title: Type II neuroblast replicate 3

status: Public on Dec 29 2015

city: Ashburn

first: Ken

last: Sugino

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters  --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were assigned to genes using HTSeq v0.6.1p1 with parameter -s no -m intersection-nonempty and using iIllumina UCSC/dm3 annotation. FPKM for a gene was calculated by dividing assigned count by the sum of lengths of all exons belonging to the gene and then by total number of reads in million.
Genome_build: dm3
Supplementary_files_format_and_content: tab deliminated files include TPM values, raw count values

source_name: Brain

growth_protocol: Newly hatched Fly larvae were first synchronized with maxiumum 2 hour age difference and then grew at 25C until dissection

extract_protocol:
30 fly larvae brain tissues were dissected at defined ages, digested with a mixture of pronase(1mg/ml) and dispase (1mg/ml) for 30 min at 25C, washed, triturated and 10 GFP labeled cells were sorted with a robotic sorter and stored at -80C in XB buffer from PicoPure kit (life technologies, KIT0204). Total RNA from around 100 pooled cells was extracted using PicoPure kit.
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).

tag: cell type

value: neuroblast

tag: age

value: 50hr after larva hatch

tag: num_cells (number of cells in the sample)

tag: ercc_mix (1 or 2)

tag: ercc_5 (10^-5 dilution of ercc in ul)


title: Type II neuroblast replicate 2

type: SRA

state: VA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Drosophila melanogaster


title: Neuron replicate 2

value: neuron

value: wandering larva


title: pH 6.8

status: Public on Dec 30 2015

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: RPKM=10^6C/(NL/10^3). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: text files containing RPKM values for each Sample

organism: Candida albicans

source_name: candida albicans_ph6.8

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: WT


title: Mushroom body neuroblast replicate 1

source_name: Mushroom body


title: Mushroom body neuroblast replicate 2


title: H471-ck-1

first: Fan

last: Zhang

state: Beijing

address: 12 South Zhong-Guan-Cun St.

institute: CAAS

description:
replicate 1
CP16

data_processing:
Primary data analysis and base calling was performed by the Illumina instrument software.
The raw reads were first filtered by removing adaptor sequences and low-quality sequences by using in-house perl script. Low quality nucleotides (< Q20) were trimmed from raw sequences for each sample, and then pair-end reads with either of both with length less than 30 bp were removed, and the retained high quality pair-end reads of rice for each sample were mapped to the rice genome of RGAP at MSU (Kawahara et al., 2013) by tophat (Trapnell et al., 2009) and then assembled with Cufflinks (Trapnellet al., 2010) to construct unique transcipts sequences, using the parameter:-g -b -u -o.
The retained high quality pair-end reads of each sample were mapped to the rice genome using Tophat2(v2.0.11) with default parameters. Then gene expression abundance was quantified by FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks(v2.1.1), and differentially-expressed genes (DEGs) between samples were identified by Cuffdiff, a component of the Cufflinks package.
Genome_build: MSU Release 7.0 (Os-Nipponbare-Reference-IRGSP-1.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: leaves

growth_protocol: Seeds of H471, HHZ, and P28 were sown in a seedling nursery and 30-day-old seedlings were transplanted into a screenhouse of the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China. There were nine plants in each row, with a spacing of 20 × 17 cm.

extract_protocol:
For all RNA-seq samples, total RNA was extracted with TRIzol Reagent (Invitrogen, Carlsbad, California, USA), and quantified using a Qubit RNA assay kit (Applied Biosystems, Foster City, California, USA). RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA samples from three independent replicates for each treatment were pooled.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Philippine’s representative strain of Xoo, PXO349, was used to artificially inoculate H471 and its parents. The strain was incubated on peptone sucrose agar at 30°C for 2 days, and the inoculum was prepared by suspending the bacterial mass in sterile water at a concentration of 108 cells mL-1. Five plants of each line were inoculated with PXO349 in the four to five uppermost leaves of each plant using the leaf-clipping method in three replications at the tillering stage (plant age of 65 days). LLs were measured on all inoculated leaves at 14 dpi when the lesions were stable.

value: introgression line

tag: developmental stage

value: tillering phase

tag: treatment

value: normal condition


title: Mushroom body neuroblast 3 wash replicate 2


title: H471-ck-2

description:
replicate 2
CP16


title: P28-ck-2

description:
replicate 2
CP3

value: donor parent


title: P-LM

city: Ya’an

first: Rongping

state: Sichuan

address: NO.46 xinkang road

institute: Sichuan Agricultural University

data_processing:
The library preparations were sequenced on an Illumina Hiseq 2000/2500 platform and 100 bp/50bp single-end reads were generated.
Index of the reference genome was built   using Bowtie v2.0.6 and  single-end clean reads were aligned to the reference   genome using TopHat v2.0.9.
HTSeq v0.5.4p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two groups  was performed using the DESeq R package (1.10.1).
Genome_build: RefSeq assembly accession: GCF_000355885.1
Supplementary_files_format_and_content: text files include RPKM values for each Sample

organism: Anas platyrhynchos

source_name: Peking_skeletal muscle_leg

growth_protocol: All duck eggs were incubated at the same condition, 37±0.5℃ and 86-87% humidity.

extract_protocol:
Total RNA for four group muscles was extracted using Trizol reagent (Takara, china) according to manufacturer’s instructions. Five RNA samples per group were equally mixed to get a RNA pool.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent captions under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: breed

value: Peking

tag: tissue

value: skeletal muscle

tag: embryonic stage

value: E15, embryonic 15 days


title: P-PM

source_name: Peking_skeletal muscle_pectoral


title: Mushroom body neuroblast 2hr wait replicate 2


title: H-PM

source_name: Heiwu_skeletal muscle_pectoral

value: Heiwu


title: Mushroom body neuroblast 2hr wait replicate 3


title: HHZ-ck-2

description:
replicate 2
CP1

value: recurrent parent


title: Glia replicate 2

value: glia


title: H-LM

source_name: Heiwu_skeletal muscle_leg


title: P28_3d

data_processing:
Primary data analysis and base calling was performed by the Illumina instrument software.
Low quality nucleotides (< Q20) were trimmed from raw sequences for each sample, and then pair-end reads with either of both with length less than 30 bp were removed using an in-house Perl script.
High quality reads were mapped to the MSU Rice Genome Annotation Project (MSU RGAP; ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0), and to Xoo strain PXO99A genome reference information downloaded from the NCBI (http://www.ncbi.nlm.nih.gov/nuccore/NC_010717.1) using Bowtie. To avoid contamination of reads from interaction partners, reads were also mapped against the reference genome of the interaction partner.
Retained high quality pair-end reads of rice for each sample were mapped to the rice genome of MSU RGAP using TopHat, and assembled with Cufflinks to construct unique transcripts sequences using the parameter –g –b –u –o. Cuffcompare was used to compare the assembled transfrags of each sample to the reference annotation, and to build up a non-redundant transcript dataset among the samples. Next, Cuffdiff was used to identify DEGs, and genes with a P value ≤ 0.05 marked as significantly different between the two samples.
Similar to credibility interval approaches reported for the analysis of SAGE data, we employed IDEG6  to identify genes showing statistically significant difference in relative abundance (as reflected by total count of individual sequence reads) between the two samples.A general Chi2 test was employed, as this has proved to be an efficient test. Finally, genes with P value ≤ 0.05 were determined to be significantly different between the two samples.
Genome_build: Nipponbare and PXO99A
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism:
Oryza sativa
Xanthomonas oryzae pv. oryzae

source_name: inoculated leaves

extract_protocol:
For all RNA-seq samples, total RNA was extracted with TRIzol Reagent (Invitrogen, Carlsbad, California, USA), and quantified using a Qubit RNA assay kit (Applied Biosystems, Foster City, California, USA). RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA samples from three independent replicates for each treatment were pooled. Ribosomal RNA (rRNA) was removed from 8 μg of total RNA using a RiboMinus™ Plant Kit (Invitrogen) followed by a Ribo-Zero Gram-Negative Bacteria kit (Epicentre, Madison, Wisconsin, USA) in accordance with manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rice genotype

tag: xanthomonas oryzae race

tag: host-pathogen compatibility status

value: compatible

tag: Stage

value: inoculated by Xoo for 3 days

tag: rice strain number


title: HHZ-ck-1

description:
replicate 1
CP1


title: Antennal lobe neuroblast replicate 1

source_name: Antennal lobe

value: neuroblast


title: All neuroblast replicate 3

value: 50hr after larva hatch


title: Type II neuroblast replicate 1


title: Neuron replicate 1

value: neuron


title: mcidas_TCC_9h

city: La Jolla

first: Ian

middle: K

last: Quigley

state: CA

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

description: Proximity-ligated genomic DNA

library_source: genomic

data_processing:
Library strategy: Proximity ligation (TCC/HiC)
TCC reads were aligned to X. laevis genome build v9.1 or v7.1 with bwa mem (PMID: 19451168)
Reads trimmed to nearest mboI site (homerTools, PMID: 20513432)
Reads were combined into tag directories and TADs called with HOMER (PMID: 20513432, 23064439)
Proximity ligation data were used to assemble chromosomes from scaffolds in genome build v7.1 with either Lachesis (PMID: 24185095) or HighRise (arXiv:1502.05331)
Genome_build: X. laevis build v9.1 or v7.1 (http://www.xenbase.org/)
Supplementary_files_format_and_content: Bed file of TADs from all 9h timepoints (stage 18 ectoderm)

molecule: genomic DNA

organism: Xenopus laevis

source_name: animal cap (dissected ectoderm)

growth_protocol: Whole embryos or animal caps (ectoderm) dissected from embryos at stage 10 were cultured in 0.5x MMR.

extract_protocol:
Embryos were fixed in 1% paraformaldehyde in PBS for 30 minutes at 22 degrees and fix was quenched with 0.125M glycine. TCC was performed as described (PMID: 22198700) with the following modifications: Tissue was thawed, rinsed in PBS, and lysed directly in 250 ul ice-cold wash buffer with SDS added (50 mM Tris.HCl pH=8.0, 50 mM NaCl, 1 mM EDTA, 0.56% SDS) rather than using lysis buffer.
Following sonication of ligated fragments, we polished and adenylated ends (NEB End-It and A-tailing modules) and ligated Truseq v2 adapters (Illumina).

treatment_protocol: Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.

value: animal cap (dissected ectoderm)

tag: harvest time/stage

value: 9h @ 22 deg after mid-11 (stage 18)

tag: injected mrna

value: Mcidas-HGR


title: wt_TCC_9h

description: Proximity-ligated genomic DNA


title: Mushroom body neuroblast replicate 3

tag: cell type

tag: age


title: Mushroom body neuroblast 3 wash replicate 3

tag: num_cells (number of cells in the sample)

tag: ercc_mix (1 or 2)


title: Glia replicate 1

value: wandering larva

tag: ercc_5 (10^-5 dilution of ercc in ul)


title: sRNAs from siCtl transfected and SINV-infected HEK293 cells expressing Dicer-2, 6 hpi

status: Public on Dec 28 2015

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description:
Small RNA
siCtl transfection was performed 2 days before SINV infection

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2.
Sequencing reads were preprocessed using the Dustmasker program and FASTX-Toolkit to filter out low complexity reads and remove instances of the 3' adapter. Degenerate bases incorporated during the library preparation protocol were then trimmed and remaining reads were further size-selected by keeping only the 18- to 32-nt long ones. In the case of human libraries, exogenous siRNA sequences were also excluded before further analysis.
Preprocessed reads were then mapped simultaneously to the host (D. melanogaster or H. sapiens) and the pathogen (SINV) genomes using Bowtie 1.0.0. In the case of fly libraries, small RNA reads were also mapped to the white-inverted repeats, wIR, transgene, as previously shown (Marques et al., 2010). Initially, only alignments of reads with 0 mismatch were recorded and reads that could map to more than 50 loci were discarded.
For each library, small RNAs deriving solely from SINV, in either sense or antisense orientation, were computationally extracted and profiled based on their length distribution and their coverage along the viral genome. The same approach was used to deal with reads deriving from the wIR transgene in fly libraries.
In order to establish the host miRNA expression profiling, host-specific reads presenting with up to 2 mismatches in total with no more than 1 mismatch in their first 15 nucleotides were taken into account.
Fly or human miRNAs (miRBase 20) were annotated in each library using BEDTools 2.16.2. During the quantification process, multiple mapped reads were weighted by the number of mapping sites in miRNAs.
To visually explore miRNA expression profiles in each library set, we produced heatmaps showing the expression data of the 100 most highly expressed miRs, after regularized log transformation (rlog2), as recommended in the DESeq2 package.
Genome_build: Dmel r5.54 + NC_001547.1 (samples 1 to 3) and GRCh37/hg19 + NC_001547.1 (samples 4 to 11).
Supplementary_files_format_and_content: Alignment files of the only viral reads are provided in BED format (*-onlyviral-alignments.bed) as well as the annotation files of the 100 most abundant miRNAs in tab-delimited format (*-top100-cellular-miRs-annot.txt: Column 1: miR, Column 2: rlog2).

organism:
Homo sapiens
Sindbis virus

source_name: HEK293 cell line

extract_protocol:
(Included as an additional column of the SAMPLES, see section above)
Small RNA libraries were prepared from 10 μg of total RNA as previously described (Contrant et al. Importance of the RNA secondary structure for the relative accumulation of clustered viral miRNAs. Nucleic Acids Res. 2014;42(12):7981-96)

tag: cell line

tag: construct

tag: growth protocol

value: HEK293 cells were maintained in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere of 5% CO2 at 37°C.

tag: viral infection condition

value: 6 hours post-infection, SINV MOI 0.01

tag: extract protocol

value: Total RNA was extracted from infected cells using TRI-Reagent (Ambion, AM9738)


title: Mushroom body neuroblast 3 wash replicate 1


title: Antennal lobe neuroblast replicate 3


title: Mushroom body neuroblast 2hr wait replicate 1


title: All neuroblast replicate 2


title: All neuroblast replicate 1


title: wt_TCC_st10.5_rep2

description: Proximity-ligated genomic DNA

source_name: whole embryo

tag: tissue

value: whole embryo

value: Stage 10.5


title: wt_TCC_st10.5_rep1

description: Proximity-ligated genomic DNA


title: sRNAs from SINV-infected HEK293 cells expressing DAR (=Dicer-2 and R2D2), 16 hpi

description:
Small RNA
None

growth_protocol: (Included as an additional column of the SAMPLES, see section above)

value: 16 hours post-infection, SINV MOI 0.01


title: sRNAs from sihDicer transfected and SINV-infected HEK293 cells expressing DAR (=Dicer-2 and R2D2), 6 hpi

description:
Small RNA
sihDicer transfection was performed 2 days before SINV infection


title: Foxf2+/-Osr2RFP/+

city: Cincinnati

first: Jingyue

last: Xu

state: Ohio

address: 3333 burnet avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7
Cufflink files include FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each sample were generated by DNA Sequencing and Genotyping Core, Cincinnati Children's Hospital, Medical center
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: embryonic palatal mesenchymal cells

extract_protocol:
Palatal shelves were microdissected,digested with trypsin-EDTA solution at 37°C for 4 minutes. After inactivation of trypsin with DMEM containing 10% FBS, cells were dissociated by pipetting. The dissociated palatal cells were resuspended in PBS with 2% FBS and 10 mM EDTA, and filtered through a 40 μm nylon cell strainer, RFP+ cells were isolated using BD FACSAria II. RNA was extracted by Qiagen RNase Micro kit. Sequencing libraries were generated by using Illumina Nextera DNA Sample Prep kit.
Sequencing libraries were generated by using Illumina Nextera DNA Sample Prep kit.

tag: strain

value: mixed background

value: embryonic palate

value: embryonic day 13.5

tag: genotype


title: Foxf2-/-Osr2RFP/+ rep2


title: Foxf2-/-Osr2RFP/+ rep1


title: sRNAs from SINV-infected HEK293 cells expressing Dicer-2, 16 hpi

description:
Small RNA
None


title: sRNAs from siCtl transfected and SINV-infected HEK293 cells expressing DAR (=Dicer-2 and R2D2), 6 hpi


title: 110040 GICs 1% O2 6h rep2

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

description:
small RNA
microRNA expression after GICs cultured in 1% O2 for 6hrs

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
From sequenced reads, the adaptor sequences were first trimmed off and then the remaining sequences were mapped to Homo Sapiens mature microRNAs from microRNA database (miRBase, www.mirbase.org) using bowtie v0.12.7
The mapped reads were counted for each miRNAs for each samples.
Genome_build: Homo Sapiens mature microRNAs from microRNA database (miRBase, www.mirbase.org)
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each miRNAs for each samples

organism: Homo sapiens

growth_protocol: CD133+ 110040 GICs were cultured in Neurobasal media (Invitrogen) supplemented with B27 (without vitamin A from Invitrogen), L-glutamine (Invitrogen), sodium pyruvate (Invitrogen), 10 ng/ml bFGF, and 10 ng/ml EGF (Millipore).

extract_protocol:
Total RNA was prepared using Trizol (Invitrogen).
Ten μg of total RNA was used for library construction using the small RNA library preparation kit (Illumina) with the alternative v1.5 protocol. After ligated with 3’ and 5’ RNA adapters, RNA samples were reverse transcribed using diluted SRA RT primer and then PCR amplified with 10 cycles using multiplex primers. The PCR products were then separated on 15% Novex TBE gel (Life Technology) and size selected between 90-100 bp and then quantified using Qubit fluorometer (Life Technology). Finally, 2 ng of each sample was pooled together for sequencing.

treatment_protocol: CD133+ 110040 GICs were cultured in 1% O2 for 0h, 6h, 12h, 24h and then harvested.

tag: tumor stage

value: Glioblastoma Grade IV


title: 110040 GICs 1% O2 12h rep1

description:
small RNA
microRNA expression after GICs cultured in 1% O2 for 12hrs


title: sRNAs from SINV-infected HEK293 cells, 16 hpi

description:
Small RNA
None

value: empty pDEST Flag-HA vector


title: sRNAs from siCtl transfected and SINV-infected HEK293 cells, 6 hpi


title: Antennal lobe neuroblast replicate 2

value: neuroblast

value: 50hr after larva hatch


title: LM11.5 Dis-RING1B

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: Distal forelimb bud from mouse E11.5, antibody: RING1B

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq reads were aligned to mm9 genome using bowtie2 (version 2.1.0) with default parameters.
Mapped reads were normalized with total mapped reads and bin size (100bp) with cutoff threshold 4 reads / bin.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files having normalized read counts.

source_name: forelimb buds

extract_protocol:
Antibodies against RING1B (Active Motif 39664, Lot. 23012002) was used for immunoprecipitation. Purified immunoprecipitated DNA prepared using the TruSeq ChIP Sample Preparation Kit. Samples were sequenced on the Illumina HiSeq system using 100 bp single-end reads according to the manufacturer’s specifications.
Illumina TruSeq protocol

treatment_protocol: Proximal or distal forelimb buds at E11.5 from wild type embryos were fixed in 1% formaldehyde/PBS for 20 min at room temperature, washed three times with cold PBS containing protease inhibitors and stored at -80°C. Pools of forelimb buds were used for ChIP and it was performed as described previously (Endoh et al., 2012).

tag: antibody

value: RING1B (Activ Motif 39664, Lot. 23012002)


title: LM11.5 Prox-RING1B

description: Proximal forelimb bud from mouse E11.5, antibody: RING1B


title: 110040 GICs 1% O2 24h rep2

description:
small RNA
microRNA expression after GICs cultured in 1% O2 for 24hrs


title: 110040 GICs 20% O2 rep1

description:
small RNA
microRNA expression after GICs cultured in 20% O2


title: D456MG GICs shKDM1B rep1

description: gene expression after GICs infected with shKDM1B

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to hg19 human whole genome using bowtie v0.12.7
Counted the mapped reads for each genes for each samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each genes for each samples

source_name: D456MG GICs expressing shKDM1B rep1

growth_protocol: CD133+ D456MG GICs were cultured in Neurobasal media (Invitrogen) supplemented with B27 (without vitamin A from Invitrogen), L-glutamine (Invitrogen), sodium pyruvate (Invitrogen), 10 ng/ml bFGF, and 10 ng/ml EGF (Millipore).

extract_protocol:
Total RNA was prepared using the mirVanaTM miRNA Isolation Kit (Ambion)
Briefly, 1 ug of total RNA was converted to cDNA by superscript III first strand synthesis kit with primer Biotin-P7-dT(20)VN. The cDNA was purified with NucleoSpin Gel and PCR Clean-Up Kit (Clontech) to remove free primers and enzyme. Then terminal transferase (NEB) was applied to block the terminal of cDNA 3’ends.  Streptavidin-coated magnetic beads (Life Technology) were further applied to isolate the cDNAs.  After RNA degradation by sodium hydroxide, the second strand cDNA was synthesized by random priming with primer Adaptor-N6. The second strand cDNA was eluted from beads by heat denaturing.  The cDNA was then used as template to construct libraries by PCR amplification with index primers (P5-index-adaptor) and primer P7. The constructed libraries were sequenced on Hiseq 2000 system (Methods Mol Biol. 2014;1125:169-78).

treatment_protocol: CD133+ D456MG GICs were infected with lenti-virus expressing a non-targeting control (PLK0.1 NT) and shRNA targeting KDM1B. Cells were selected by putomycin 48hrs after infection and then harvested 7 days after selection.


title: D456MG GICs NT rep3

description: gene expression after GICs infected with shNT

source_name: D456MG GICs expressing non-targeting control rep3


title: 110040 GICs 1% O2 24h rep1


title: sRNAs from sihDicer transfected and SINV-infected HEK293 cells, 6 hpi


title: 110040 GICs 1% O2 6h rep1


title: Osr2RFP/+


title: 110040 GICs 20% O2 rep2


title: D456MG GICs NT rep2

source_name: D456MG GICs expressing non-targeting control rep2


title: 110040 GICs 1% O2 12h rep2


title: sRNAs from SINV-infected transgenic flies expressing RFP tagged hDicer in a Dicer-2 null background, 5 dpi

description:
Small RNA
None

organism:
Drosophila melanogaster
Sindbis virus

source_name: Transgenic flies with a Dicer-2 null background

value: Flies were fed on standard cornmeal-agar medium at 25°C, tested for Wolbachia infection and cured whenever necessary.

value: 5 days post-infection by intrathoracic injection with viral particles prepared in 10 mM Tris-HCL, pH 7.5 (SINV 5x10^8 PFU/ml)

value: Total RNA was extracted from infected flies using TRI Reagent RT bromoanisole solution (MRC)


title: D456MG GICs shKDM1B rep3

source_name: D456MG GICs expressing shKDM1B rep3


title: D456MG GICs shKDM1B rep2

source_name: D456MG GICs expressing shKDM1B rep2


title: met18-2_MethylC-Seq_rep2

status: Public on Dec 27 2015

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

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

organism: Arabidopsis thaliana

source_name: Seedlings

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

value: seedling


title: met18-1_MethylC-Seq_rep1

description: treated with bisulfite


title: met18-2_MethylC-Seq_rep1

description: treated with bisulfite


title: Barrett’s Esophagus 2

status: Public on Dec 26 2015

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: HpaII test for HELP

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions 1.3-1.4).  Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg18 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation scores for each Sample

source_name: Barrett’s esophageal tissue from patient 2

extract_protocol:
Genomic DNA from cell lines were isolated by Puregene Core Kit A (Qiagen)
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

value: Barrett’s esophageal tissue

tag: disease state

value: Barrett’s esophagus

tag: subject

value: patient 2


title: Barrett’s Esophagus 3

description: HpaII test for HELP

source_name: Barrett’s esophageal tissue from patient 3

value: patient 3


title: met18-1_MethylC-Seq_rep2

description: treated with bisulfite


title: Barrett’s Esophagus 1

description: HpaII test for HELP

source_name: Barrett’s esophageal tissue from patient 1

value: patient 1


title: Healthy Esophagus 3

description: HpaII test for HELP

source_name: healthy esophageal tissue from patient 3

value: healthy esophageal tissue


title: Healthy Esophagus 2

description: HpaII test for HELP

source_name: healthy esophageal tissue from patient 2


title: Healthy Esophagus 1

description: HpaII test for HELP

source_name: healthy esophageal tissue from patient 1


title: notch-icd_foxi1_RNAseq_3h_rep_2

status: Public on Dec 25 2015

data_processing:
RNAseq reads aligned to transcriptome with RNA-STAR (PMID: 23104886)
RNAseq aligned reads counted with eXpress (PMID: 23160280)
RNAseq counts normalized and differential expression tested with DESeq (PMID: 23975260)
Genome_build: Transcriptome: Mayball interim models, http://daudin.icmb.utexas.edu/
Supplementary_files_format_and_content: RNAseq files are output from eXpress

molecule: polyA RNA

source_name: animal cap (dissected ectoderm)

growth_protocol: Animal caps (ectoderm) dissected from embryos at stage 10 and cultured in 0.5x MMR. 20 animal caps per condition were used for RNAseq.

extract_protocol:
mRNAs were obtained with proteinase K digestion, phenol chloroform extraction and precipitated with ethanol, treated with DNAse, extracted with phenol chloforom, and precipitated with lithium and again with ethanol. See our manuscript (PMID: 24934224) for a more detailed protocol.  RNAseq libraries were constructed with Illumina Truseq v2 non-stranded mRNA kits.
Illumina Truseq v2, poly-a+

value: animal cap (dissected ectoderm)

tag: harvest time/stage

value: 3h @ 22 deg after mid-11 (st 13)

tag: injected mrna


title: notch-icd_foxi1_RNAseq_9h_rep_1

value: 9h @ 22 deg after mid-11 (st 18)


title: wt_RNAseq_9h_rep_2

value: wild-type


title: notch-icd_foxi1_RNAseq_9h_rep_2


title: wt_RNAseq_9h_rep_1


title: notch-icd_foxi1_RNAseq_6h_rep_2

value: 6h @ 22 deg after mid-11 (st 16)


title: wt_RNAseq_6h_rep_2


title: notch-icd_foxi1_RNAseq_6h_rep_1


title: wt_RNAseq_3h_rep_1


title: dbm_dnmcidas_RNAseq_9h_rep_1

value: DNA binding mutant of Suppressor of Hairless (dbm) + dominant negative mcidas (dnmcidas)


title: dbm_dnmcidas_RNAseq_6h_rep_2


title: dbm_dnmcidas_RNAseq_6h_rep_1


title: notch-icd_mcidas_RNAseq_9h_rep_2

value: notch-icd+mcidas-HGR


title: sRNAs from SINV-infected transgenic flies expressing RFP tagged Dicer-2 in a Dicer-2 null background, 5 dpi

description:
Small RNA
None

value: Flies were fed on standard cornmeal-agar medium at 25°C, tested for Wolbachia infection and cured whenever necessary.


title: sRNAs from SINV-infected transgenic flies with a Dicer-2 null background, 5dpi

description:
Small RNA
None

value: 5 days post-infection by intrathoracic injection with viral particles prepared in 10 mM Tris-HCL, pH 7.5 (SINV 5x10^8 PFU/ml)


title: wt_RNAseq_6h_rep_1


title: D456MG GICs NT rep1

source_name: D456MG GICs expressing non-targeting control rep1

value: Glioblastoma Grade IV


title: wt_RNAseq_3h_rep_2


title: notch-icd_mcidas_RNAseq_9h_rep_1


title: notch-icd_foxi1_RNAseq_3h_rep_1


title: dbm_dnmcidas_RNAseq_9h_rep_2


title: dbm_dnmcidas_RNAseq_3h_rep_1


title: dbm_RNAseq_6h_rep_2

value: DNA binding mutant of Suppressor of Hairless (dbm)


title: dbm_RNAseq_6h_rep_1


title: dbm_RNAseq_9h_rep_1


title: dbm_RNAseq_3h_rep_2


title: notch-icd_RNAseq_9h_rep_2

value: notch-icd


title: notch-icd_mcidas_RNAseq_6h_rep_2


title: notch-icd_mcidas_RNAseq_6h_rep_1


title: notch-icd_mcidas_RNAseq_3h_rep_2


title: notch-icd_RNAseq_6h_rep_2


title: notch-icd_RNAseq_6h_rep_1


title: notch-icd_RNAseq_3h_rep_1


title: dbm_dnmcidas_RNAseq_3h_rep_2


title: dbm_RNAseq_3h_rep_1


title: GM19204 ribosome protected fragments

city: Chicago

first: Sidney

last: Wang

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Harringtonine treated

data_processing:
Sequencing image analysis and basecalling were performed using CASAVA version 1.7.0
Raw data provided are fastq files after the following processing. FASTX-Toolkit were used to clip the adaptor sequence and trim the 5' most base for each read. Reads that are shorter than 22-nt or that are mapped to rRNA, tRNA, snoRNA using bowtie were removed from the file.
Processed reads are then map to human genome (hg19) using TopHat. Uniquely mapped reads are used for the aggregate plots presented in the paper.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file contains hg19 genome coordinates of each novel CDS indentified in this study.

molecule: cytoplasmic RNA

source_name: HapMap Lymphoblastoid Cell Line

growth_protocol: Cells were cultured at 37 degree Celsius and 5% CO2 in RPMI 1640 (supplemented with 2mM L-glutamine and 15% fetal bovine serum)

extract_protocol:
Ribosome footprint profiling experiments were performed using ARTseqTM Ribosome Profiling kit for mammalian cells (RPHMR12126) following vendor’s instructions. Cell lysates were prepared from flash frozen pellets of 30 to 50 million live cells by repeat pipetting in 1 ml cold lysis buffer. Sephacryl S400 spin column (GE; 27-5140-01) was used for monosome isolation. For rRNA depletion, Ribo-Zero Magnetic Kit (Epicentre; MRZH11124) was used.
Ribosome footprint cDNA libraries were PCR amplified (12 to 15 thermo-cycles) and barcoded using ScriptMiner Index PCR Primers (Epicentre; SMIP2124). Indexed libraries were pooled to sequence on an Illumina HiSeq 2500.

treatment_protocol: Each culture was treated with 2 μg/ml harringtonine (final concentration in media) for 2 minutes followed by 100 μg/ml cycloheximide (final concentration in media).

tag: gender

value: Female

tag: enrichment type

value: ribosome protected fragments


title: notch-icd_RNAseq_9h_rep_1


title: notch-icd_RNAseq_3h_rep_2


title: STT7092_run_2

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

description: Experiment type: RNA-Seq

data_processing:
Sequences were aligned against the human genome (Hg19) with TopHat.
Cufflinks was used to quantify the gene expression; expression values were then normalized to FPKM (fragments per kilo bases for per million mapped reads).
TopHat-fusion was used to identify the fusion candidates with at least 1 spanning reads, at least two spanning mate pairs and at least 5 summed number of above spanning reads and mate pairs.
Genome_build: hg19
Supplementary_files_format_and_content: expressional matrix with sample by column and gene by row

source_name: normal smooth muscle

extract_protocol:
Multiple 2mm-diameter cores were taken from diagnostic FFPE material for RNA isolation. Then, total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
After ribo-depletion, RNA-SEQ libraries were constructed with a modified TruSeq Sample Preparation Kit using random primer (TruSeq™ RNA Sample Prep Kit v2 -Set A (48rxn) , RS-122-2001, Illumina, San Diego, CA, USA). Then the libraries were sent to Stanford Center for Genomics and Personalized Medicine to be sequenced on an Illumina HiSeq2000 platform with a paired-end 2X101-base protocol.

treatment_protocol: Clinical tissue samples were formalin-fixed and paraffin-embedded (FFPE).

value: Soft Tissue

tag: tissue type

value: normal smooth muscle

tag: tissue archive method

value: FFPE

tag: subtypes

value: Unknown

tag: insert size


title: STT7091_run_2

description: Experiment type: RNA-Seq


title: STT7089_run_1

description: Experiment type: RNA-Seq


title: GM19238 ribosome protected fragments

description: Harringtonine treated

tag: cell line


title: STT7093_run_2

description: Experiment type: RNA-Seq


title: STT7093_run_1

description: Experiment type: RNA-Seq


title: STT7087_run_2

description: Experiment type: RNA-Seq

source_name: normal lung

value: normal lung


title: STT7091_run_1

description: Experiment type: RNA-Seq


title: STT7092_run_1

description: Experiment type: RNA-Seq


title: STT6785_run_1

description: Experiment type: RNA-Seq

source_name: leimyosarcoma

value: leimyosarcoma

value: III


title: STT6783_run_1

description: Experiment type: RNA-Seq


title: STT6652_run_2

description: Experiment type: RNA-Seq

value: II


title: STT7090_run_2

description: Experiment type: RNA-Seq


title: STT7090_run_1

description: Experiment type: RNA-Seq


title: STT6785_run_2

description: Experiment type: RNA-Seq


title: STT6783_run_2

description: Experiment type: RNA-Seq


title: STT6620_run_2

description: Experiment type: RNA-Seq


title: STT7089_run_2

description: Experiment type: RNA-Seq


title: STT6620_run_1

description: Experiment type: RNA-Seq


title: STT6652_run_1

description: Experiment type: RNA-Seq


title: STT6038_run_2

description: Experiment type: RNA-Seq


title: dbm_RNAseq_9h_rep_2

value: animal cap (dissected ectoderm)

value: 9h @ 22 deg after mid-11 (st 18)


title: STT6043_run_2

description: Experiment type: RNA-Seq


title: STT6043_run_1

description: Experiment type: RNA-Seq


title: STT6032_run_2

description: Experiment type: RNA-Seq


title: STT6038_run_1

description: Experiment type: RNA-Seq


title: STT6023_run_2

description: Experiment type: RNA-Seq

value: I


title: STT6023_run_1

description: Experiment type: RNA-Seq


title: STT7088_run_2

description: Experiment type: RNA-Seq

source_name: normal skeletal muscle

value: normal skeletal muscle


title: STT6021_run_2

description: Experiment type: RNA-Seq


title: STT7088_run_1

description: Experiment type: RNA-Seq


title: STT6021_run_1

description: Experiment type: RNA-Seq


title: STT6032_run_1

description: Experiment type: RNA-Seq


title: STT7087_run_1

description: Experiment type: RNA-Seq


title: STT5979_run_2

description: Experiment type: RNA-Seq


title: STT5975_run_2

description: Experiment type: RNA-Seq


title: STT5859_run_2

description: Experiment type: RNA-Seq


title: STT5979_run_1

description: Experiment type: RNA-Seq


title: STT5859_run_1

description: Experiment type: RNA-Seq


title: STT5861_run_2

description: Experiment type: RNA-Seq


title: longissimus dorsi  rep1_7Y-1

city: Sichuan

first: Chaowei

last: Zhou

description: small RNA

data_processing:
The reads that passed through a series of additional filters are called “mappable reads”, which are sequences satisfy the following criteria from the statistics of mammalian miRNAs in miRBbase 19.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing not only A and C or G and T, (5) containing no stretches of A7, C8, G6, or T7; (6) being longer than 14 nt and shorter than 27 nt; (7) not containing more than nine repeats of any dimer, more than five repeats of any trimer, or more than four repeats of any tetramer; (8) been observed more than two times; and (9) not originating from porcine known classes of RNAs (i.e., mRNA in NCBI database; rRNA, tRNA, snRNA and snoRNA in Rfam database; and repetitive sequence elements in Repbase database).
Genome_build: miRBbase 19.0
Supplementary_files_format_and_content: Excel files with read counts

organism: Sus scrofa

source_name: muscle tissues

extract_protocol:
The longissimus dorsi muscle tissues from the same area were collected at E90, 0, 30, 180 days and 7 years. Subsequently, the samples were immediately frozen in liquid nitrogen and stored at −80°C until RNA extraction. Total RNAs were isolated from each sample using Trizol (Takara) according to the manufacturer’s protocol.
The small RNA fraction between 10-40 nt was isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). The short RNAs were then converted to cDNA by RT-PCR and each small RNA library was sequenced individually using Illumina Genome Analyzer II according to manufacturer instructions.

value: female

value: Jinhua

value: muscle

tag: developmental stage

value: 7 years


title: STT5975_run_1

description: Experiment type: RNA-Seq

tag: tissue


title: STT5857_run_2

description: Experiment type: RNA-Seq


title: longissimus dorsi  rep3_7Y-3

description: small RNA

tag: strain


title: longissimus dorsi  rep2_7Y-2

description: small RNA


title: STT5861_run_1

description: Experiment type: RNA-Seq


title: longissimus dorsi  rep1_180d-1

description: small RNA

value: 180 days


title: notch-icd_mcidas_RNAseq_3h_rep_1

value: 3h @ 22 deg after mid-11 (st 13)

value: notch-icd+mcidas-HGR


title: STT5858_run_2

description: Experiment type: RNA-Seq

value: Soft Tissue

value: FFPE


title: longissimus dorsi _0d

description: small RNA

value: 0 day


title: STT5857_run_1

description: Experiment type: RNA-Seq

value: leimyosarcoma


title: longissimus dorsi  rep2_180d-2

description: small RNA


title: longissimus dorsi_E90d

description: small RNA

value: E90 day


title: STT5528_run_1

description: Experiment type: RNA-Seq


title: longissimus dorsi  rep3_180d-3

description: small RNA


title: STT5858_run_1

description: Experiment type: RNA-Seq


title: STT5848_run_2

description: Experiment type: RNA-Seq


title: STT5848_run_1

description: Experiment type: RNA-Seq


title: STT5835_run_2

description: Experiment type: RNA-Seq

value: III


title: STT1220_run_1

description: Experiment type: RNA-Seq

value: II


title: STT5835_run_1

description: Experiment type: RNA-Seq


title: STT1220_run_2

description: Experiment type: RNA-Seq


title: STT5528_run_2

description: Experiment type: RNA-Seq


title: STT516_run_2

description: Experiment type: RNA-Seq


title: STT516_run_1

description: Experiment type: RNA-Seq


title: 2i_H12 [RNA-seq]

status: Public on Dec 24 2015

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
Sample name: H12
Processed data file: none

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
RNA-Seq reads were mapped using Mapping GSNAP (v2014-02-28). Raw counts for each gene were generated using SAMtools (v0.1.18), bedtools (v2.19.1) and DESEQ2 sizeFactor.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq_raw_counts.txt: The raw counts file is a tab-delimited matrix for each gene (annotation Ensembl 75) and all 61 cells which passed the QC requirements in both RNA-Seq and BS-Seq.
Supplementary_files_format_and_content: RNA-seq_normalized_counts.txt: The normalized counts file is a tab-delimited matrix that includes the size-factor-normalized TPM counts (as explained in the associated manuscript). The first column is the Ensembl gene ID, the other columns correspond to the 61 cells which passed the QC requirements, and the rows correspond to the different genes.
Supplementary_files_format_and_content: GSE74535_source_code.tar.gz: Intermediate data files required to reproduce the results with the provided source code (https://github.com/PMBio/scMT-seq).

source_name: Single E14 ES cell, 2i

growth_protocol: ESCs were cultured in serum/LIF or 2i conditions as described previously (Ficz et al., Cell Stem Cell, 2013, 13:351-359).

extract_protocol:
DNA and mRNA were separately purified from single cells using the G&T-seq protocol described previously (Macaulay et al., Nature Methods, 2015).
RNA sequencing libraries were prepared from the single-cell cDNA libraries using the Nextera XT kit (Illumina) as per the manufacturer's instructions, but using one-fifth volumes.

tag: cell type

value: embryonic stem cell

tag: strain/background

tag: genotype/variation

value: wild-type

tag: growth condition


title: Negative_H05 [RNA-seq]

description:
Sample name: H05
Processed data file: none

source_name: No cells

tag: sample type

value: negative control


title: Negative_H06 [RNA-seq]

description:
Sample name: H06
Processed data file: none


title: 2i_H11 [RNA-seq]

description:
Sample name: H11
Processed data file: none


title: Negative_H04 [RNA-seq]

description:
Sample name: H04
Processed data file: none


title: Serum_H03 [RNA-seq]

description:
Sample name: H03
Processed data file: RNA-seq_raw_counts.txt

source_name: Single E14 ES cell, serum/LIF

value: serum/LIF


title: Serum_H09 [RNA-seq]

description:
Sample name: H09
Processed data file: RNA-seq_raw_counts.txt


title: Serum_H10 [RNA-seq]

description:
Sample name: H10
Processed data file: RNA-seq_raw_counts.txt


title: Negative_H07 [RNA-seq]

description:
Sample name: H07
Processed data file: none


title: Serum_H01 [RNA-seq]

description:
Sample name: H01
Processed data file: RNA-seq_raw_counts.txt


title: Serum_H02 [RNA-seq]

description:
Sample name: H02
Processed data file: RNA-seq_raw_counts.txt


title: longissimus dorsi _30d

description: small RNA

value: female

value: Jinhua

value: 30 days


title: Serum_H08 [RNA-seq]

description:
Sample name: H08
Processed data file: none


title: Serum_G08 [RNA-seq]

description:
Sample name: G08
Processed data file: none


title: Serum_G10 [RNA-seq]

description:
Sample name: G10
Processed data file: RNA-seq_raw_counts.txt


title: Serum_G06 [RNA-seq]

description:
Sample name: G06
Processed data file: RNA-seq_raw_counts.txt


title: Serum_G07 [RNA-seq]

description:
Sample name: G07
Processed data file: RNA-seq_raw_counts.txt


title: Serum_G05 [RNA-seq]

description:
Sample name: G05
Processed data file: RNA-seq_raw_counts.txt


title: Serum_G03 [RNA-seq]

description:
Sample name: G03
Processed data file: RNA-seq_raw_counts.txt


title: Serum_G09 [RNA-seq]

description:
Sample name: G09
Processed data file: RNA-seq_raw_counts.txt


title: Serum_G04 [RNA-seq]

description:
Sample name: G04
Processed data file: none


title: Serum_G01 [RNA-seq]

description:
Sample name: G01
Processed data file: RNA-seq_raw_counts.txt


title: Serum_F10 [RNA-seq]

description:
Sample name: F10
Processed data file: none


title: 2i_F11 [RNA-seq]

description:
Sample name: F11
Processed data file: none


title: 2i_F12 [RNA-seq]

description:
Sample name: F12
Processed data file: none


title: Serum_F09 [RNA-seq]

description:
Sample name: F09
Processed data file: RNA-seq_raw_counts.txt


title: 2i_G12 [RNA-seq]

description:
Sample name: G12
Processed data file: none


title: Serum_F08 [RNA-seq]

description:
Sample name: F08
Processed data file: none


title: Serum_F06 [RNA-seq]

description:
Sample name: F06
Processed data file: RNA-seq_raw_counts.txt


title: 2i_G11 [RNA-seq]

description:
Sample name: G11
Processed data file: none


title: Serum_F01 [RNA-seq]

description:
Sample name: F01
Processed data file: RNA-seq_raw_counts.txt


title: Serum_F03 [RNA-seq]

description:
Sample name: F03
Processed data file: RNA-seq_raw_counts.txt


title: Serum_F02 [RNA-seq]

description:
Sample name: F02
Processed data file: RNA-seq_raw_counts.txt


title: 2i_E12 [RNA-seq]

description:
Sample name: E12
Processed data file: none


title: Serum_E09 [RNA-seq]

description:
Sample name: E09
Processed data file: RNA-seq_raw_counts.txt


title: Serum_F05 [RNA-seq]

description:
Sample name: F05
Processed data file: RNA-seq_raw_counts.txt


title: Serum_E10 [RNA-seq]

description:
Sample name: E10
Processed data file: RNA-seq_raw_counts.txt


title: Serum_F07 [RNA-seq]

description:
Sample name: F07
Processed data file: RNA-seq_raw_counts.txt


title: 2i_E11 [RNA-seq]

description:
Sample name: E11
Processed data file: none


title: Serum_E08 [RNA-seq]

description:
Sample name: E08
Processed data file: none


title: Serum_E07 [RNA-seq]

description:
Sample name: E07
Processed data file: RNA-seq_raw_counts.txt


title: Serum_G02 [RNA-seq]

description:
Sample name: G02
Processed data file: RNA-seq_raw_counts.txt


title: Serum_E05 [RNA-seq]

description:
Sample name: E05
Processed data file: RNA-seq_raw_counts.txt


title: 2i_D12 [RNA-seq]

description:
Sample name: D12
Processed data file: none


title: Serum_D10 [RNA-seq]

description:
Sample name: D10
Processed data file: RNA-seq_raw_counts.txt


title: Serum_D06 [RNA-seq]

description:
Sample name: D06
Processed data file: RNA-seq_raw_counts.txt


title: 2i_D11 [RNA-seq]

description:
Sample name: D11
Processed data file: none


title: Serum_E02 [RNA-seq]

description:
Sample name: E02
Processed data file: RNA-seq_raw_counts.txt


title: Serum_D09 [RNA-seq]

description:
Sample name: D09
Processed data file: RNA-seq_raw_counts.txt


title: Serum_D08 [RNA-seq]

description:
Sample name: D08
Processed data file: none


title: Serum_D04 [RNA-seq]

description:
Sample name: D04
Processed data file: RNA-seq_raw_counts.txt


title: Serum_D03 [RNA-seq]

description:
Sample name: D03
Processed data file: none


title: 2i_C11 [RNA-seq]

description:
Sample name: C11
Processed data file: none


title: Serum_C08 [RNA-seq]

description:
Sample name: C08
Processed data file: none


title: Serum_F04 [RNA-seq]

description:
Sample name: F04
Processed data file: RNA-seq_raw_counts.txt


title: Serum_E06 [RNA-seq]

description:
Sample name: E06
Processed data file: none


title: Serum_D02 [RNA-seq]

description:
Sample name: D02
Processed data file: RNA-seq_raw_counts.txt


title: Serum_D05 [RNA-seq]

description:
Sample name: D05
Processed data file: RNA-seq_raw_counts.txt


title: Serum_E04 [RNA-seq]

description:
Sample name: E04
Processed data file: none


title: Serum_E03 [RNA-seq]

description:
Sample name: E03
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C07 [RNA-seq]

description:
Sample name: C07
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C09 [RNA-seq]

description:
Sample name: C09
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C06 [RNA-seq]

description:
Sample name: C06
Processed data file: none


title: Serum_D01 [RNA-seq]

description:
Sample name: D01
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C05 [RNA-seq]

description:
Sample name: C05
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C02 [RNA-seq]

description:
Sample name: C02
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C04 [RNA-seq]

description:
Sample name: C04
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C01 [RNA-seq]

description:
Sample name: C01
Processed data file: RNA-seq_raw_counts.txt


title: Serum_B08 [RNA-seq]

description:
Sample name: B08
Processed data file: none


title: Serum_B10 [RNA-seq]

description:
Sample name: B10
Processed data file: RNA-seq_raw_counts.txt


title: 2i_B11 [RNA-seq]

description:
Sample name: B11
Processed data file: none


title: Serum_B07 [RNA-seq]

description:
Sample name: B07
Processed data file: RNA-seq_raw_counts.txt


title: 2i_B12 [RNA-seq]

description:
Sample name: B12
Processed data file: none


title: Serum_B05 [RNA-seq]

description:
Sample name: B05
Processed data file: RNA-seq_raw_counts.txt


title: Serum_C03 [RNA-seq]

description:
Sample name: C03
Processed data file: RNA-seq_raw_counts.txt


title: Serum_B06 [RNA-seq]

description:
Sample name: B06
Processed data file: RNA-seq_raw_counts.txt


title: Serum_B04 [RNA-seq]

description:
Sample name: B04
Processed data file: RNA-seq_raw_counts.txt


title: Serum_D07 [RNA-seq]

description:
Sample name: D07
Processed data file: RNA-seq_raw_counts.txt


title: 2i_C12 [RNA-seq]

description:
Sample name: C12
Processed data file: none


title: Serum_C10 [RNA-seq]

description:
Sample name: C10
Processed data file: RNA-seq_raw_counts.txt


title: Serum_B03 [RNA-seq]

description:
Sample name: B03
Processed data file: RNA-seq_raw_counts.txt


title: Serum_B01 [RNA-seq]

description:
Sample name: B01
Processed data file: RNA-seq_raw_counts.txt


title: Serum_E01 [RNA-seq]

description:
Sample name: E01
Processed data file: RNA-seq_raw_counts.txt


title: Serum_A09 [RNA-seq]

description:
Sample name: A09
Processed data file: RNA-seq_raw_counts.txt


title: 2i_A12 [RNA-seq]

description:
Sample name: A12
Processed data file: none


title: Serum_A06 [RNA-seq]

description:
Sample name: A06
Processed data file: RNA-seq_raw_counts.txt


title: Serum_A10 [RNA-seq]

description:
Sample name: A10
Processed data file: RNA-seq_raw_counts.txt


title: 2i_A11 [RNA-seq]

description:
Sample name: A11
Processed data file: none


title: Serum_A08 [RNA-seq]

description:
Sample name: A08
Processed data file: none


title: Serum_A02 [RNA-seq]

description:
Sample name: A02
Processed data file: RNA-seq_raw_counts.txt


title: Serum_B02 [RNA-seq]

description:
Sample name: B02
Processed data file: RNA-seq_raw_counts.txt


title: Serum_A04 [RNA-seq]

description:
Sample name: A04
Processed data file: RNA-seq_raw_counts.txt


title: Serum_A01 [RNA-seq]

description:
Sample name: A01
Processed data file: none


title: Serum_B09 [RNA-seq]

description:
Sample name: B09
Processed data file: RNA-seq_raw_counts.txt


title: 2i_H12 [BS-seq]

description: Sample name: H12

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence reads had the first 6 base pairs clipped off the 5' end to remove 6N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.0, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 6, Cutadapt v1.8.1). Remaining sequences were then aligned to the mouse genome (build GRCm38) with Bismark (v0.14.5) in single-end mode (parameters: --non_directional). Methylation calls were extracted after duplicate sequences had been excluded.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bismark CpG coverage report files are available in a tar archive on the series record. Bismark CpG coverage report files  (ending in .cov.gz) are tab-delimited, use 1-based genomic coordinates (for the genome build GRCm38) for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome> <position> <strand> <count methylated> <count non-methylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: GSE74535_source_code.tar.gz: Intermediate data files required to reproduce the results with the provided source code (https://github.com/PMBio/scMT-seq).

extract_protocol:
DNA and mRNA were separately purified from single cells using the G&T-seq protocol described previously (Macaulay et al., Nature Methods, 2015).
Single-cell bisulfite libraries were prepared from the purified genomic DNA as previously described (Smallwood et al., Nature Methods, 2014) but with the following modifications. Conversion was carried out using EZ Methylation Direct bisulfite reagent (Zymo) on purified DNA in the presence of AMPure XP beads (Beckman Coulter) following G&T-seq. Purification and desulphonation of converted DNA was performed with magnetic beads (Zymo) on a Bravo Workstation pipetting robot (Agilent) eluting into the mastermix for the first strand synthesis. Primers for first and second strand synthesis contained a 3' random hexamer instead of nonamer and biotin capture of first strand products was omitted substituting an extra 0.8x AMPure XP (Beckman Coulter) purification between second strand synthesis and PCR. Each pre-PCR AMPure XP cleanup was carried out using a Bravo Workstation (Agilent). To avoid batch effects, all libraries were prepared in parallel in 96 well plates.


title: 2i_H11 [BS-seq]

description: Sample name: H11


title: Serum_H09 [BS-seq]

description: Sample name: H09


title: Negative_H04 [BS-seq]

description: Sample name: H04


title: Negative_H06 [BS-seq]

description: Sample name: H06


title: Negative_H07 [BS-seq]

description: Sample name: H07


title: Negative_H05 [BS-seq]

description: Sample name: H05


title: Serum_A03 [RNA-seq]

description:
Sample name: A03
Processed data file: RNA-seq_raw_counts.txt


title: Serum_H03 [BS-seq]

description: Sample name: H03


title: Serum_H02 [BS-seq]

description: Sample name: H02


title: 2i_G12 [BS-seq]

description: Sample name: G12


title: Serum_G10 [BS-seq]

description: Sample name: G10


title: 2i_G11 [BS-seq]

description: Sample name: G11


title: Serum_G08 [BS-seq]

description: Sample name: G08


title: Serum_G09 [BS-seq]

description: Sample name: G09


title: Serum_G07 [BS-seq]

description: Sample name: G07


title: Serum_A07 [RNA-seq]

description:
Sample name: A07
Processed data file: RNA-seq_raw_counts.txt


title: Serum_H01 [BS-seq]

description: Sample name: H01


title: Serum_G06 [BS-seq]

description: Sample name: G06


title: Serum_F10 [BS-seq]

description: Sample name: F10


title: Serum_H08 [BS-seq]

description: Sample name: H08


title: Serum_G05 [BS-seq]

description: Sample name: G05


title: Serum_A05 [RNA-seq]

description:
Sample name: A05
Processed data file: RNA-seq_raw_counts.txt


title: Serum_F08 [BS-seq]

description: Sample name: F08


title: 2i_F12 [BS-seq]

description: Sample name: F12


title: Serum_G04 [BS-seq]

description: Sample name: G04


title: Serum_F09 [BS-seq]

description: Sample name: F09


title: Serum_G03 [BS-seq]

description: Sample name: G03


title: 2i_F11 [BS-seq]

description: Sample name: F11


title: Serum_G02 [BS-seq]

description: Sample name: G02


title: Serum_F03 [BS-seq]

description: Sample name: F03


title: Serum_F06 [BS-seq]

description: Sample name: F06


title: Serum_F07 [BS-seq]

description: Sample name: F07


title: Serum_F01 [BS-seq]

description: Sample name: F01


title: 2i_E12 [BS-seq]

description: Sample name: E12


title: Serum_F02 [BS-seq]

description: Sample name: F02


title: 2i_E11 [BS-seq]

description: Sample name: E11


title: Serum_F05 [BS-seq]

description: Sample name: F05


title: Serum_E06 [BS-seq]

description: Sample name: E06


title: Serum_E05 [BS-seq]

description: Sample name: E05


title: Serum_E08 [BS-seq]

description: Sample name: E08


title: Serum_E07 [BS-seq]

description: Sample name: E07


title: Serum_G01 [BS-seq]

description: Sample name: G01


title: Serum_E04 [BS-seq]

description: Sample name: E04


title: Serum_E10 [BS-seq]

description: Sample name: E10


title: Serum_E01 [BS-seq]

description: Sample name: E01


title: 2i_D12 [BS-seq]

description: Sample name: D12


title: Serum_E02 [BS-seq]

description: Sample name: E02


title: Serum_D10 [BS-seq]

description: Sample name: D10


title: Serum_D09 [BS-seq]

description: Sample name: D09


title: Serum_F04 [BS-seq]

description: Sample name: F04


title: 2i_D11 [BS-seq]

description: Sample name: D11


title: Serum_H10 [BS-seq]

description: Sample name: H10


title: Serum_D05 [BS-seq]

description: Sample name: D05


title: Serum_D04 [BS-seq]

description: Sample name: D04


title: Serum_E09 [BS-seq]

description: Sample name: E09


title: Serum_D07 [BS-seq]

description: Sample name: D07


title: Serum_D06 [BS-seq]

description: Sample name: D06


title: Serum_E03 [BS-seq]

description: Sample name: E03


title: Serum_D02 [BS-seq]

description: Sample name: D02


title: Serum_D03 [BS-seq]

description: Sample name: D03


title: Serum_D01 [BS-seq]

description: Sample name: D01


title: 2i_C12 [BS-seq]

description: Sample name: C12


title: Serum_D08 [BS-seq]

description: Sample name: D08


title: Serum_C08 [BS-seq]

description: Sample name: C08


title: Serum_C10 [BS-seq]

description: Sample name: C10


title: Serum_C09 [BS-seq]

description: Sample name: C09


title: Serum_C06 [BS-seq]

description: Sample name: C06


title: Serum_C07 [BS-seq]

description: Sample name: C07


title: Serum_C04 [BS-seq]

description: Sample name: C04


title: Serum_C02 [BS-seq]

description: Sample name: C02


title: Serum_C05 [BS-seq]

description: Sample name: C05


title: Serum_C01 [BS-seq]

description: Sample name: C01


title: 2i_B12 [BS-seq]

description: Sample name: B12


title: Serum_C03 [BS-seq]

description: Sample name: C03


title: 2i_B11 [BS-seq]

description: Sample name: B11


title: Serum_B06 [BS-seq]

description: Sample name: B06


title: Serum_B07 [BS-seq]

description: Sample name: B07


title: Serum_B10 [BS-seq]

description: Sample name: B10


title: Serum_B09 [BS-seq]

description: Sample name: B09


title: Serum_B03 [BS-seq]

description: Sample name: B03


title: Serum_B02 [BS-seq]

description: Sample name: B02


title: Serum_B01 [BS-seq]

description: Sample name: B01


title: Serum_A10 [BS-seq]

description: Sample name: A10


title: 2i_A11 [BS-seq]

description: Sample name: A11


title: Serum_A08 [BS-seq]

description: Sample name: A08


title: 2i_C11 [BS-seq]

description: Sample name: C11


title: Serum_B04 [BS-seq]

description: Sample name: B04


title: Serum_A05 [BS-seq]

description: Sample name: A05


title: Serum_A06 [BS-seq]

description: Sample name: A06


title: Serum_A04 [BS-seq]

description: Sample name: A04


title: Serum_A02 [BS-seq]

description: Sample name: A02


title: Serum_A01 [BS-seq]

description: Sample name: A01


title: Serum_A03 [BS-seq]

description: Sample name: A03


title: WGC023779R

city: Shanghai

first: Jianru

last: Xiao

address: 415 Fengyang Road

department: Department of Orthopedics Oncology

institute: Changzheng Hospital, Second Military Medical University

data_processing:
Illumina RTA1.18.61 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome and transcriptome (Refseq) using TopHat v2.0.12 with parameters --bowtie1 --mate-inner-dist 0 --mate-std-dev 80 --prefilter-multihits --read-realign-edit-dist 0 --read-mismatches 2 --no-coverage-search --no-novel-juncs --no-novel-indels --microexon-search. The version of Bowtie was 1.1.0.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) for Refseq genes were calculated using Cufflinks v2.0.2 with parameters --frag-bias-correct --multi-read-correct --compatible-hits-norm.
The gene expression differences were calculated using Cuffdiff with parameters --frag-bias-correct --multi-read-correct --compatible-hits-norm --library-norm-method geometric --dispersion-method pooled. And genes with false discovery rate (FDR) < 0.01 and fold change > 2 were defined as differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: 6 files for corresponding samples include FPKM values of genes, 1 file lists all differentially expressed genes and 1 file lists differentially expressed genes after screening.

source_name: Lung cells

growth_protocol: A549 was cultured with MEM which was supplemented with 10% fetal bovine serum (FBS), 2 mmol/ l glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin in a humidified atmosphere of 95% air and 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using Qiagen RNeasy MinElute Cleanup Kit
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA Sample Preparation Kit )

treatment_protocol: A549 is a human non-small-cell lung cancer (NSCLC) cell line and it was used for constructing cell strain with FOXD3 knockdown. FoxD3 SMART pool(Cat. L-009152-00-0005) was purchased from Dharmacon/Thermo Fisher Scientific. Transfection of the siRNA oligonucleotide duplexes was performed in a 6-well plate (1 × 10 5cells per well) with Lipofectamine 2000 (Invitrogen, Inc.), using the methods recommended by the manufacturer. Using western blotting and real-time PCR, knockdown of FoxD3 with siRNA was examined 72 h after siRNA transfection.

value: Non-small-cell lung cancer (NSCLC) cells

tag: genotype

value: FOXD3 knockdown


title: WGC023780R


title: WGC023778R


title: Serum_B08 [BS-seq]

description: Sample name: B08


title: WGC023777R

value: Wild type

value: Control


title: WGC023775R


title: WGC023776R


title: Serum_B05 [BS-seq]

description: Sample name: B05


title: Serum_A07 [BS-seq]

description: Sample name: A07


title: deg-Tubers4C

city: Wuhan

first: Yongbin

last: Ou

state: Hubei

address: No.1 Shizishan Street, Hongshan Distrit

department: Key Laboratory of Horticultural Plant Biology

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.5 software used for basecalling.
All reads  with low quality or 5' adapter contaminants, reads without 3’ adapter or the insert tag and reads shorter than 18nt were removed by Beijing Genomics Institute (BGI) small RNA pipeline and degradome pipeline.
Sequence count by BGI small RNA pipeline and degradome pipeline.
Reads aligned to S. tuberosum Group Phureja DM1-3 516R44 (CIP801092) Assembly Version 3 DM, PGSC Version 2.1.11 Pseudomolecule Sequences
Genome_build: PGSC_DM_v3_2.1.11_pseudomolecules.zip (http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml)
Supplementary_files_format_and_content: tab-delimited text files include count for each read

organism: Solanum tuberosum

source_name: Tubers

growth_protocol: Potato (Solanum tuberosum) diploid line 10908-06 was planted in the green house at National Centre for Vegetable Improvement (Centre China), Huazhong Agricultural University in Wuhan.

extract_protocol:
Tuber samples were ground in liquid nitrogen and the total RNA was individually extracted using an improved method for potato tubers (Yang et al., 2006)
Total RNA of 10908-06 tubers was normalized and pooled into 4 ºC treated sample (designated as Tubers4C) and control (designated as Tubers20C). Small RNAs were enriched by poly-ethylene glycol precipitation and separated on 15% denaturing PAGE. Small RNAs were gel-purified, ligated to a 5' adapter and a 3' adapter and amplified by reverse-transcription polymerase chain reaction (RT-PCR). PCR products were collected by gel purification and used for small RNA sequencing.
The potato tuber degradome libraries were constructed as previously described (Addo-Quaye et al, 2008; German et al, 2008).

treatment_protocol: Tubers were kept for 10 days at 20 ºC for skin set and divided into two sets. One set was stored at 4 ºC and the other at 20 ºC. Tubers were sampled 1, 2, 5 and 15 days after storage.

value: tubers, modified stem

value: mature

tag: storage temperature

value: 4 ºC


title: Serum_A09 [BS-seq]

description: Sample name: A09


title: ATAC-seq Acinar2

status: Public on Dec 23 2015

city: Philadelphia

first: Paul

state: PA

address: 3700 Hamilton Walk

institute: University of Pennsylvania

data_processing:
Library strategy: ATAC-seq
ATACseq: Illumina adapters were trimmed by Trimmomatic, and the 50 bp reads were trimmed by 10 bp with fastx_trimmer, then all reads were combined for each sample and aligned to hg18 with bowtie2 using default settings. Reads mapped to mitochrondrial DNA and low quality reads (MAPQ<10, duplicates and reads in Encode blacklist regions) were removed. All reads left were offset by +4 bp for + strand and −5 bp for – strand. Peaks were called for each sample using MACS2 with parameters “-q 0.05 --nomodel --shift 37 --extsize 73”.
RNAseq: High quality RNA-seq reads were aligned to the human genome and transcriptome (hg18) using the RNA-seq Unified Mapper (RUM). Aligned reads were filtered for rRNA reads using BLAST alignment against the known rRNA sequences, and all reads aligning to the mitochondrial genome were also discarded. Aligned reads were used to determine unambiguous read counts for each gene in the refGene database using HTSeq, i.e., only reads uniquely assigned to a single gene were counted. All differential expression analysis was performed using the GLM functions in the EdgeR package.
Genome_build: hg18
Supplementary_files_format_and_content: bed files from MACS2 for ATACseq peak summit locations;  tab-delimited text files include read counts for each RNAseq ample

source_name: pancreatic islets

growth_protocol: Islets were cultured either in CMRL1066 with 0.5% human albumin, 2 mM L-glutamine, 1% heparin, and 1% penicillin/streptomycin or in Prodo PIM(S) media supplemented with 5% PIM(ABS) and 1% PIM(G) at 37oC with 5% CO2.

extract_protocol:
Nuclei were isolated from cells by lysing in 50 ul/50,000 cells of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40), followed by centrifugation at 500 x g for 10 minutes at 4 degrees Celsius.  Transposition was performed using 50 ul/50,000 cells of transposition reaction mix (25 ul TD buffer, 2.5 ul Tn5 transposase, 22.5 ul nuclease-free water) from the Illumina-Compatible Nextera DNA Sample Prep Kit (Part# FC-121-1030) for 30 minutes at 37 degrees Celsius.  DNA was then purified using the Qiagen MinElute PCR Purification Kit (Part# 28004) and eluted in 10 ul of elution buffer.
Libraries were prepared using Nextera barcoded primers and NEBNext High-Fidelity 2X PCR Master Mix (Part# M0541).

treatment_protocol: Islets underwent fluorescence-activated cell sorting using cell-surface antibodies (HIC1-2B4, HIC3-2D12, and HIC1-1C10) to separate alpha, beta, and acinar cells.

value: acinar

tag: donor


title: ATAC-seq Acinar3


title: ATAC-seq Beta3

value: beta


title: ATAC-seq Beta2


title: sr-Tubers4C


title: sr-Tubers20C

value: 20 ºC


title: deg-Tubers20C


title: ATAC-seq Alpha2

value: alpha


title: ATAC-seq Alpha1


title: ATAC-seq Alpha3


title: Cell95

first: Raphael

last: Kopan

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

description: total RNA from single-cells

data_processing:
Illumina Off-Line Basecaller(OLB) v1.9.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to mm10 whole genome using tophat v2.0.9 –p 4 –G (UCSC gtf)
Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Nephron_progenitors_p0 single cell

extract_protocol:
Single-cell were loaded onto a Fluidigm Single-cell 10uM-17uM chip using the C-1 Autoprep system.   Cells were lysed and cDNAs generated following manufacturer's protocol.
The construction of RNA libraries were generated using Illumina Tagmentation following manufactuer's protocols

treatment_protocol: Nephron progenitors from various embryonic stages were purifed from the kidneys of Cited1-GFP transgenic mice by FACS.

value: Mixed

value: Kidney

value: Neonatal day 0


title: Cell91

description: total RNA from single-cells


title: Cell89

description: total RNA from single-cells


title: ES-R2_RNA

city: Worcester

first: Troy

middle: W.

last: Whitfield

address: 55 Lake Ave. N.

institute: University of Massachusetts Medical School

data_processing:
ChIP-Seq
Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina).
Reads were mapped to the human genome (GRCh37, hg19) using bowtie (version 0.12.8) with up to two mismatches allowed.
For each cellular condition (i.e. defined by cell cycle phase and differentiation state), genome-wide enrichment profiles were generated from pooled ChIP-seq replicates versus input for H3K27me3 and H3K4me3, respectively using SPP. The resulting enrichment profiles are conservative (alpha=0.01) statistical estimates of log2 fold-enrichment  across the genome.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: BigWig files correspond to enrichment profiles that are conservative (alpha=0.01) statistical estimates of log2 fold-enrichment  across the genome.
RNA-Seq
Base calls and sequence reads were generated by Illumina CASAVA software (CASAVA 1.8 pipeline, Illumina).
Raw sequences from RNA-seq libraries were mapped using TopHat (version 2.0.8b) with the parameters of “--b2-sensitive -r 80 -g 10”.
Mapped reads were analyzed using SeqMonk software (v0.27.0; Babraham Bioinformatics Institute). Expression profiles were calculated using the RNA-seq quantitation pipeline and normalized by adjusting globally count distributions at the 75th percentile. Differential expression was calculated using the intensity difference statistical test included in the software. Differential expression was called on log2 transformed counts by selecting transcripts that changed with a significance of p < 0.05 after Benjamini and Hochberg correction using a null model constructed from the 1% of transcripts showing the closest average level of observation to estimate experimental noise.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text files include RPKM values for each sample.

source_name: H9 Human ESCs

growth_protocol: The H9 human ESC line from WiCell Research Institute (Madison, WI) was maintained on hESC-qualified Matrigel (BD Bioscience, Catalog number 354277) in mTeSR-1 medium (Stemcell Technologies, Catalog number 05850) or Essential E8 medium (Life Technologies, Catalog number A1517001), as recommended by the supplier. Cells were expanded every 5–6 days, using non-enzymatic passaging following WiCell standard protocols. To generate PAX6 cells, undifferentiated ESCs were incubated in mTeSR-1 medium supplemented with 10 mM of Retinoic Acid (Sigma-Aldrich, Catalog number R2625-50MG) for 5 days. The treatment started one day after plating the cells, and medium was changed every day. hESC research was approved by the Institutional Embryonic Stem Cell Research Oversight Committee at University of Vermont.

extract_protocol:
Total RNAs from undifferentiated H9 cells or PAX6 cells, were isolated by using Trizol (Invitrogen). Subsequently, we removed DNA contaminants by using DNA-free RNA extraction kit (Zymo Research). Following Illumina’s manual, 2 µg of DNA-free total RNAs was used to construct each paired-end RNA-Seq library with TruSeq RNA Sample Preparation Kit v2 (Illumina). Libraries were subjected to 15 cycles of amplification with pair-end PCR primers (Illumina). Libraries were quantified in Bioanalyzer and sequenced were on the HiSeq-1000 platform (Illumina) for the read length of 100 bases. To address the influence of culture medium on RNA expression, RNA-seq libraries were built from stocks of ESCs maintained in either mTeSR-1 or Essential E8 medium. The RNA-seq libraries for PAX6 cells were generated from original cellular stocks maintained in either mTeSR-1 or E8. No major differences in RNA expression were detected among different stocks. Therefore, libraries of similar cellular condition (Control or Differentiated) were considered biological replicates. R1: mTeSR medium; R2: E8 medium.
Before every cell sorting experiment, cells were allowed to establish robust colonies. Normally, they were collected 4-5 days after plating. To improve the yield of sorting, we synchronized hESCs at either G2/M or G1 phase of the cell cycle one day before the collection, by incubation with Nocodazole (Sigma–Aldrich, Catalog number M1404-2MG) (200 ng/ml for 16 hr when cells were grown in mTeSR-1) (Figure 2B). Blocking of hESCs in G2/M phase was reversible, and cells were able to resume the cell cycle and progress into G1 after withdrawing of Nocodazole from the culture medium (Figure 1C). For cells growing in E8 medium, 25 ng/ml of Nocodazole for 16 hr was enough to block most of the cells in G2/M and allowed progression into G1 after withdrawing of Nocodazole from the medium (data not shown). After synchronization, cells were collected as single cells by treatment with Acutase (MP Biomedicals, Catalog number 1000449), and subsequently fixed with 1% formaldehyde for 10 minutes followed by 5 minutes of incubation with 0.125M glycine (Sigma-aldrich, Catalog number G8790-100G). Cells were counted and stored at -80ºC.
Pure populations of cells at G2, mitosis or G1 phase of the cell cycle were isolated by FACS, taking advantage of differences in DNA content that allow us to distinguish cells in G2/M from cells in G1, and the exclusive presence of histone H3 phosphorylated in serine 28 (H3S28p) in mitosis that permits us to discriminate between cells in G2 or M phase. Subsequent to cell synchronization and fixation, cells were permeabilized for 10 minutes using a mild permeabilization/wash buffer containing Saponin (BD Bioscience, Catalog number 51-2091KZ). For ESCs isolation, staining was performed with antibodies against OCT4 (PE-conjugated, BD Bioscience, Material number 561556), H3S28p (Alexa fluor 647-conjugated, BD Bioscience, Material number 558609), for 30 min. For PAX6 cells, staining was performed with antibodies against PAX6, instead of OCT4 (PE-conjugated, BD Bioscience, Material number 561552). After staining, cells were washed with permeabilization/wash buffer, resuspended in 2% fetal bovine serum (FBS) in phosphate buffer saline (PBS) and counterstained with 1 μg/ml DAPI (Life Technologies, Catalog number D1306) for 30 min. FACS was performed on a BD FACSAria II using linear FSC and SSC scaling, followed by height and area-based doublets discrimination. Compensation was calculated using FACS Diva autocompensation algorithms, and supplemented by manual compensation to correct for autofluorescence. Cells with sub-normal DNA content were filtered out during the gating and only samples with a purity of 95% or higher were used in the following experiments.
Cells at specific phases of the cell cycle, obtained from 3-4 different cell-sorting experiments, were pooled and treated as a single sample (or biological replicate). Two biological replicates were analyzed for each cell cycle phase, and for each cellular condition (ESCs and PAX6 cells). Cells were washed twice with PBS and subjected to extraction of nuclei according to (Siegel et al., 2009) with modifications. Isolated nuclei were sonicated using a Misonix S-4000 Ultrasonic Processor (QSonica,) to obtain sheared chromatin ranging from 0.2 to 0.6 kilobases (Figure S1). 4 μg of sheared chromatin were immunoprecipitated with either anti H3K4me3 (Abcam, ab1012) or anti H3K27me3 (Millipore, 07-449). Immunoprecipitated complexes were purified by Protein-G Dynabeads (Invitrogen), eluted, reverse crosslinked, quantified, and subjected to library preparation.

value: H9 Human ESCs

tag: passages

tag: chip antibody


title: PAX6-R2_RNA

source_name: H9 Human ESCs-derived PAX6 positive cells


title: ES-R1_RNA


title: Cell68

description: total RNA from single-cells


title: Cell79

description: total RNA from single-cells


title: 2i_A12 [BS-seq]

description: Sample name: A12

value: embryonic stem cell

value: wild-type


title: Cell75

description: total RNA from single-cells


title: Cell77

description: total RNA from single-cells


title: Cell57

description: total RNA from single-cells


title: Cell56

description: total RNA from single-cells


title: Cell65

description: total RNA from single-cells


title: Cell48

description: total RNA from single-cells


title: ATAC-seq Beta1


title: Cell43

description: total RNA from single-cells


title: Cell96

description: total RNA from single-cells

source_name: Nephron_progenitors_e18 single cell

value: embryonic day 18


title: Cell40

description: total RNA from single-cells


title: Cell29

description: total RNA from single-cells


title: Cell49

description: total RNA from single-cells


title: Cell69

description: total RNA from single-cells


title: Cell22

description: total RNA from single-cells


title: Cell94

description: total RNA from single-cells


title: PAX6-R1_RNA


title: Cell90

description: total RNA from single-cells


title: Cell87

description: total RNA from single-cells


title: Cell80

description: total RNA from single-cells


title: Cell85

description: total RNA from single-cells


title: Cell82

description: total RNA from single-cells


title: Cell67

description: total RNA from single-cells


title: Cell76

description: total RNA from single-cells


title: Cell8

description: total RNA from single-cells


title: Cell70

description: total RNA from single-cells


title: Cell6

description: total RNA from single-cells


title: Cell52

description: total RNA from single-cells


title: Cell55

description: total RNA from single-cells


title: Cell58

description: total RNA from single-cells


title: Cell54

description: total RNA from single-cells


title: Cell61

description: total RNA from single-cells


title: Cell73

description: total RNA from single-cells


title: Cell10

description: total RNA from single-cells


title: Cell51

description: total RNA from single-cells


title: Cell44

description: total RNA from single-cells


title: Cell46

description: total RNA from single-cells


title: Cell39

description: total RNA from single-cells


title: Cell42

description: total RNA from single-cells


title: Cell5

description: total RNA from single-cells


title: Cell50

description: total RNA from single-cells


title: Cell83

description: total RNA from single-cells


title: Cell4

description: total RNA from single-cells


title: Cell35

description: total RNA from single-cells


title: Cell36

description: total RNA from single-cells


title: Cell34

description: total RNA from single-cells


title: Cell71

description: total RNA from single-cells


title: Cell30

description: total RNA from single-cells


title: Cell26

description: total RNA from single-cells


title: Cell28

description: total RNA from single-cells


title: Cell23

description: total RNA from single-cells


title: Cell25

description: total RNA from single-cells


title: Cell21

description: total RNA from single-cells


title: Cell24

description: total RNA from single-cells


title: Donor 36 CD14+ mono

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Reads were trimmed for adaptors and quality using Trimmomatic
Reads were mapped against Human reference GRCh37using bowtie2
BAM files were converted to counts per gene using htseq-count counting reads mapping to exons
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: CSV file containing raw read counts per gene

source_name: Blood derived APC_CD14+ mono

extract_protocol:
PBMC were isolated by Ficoll-Paque density gradient centrifugation (GE Healthcare, Chalfont St. Giles, United Kingdom) from healthy buffy coats obtained from the Australian Red Cross. PBMC were further separated into three populations by counter-current elutriation using Beckman J-6 M/E centrifuge equipped with a JE 5.0 rotor (Beckman Coulter, Pasedena, CA, USA). The three fractions were isolated at rates of 12 (small lymphocytes), 16 (large lymphocytes) and 20 (DC/Monocytes fractions) ml/min. dendritic cells and monocytes were islated from the large cell fraction. The large cell fraction was first stained with antibodies specific for the DC subsets, which included CD1c-APC (Miltenyi), CD141-VioBlue (Miltenyi), CD123-PE (BD BioSciences, Franklin Lakes, NJ, USA) and SLAN-FITC (Miltenyi), and labeled with anti-IgG beads (Miltenyi). DC were then isolated using an AutoMACS (Miltenyi) into positive and negative fractions. The positive fraction (DC enriched) was further sorted into four DC subsets: CD1c+ mDC, SLAN+ DC, CD141+ mDC and CD123+ pDC, using a FACSAria (BD BioSciences). The negative fraction (DC depleted/mono) was stained with anti-CD14-FITC and anti-CD16-PE (BD Biosciences) antibodies, labeled with IgG beads (Miltenyi) and a positive selection performed using an AutoMACS (Miltenyi) to obtain a bulk monocyte population. These cells were further sorted to obtain the CD14+CD16- (CD14+) and CD16+CD14lo (CD16+) monocyte subsets using a FACSAria. Cell populations with a purity ≥90% were used, as determined by flow cytometry (LSR II or FACSAria; BD Bioscience).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: Healthy controls

tag: donor id

value: Donor 36

value: Blood

value: Monocyte

tag: cell subtype

value: CD14+ monocytes


title: Donor 36 CD1c+ mDC

source_name: Blood derived APC_CD1c+ mDC

value: Dendritic cell

value: CD1c+ myleoid dendirtic cells (mDC)


title: Donor 36 SLAN DC

source_name: Blood derived APC_SLAN DC

value: slan(+) Dendritic cells


title: Cell20

description: total RNA from single-cells


title: Cell19

description: total RNA from single-cells


title: Donor 36 pDC

source_name: Blood derived APC_pDC

value: plasmacytoid dendritic cells (pDC)


title: Cell2

description: total RNA from single-cells


title: Cell41

description: total RNA from single-cells


title: Donor 28 CD14+ Mono

value: Donor 28


title: Cell15

description: total RNA from single-cells

value: Mixed


title: Cell14

description: total RNA from single-cells

value: Kidney


title: Donor 28 CD1c+ mDC


title: Donor 28 pDC


title: Cell93

description: total RNA from single-cells

source_name: Nephron_progenitors_e14 single cell

value: embryonic day 14


title: Donor 28 SLAN DC


title: Cell1

description: total RNA from single-cells


title: Donor 97 CD14+ mono

value: Donor 97


title: Donor 97 SLAN DC


title: Cell31

description: total RNA from single-cells


title: Cell86

description: total RNA from single-cells


title: Cell81

description: total RNA from single-cells


title: Donor 97 CD1c+ mDC


title: Cell92

description: total RNA from single-cells


title: Donor 97 pDC


title: Cell78

description: total RNA from single-cells


title: Cell62

description: total RNA from single-cells


title: Cell59

description: total RNA from single-cells


title: Cell53

description: total RNA from single-cells


title: Cell47

description: total RNA from single-cells


title: Cell66

description: total RNA from single-cells


title: Cell60

description: total RNA from single-cells


title: Cell38

description: total RNA from single-cells


title: Cell63

description: total RNA from single-cells


title: Cell45

description: total RNA from single-cells


title: Cell32

description: total RNA from single-cells


title: Cell37

description: total RNA from single-cells


title: Cell33

description: total RNA from single-cells


title: Cell18

description: total RNA from single-cells


title: Cell17

description: total RNA from single-cells


title: Cell13

description: total RNA from single-cells


title: Cell16

description: total RNA from single-cells


title: Cell11

description: total RNA from single-cells


title: Cell27

description: total RNA from single-cells


title: Cell7

description: total RNA from single-cells


title: Cell12

description: total RNA from single-cells


title: T22

city: Yangling

first: Yuejin

state: Shaanxi

address: Shaanxi, China

institute: Northwest A&F University

description: E-L 38 rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to grape reference genome using TopHat2
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using a protocol from Trapnell C et al. Nature Biotechnology 2010
Genome_build: Vitis vinifera
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Vitis quinquangularis

source_name: Grape skin

extract_protocol:
Total RNA was extracted using  OMEGA plant RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Grape skin


title: T24

description: E-L 38 rep3


title: T23

description: E-L 38 rep2


title: T21

description: E-L 35 rep3


title: T20

description: E-L 35 rep2


title: T19

description: E-L 35 rep1


title: T17

description: E-L 34 rep2


title: Cell3

description: total RNA from single-cells

tag: developmental stage


title: T18

description: E-L 34 rep3

tag: tissue


title: T14

description: E-L 33 rep2


title: T16

description: E-L 34 rep1


title: T15

description: E-L 33 rep3


title: T12

description: E-L 38 rep3

organism: Vitis vinifera

value: Cabernet Sauvignon


title: T11

description: E-L 38 rep2


title: T13

description: E-L 33 rep1


title: T09

description: E-L 35 rep3


title: T05

description: E-L 34 rep2


title: T07

description: E-L 35 rep1


title: T08

description: E-L 35 rep2


title: T06

description: E-L 34 rep3


title: T02

description: E-L 33 rep2


title: T03

description: E-L 33 rep3


title: PY9mat

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

data_processing:
Allelic methylation levels were extracted from the Bismark BAM files for reads with a linear match to the genome using a custom script (Supplementary material in manuscript), which compared the bases in the reads to the expected SNPs designed into the amplicons.
Genome_build: GRCh37
Supplementary_files_format_and_content: Average DNA methylation for each read, with a minimum of 5 informative CpGs, corresponding to allele 1 or allele 2 of SNPs for each assayed region in each sample.

source_name: whole blood

extract_protocol:
submitter states "custom" (no  meaningful entry)
DNeasy Blood and Tissue Kit DNA extraction
Parallel PCR reactions to assay 151 imprinted differentially methylated domains (Supplementary material in manuscript) with a final concentration of 1xHotStar PCR buffer, 0.2mM dNTPs, 1U HotStar taq and 0.4uM each primer pair and 2ng DNA were performed in a 15uL reaction volume in 384-well plates.  The plates were prepared on the Agilent Bravo Workstation.  The cycling conditions included a 15 minute 95°C denaturation, followed by 30 cycles of 95°C for 30 seconds, 50°C for 30 seconds, 72°C for 90 seconds, with a 5 minute final extension at 72°C and were performed on the C1000 Touch Thermal Cycler.  PCR products were pooled for each sample and SPRI-purified using Sera-Mag carboxylate-modified Magnetic SpeedBeads as per manufacturer’s recommendations.  A-overhang addition was done using 1x NEB buffer 2, 0.2mM dATP, 12.5U Klenow fragment (3’->5’ exo-) in a 25uL reaction incubated at 37°C for 30 minutes.  Following SPRI purification, Illumina adapters were ligated using the Quick ligation kit in a 40uL reaction.  Following another SPRI purification, libraries were amplified (11 cycles) and barcoded using the Sanger 8-base index in a 50uL reaction containing: 1x High Fidelity buffer, 1U Phusion High Fidelity taq, 0.2mM dNTPs, 0.1uM each primer .  Final libraries were SPRI purified and concentration and quality were assessed by the 2100 Bioanalyzer system and Kapa library quantification.  The 48 barcoded libraries were pooled and multiplexed.

value: whole blood

value: adult

value: Control


title: PY9

source_name: placental villi

value: placental villi

value: 3rd trimester


title: PY3pat


title: PY3mat


title: PX4pat


title: T04

description: E-L 34 rep1


title: PX4mat


title: PX4


title: PY3


title: PX23tro

source_name: trophoblast

value: trophoblast


title: PX4tro


title: PX23pat


title: T10

description: E-L 38 rep1


title: PM285tro


title: PX23