic Cancer


title: Sample_PC6

description: exRNA seq


title: Sample_4S13

description: exRNA seq


title: Sample_4S16

description: exRNA seq


title: Male 1-rRNA

value: Day 12

value: gametocyte at stage V


title: Sample_4S1

description: exRNA seq


title: Sample_1S23

description: exRNA seq


title: Sample_1S25

description: exRNA seq


title: Transcriptome sequencing analysis [PB-Lef1 P2]


title: Sample_Pan05

description: exRNA seq


title: Sample_1S20

description: exRNA seq


title: Sample_1S17

description: exRNA seq


title: Sample_1S14

description: exRNA seq


title: Sample_1S11

description: exRNA seq


title: Sample_1S2

description: exRNA seq


title: Sample_1S5

description: exRNA seq


title: 4x (double diploid) rep2

city: Wuhan

first: Fengquan

last: Tan

address: Hongshan

institute: HZAU

description: RNA-seq data of doubled diploid mature leaves

data_processing:
For mRNA RNA-Seq data, TopHat (v2.0.9) for mapping, HTSeq (v0.5.4p3) for estimating their abundances
tests for differential expression and regulation in RNA-Seq samples using  the DESeq R package (1.10.1)
Genome_build: Index of the reference genome was built using Bowtie (v2.0.6). Reference genome sequences and annotations were downloaded from the citrus sinensis  genome websit. (http://citrus.hzau.edu.cn/orange/download/data.php)
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

organism: Citrus junos

source_name: leaves

growth_protocol: mature leaves

extract_protocol:
Total RNA was extracted by Trizol method
20 mg total RNA was prepared to enrich mRNA by using the oligo (dT) magnetic beads. After adding fragmentation buffer, the mRNA was interrupted to short fragments (approximately 200 bp). The first strand cDNA was then synthesized with random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments.

treatment_protocol: No treatment

tag: development stage

value: 3-5 month old

tag: cultivar

value: Ziyang xiangcheng

value: fourth or fifth leaf from the plant top


title: Sample_1S8

description: exRNA seq


title: 4x (double diploid) rep1


title: 2x (diploid) rep2

description: RNA-seq data of diploid mature leaves


title: Sample_4S7

description: exRNA seq


title: Sample_4S4

description: exRNA seq


title: Sample_N50

description: exRNA seq

value: Male


title: Sample_3S24

description: exRNA seq


title: 2x (diploid) rep1

description: RNA-seq data of diploid mature leaves


title: Sample_PC17

description: exRNA seq


title: Sample_PC5

description: exRNA seq


title: MethylC-Seq_mm_E9_5

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (mm10) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0.
Supplementary_files_format_and_content: For "*.allC" processed data files (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.

source_name: embryo

extract_protocol: For DNA extraction, embryos were lysed in 20 mM Tris pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS, 0.5 mg/ml proteinase K, for 3h at 55ºC. This was followed by two Phenol/Chlorophorm/Isoamylalcohol (25:24:1, PCI) extractions and subsequent centrifugation (5 minutes at 13,000 rpm). The DNA was then precipitated by adding 1/5 volumes of 4 M NH4Ac and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 minutes. The DNA precipitate was centrifuged for 20 minutes at 4°C (13,000 rpm) and the pellet was washed with 500 μL of 70% ethanol and centrifuged for 5 minutes (13,000 rpm) at room temperature. The pellet was then resuspended in 200 μL of TE buffer and 1 μl of RNAse A (20 μg/μl) was added. The reaction was left to proceed for 30 minutes at room temperature after which it was precipitated with 0.1 volumes of 4 M NH4Ac and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 minutes at 4°C (13,000 rpm) and the pellet resuspended in TE buffer. MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

value: whole embryo

tag: genetic background

tag: transgenic embryos

value: NO


title: Sample_Pan04

description: exRNA seq


title: Sample_3S25

description: exRNA seq


title: Sample_3S18

description: exRNA seq


title: MethylC-seq_mm_E14_5

tag: tissue


title: Sample_3S21

description: exRNA seq


title: RNA-seq_mm_E9_5_rep1

data_processing:
RNA-seq reads were mapped using Kallisto (http://pachterlab.github.io/kallisto/) with default settings (kallisto quant -i index -o outputDIR --single -l 100 file.fastq). The reference transcriptome was generated using canonical transcript isoforms as identified by ENSEMBL.
Supplementary_files_format_and_content: The column headers are as follows: column 1 – target ID. column 2 – length. column 3 – effective length. column 4 – estimated counts. column 5 – TPM (transcripts per million).

molecule: polyA RNA

extract_protocol: Total RNA was purified from tissue using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). Strand-specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al., High-Throughput Illumina Strand-Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011, 940-949 (2011)].

tag: developmental stage


title: RNA-seq_mm_E14_5_rep1


title: Sample_PC11

description: exRNA seq


title: Sample_PC35

description: exRNA seq


title: Sample_3S15

description: exRNA seq


title: RNA-seq_mm_E14_5_rep2


title: KJ201_dmt2 (mycelia)

city: Gangneung

first: Jaeyoung

last: Choi

address: 679 Saimdang-ro

country: South Korea

institute: Korea Institute of Science and Technology

data_processing:
Adaptor sequences, contamination and low-quality reads were filtered from the raw reads.
The filtered reads were mapped to the reference genome by SOAP aligner. (Observed cytosines on the forward read of each pair were replaced by thymines and observed guanines on the reverse read of each pair were replaced by adenines.)
Methylation sites were determined by detect the number of reads covering each methyl-C.
Magnaporthe oryzae 70-15 downloaded from Broad Institute (http://www.broadinstitute.org/)
Genome_build: GCF_000002495.2
Supplementary_files_format_and_content: Information for methyl-C sites were listed in each tab of Excel spreadsheet file.

organism: Pyricularia oryzae KJ201

growth_protocol: For mycelia, fungus was culture for 3 days in liquid complete media (0.6% yeast extract, 0.6% casamino acid, 1% glucose) with 150rpm shaking; For conidia, fungal cultures were suspended using distilled water and filtered with miracloth to exclude mycelia; For appressoria, conidia (~106 spores/ml) suspension were dropped on hydrophobic green mirror and incubated overnight for appressorium induction. Appressoria were collected by scraping the surface thoroughly.

extract_protocol:
Genomic DNAs were extracted from lyophilized samples according to manufacturer's instructions using DNeasy Plant Mini Kit (Qiagen)
Libraries were constructed from DNA using the ZYMO EZ DNA Methylation-Gold kit (Cat#D5005) following manufacturer's protocols.

treatment_protocol: All extracted genomic DNAs were treated with bisulphite for conversion of unmethylated cytosines into thymidines according to manufacturer's instruction using EZ DNA methylation kit (Zymo Research)

value: mycelia

tag: genotype


title: KJ201_appressorium

value: appressorium

value: wildtype


title: KJ201_dmt1 (mycelia)


title: Sample_3S9

description: exRNA seq


title: KJ201_conidia

value: conidia


title: KJ201_mycelia


title: RNA-seq_mm_E9_5_rep2

data_processing:
All data were mapped to the following reference genomes: Danio rerio (zv9), Xenopus tropicalis (JGI 7.1), Mus musculus (mm10). MethylC-Seq and TAB-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013). RNA-seq data was mapped using Kallisto (http://arxiv.org/abs/1505.02710). Processed RNA-seq data tables contain both read counts and expression values represented as transcripts per million (TPMs). ATAC-seq libraries were sequenced on the Illumina Hi-Seq 2000 sequencing platform. Reads were aligned using zebrafish Danio rerio (zv9) as the reference genome. Duplicated pairs or those ones separated by more than 2Kb were removed. The processed data files (BED) contain positions of the enzyme cleavage site that was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Supplementary_files_format_and_content: For "*.allC" processed data files (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.


title: Sample_3S6

description: exRNA seq

value: Cancer


title: Sample_3S3

description: exRNA seq

value: Colorectal Cancer


title: KJ201_dmt2_mRNA

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality sequence and removed short read (N<20bp)
Mapped to MG8 whole genome using Tophat version 2.0.5 with parameters -p 8 -r --mate-std-dev --read-realign-edit-dist 0 --min-intron-length --max-intron-length.
Transcripts were assembled and quantitated using Cufflinks version 2.0.2.
Magnaporthe oryzae 70-15 downloaded from Broad Institute (http://www.broadinstitute.org/)
Genome_build: GCF_000002495.2
Supplementary_files_format_and_content: abundance measurements

growth_protocol: 3 day culture in complete media (0.6% yeast extract, 0.6% casamino acid, 1% glucose)  with 150rpm shaking

extract_protocol:
According to manufacturer's instructions using Easy-spin™ total RNA extraction kit (iNtRON Biotechnology, Seoul, Korea)
Libraries were constructed from mRNA using the Illumina TruSeq RNA sample preparation kit (Cat#FC-122-1001) following  manufacturer's protocols.


title: Sample_PC25

description: exRNA seq

value: Prostate Cancer


title: TAB-seq_mm_E9_5

description: TAB-seq

data_processing:
Single-read TAB-seq libraries were sequenced on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (mm10) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 1.
Supplementary_files_format_and_content: For "*.allC" processed data files (for TAB-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - hmc: number of reads supporting a hydroxymethylated cytosine.column 6 - h: total number of reads at that position.

extract_protocol: For DNA extraction, embryos were lysed in 20 mM Tris pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS, 0.5 mg/ml proteinase K, for 3h at 55ºC. This was followed by two Phenol/Chlorophorm/Isoamylalcohol (25:24:1, PCI) extractions and subsequent centrifugation (5 minutes at 13,000 rpm). The DNA was then precipitated by adding 1/5 volumes of 4 M NH4Ac and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 minutes. The DNA precipitate was centrifuged for 20 minutes at 4°C (13,000 rpm) and the pellet was washed with 500 μL of 70% ethanol and centrifuged for 5 minutes (13,000 rpm) at room temperature. The pellet was then resuspended in 200 μL of TE buffer and 1 μl of RNAse A (20 μg/μl) was added. The reaction was left to proceed for 30 minutes at room temperature after which it was precipitated with 0.1 volumes of 4 M NH4Ac and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 minutes at 4°C (13,000 rpm) and the pellet resuspended in TE buffer. TAB-seq library generation was performed with the 5hmC TAB-seq Kit (WiseGene, USA - Cat# K001) as per manufacturer’s instructions, with minor modifications related to the amount of starting material (100 ng).


title: KJ201_dmt1_mRNA


title: Sample_1S19

description: exRNA seq

value: Female


title: Sample_1S16

description: exRNA seq


title: Sample_3S12

description: exRNA seq


title: Sample_1S10

description: exRNA seq


title: KJ201_mycelia_mRNA

value: wild type


title: Sample_1S4

description: exRNA seq


title: Sample_1S7

description: exRNA seq


title: Sample_1S13

description: exRNA seq


title: Sample_1S1

description: exRNA seq


title: Sample_PC24

description: exRNA seq


title: Sample_PC34

description: exRNA seq


title: Sample_PC4

description: exRNA seq


title: Sample_Pan03

description: exRNA seq

value: Pancreatic Cancer


title: Sample_N42

description: exRNA seq

value: Normal

value: Healthy Control


title: Sample_N48

description: exRNA seq


title: Sample_PC30

description: exRNA seq


title: Sample_N24

description: exRNA seq


title: Sample_N36

description: exRNA seq


title: Sample_PC10

description: exRNA seq


title: Sample_N30

description: exRNA seq


title: Sample_3S20

description: exRNA seq


title: Sample_N12

description: exRNA seq


title: Sample_3S17

description: exRNA seq


title: Sample_3S14

description: exRNA seq


title: Sample_N18

description: exRNA seq


title: Sample_N6

description: exRNA seq


title: Sample_3S23

description: exRNA seq


title: Sample_1S22

description: exRNA seq


title: Sample_PC16

description: exRNA seq


title: Sample_3S11

description: exRNA seq


title: Sample_3S8

description: exRNA seq


title: Sample_PC29

description: exRNA seq


title: Sample_PC20

description: exRNA seq


title: Sample_PC23

description: exRNA seq


title: Sample_PC33

description: exRNA seq


title: Sample_3S5

description: exRNA seq


title: Sample_3S2

description: exRNA seq


title: Sample_PC9

description: exRNA seq


title: Sample_2S25

description: exRNA seq


title: Sample_PC3

description: exRNA seq


title: Sample_N29

description: exRNA seq


title: Sample_PC15

description: exRNA seq


title: Sample_N41

description: exRNA seq


title: Sample_Pan02

description: exRNA seq


title: Sample_N23

description: exRNA seq


title: Sample_N35

description: exRNA seq


title: Sample_N17

description: exRNA seq


title: Sample_N11

description: exRNA seq


title: Sample_N47

description: exRNA seq


title: Sample_3S16

description: exRNA seq


title: Sample_3S10

description: exRNA seq


title: Sample_3S19

description: exRNA seq


title: Sample_3S7

description: exRNA seq


title: Sample_3S4

description: exRNA seq


title: Sample_3S13

description: exRNA seq


title: Sample_3S22

description: exRNA seq


title: Sample_N5

description: exRNA seq


title: Sample_3S1

description: exRNA seq


title: Sample_PC22

description: exRNA seq


title: Sample_PC28

description: exRNA seq


title: Sample_PC32

description: exRNA seq


title: Sample_PC14

description: exRNA seq


title: Sample_PC19

description: exRNA seq


title: Sample_Pan01

description: exRNA seq


title: Sample_N46

description: exRNA seq


title: Sample_PC8

description: exRNA seq


title: Sample_N28

description: exRNA seq


title: Sample_N10

description: exRNA seq


title: Sample_N16

description: exRNA seq


title: Sample_N40

description: exRNA seq


title: Sample_N22

description: exRNA seq


title: Sample_N34

description: exRNA seq


title: Sample_2S21

description: exRNA seq


title: Sample_2S18

description: exRNA seq


title: Sample_N4

description: exRNA seq


title: Sample_2S24

description: exRNA seq


title: Sample_2S15

description: exRNA seq


title: Sample_2S12

description: exRNA seq


title: Sample_2S6

description: exRNA seq


title: Sample_PC36

description: exRNA seq


title: Sample_PC27

description: exRNA seq


title: Sample_PC13

description: exRNA seq


title: Sample_2S3

description: exRNA seq


title: Sample_2S9

description: exRNA seq


title: Sample_PC31

description: exRNA seq


title: Sample_PC21

description: exRNA seq


title: Sample_PC2

description: exRNA seq


title: Sample_N45

description: exRNA seq


title: Sample_PC7

description: exRNA seq


title: Sample_PC18

description: exRNA seq


title: Sample_PC1

description: exRNA seq


title: Sample_N21

description: exRNA seq


title: Sample_N33

description: exRNA seq


title: Sample_N15

description: exRNA seq


title: Sample_N39

description: exRNA seq


title: Sample_2S20

description: exRNA seq


title: Sample_N3

description: exRNA seq


title: Sample_2S14

description: exRNA seq


title: Sample_2S11

description: exRNA seq


title: Sample_2S17

description: exRNA seq


title: Sample_2S23

description: exRNA seq


title: Sample_N44

description: exRNA seq


title: Sample_2S2

description: exRNA seq


title: Sample_2S8

description: exRNA seq


title: Sample_N14

description: exRNA seq


title: Sample_N2

description: exRNA seq


title: Sample_N8

description: exRNA seq


title: Sample_N26

description: exRNA seq


title: Sample_N20

description: exRNA seq


title: Sample_4S24

description: exRNA seq


title: Sample_N27

description: exRNA seq


title: Sample_4S21

description: exRNA seq


title: Sample_4S15

description: exRNA seq


title: Sample_4S18

description: exRNA seq


title: Sample_4S12

description: exRNA seq


title: Sample_N9

description: exRNA seq


title: Sample_4S9

description: exRNA seq


title: Sample_4S6

description: exRNA seq


title: Sample_4S3

description: exRNA seq


title: RNA-seq_dr_24hpf_tet123_wt_rep1

organism: Danio rerio

value: mixed AB and Tübingen


title: Sample_2S5

description: exRNA seq


title: RNA-seq_dr_24hpf_tet123_wt_rep2


title: Sample_2S19

description: exRNA seq


title: RNA-seq_dr_24hpf_tet123_MO_rep2

value: Morpholino against Tet1/Tet2/Tet3


title: RNA-seq_dr_24hpf_tet123_MO_rep1


title: Sample_2S22

description: exRNA seq


title: Sample_N38

description: exRNA seq


title: Sample_N32

description: exRNA seq


title: Sample_2S13

description: exRNA seq


title: Sample_2S10

description: exRNA seq


title: MethylC-seq_dr_24hpf_tet3

data_processing:
MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (danRer7) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0.
Supplementary_files_format_and_content: For "*.allC" processed data files (for MethylC-Seq) the column headers are as follows: column 1 - assembly (chromosome).column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0).column 3 - strand: + or - strand.column 4 - class: context of the cytosine and the two following bases from the same strand.column 5 - mc: number of reads supporting a methylated cytosine.column 6 - h: total number of reads at that position.

growth_protocol: Danio rerio embryos used for MethylC-Seq were obtained from a natural mating procedure and dechorionated by pronase treatment prior to gDNA isolation.

value: 24 hpf (pharyngula)

value: Morpholino against Tet3


title: MethylC-seq_dr_24hpf_wt

value: whole embryo

value: NO