title: sample 2539382 Tumor tissue_rna

description: processed data file: 2539382T-VS-2539382N.GeneDiffExp.txt


title: sample 2539382 Tumor tissue_hmedip

status: Public on Dec 31 2018

type: SRA

city: Hangzhou

first: Yimin

last: Zhu

state: Zhejiang

address: Yuhangtang Road

country: China

institute: Zhejiang university

library_source: genomic

data_processing:
Library strategy: MeDIP-Seq with anti-hydroxymethylcytosine antibody
After base calling, low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21). Mismatches of no more than two bases were allowed in the alignment.
Identification of group-wise DMR and DhMR was performed by a strategy of sliding windows along the whole genome descripted in our previous research. This strategy identified DMR and DhMR between tumor and corresponding normal tissues based on the threshold with P-value < 0.05 and at least 5 CG sites.
genome build: hg19
processed data files format and content: wig format

molecule: genomic DNA

organism: Homo sapiens

source_name: colonrectal

extract_protocol:
DNA extraction protocol not provided.
Prior to immunoprecipitation, 5 μg of genomic DNA was sonicated to a mean size of 200 bp fragments, followed with end repair, <A> base addition and adaptor ligation steps according to Illumina Paired-End protocol. The libraries were sequenced using Illumina HiSeq analyzer according to the manufacturer’s instructions. After base calling, low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21). Mismatches of no more than two bases were allowed in the alignment.

tag: disease state

value: tumor

tag: tissue

value: colorectal


title: sample 2539382 Normal tissue_hmedip

value: normal


title: sample 2512618 Tumor tissue_hmedip


title: sample S12 Normal tissue_hmedip


title: sample 2539382 Normal tissue_medip

data_processing:
After base calling, low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21). Mismatches of no more than two bases were allowed in the alignment.
Identification of group-wise DMR and DhMR was performed by a strategy of sliding windows along the whole genome descripted in our previous research. This strategy identified DMR and DhMR between tumor and corresponding normal tissues based on the threshold with P-value < 0.05 and at least 5 CG sites.
genome build: hg19
processed data files format and content: wig format


title: sample 2512618 Tumor tissue_rna

description: processed data file: 2512618T-VS-2512618N.GeneDiffExp.txt

library_source: transcriptomic

data_processing:
The following data processing including gene expression level and differentially expressed genes were statistically analyzed by the method of Audic andClaverie3. The gene expression level was calculated by using RPKM (Reads Per kb per Million reads). If there was more than one transcript for one gene, the longest one was used to calculate its expression level and coverage. The RPKM values can be directly used for comparing the difference of gene expression among samples. The significantly differentially expressed genes (DEG) were determined at a threshold false discovery rate (FDR) ≤0.05 and the absolute value of log2Ratio ≥ 0.585.
genome build: hg19
processed data files format and content: text file with RPKM and statistics

molecule: total RNA

extract_protocol:
RNA extraction protocol not provided.
The total RNA samples were first treated with DNase I to degrade any possible DNA contamination. Then the mRNA was enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments (about 200 bp). The first strand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, Agilent2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used to qualify and quantify of the sample library. The library products were ready for sequencing via Illumina HiSeq2000.


title: sample 2512618 Tumor tissue_medip


title: sample 2512618 Normal tissue_rna


title: sample 2512618 Normal tissue_medip


title: sample 2512618 Normal tissue_hmedip


title: sample 2504588 Tumor tissue_hmedip


title: sample 2504588 Normal tissue_rna

description: processed data file: 2504588T-VS-2504588N.GeneDiffExp.txt


title: sample 2504588 Normal tissue_medip


title: sample 2504588 Normal tissue_hmedip


title: 7dayC57CS0

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

country: USA

institute: NIEHS

data_processing:
Fastq data files were aligned to the mouse Mm10 Ensembl genome with Novoalign read aligner version 2.08.02
Novoaligned SAM files were parsed into binary BAM files and differentially expressed genes identified using the RNASeq application from USeq software version 8.7.4
RNASeq application calculates fraction of reads that are exonic, intronic and intergenic and makes normalized read data tracks (FPKM) for visualization in the Integrated Genome Browser
RNASeq application runs DefinedRegionsDifferentialSeq for calculating differential expression using Anders DESeq2 negative binomial statistics and Benjamini and Hochberg mulitple testing correction
Genome_build: Ensembl Mus musculus Mm10
Supplementary_files_format_and_content: Excel file with Ensembl IDs, chromosome coordinates, individual sample raw read counts, FPKM counts, Log2 ratio and false discovery rate

organism: Mus musculus

source_name: Alveolar macrophages

extract_protocol:
Qiagen RNAeasy mini kit
Illumina TruSeq RNA sample prep with oligo dT selection

tag: strain

tag: genotype

value: Wild-type

tag: exposure

value: cigarette smoke

tag: time point


title: LNCap_SP2509_24h_3

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

description: 1uM SP-2509 24hrs

data_processing:
Tophat version 2.0.9 for alignment
Cufflinks version 2.1.1 for transcript assembly
STAR version 2.4.2a for alignment and assembly (LNCaP 24h only)
Genome_build: hg19
Genome_build: GRCh38 (LNCaP 24hr only)
Supplementary_files_format_and_content: Text file with fpkm-like measurement for each UCSC (v. hg19) transcript
Supplementary_files_format_and_content: Tab-delimited STAR output file with raw read counts for each GRCh38 gene (LNCaP 24h only)

source_name: Cell line

growth_protocol: C42B cells were plated in triplicate in 6-well plates, 250,000 cells/well in RPMI+10% charcoal-stripped FBS. PC3 cells were plated in triplicate in 6-well plates, 250,000 cells/well in RPMI+10% FBS. LNCaP cells were plated in triplicate in 6-well plates, 350,000 cells/well in RPMI+10% FBS. LNCaP cells for 24hr treatment conditions were plated in triplicate in 6-well plates, 400,000 cells/well in RPMI+10% FBS.

extract_protocol:
TriZol+CHCl3
Agilent SureSelect Stranded RNAseq

treatment_protocol: C42B cells were treated with 1uM SP-2509 or 0.1% DMSO the day after plating, and harvested 72hrs post-treatment.  PC3 cells were treated with 2uM SP-2509 or 0.1% DMSO the day after plating, and harvested 72hrs post-treatment. LNCaP cells were treated with 1uM SP-2509 or 0.1% DMSO the day after plating, and harvested at 24 and 72hrs post-treatment.

value: prostate

tag: cell type

value: prostate cancer cell line LNCap

tag: treatment


title: LNCap_DMSO_24h_2

description: 0uM SP-2509 24hrs

value: DMSO


title: sample 2539382 Normal tissue_rna


title: LNCap_DMSO_24h_3

description: 0uM SP-2509 24hrs


title: LNCap_SP2509_24h_1

description: 1uM SP-2509 24hrs


title: LNCap_DMSO_24h_1

description: 0uM SP-2509 24hrs


title: Control

city: chicago

first: jun

last: liu

state: Illinois

institute: UoC

data_processing: RNA-seq was aligned to human genome hg38 by Tophat version 2.0 without any gaps and allowed for at most two mismatches. Then DESeq were used to generate RPKM (reads per kilobase, per million reads)  and differential expressed gene.

molecule: polyA RNA

source_name: HeLa

growth_protocol: Human HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100× Pen Strep (Gibco, 15140).

extract_protocol:
HeLa cells were transfected with the plasmid PCMV6-Entry by using Lipofectamine2000 (Invitrogen). After 24 h post-transfection, total RNA were isolated from transfected cells using TRIZOL reagent (Invitrogen).Poly-adenylated RNA were extracted using PolyATract mRNA Isolation Systems (Promega). Library preparation were performed following Tru-seq mRNA sample preparation kit (Illumina)
TruSeq RNA Sample Preparation Kit (Illumina)
Total RNA from separated cell fractions was isolated with TRIZOL reagent (Invitrogen). mRNA was extracted using PolyATract mRNA Isolation Systems (Promega)
Tru-seq mRNA sample preparation kit (Illumina)

treatment_protocol:
Plasmid empty vector were transfected into HeLa cells, respectively, by using Lipofectamine 2000 reagent (Invitrogen)
treated with Empty vector or RTKN plasmid by using Lipofectamine 2000 reagent (Invitrogen)

tag: cell line

value: HeLa

tag: condition

value: Empty vector overexpression


title: sample 2504588 Tumor tissue_rna


title: RTKN

extract_protocol:
HeLa cells were transfected with the plasmid containing flag-tagged RTKN by using Lipofectamine2000 (Invitrogen). After 24 h post-transfection, total RNA were isolated from transfected cells using TRIZOL reagent (Invitrogen).Poly-adenylated RNA were extracted using PolyA
TruSeq RNA Sample Preparation Kit (Illumina)
Total RNA from separated cell fractions was isolated with TRIZOL reagent (Invitrogen). mRNA was extracted using PolyATract mRNA Isolation Systems (Promega)
Tru-seq mRNA sample preparation kit (Illumina)

treatment_protocol:
Plasmid RTKN were transfected into HeLa cells, respectively, by using Lipofectamine 2000 reagent (Invitrogen)
treated with Empty vector or RTKN plasmid by using Lipofectamine 2000 reagent (Invitrogen)

value: RTKN overexpression


title: JmjC*_rep3

city: Bronx

first: Julie

last: Secombe

state: NY

address: 1300 Morris park ave

department: Genetics

institute: Albert Einstein College of Medicine

description:
mRNA-seq
JmjC_vs_WT.txt

data_processing:
Alignment of raw reads was carried out using STAR aligner
Normalized and differential expression determined with DESeq2.
Supplementary_files_format_and_content: log fold change

organism: Drosophila melanogaster

source_name: adult Drosophila head

growth_protocol: Flies were grown on standard media.

extract_protocol:
RNA was extracted using Trizol and Rneasy.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit in accordance with the manufacturer’s instructions. Briefly, 500ng of total RNA was used for purification and fragmentation of mRNA. Purified mRNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 8 cycles). Final libraries were evaluated using fluorescent-based assays including PicoGreen (Life Technologies) or Qubit Fluorometer (invitrogen) and Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent 2100), and were sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 2 x 50bp cycles.

treatment_protocol: No treatment

tag: age

value: 3-5 days old

value: whole adult head

value: JmjC (demethylase inactive) mutant


title: JmjC*_rep2

description:
mRNA-seq
JmjC_vs_WT.txt


title: JmjC*_rep1

description:
mRNA-seq
JmjC_vs_WT.txt


title: LNCaP_SP-2509_3

description: Sample 18

data_processing:
Tophat version 2.0.9 for alignment
Cufflinks version 2.1.1 for transcript assembly
Genome_build: hg19
Supplementary_files_format_and_content: Text file with fpkm-like measurement for each UCSC (v. hg19) transcript

source_name: prostate cancer cell line

growth_protocol: C42B cells were plated in triplicate in 6-well plates, 250,000 cells/well in RPMI+10% charcoal-stripped FBS. PC3 cells were plated in triplicate in 6-well plates, 250,000 cells/well in RPMI+10% FBS. LNCaP cells were plated in triplicate in 6-well plates, 350,000 cells/well in RPMI+10% FBS.

treatment_protocol: C42B cells were treated with 1uM SP-2509 or 0.1% DMSO the day after plating, and harvested 72hrs post-treatment.  PC3 cells were treated with 2uM SP-2509 or 0.1% DMSO the day after plating, and harvested 72hrs post-treatment. LNCaP cells were treated with 1uM SP-2509 or 0.1% DMSO the day after plating, and harvested 72hrs post-treatment.

value: prostate cancer cell line LNCaP


title: PC3_SP-2509_3

description: Sample 12

value: prostate cancer cell line PC3


title: LNCaP_SP-2509_1

description: Sample 16


title: LNCaP_control_2

description: Sample 14

value: control


title: LNCaP_control_3

description: Sample 15


title: PC3_SP-2509_1

description: Sample 10


title: PC3_SP-2509_2

description: Sample 11


title: LNCaP_SP-2509_2

description: Sample 17


title: PC3_control_3

description: Sample 9


title: A512P_rep3

description:
mRNA-seq
A512P_vs_WT.txt

value: A512P mutant


title: LNCaP_control_1

description: Sample 13


title: sample 2504588 Tumor tissue_medip

value: tumor

value: colorectal


title: LNCap_SP2509_24h_2

description: 1uM SP-2509 24hrs


title: PC3_control_1

description: Sample 7


title: A512P_rep2

description:
mRNA-seq
A512P_vs_WT.txt


title: WT_rep2

description: mRNA-seq

value: wildtype


title: C42B_SP-2509_3

description: Sample 6

value: prostate cancer cell line C42B


title: PC3_control_2

description: Sample 8

value: prostate


title: WT_rep1

description: mRNA-seq


title: C42B_SP-2509_1

description: Sample 4


title: C42B_control_3

description: Sample 3


title: C42B_control_1

description: Sample 1


title: C42B_control_2

description: Sample 2


title: 24-32lps001

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

description: barcode: CGATGT

data_processing:
bcl2fastq for both demultiplexing data and converting bcl files generated by Illumina sequencing to fastq files
FastQC (v0.11.5) was used for quality control of reads
Raw reads were trimmed adapters, low-quality bases and reads by cutadapt (v1.12)
Trimmed reads were mapped to zebrafish transcriptome and genome by Tophat2 (v2.1.0) with parameters: --library-type fr-unstranded -r 100 --mate-std-dev 100
Mapped reads were sorted by samtools (v0.1.19-96b5f2294a), and counted by htseq-count (v0.6.1p1)
Reads counts of each library were combined into a matrix, and were used for gene differential expression analysis by DESeq2 (v1.11.1), with parameters: design=~treatment, adjusted p-value < 0.05
Genome_build: GRCz10 (Ensembl)
Supplementary_files_format_and_content: tab-delimited matrix containing read counts of each library

organism: Danio rerio

source_name: first-feeding larva

growth_protocol: Zebrafish embryos were incubated in sterile E3 medium containing 0.1 mg/L methylene blue (Sigma-Aldrich, USA) until the first-feeding stage. One-third of the medium was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C, 28 ± 0.5 °C or 32 ± 0.5 °C, according to the experimental design. The photoperiod was 12 h light: 12 h dark.

extract_protocol:
Total RNA was extracted from whole larvae following the QIAzol (Qiagen, Germany) protocol. RNA concentration, purity and quality were measured by NanoDrop 1000 (Thermo Scientific, USA) and TapeStation 2200 (Agilent Technologies, USA).
Libraries were built from total RNA using the TruSeq RNA Library Prep Kit v2 (Illumina, USA). After purification with oligo-dT beads, mRNAs were fragmented into an average length of 508-541 base pairs. The first strand of complementary DNA was synthesized with random hexamer primers (Illumina, USA), and the second strand was synthesized by Second Strand Master Mix (Illumina, USA). All 18 libraries were barcoded uniquely, and normalized with the KAPA library quantification kit (Kapa Biosystems, USA). The pooled libraries were denatured following the NextSeq System Denature and Dilute Libraries Guide (Illumina, USA), and loaded at 11 pM on a NextSeq 500 reagen cartridge (Illumina, USA) for 150 cycle, paired-end sequencing.

treatment_protocol: Larvae were gently transferred to distilled water containing 10 mg/L LPS from Pseudomonas aeruginosa 10 (Sigma-Aldrich, USA), and kept for 24 h. Then, larvae were euthanized by immersing in 300 mg/L tricaine methanesulfonate, followed by snap-freezing with liquid nitrogen and stored at -80 °C until use.

value: AB

tag: developmental stage

value: first-feeding stage

value: whole larva


title: 32-24lps001

description: barcode: GTGAAA


title: 24-32lps002

description: barcode: ACAGTG


title: 32-24ct001

description: barcode: CAGATC


title: A512P_rep1

description:
mRNA-seq
A512P_vs_WT.txt


title: 24-32ct002

description: barcode: ACTGAT


title: 24-32ct001

description: barcode: GTGGCC


title: 24-32lps003

description: barcode: TGACCA


title: 24-24lps003

description: barcode: GGCTAC


title: 24-24lps001

description: barcode: TAGCTT


title: 32-24lps003

description: barcode: CCGTCC


title: WT_rep3

description: mRNA-seq


title: 24-24ct003

description: barcode: ACTTGA


title: 32-24lps002

description: barcode: ATGTCA


title: 32-24ct002

description: barcode: GCCAAT


title: 24-32ct003

description: barcode: CGTACG


title: 24-24ct002

description: barcode: TTAGGC


title: C42B_SP-2509_2

description: Sample 5


title: Ku50_RT00

city: HaiKou

first: Zehong

last: Ding

state: HaiNan

address: No.4 XueYuan Rd

institute: ITBB

data_processing:
Sequence quality was examined using FastQC
low quality reads were ﬁltered also using FASTX-toolkit
Clean reads weremapped to cassava genome (version 4.1) using Tophat v2.0.13
Raw count data were obtained and normalized by Cufﬂinks pipeline v2.1.1
Genome_build: cassava genome version 4.1  The genome assembly file (‘Mesculenta_147.fa.gz’) and GFF annotation file (‘Mesculenta_147_gene.gff3.gz’) were downloaded from phytozome website (Version 9) at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Manihot esculenta

source_name: root

extract_protocol:
Fresh samples were frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: 60 days

tag: treated with

value: PEG for 0h

value: root


title: 32-24ct003

description: barcode: AGTCAA


title: Ku50_FL24

source_name: folded leaf

value: PEG for 24h

value: folded leaf


title: EoE-D3

description: processed data file: EoE_GERDvsControl_Distal_AllGenes.txt

data_processing:
Fastq data files aligned to human Hg19 genome with Bowtie short read aligner version 0.12.7
Bowtie aligned sam files were parsed into binary point data files and differentially expressed genes identified using the RNASeq application from USeq software version 7.8.
RNASeq application calculates fraction of reads that are exonic, intronic and intergenic and makes normalized read data tracks (RPKM) from the point data for visualization in the Integrated Genome Browser.
RNASeq application runs MultipleReplicaDefinedRegionScanSeqs (MRDRSS) for calculating differential expression using Anders DESeq negative binomial statistics and Benjamini and Hochberg mulitple testing correction.
Disease specific unannotated (novel) RNAs were identified using Cufflinks and Cuffcompare software and differential expression calcuated using MRDRSS application.
Genome_build: Human Hg19
Supplementary_files_format_and_content: text files with individual sample RPKM values, fold change and false discovery rate

source_name: EoE_distal esophagus

extract_protocol:
TriZol
Illumina TruSeq RNA sample prep kit using barcodes for mulitplexing

tag: gender

value: male

tag: disease

value: eosinophilic esophagitis

value: Esophageal biopsies

tag: location

value: distal esophagus


title: Ku50_RT03

value: PEG for 3h


title: Ku50_RT24


title: 24-24lps002

description: barcode: GATCAG


title: Ulmus pumila（MSL）_HIGSeq

city: Beijing

first: Zhu

last: Jianfeng

address: Haidian District, Xiang Shan Road

department: Research Center of Saline and Alkali Land of State Forestry Administration

institute: Chinese Academy of Forestry

description: The seedlings subjected to salt stress (NaCl, 200 mM) for 24 hours.

data_processing:
Novogene small RNA analysis pipline software used for basecalling.
Remove low qulity reads strictly, trim 3' adaptor sequence and remove 5' adaptor contaminants, remove too small and polyA.
Identification of conserved miRNAs by software mirdeep2 and srna-tools-cli.
Discovery of Novel miRNAs by software miREvo and mirdeep2.
Custom scripts were used to obtain the identified miRNA counts.
Genome_build: Transcriptome sequences of Ulmus pumila (unpublished data) used for read alignment.
Supplementary_files_format_and_content: tab-delimited xls files include  the expression abundance for each conserved and novel miRNAs in different samples.

organism: Ulmus pumila

source_name: seedlings

extract_protocol:
Roots were collected from 30 days old seedlings, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: roots of seedlings

value: 30 days after germination

value: wild type

tag: protocol


title: Ku50_FL03

tag: tissue


title: Ulmus pumila（LSS）_HIGSeq

description: The seedlings subjected to salt stress (NaCl, 50 mM) for 6 hours.

value: salt stress (NaCl, 50 mM) for 6 hours.


title: Ulmus pumila（CK）_HIGSeq

description: The seedlings grown under normal conditions without salt stress.


title: Ku50_BL03

source_name: bottom leaf

value: bottom leaf


title: Arg7_MSR

source_name: middle storage root

value: 150 days

value: normal condition

value: middle storage root


title: Ku50_FEL03

source_name: full expanded leaf

value: 60 days

value: full expanded leaf


title: Ku50_BL24

value: PEG for 24h


title: Ku50_BL00

value: PEG for 0h


title: Arg7_LSR

source_name: last storage root

value: 210 days

value: last storage root


title: KU50_LSR


title: KU50_MSR


title: Ku50_FL00

value: folded leaf


title: KU50_ESR

source_name: early storage root

value: 90 days

value: early storage root


title: Ku50_FEL00


title: Arg7_ESR


title: 24-24ct001

description: barcode: ATCACG

tag: strain

value: AB

value: first-feeding stage

value: whole larva


title: Arg7_stem

source_name: stem

value: stem


title: KU50_leaf

source_name: leaf

value: leaf


title: W14_root

value: root


title: W14_stem

value: normal condition


title: Japanese quail 2K3

city: University Park

first: Suresh

middle: Varma

last: Kuchipudi

state: PA

address: Animal Diagnostic Laboratory, Wiley Lane

department: Veterinary and Biomedical Sciences

institute: The Pennsylvania State University

data_processing:
Illumina HiSeq 2000 used for high-throughput sequencing of cDNA library
Read quality check parameters such as base quality score distribution, sequence quality score distribution, average base content per read, GC distribution in the reads, PCR amplification issues, over-represented sequences, biasing of kmers, and read-length distribution were analysed from the obtained FASTQ file. Based on quality of sequence reads, trimming was done to retain only high quality sequences for further analysis. In addition, the low-quality sequence reads were excluded from the analysis.
From the trimmed paired-end reads, contaminating sequences were removed, including non-polyA tailed RNAs, mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences and others. The contamination removal step was performed for chicken samples using the help of Bowtie 2 (version 2.2.2), in-house Perl scripts and Picard tools (version 1.115).  No contamination removal step was performed for Japanese quail samples as the transfer RNA and ribosomal RNA sequences were not available for Japanese quail.
The gene expression estimation was performed using cufflinks program.
The differential gene expression analysis was performed using cuffdiff program of cufflink package with default settings
Genome_build: Galgal4
Supplementary_files_format_and_content: tab-delimited files show FPKM values of control and virus-infected samples

organism: Coturnix japonica

source_name: spleen

extract_protocol:
TRIzol followed by DNase treatment.  Quality and quantity were determined by Agilent 2100 Bioanallyzer per manufacturer's instructions.  Ribosomal RNA contamination was evaluated by RNA 6000 Pico Chip kit (Agilent, USA) using an Agilent 2100 BioAnalyzer.  Ribosomal RNA was depleted using a RiboMinus Transcriptome Isolation kit (Agilent, USA).
RNA was subjected to fragmentation to obtain approximately 200 bp length fragments, which were reverse transcribed into double-stranded cDNA. The cDNA was treated to generate blunt ends, then adapter sequences were ligated to both ends of the cDNA. High-throughput sequencing of the cDNA library was carried out on an Illumina HiSeq 2000 platform (Illumina, USA)

treatment_protocol: Three-week old chickens or Japanese quails were infected with 10^7 EID50 of LaSota or 2K3 strains of NDV by the oculo-nasal route. Mock-infected animals received phosphate buffered saline.  Animals were euthanized 24 hour following infection.

tag: species

value: Japanese quail

tag: infection status

value: spleen

value: 3 weeks


title: W14_leaf


title: HeLa.U6

city: Madison

first: Heidi

last: Dvinge

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: UW-Madison

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the hg19 human genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie  with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with RSEM-based expression estimates for coding and non-coding RNA transcripts.

source_name: HeLa cells

extract_protocol:
totalRNA was extracted using NucleoSpin miRNA (Macherey-Nagel)
The KAPA Stranded mRNA-Seq kits (KAPA Biosystems) was used with 500ng of total RNA for the construction of sequencing libraries.  Samples were multiplexed using Illumina barcodes to run 3 samples per sequencing lane.

treatment_protocol: Oligos were added to cells at a concentration of 200pM for 48 hours.

value: U6 knock-down

value: HeLa cells


title: Japanese quail LaSota

value: LaSota


title: Japanese quail mock-infection

value: mock


title: Ku50_FEL24

value: 60 days

value: PEG for 24h

value: full expanded leaf


title: HeLa.U1

value: U1 knock-down


title: HeLa.U2

value: U2 knock-down


title: HeLa.control

value: control


title: MCF7.U2

source_name: MCF7 cells

value: MCF7 cells


title: MCF7.control


title: 28792

city: Philadelphia

first: Blanca

middle: E

last: Himes

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_asthma.txt
Barcode: CGATGT

data_processing:
Sample 28782 was excluded from analyses due to having low reads; its corresponding vehicle sample from the same donor (28779) was therefore excluded as well
kallisto was used to obtain TPM per transcript
sleuth was used to perform differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Space-delimited text files include TPM values per gene for each sample that passed QC (PostQC_all_sample_TPM.txt) and transcript-based differential expression results for pairs of samples that passed QC for the BUD vs. vehicle comparison in asthma and non-asthma (Differential_expression_BUD_vs_vehicle_asthma.txt and Differential_expression_BUD_vs_vehicle_non-asthma.txt, respectively).

source_name: airway smooth muscle

extract_protocol:
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc., San Diego, CA)

treatment_protocol: cells were treated with budesonide (100nM for 24h) or vehicle control

tag: disease state

value: asthma

value: budesonide

tag: donor

value: airway smooth muscle


title: 28794

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_non-asthma.txt
Barcode: GCCAAT

tag: treatment


title: 28795

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_non-asthma.txt
Barcode: GTCCGC

value: vehicle


title: 28791

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_non-asthma.txt
Barcode: CCGTCC


title: 28790

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_non-asthma.txt
Barcode: CAGATC


title: 28797

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_asthma.txt
Barcode: TGACCA


title: 28796

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_non-asthma.txt
Barcode: GTGAAA


title: MCF7.U1

tag: cell line


title: 28786

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_asthma.txt
Barcode: ACAGTG


title: 28789

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_asthma.txt
Barcode: ATGTCA


title: HeLa.U4

value: U4 knock-down


title: 28784


title: Arg7_leaf

value: 90 days

value: normal condition

value: leaf


title: 28787

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_asthma.txt
Barcode: AGTCAA


title: 28788

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_asthma.txt
Barcode: AGTTCC


title: 28781

description:
PostQC_all_sample_TPM.txt
Differential_expression_BUD_vs_vehicle_non-asthma.txt
Barcode: CTTGTA


title: 28783


title: 28780


title: MCF7.U6

value: U6 knock-down


title: MCF7.U4


title: 28777


title: 28775


title: 28778


title: 28774


title: 28773


title: 28776


title: 28770


title: 28793


title: 28771


title: 28768


title: 28769


title: 28765


title: 28767


title: 28766


title: 28785


title: 28763


title: 28762


title: C2

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

data_processing:
Reads have been aligned using STAR (version 2.3.0e_r291) on hg19 reference with default parameters. Samples A4 and A5 have been merged with their specific re-runs at BAM level using samtools merge software (version 1.2-17-ge91985a)
Gene-level counts have been calculated using Rsubread package (version 1.16.1) for R statistical program using the ensmbl Gene annotation file for hg19 in GTF format.
Counts have been tested for gene-level differential expression using limma-voom package (version 3.22.7) for R with a TMM normalization and taking account for quality weights.
Design has been built to test condition-related differences in Amyloid in respect to control samples.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] Tab-delimited file containing the matrix output by Rsubread. Columns correspond to samples, rows correspond to single genes

source_name: Control, HAOEC

growth_protocol: HAOEC cells were grown in EGM-2 (Lonza) complete containing 2& FBS

extract_protocol:
RNA extraction by TRIZOL method
The TruSeq™ RNA Sample preparation kit (Illumina) was used to generate poly-A selected, indexed cDNA libraries, according to the manufacturer’s instructions.

treatment_protocol: Cells were stimulated or not with 400nM β-amyloid in EGM-2 medium containing 0.5% FBS, 0.5 ng/ml VEGF, 1 μg/ml ascorbic acid and 0.1% Heparin  for 24 hours

value: HAOEC cells treated with growth medium only

value: HAOEC


title: C4


title: A5 rerun

source_name: 400nM β-amyloid, HAOEC

value: HAOEC cells treated with 400nM β-amyloid


title: C3


title: C6


title: A6


title: A4 rerun


title: A4


title: C1


title: A2


title: 28772


title: 105

data_processing:
fastq files from three donors who were sequenced in replicate were concatenated for each donor
STAR was used to align reads to the hg38 reference genome
HTSeq was used to obtain raw read counts per gene
DESeq2 was used to perform differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: counts_matrix.tsv: tab-separated values of HTSeq raw counts
Supplementary_files_format_and_content: ardsVardsBMT.csv: comma-separated values of DESeq2 results output

source_name: Whole blood

extract_protocol:
Total RNA was extracted using Paxgene Blood RNA kit (Qiagen Sciences, Inc., Germantown, MD). RNA was globin-cleared using the Ambion GLOBINclear kit.
Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA).

value: SEPSIS

value: Whole blood


title: 37


title: A3


title: 134


title: A1


title: 310


title: 242

value: SEPSIS/BMT


title: 210


title: 406


title: 252


title: 282


title: 18


title: 473


title: 252_1


title: 28764


title: 495_1

value: ARDS


title: A5


title: 19_1


title: 221


title: 19


title: 204


title: 495


title: 239


title: 223

value: ARDS/BMT


title: 266


title: 92


title: 247


title: 427


title: HeLa Rsf1 siRNA [RNA-Seq]

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

description:
polyA RNAseq
hg19_CsiRNA_Rsf1siRNA_Cuffdiff_on_data_1,_data_2,_and_data_17__gene_differential_expression_testing.tabular
hg19_Rsf1siRNA_RNF2siRNA_Cuffdiff_on_data_2,_data_3,_and_data_17__gene_differential_expression_testing.tabular

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed to remove adapters and low quality bases
Reads were mapped to mm10 or hg19 with TopHat (tophat -p 12 --mate-inner-dist=200 --mate-std-dev=40 --no-mixed --no-coverage-search) for RNAseq or BWA samse for ChIPseq
Transcripts were assembled with Cufflinks.
Differential gene expression was performed by Cuffdiff
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Gene expression values are a direct output of Cuffdiff. Bedgraph files were scaled to 10 million reads

source_name: HeLa Rsf1 siRNA

extract_protocol:
 HeLa cells (3X105) were treated with either scrambled siRNA, or RNF2 siRNA, or RSF1 siRNA. 48 hrs later, cells were harvested and total RNA was extracted with Trizol. For mouse ESC, total RNA was extracted directly from wild type and RSF1 KO cells. For ChIP sequencing experiments, ChIP was performed with anti-FLAG antibody in a mouse ESC line stably expressing FLAG-RSF1.
RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP and Mnase libraries were prepared for sequencing using standard illumina protocols

value: HeLa


title: HeLa Control [RNA-Seq]

description:
polyA RNAseq
hg19_CsiRNA_RNF2siRNA_Cuffdiff_on_data_1,_data_3,_and_data_17__gene_differential_expression_testing.tabular
hg19_CsiRNA_Rsf1siRNA_Cuffdiff_on_data_1,_data_2,_and_data_17__gene_differential_expression_testing.tabular

source_name: HeLa Control


title: HeLa RNF2 siRNA [RNA-Seq]

description:
polyA RNAseq
hg19_CsiRNA_RNF2siRNA_Cuffdiff_on_data_1,_data_3,_and_data_17__gene_differential_expression_testing.tabular
hg19_Rsf1siRNA_RNF2siRNA_Cuffdiff_on_data_2,_data_3,_and_data_17__gene_differential_expression_testing.tabular

source_name: HeLa RNF2 siRNA


title: 453


title: bf Oxidized rep2

city: Farmington

first: Gordon

middle: G.

last: Carmichael

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
Library strategy: RibOxi-seq
RibOxi-seq. During alignment,TriTrypDB-29_TbruceiLister427.gff from the TriTryp data base was used.
Genome_build: 427
Supplementary_files_format_and_content: RibOxi-seq. During analysis, DESeq2's cooksCutoff for outliers were disabled, since the nature of the method makes many sites look like outliers. All analyzed data use only chromosome 2  (Tb427_02_v4) with the base position region indicated in files.  The analyzed region of chromosome 2 is 370000-378499 which is where one of the rRNA genes is located. Count files contain raw read 3' end base counts; *sites files contain normalized abundance measurements filtered by log 2 fold change and adjusted p values.

organism: Trypanosoma brucei

source_name: blood stream form (bf), strain 427

extract_protocol:
Total RNA is extraction using PureLink® RNA Mini Kit (ThermoFisher Scientific, 12183025) and PureLink® DNase Set (ThermoFisher Scientific, 12185010) following kit protocols.
RibOxi-seq

tag: passage

tag: life stage

value: blood stream form


title: bf Oxidized rep3


title: pf Oxidized rep1

source_name: procyclic form (pf), strain 427

value: procyclic form


title: pf Oxidized rep3


title: pf Oxidized rep2


title: bf Oxidized rep1


title: ros1-3 knockout line

city: Seoul

first: Jin Hoe

last: Huh

address: Gwanak-gu

department: Dept Plant Science

country: South Korea

institute: Seoul National University

data_processing:
Low quality trimming and artificial sequence trimming was performed with trim_galore (version 0.2.8) with parameters "--paired -t -a TACAGTCCGACGATC"
BS-seq data mapping was performed with bwa-meth (version 0.09).
The 5mC ratio calling was performed with bwa-meth (version 0.09) and Bis-SNP (version 0.82.2) with parameters "--map-q 60 -T BisulfiteGenotyper -C CG,1 -C CHG,1 -C CHH,1 -out_modes EMIT_ALL_CYTOSINES"
Biased bases at ends of mapped reads were surveyed and trimmed (--trim 3,3)
Genome_build: TAIR10
Supplementary_files_format_and_content: a tab-delimited text file contains; cytosine locus, 5mC/non-5mC reads counts and sequence context

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Twelve-d-old seedlings grown at 22 oC, 16/8 hr of light time, 70% of relative humidity

extract_protocol:
Genomic DNA was extracted from whole seedlings and sent to Macrogen (http://www.macrogen.com/eng/) for bisulfite treatment, library preparation and sequencing.
Bisulfite treatment and following library construction were performed using standard Illumina protocols.

tag: developmental stage

value: whole seedling

tag: genotype

value: ros1-3 knockout


title: ros1-4 knockout line

value: ros1-4 knockout


title: 167


title: wildtype col-0

value: wild type


title: pf non-oxidation control rep1


title: pf non-oxidation control rep2


title: DHA_hypothalamus_rep2 [RNA-seq]

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 610 Charles E. Young Dr. East

institute: UCLA

description: processed data file: Hypothalamus_fpkm_processed.txt

data_processing:
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent Technologies, CA, USA) and Qubit RNA assay (Life Technologies, NY, USA).
The RNA-Seq libraries were prepared followed the standard Illumina protocol (http://support.illumina.com/sequencing/documentation.ilmn). Briefly, about 1,000 ng total RNA was first enriched for mRNA by poly-A selection, then fragmented, and reverse transcribed using random hexamer-primers to generate first-strand cDNA. Second-strand cDNA was then generated using RNase H and DNA polymerase. Fragments of 200-400 bp in size were next enriched through PCR and multiplex barcodes were also added. Sequencing was performed on HiSeq 2000 (Illumina Inc, CA, USA). Data quality check was done on Sequencing Analysis Viewer and demultiplexing was performed with CASAVA 1.8.2 (Illumina Inc, CA, USA).

value: Sprague Dawley

value: male

tag: fed with

value: DHA for 6 wks

value: hypothalamus


title: DHA_hippocampus_rep3 [RNA-seq]

description: processed data file: Hippocampus_fpkm_processed.txt

tag: gender

value: hippocampus


title: DHA_hippocampus_rep4 [RNA-seq]


title: DHA_hypothalamus_rep1 [RNA-seq]


title: DHA_hippocampus_rep2 [RNA-seq]


title: DHA_hippocampus_rep1 [RNA-seq]


title: bf non-oxidation control rep3


title: T12_3

first: Tong

last: Chen

address: No 16 Nan-xiao-jie Dong-zhi-men-nei

department: State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica

institute: China Academy of Chinese Medical Sciences

description:
T12_3
MeJA induce for 12 hours

data_processing:
Base-calling were performed using RTA and CASAVA.
The quality of sequencing data was estimated using FastQC (v0.11.3). Then adaptors and low quality bases were removed using Trimmomatic (v0.33).
Clean reads from all samples were pooled together and feeded to de novo RNA-seq assembly software Trinity (v2.0.6) with default parameters.
The expression of assembled transcripts and genes were quantified using RSEM (v1.2.19).
Genome_build: n/a
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of each transcript for all samples.

organism: Andrographis paniculata

source_name: T12 leaves

extract_protocol:
Total RNAs from leaves induced for 0, 12, 24 and 48 hours with three biological replicates were extracted using Trizol (Invitrogen, 15596-018) according to the manufacturer’s instructions. Highly purified and intact mRNAs were enriched from total RNAs using Dynabeads® mRNA purification kit (Ambion, 61006). RNAs were fragmented into ~ 300 nt fragments by 1 min incubation at 94℃ in fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl, pH 7.0). The fragmentation reaction was stopped with 50 mM EDTA, followed by standard ethanol precipitation and collected for sequencing and expression validation.
For the strand-specific RNA-seq, fragmented RNAs were re-suspended in H2O and used for library generation with mRNA sequencing kit (Illumina Inc. San Diego, CA). Sequencing was carried out on Illumina HiSeq 4000 sequencer (Illumina Inc. San Diego, CA) according to the manufacturer’s instructions and 150 nt paired-end sequencing reads were generated.

value: leaf

tag: induction stage


title: T48_2

description:
T48_2
MeJA induce for 48 hours

source_name: T48 leaves


title: T24_1

description:
T24_1
MeJA induce for 24 hours

source_name: T24 leaves


title: T48_1

description:
T48_1
MeJA induce for 48 hours


title: bf non-oxidation control rep1


title: T24_2

description:
T24_2
MeJA induce for 24 hours


title: bf non-oxidation control rep2


title: T24_3

description:
T24_3
MeJA induce for 24 hours


title: pf non-oxidation control rep3


title: T12_2

description:
T12_2
MeJA induce for 12 hours


title: T12_1

description:
T12_1
MeJA induce for 12 hours


title: T0_3

description:
T0_3
MeJA induce for 0 hours

source_name: T0 leaves


title: T0_2

description:
T0_2
MeJA induce for 0 hours


title: T0_1

description:
T0_1
MeJA induce for 0 hours


title: DHA_hypothalamus_rep3 [RNA-seq]


title: ribo_aglaiacized_roca

status: Public on Dec 30 2018

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

description: Ribosome Profiling

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

extract_protocol:
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification
Ribosome profiling

value: RocA treatment

tag: extracted molecule

value: total RNA

value: Rnase I footprinting, ribosome pelleting, RNA extraction


title: ribo_naive_DMSO_rep2

description: Ribosome Profiling

value: control DMSO treatment


title: ribo_aglaiacized_DMSO_rep1

description: Ribosome Profiling


title: ribo_aglaiacized_DMSO_rep2

description: Ribosome Profiling


title: DN50_rep2

city: Hangzhou

first: Kexin

last: Zhang

address: No.9, Meiling South Road

institute: Tea Research Institute,Chinese Academy of Agricultural Science

data_processing:
Leaves mRNA  of soybeans were used by RNA sequencing using Illumina HiSeqTM2000.
The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample ...

organism: Glycine max

source_name: trifoliolate leaf

extract_protocol:
Trifoliolate leaves were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: trifoliolate leaf

tag: age

value: germination day 30


title: GmRAV1-ox_rep2

tag: tissue


title: GmRAV1-ox_rep3


title: ribo_naive_DMSO_rep1

description: Ribosome Profiling


title: DN50_rep3


title: ribo_naive_roca

description: Ribosome Profiling


title: T48_3

description:
T48_3
MeJA induce for 48 hours


title: DN50_rep1


title: GmRAV1-ox_rep1


title: RIP_lysate_input1

status: Public on Dec 29 2018

city: Bethesda

first: Chuanyuan

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Illumina reads were post-processed and aligned to the mouse mm9 assembly using STAR program with default parameters.
For RIP-Seq:to visualize sequencing signals in the genome browser, we generated bigwig files with bamCoverage function from deepTools
For RNA-Seq: The read count for each gene were calculate by using the summarizeOverlaps function in R package GenomicAlignments.
Further normalization was performed by rlog function in DESeq2 package
Genome_build: mm9
Supplementary_files_format_and_content: for RNA-Seq, bamfiles are mapping results. entrez_count_rld.txt contain rlog transfomed counts per Gene. For RIP-Seq, Bigwig file for each dataset was generated by deepTools software

source_name: BMDCs

growth_protocol: 20 million BMDCs were harvested and co-cultured with necrotic B16-OVA overnight.

extract_protocol:
For RIP-Seq：Cells were washed twice with cold PBS and the cell pellet was re-suspended with 2 volumes of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/mL RNase inhibitor).For RNA-Seq: Total RNA was extracted by Trizol.
For RIP-Seq：Lysate was incubated on ice for 5 min centrifuged for 15 min to clear the lysate. 1/10 volume of cell lysate was saved as input and total RNA was extracted by trizol. The rest of cell lysate was incubated with 5ug anti-YTHDF1(Proteintech) at  4°C overnight with gentle rotation followed by incubation with 40ul protein G beads for 1 hour at 4°C. The beads were then washed five times with 1 mL ice-cold washing buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/mL RNase inhibitor). The IP complex was re-suspended in 400μl 1xProteinase K and digested with 2 mg Proteinase K at 55°C for 1 hour. RNA was then extracted by RNA isolation kit (Zymo). Input and IP RNA of each sample were used to generate the library using TruSeq stranded mRNA sample preparation kit (Illumina). For RNA-Seq: Extracted RNA of each sample were used to generate the library using TruSeq stranded mRNA sample preparation kit (Illumina).

treatment_protocol: DCs were then purified and pelleted by centrifuge for 5 min.

value: wt

tag: condition

value: DC+tumor lysate


title: RIP_lysate_IP2


title: RIP_lysate_input2


title: RIP_lysate_IP1


title: Vfo_S2

city: Changsha

first: Dangquan

address: South Shaoshan Road

institute: Central South University of Forestry and Technology

description: processed data file: youtong_exp_RPKM.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
Clean reads assembly by trinity with default parameters
mapped using bowtie -k 2 -v 2
detecting different expression gene using edgeR
Genome_build: youtongshu.fasta for Vfo_S1 and Vfo_S2
Genome_build: mafengshu.fasta for Jcu_S1 and Jcu_S2
Supplementary_files_format_and_content: fasta file for genome, and tab-delimited text files include gene RPKM values for each Sample

organism: Vernicia fordii

source_name: endosperm

extract_protocol:
Total RNA was extracted using CTAB method and treated with RQ1 DNase (promega) to remove DNA.
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)- conjugated magnetic beads (Invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95°C followed by end repair and 5' adaptor ligation. The reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified, and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing.

value: 135 days after pollination

value: seeds from female flowers pollinated to mature seeds

tag: oil accumulation stage

value: S2; fast stage


title: Jcu_S1

description: processed data file: mafeng_exp_RPKM.txt

organism: Jatropha curcas

value: 29 days after pollination

value: S1; early/initial stage


title: Vfo_S1

value: 90 days after pollination


title: wt_lysate2


title: y1ko_alone2

value: DC alone


title: y1ko_lysate2


title: y1ko_alone1


title: y1ko_lysate1


title: P106a2_fruit

first: Jing

last: Li

address: xiangshan street

institute: Beijing institute of botany

data_processing:
Base calling for reads generation and lie on Illumina GA Pipeline v1.3 to base quality control.
filtering the raw reads to remove reads with adaptors or unknown nucleotides larger than 5% and low-quality reads
De novo transcriptome assembly was conducted with the short reads assembly program, Trinity (Grabherr et al., 2011)
Gene expression level was evaluated by using the RPKM method (Wagner et al., 2012). When there was more than one transcript for a gene, the longest one was used to calculate its expression level and coverage. The false discovery rate (FDR) was estimated, and an FDR ≤ 0.001 (Benjamini and Yekutieli, 2001) and the absolute value of the log2 ratio ≥ 2 were used as threshold settings in judging the significance of the difference in gene expression levels.
Genome_build: de novo transcriptome assembly was conducted with the short reads assembly program, Trinity (Grabherr et al., 2011). FASTA files are available on the series record.
Supplementary_files_format_and_content: text files with RPKM and gene annotation

organism: Physalis pubescens

source_name: fruit

growth_protocol: P. floridana P106 were grown in a glass-house under long-day conditions (16 h light /8 h darkness)

extract_protocol:
Total RNA was extracted using the TRIzolTM reagent. Equal quantity of RNA from floral buds, blooming flowers, and 5-day-old fruits of P. floridana.Approximately 20 ug of total RNA (≥ 400 ng/mL) was used to prepare a cDNA library and sequenced using using Illumina HiSeqTM 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: young fruit

tag: Stage

value: after fertilization


title: P106b2_floral_bud

source_name: floral bud

value: floral bud

value: before fertilization


title: P106b1_floral_bud


title: P106a1_fruit


title: wt_lysate1


title: wt_alone1


title: P106_floral_bud_and_fruit

description: This sample was made with RNA from both floral buds and fruits and was used to generate reads for transcriptome assembly. There are no processed data with quantified reads associated with this sample. The FASTA files of assembled transcripts are available on the series record.

source_name: floral bud- fruit mixed

value: floral bud- young fruit

value: flower-fruit transition


title: wt_alone2


title: KMS12

status: Public on Dec 28 2018

city: New York

first: Selina

last: Chen-Kiang

state: New York

address: 1300 York Avenue

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medical College

data_processing:
Cluster generation, sequencing, and processing of the images were done using the Real-Time Analysis (RTA) software on the HiSeq2000 and post-processing with CASAVA (v.1.8.2).
To optimize library preparation we used a TACON high-throughput RNA prep-station. Raw data were filtered for high median quality (Q-value > 20) and then sent to Cornell’s High Performance Computing (HPC) cluster, to be run through our RNA-seq analysis pipeline.
Raw reads were trimmed for the first and last five base pairs before alignment to  remove low quality bases.
Our RNA-Seq analysis pipeline used BWA and SAMtools.
Processed Data files (RPKM values) were obtained using Genesifter (Geospiza), which uses SAMtools and the Genome Analysis Toolkit (GATK) for base quality score recalibration and local re-alignment for indels.
Genome_build: Human (Build 37.2)
Supplementary_files_format_and_content: RPKM values

source_name: Cell line

growth_protocol: Myeloma biopsies were obtained from patients at the New York-Presbyterian Hospital after informed consent as part of a study approved by the Institutional Review Board. Primary BMMCs were purified using MACS CD138 MicroBeads (Miltenyi Biotec). The percentage of BMMCs (CD138+) was determined to be > 95% by flow cytometry. Primary BMMCs were cultured in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FBS (HyClone), 2 mM L-glutamine and 100 U/ml penicillin/streptomycin (Invitrogen), 40 U/ml IL-6 and IGF-1 (R&D).

extract_protocol:
For each experimental condition, 100 ng of high quality total RNA (RIN > 0.8 on the Agilent BioAnalyzer 2100) was isolated using the RNAEasy kit according to the manufacturer’s instructions (QIAGEN)
All RNAs were converted to cDNA, isolated with magnetic beads from the TruSeq mRNA prep kit (v2), and then ligated to Illumina adapters, as per the standard TruSeq Illumina protocol. Using these multi-plexed cDNA libraries, we generated clusters on the Illumina cBot station and paired-end sequenced each sample to 50x50 bp on the Illumina HiSeq2000 at the Weill Cornell Medical College (WCMC) Epigenomics Core

treatment_protocol: Freshly isolated CD138-positive primary BMMCs (0 h) pretreated with PD 0332991 (PD, also called palbociclib, 0.5 mM) for 5 hours were treated further with PD, lenalidomide (Len, 5 mM), or both (PDLen) for 24 hr. Untreated cells were used as control (Cntl).

tag: patient mm

value: No

tag: cell type

value: multiple myeloma cell lines

tag: disease state


title: PDLen7_D

source_name: bone marrow

tag: treatment

value: PD 0332991 + lenalidomide

value: multiple myeloma cells

value: multiple myeloma patients


title: PDLen7_C


title: PDLen7_A

value: control


title: PDLen7_B

value: lenalidomide


title: Jcu_S2

value: 37 days after pollination

value: seeds from female flowers pollinated to mature seeds

value: S2; fast stage


title: PDLen6_E

value: 0 h


title: MM.S

tag: cell line


title: PDLen6_D


title: PDLen6_C


title: PDLen6_A


title: PDLen6_B


title: PDLen5_C


title: PDLen5_A


title: PDLen5_D


title: PDLen5_B


title: PDLen4_C


title: PDLen4_D


title: PDLen4_E


title: PDLen4_A


title: PDLen4_B


title: PDLen3_C


title: PDLen3_E


title: PDLen3_D


title: PDLen3_B


title: PDLen7_E


title: PDLen2_D


title: PDLen2_E


title: PDLen3_A


title: PDLen2_C


title: PDLen2_A


title: PDLen1_E


title: PDLen2_B


title: PDLen1_D


title: PDLen1_B


title: BMPC_65

value: normal plasma cells

value: normal patient


title: PDLen1_A


title: BMPC_57


title: BMPC_56


title: BMPC_49


title: ECAD_Dex_cKO_Rep3

first: Kenneth

last: Lay

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Alignment of sequencing reads was performed using STAR version 2.5.2a.
Transcripts were annotated using Gencode release M10 of the mouse genome.
Gene count output from STAR read aligner was used to perform differential gene expression analysis with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are .txt files containing gene count output from STAR read aligner.

source_name: Skin

extract_protocol: HFSCs were isolated by fluorescence-activated cell sorting (FACS) and total RNA was extracted. mRNA libarary was prepared using Illumina TruSeq mRNA sample preparation kit and single end sequencing was performed using Illumina HiSeq 4000.

tag: strain

value: post-natal week 12

value: skin


title: WT_AnaIII_Rep2

value: post-natal day 23

tag: genotype

value: wild type


title: WT_AnaIII_Rep1


title: ECAD_Dex_cKO_Rep1


title: ECAD_Dex_cKO_Rep2


title: ECAD_cKO_Rep4


title: ECAD_Dex_Het_Rep3


title: ECAD_Dex_Het_Rep1


title: ECAD_Het_Rep4


title: ECAD_cKO_Rep2


title: ECAD_cKO_Rep3


title: ECAD_Het_Rep3


title: ECAD_Dex_Het_Rep2


title: ECAD_Het_Rep2


title: ECAD_cKO_Rep1


title: ECAD_Het_Rep1


title: PDLen1_C


title: SA_MT1

city: bangkok

first: Sirirak

last: Supa-amornkul

address: 272 Payatai

department: Microbiology

country: Thailand

institute: Mahidol University

description: rRNA depleted RNA

data_processing:
.sff file from Ion torrent machine was converted to fastq file.
FastQC program was obtained to determine quality of output sequences.
Sequences were trimmed before alignment. Quality of the sequences was at Phred score of 30.
EDGE-pro was obtained to align the sequences to RF122 reference genome and to detemine differentially expressed genes between the two stains of S. aureus
RPKM data from EDGE-pro were compared and sorted in Microsoft Excel.
Genome_build: NC_007622.1
Supplementary_files_format_and_content: (.xlsx) excel file include RPKM values for each sample

organism: Staphylococcus aureus RF122

source_name: RF122 null sigB strain

growth_protocol: S. aureus strains RF122 were grown until early stationary phase. Early stationary phase is defined as a culture incubated at 37C with 200 rpm agitation until OD 600 reached 1.0 with 3 additional hours of incubation.

extract_protocol:
RNA was obtained by Ribopure RNA extraction kit (Ambion).   rRNA in RNA samples was depleted by MICROBExpress bacterial mRNA enrichment kit.
The whole transcriptome library was constructed by Ion total RNAseq kit.

tag: genotype/variation

value: sigB null


title: SA_WT1

description: rRNA depleted RNA

value: sigB wild-type


title: SA_MT2

description: rRNA depleted RNA


title: SA_WT2

description: rRNA depleted RNA


title: Delta-Input

status: Public on Dec 27 2018

city: Oxford

first: Hedia

last: Chagraoui

address: john radcliffe hospital headley way headington

department: Molecular Hematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

data_processing:
Base calling performed on illumina 1.9 platform
Chipseq reads were aligned to the mm9 and drosophila dm3 genome references. Data were analysed using in-house pipeline that automatically assesses the quality of data, trims adaptors, merges short reads, maps reads to the reference genome, and filters data for duplicates: http://userweb.molbiol.ox.ac.uk/public/telenius/PipeSite.html
mapping : bowtie -m 1 --maxIns 350  --lanes 4
for un-mapping reads : trim_galore -- length 10, --noFlash
removing duplicates : samtools rmdup
no ploidy region (bedtools pairtobed )
reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
pileup of fragments (bedtools genomecov -counts)
generating bigwig tracks (ucsctools bedGraphToBigWig)
peak calling were performed using Macs2 v2.0.10
Genome_build: mm9, dm3
Supplementary_files_format_and_content: broadPeak files were generated using Macs2 with the following parameters  --broad-cutoff 0.05

source_name: mcherry+ mesoderm

extract_protocol:
Complexes were eluted from beads in a thermomixer at 65 degres for 15 min and the eluates and reserved inputs were reverse cross-linked overnight at 65C. The samples were then treated with RNaseA, proteinase K and phenol/chloroform purified.
ChIP samples were submitted to library preparation using NEBNext Ultra DNA Library prep kit for Illumina (NEB 7370) and multiplexing barcodes (NEB E7500) following Illumina’s instructions.

value: ES cell-derived embryoid bodies

tag: ebs stage

value: day 4

value: Scl d/d

tag: antibody

tag: chiprx

value: spike in drosophila S2 cells


title: H3K4me3-WT

value: Scl wt

value: H3K4me3 (ab8580,Abcam)


title: Input-WT


title: H3K4me3-Delta


title: H3K27ac-WT

value: H3K27ac (ab4729,Abcam)


title: H3K27me3-WT

value: H3K27me3 (39155,Active motif)


title: H3K27ac-Delta


title: H3K27me3-Delta


title: H2K119ub-WT

value: H2AK119ub (D27C4,Cell Signaling)


title: ETO2_Chip_replicate2

data_processing:
Base calling performed on illumina 1.9 platform
Chipseq reads were aligned to the mm9  genome reference. Data were analysed using in-house pipeline that automatically assesses the quality of data, trims adaptors, merges short reads, maps reads to the reference genome, and filters data for duplicates: http://userweb.molbiol.ox.ac.uk/public/telenius/PipeSite.html
mapping : bowtie -m 1 --maxIns 350  --lanes 4
for un-mapping reads : trim_galore -- length 10, --noFlash
removing duplicates : samtools rmdup
no ploidy region (bedtools pairtobed )
reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
pileup of fragments (bedtools genomecov -counts)
generating bigwig tracks (ucsctools bedGraphToBigWig)
peak calling were performed using Macs2 v2.0.10 with the following parameters -B -q 0.05 --to-large
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak files were generated with macs2
Supplementary_files_format_and_content: bed file: tab delimited text file containing peakcalling union of replicate 1 and 2

value: ETO2 (sc-9741x,santa cruz)


title: ETO2_Chip_input1


title: H2K119ub-Delta

value: ES cell-derived embryoid bodies (EBs)


title: ETO2_Chip_replicate1


title: SCL_Chip_replicate2

data_processing:
Basecalls were performed using Illumina 1.9
Chip-seq reads were aligned to the mm9 genome using Bowtie v1.1.2 with the following parameters bowtie  -q  -n 2 -m 2
Peaks were called using Macs2  v2.0.10 with the following parameters -B -q 0.01
The two replicates were merged and peak called using IDR: https://sites.google.com/site/anshulkundaje/projects/idr
Supplementary_files_format_and_content: bed file: tab delimited text representing the union of the 2 replicates peak calls

value: day 3.5

value: SCL rabbit anti-serum (in-house)


title: SCL_Chip_input2


title: SCL_Chip_replicate1


title: SCL_Chip_input1


title: j1.scl2

data_processing:
Fastq reads were mapped to the mm9 reference genome using tophat version 2.0.8b
Duplicate reads pairs were removed and reads filtered for mapq> 15 using SAMtools version 0.1.19
Data normalisation and dufferential expression analysis was carried out using EdgeR. Data normalisation to account for differences in sequencing depth and RNA composition was performed using the TMM method (Trimmed Mean of M-values) provided by the edgeR package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include CPM values for each Sample

extract_protocol:
RNA was extracted using RNA minikit (Qiagen). The samples were sent to the Wellcome Trust Center, Oxford University, UK (WTCHG) for sequencing
Libraries and sequencing were done at the WTCHG, university of Oxford, UK

value: Scl -/-

tag: replicate


title: j1.wt3

value: WT


title: sampleWT-1I

data_processing:
Base calling performed on illumina 1.9 platform
Chip-seq reads were aligned to the mm9 genome using Bowtie v1.1.2b with the following parameters:  -q -p 8 --chunkmbs 10000 -n 2 -m 2
Peaks were called using Macs2  v2.0.10 with the following parameters  -B -q 0.05
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak file were generated using Macs2 narrowPeak -q 0.05
Supplementary_files_format_and_content: The bed file is the intersection of the 2 narrowPeak files and was generated with bedtools intersect

source_name: single FLK1+mesoderm

tag: samples

value: input 1


title: j1.wt2


title: sampleWT-2I

value: input 2


title: j1.scl3

value: ES cell-derived embryoid bodies


title: sampleWT-1A

value: anti DEDAF (AB3637,) Millipore


title: j1.scl1


title: j1.wt1


title: KO_UN_2_S8

first: Mikhail

last: Dozmorov

address: 830 E Main St

department: Biostatistics

data_processing:
All sequencing reads were quality controlled using FastQC v0.11.2. Illumina adapters were trimmed using Cutadapt v1.9.dev2, replicates were merged and aligned with their reference genome (UCSC mouse genome build mm10) using subread-align v1.4.6-p4. The BAM files from alignment were processed using featureCounts v1.4.6-p4 to obtain the counts per gene in all samples. Mus_musculus.GRCm38.83.gtf gene definition file was used. The differential expression analysis was performed using edgeR v3.18.1. Genes having counts per million less than 2 in all samples were excluded. Differentially expressed genes were defined using p-value < 0.01 and FDR-corrected p-value < 0.1 cutoffs. All bioinformatics analyses were conducted in R/Bioconductor computing environment v3.4.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text, counts

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow cells were isolated from femurs of C57BL/6 WT and AEG-1KO mice and were differentiated into macrophages using RMPI-1640 medium supplemented with 10% heat-inactivated FBS and 20% L929 conditioned media for 7days at which point cells were harvested.

extract_protocol:
Trizol extraction of total RNA was performed using QIAGEN columns according to the manufacturer's instruction.
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and sequenced on Illumina HiSeq3000 platform.
RNA-Seq libraries were pooled together to aim about 25-40M read passed filtered reads per sample.

value: AEG-1 knockout


title: WT_UN_3_S3

value: Wild-type


title: KO_UN_3_S9


title: WT_UN_1_S1


title: WT_UN_2_S2


title: KO_UN_1_S7


title: sampleWT-2A


title: Day7-2_H3K9ac IP

city: Raleigh

first: Vincent

middle: L

last: Chiang

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

data_processing:
ChIP-seq reads were aligned to the P.trichocarpa genome version 3 by using Bowtie.
Differential peaks between drought treated samples after day 5 and untreated day 0 samples, and between day 7 and day 0, were identified by using DiffReps (ver 1.55.4) with input samples (No antibody in experiments) as background. The peak identification using the window size of 1000 with other default parameters for diffReps.  This software does not provide intermediate files for the peak called from each library.
Genome_build: P. trichocarpa version 3 [http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa]
Supplementary_files_format_and_content: .txt files were generated using diffReps to identify differential peaks between drought-treated samples with untreated control samples.

organism: Populus trichocarpa

source_name: Day7, H3K9ac IP

growth_protocol: P. trichocarpa plants were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 3 months (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterization.

extract_protocol:
Stem differentiating xylem (SDX) isolated from the P.trichocarpa plants and anti-H3K9ac antibodies were used for ChIP assays: SDX were treated with formaldehyde to stabilize protein-DNA interactions. Nuclei were isolated and chromatin were sonicated into 200 to 1,000-bp fragmets, followed by immunoprecipitation of the acetylated H3K9-DNA complexes using anti-H3K9ac antibodies and protein G magnetic beads. An equal amount of IgG from the same source as the anti-H3K9ac antibodies were used as the mock control. The immune complexes were collected and eluted. The acetylated H3K9-DNA cross-linking were reversed, and treated with proteinase K. The DNA were precipitated, dissolved in water and stored at -80°C.
Sequencing libraries were constructed from the prepared DNAs mainly followed manual of Illumina ChIP-seq library kit. The ends of DNA fragments were repaired and ligated to the adaptors. DNA fragments of approximately 250-bp were recovered from the gels and PCR amplified for 18 cycles. The amplified DNA products wer purified and checked for quality (Bioanalyzer) and quantified by qPCR, and sequenced (Illumina HiSeq 2000).

treatment_protocol: Control plants (day 0) were fully irrigated, the soil water content is 74% and the xylem water content is 80.6%. After 5 days without watering, the drought treated plants (day 5) are under a mild drought state, and the soil and xylem water content dropped to 33% and 75.3%, respectively. After 7 days without watering, the drought treated plants (day 7) are under a severe drought state where the soil and xylem water content continued decreasing to 29% and 74.3%, respectively.

tag: time

value: 7 days after drought treatment

tag: chip antibody

value: H3K9ac (Abcam, cat. no. ab10812)

tag: tissue

value: Stem differentiating xylem


title: Day5-2_H3K9ac IP

source_name: Day5, H3K9ac IP

value: 5 days after drought treatment


title: Day7-4

data_processing:
Twelve libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for HiSeq 2000 sequencing
100 bp average read lengths were obtained after removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (Phytozome V10.0, http://www.phytozome.com) using the program “TOPHAT”.
Genome_build: P. trichocarpa
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3) and the read counts

source_name: Stem differentiating xylem

growth_protocol: P. trichocarpa  trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 3 monthes (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterzation. Due to limited greenhouse space, different batch of transgenic trees with respective wild type were planted in soil and harvest at different time, there are total six batch trees were labeled with NSF1 to NSF6

extract_protocol:
Stem defferentiating xylem were scraped from the surface of the debark stem 5cm above soil using a single-edge razor into liquid nitrogen immediately. collected tissues were ground into powder and stored in liquid nitrogen. Total RNA of SDX sample were extracted by uing Qiagen RNeasy Mini Kit (Invitrogen/Life Technologies, Grand Island, NY) with DNase I treatment option as suggested by kit manunal.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control plants (day 0) are with fully irrigation, the soil water content is 74% and the xylem water content is 80.6%. After 5 days without watering, the drought treated plant (day 5) are under a mild drought state, and the soil and xylem water content in dropped to 33% and 75.3%, respectively. After 7 days without watering, the drought treated plant (day 7) is in a severe drought state  where the soil and xylem water content continued decreasing to 29% and 74.3%, respectively.

tag: days after drought treatment

value: 7 day


title: Day0-2_H3K9ac IP

description: diffresp_dr5_2rep & diffresp_dr7_2rep

source_name: Day0, H3K9ac IP

value: 0 days after drought treatment


title: Day0-1_H3K9ac IP

description: diffresp_dr5_2rep & diffresp_dr7_2rep


title: Day5-2_Input

source_name: Day5, Input


title: Day0-2_Input

description: diffresp_dr5_2rep & diffresp_dr7_2rep

source_name: Day0, Input


title: Day0-1_Input

description: diffresp_dr5_2rep & diffresp_dr7_2rep


title: Day5-1_H3K9ac IP


title: Day7-3


title: Day5-4

value: 5 day


title: Day5-2


title: Day7-1


title: Day5-1


title: Day7-2_Input

source_name: Day7, Input


title: Day0-4

value: 0 day


title: Day7-1_H3K9ac IP


title: Day0-2


title: Day7-1_Input


title: Day0-3


title: Day0-1


title: T_20W_2

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Overall read quality was checked using FASTQC v.0.11.2. Overall these plots showed that the base data off sequencer is of acceptable quality for analysis. For RNA QC the tool RNA-SeQC (v1.1.7) was used. Overall the RNA sequencing quality is acceptable for further analysis.
The raw sequence data, in the form of FASTQ files, was aligned to the human genome (mm10, iGenome GTF definition file) using the BOWTIE/TOPHAT pipeline (BOWTIE v2.2.3, TOPHAT 2.0.13).  Accessory programs for the alignment stage include SAMTOOLS (v1.0) and cutadapt (1.7.1).  Transcript assembly, abundance estimation, and tests for differential regulation were done using CUFFLINKS (v2.2.1).
Results of differential expression testing were loaded into the CummeRBund software in R (v3.1.1) for final output of results and graphing.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: skin

extract_protocol:
Skin samples were macrodissected and snap frozen in liquid nitrogen. Samples were pulvarized in liquid nitrogen and RNA was isolated using Qiagen Rneasy.
Library prep and seq:  All of the RNA samples were quantified using the qubit RNA kit (Life Technologies) on the Qubit 2.0 fluorometer. The RNA integrity was assessed using the Agilent RNA 6000 nano chip on the Agilent Bioanalyzer 2100. Each sample had a RIN score greater than 8.0 and 250ng of each sample was used for library prep. Libraries were prepared using the TruSeq Stranded mRNA library prep kit (Illumina). Briefly, 250 ng of RNA from each sample was purified using poly-T coated magnetic beads before being fragmented for first strand cDNA synthesis. Samples are reverse transcribed in the first strand cDNA synthesis step using random primers, then amplified using DNA Polymerase I in the second strand cDNA synthesis step. Samples were cleaned using AMPure beads before being single “A” base extended in preparation for adaptor ligation to generate indexed, cDNA libraries. Final cDNA libraries were size validated using the Agilent Bioanalyzer 2100 and quantified by qPCR (Kapa Biosystems). All libraries were normalized to 10nM, pooled 5 samples per pool and diluted down to 2nM. 2nM pools were denatured using 0.2N NaOH and diluted to a final concentration of 10 pM. 10pM pools were loaded onto the Illumina cBot for cluster generation. The clustered flow cell was sequenced paired-end 101 cycles using v3 reagents on the Illumina HighSeq 2000 to achieve a minimum of ~30 million reads per sample.

value: CD36highCD90+ Treated

value: C3H/HeJ mice

tag: time point

value: 20 weeks


title: T_20W_3

tag: cell type


title: T_20W_1


title: F_20W_3

value: fibrotic tissue


title: F_20W_2


title: F_20W_1


title: Day5-1_Input


title: F_6W_3

value: 6 weeks


title: N1

value: normal tissue

tag: Time point 0


title: Day7-2


title: F_6W_2


title: N2


title: PANC1 cells treated with 1mM pilocarpine for 72 hours sample 4 [YT008]

status: Public on Dec 26 2018

first: Timothy

middle: Cragin

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie 2, Tophat 2.04 and HTSeq 0.6.1 .
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: excel file with raw counts for each gene

organism: Homo sapiens

source_name: PANC1_1mM pilocarpine

extract_protocol:
RNA was extracted from each group using RNAqueous®-Micro Total RNA Isolation Kit (Thermo Sci,catalog no. AM1931) (n=4).
The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA Pico kit.
RNAs with RNA Integrity Number (RIN) values greater than 8.0 were used to generate sequencing libraries.
Extracted RNA samples were amplified by Ovation® RNA-Seq System V2 (NuGEN) Kit. Amplified cDNA was labeled with Encore biotin module Kit (NuGEN)for RNA-Seq applications.

treatment_protocol: Panc-1 cells were treated with 1mM pilocarpine.

value: pancreatic cancer cells

tag: treated with

value: 1mM pilocarpine


title: PANC1 cells treated with 1mM pilocarpine for 72 hours sample 1 [YT005]

tag: cell line


title: F_6W_1

organism: Mus musculus

tag: strain


title: Day5-3


title: N3


title: PANC1 cells untreated sample 4 [YT004]


title: PANC1 cells untreated sample 2 [YT002]


title: HSR-RNA-GBM1-RNA-2

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer.
The Illumina bcl2fastq 2.19.0.316 pipeline was used to generate the sequence data.
Sequences were mapping to the human genome hg38 using STAR software 2.5.3a.
Porvides uniquely mapped reads in counts for each gene by the featureCounts function in Rsubread package (1.26.0) using the inbuilt annotation hg38.
Identification of differentially expressed genes by edgeR package (3.16.5).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing read counts values of each gene for each sample; csv file containing statistical results by edgeR package.

source_name: HSR-GBM1 glioblastoma cells replicate 2

growth_protocol: HSR-GBM1 cells were cultured as neurospheres on ultra-low attachment plates (Sigma) in Dulbecco's Modified Eagle Medium /Nutrient Mixture (DMEM/F-12) Media (Gibco) containing 2% StemPro neural supplement (Invitrogen Life Technologies), 20 ng/ml basic fibroblast growth factor (bFGF; Millipore) and 20 ng/ml epidermal growth factor (EGF; Millipore) at 37 °C, 5% CO2 and 95% humidity.

extract_protocol:
Total genomic RNA were extracted from cultured cell pellets using the RNeasy and QiaShredder Kits (Qiagen) according to manufacturer’s protocols . The DNA samples were treated with 3 μL of RNase solution (Qiagen) and Proteinase K Solution (20 μg/μL; Qiagen) at 65 °C for 10 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HSR-GBM1 cells were cultured in the presence of 0.5 μM of 5-azacytidine (Sigma-Aldrich) for 48 hours or 100 μg/mL of Vitamin C (L-ascorbic acid, Sigma-Aldrich) for 72 hours. Culture media was changed every 24 hours.

value: cell line derived from human glioblastoma

tag: cell-subtype

value: astrocytoma

value: Glioblastoma multiforme


title: HSR-RNA-GBM1+VitC-RNA-1

source_name: HSR-GBM1 glioblastoma cells cultured with vitaminC replicate 1


title: HSR-RNA-GBM1+5Aza-RNA-2

source_name: HSR-GBM1 glioblastoma cells cultured with 5azacytidine replicate 2


title: PANC1 cells untreated sample 1 [YT001]


title: HSR-RNA-GBM1+VitC-RNA-3

source_name: HSR-GBM1 glioblastoma cells cultured with vitaminC replicate 3


title: HSR-RNA-GBM1+5Aza-RNA-3

source_name: HSR-GBM1 glioblastoma cells cultured with 5azacytidine replicate 3


title: HSR-RNA-GBM1-RNA-3

source_name: HSR-GBM1 glioblastoma cells replicate 3


title: HSR-RNA-GBM1+VitC-RNA-2

source_name: HSR-GBM1 glioblastoma cells cultured with vitaminC replicate 2


title: HSR-RNA-GBM1+5Aza-RNA-1

source_name: HSR-GBM1 glioblastoma cells cultured with 5azacytidine replicate 1


title: HSR-RNA-GBM1-RNA-1

source_name: HSR-GBM1 glioblastoma cells replicate 1


title: PANC1 cells treated with 1mM pilocarpine for 72 hours sample 2 [YT006]


title: M12_P1

city: Crawley

first: Alecia-Jane

last: Twigger

state: WA

address: 35 Stirling Highway

department: Chemistry and Biochemistry

institute: The University of Western Australia

data_processing:
Illumina HiSeq Control Software (HCS) v2.2.58 with RTA 1.18.64 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using SOAP2. No more than 2 mismatches were allowed in the alignment
Gene expression levels were estimated and expressed as RPKM (Reads Per Kilobase per Million mapped reads) (Mortazavi et al. 2008) and annotated with BLAST (-p blastx -e 1e-5 -m 7/8) sequences to Nr database of NCBI
Genome_build: hg38
Supplementary_files_format_and_content: a single tab-delimited text file include RPKM values for all samples

source_name: Human milk cells_month 12_participant 1

extract_protocol:
Cells were isolated by centrifugation from either prepartum secretions or human milk. mRNA was extracted using the Qiagen mini RNeasy extraction kit using extraction techniques previously described (Hassiotou et al 2012). Mammary tissue mRNA from breast biopsies was purchased from Agilent Technologies, representative of a pool of donors. Library preparation was done by degrading DNA contaminant, enrichment with oligo(dT) magnetic beads and fragmentation with fragmentation buffer using the standard Illumina reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mammary gland development stage

value: mature lactation

tag: participant

value: human milk cells


title: M12_P2

source_name: Human milk cells_month 12_participant 2


title: PANC1 cells treated with 1mM pilocarpine for 72 hours sample 3 [YT007]

last: Wang


title: M12_P4

source_name: Human milk cells_month 12_participant 4


title: M6_P4

source_name: Human milk cells_month 6_participant 4


title: M6_P3

source_name: Human milk cells_month 6_participant 3


title: M6_P2

source_name: Human milk cells_month 6_participant 2


title: M6_P1

source_name: Human milk cells_month 6_participant 1


title: M3_P4

source_name: Human milk cells_month 3_participant 4


title: M3_P2

source_name: Human milk cells_month 3_participant 2


title: M3_P1

source_name: Human milk cells_month 3_participant 1


title: PANC1 cells untreated sample 3 [YT003]


title: M1_P3

source_name: Human milk cells_month 1_participant 3


title: PS_P4

source_name: Prepartum secretion cells_participant 4

value: pregnancy

value: prepartum secretion cells


title: M1_P1

source_name: Human milk cells_month 1_participant 1


title: M1_P2

source_name: Human milk cells_month 1_participant 2


title: M1_P4

source_name: Human milk cells_month 1_participant 4


title: PS_P2

source_name: Prepartum secretion cells_participant 2


title: PS_P3

source_name: Prepartum secretion cells_participant 3


title: RMT

source_name: Resting mammary tissue

value: resting

value: pool of 5 participants

value: resting mammary tissue


title: M12_P3

source_name: Human milk cells_month 12_participant 3


title: PS_P1

source_name: Prepartum secretion cells_participant 1


title: psp RNAi line 17, end of night_3

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.9software used for basecalling.
The software kallisto (v 0.43.0) was used for quantification with the Arabidopsis thaliana genome as a reference (TAIR10 cDNA). The resulting normalized counts (transcripts per million, tpm) were used for downstream analyses.
Kallisto was run with 30 bootstrapping replications. The resulting .h5 files were fed forward into differential gene expression analysis using sleuth (v 0.28.1).
Means and standard deviation of tpm of biological triplicates group were calculated.
Supplementary_files_format_and_content: Tab-separated table (.tsv) file including Arabidopsis Gene Identifier (AGI) and TAIR10 description, raw estimated counts (kallisto), tpm (kallisto) for each sample and mean and standard deviation of tpm for biological triplicates, sleuth results of differential gene expression comparing each of the mutant lines against the wildtype at the respective time of sampling

source_name: Leaf

extract_protocol:
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in paired-end mode (150 bp read length) on an Illumina HiSeq 3000 platform.

tag: genotype

value: psp RNAi line 17

tag: time of sampling

value: end of night


title: psp RNAi line 18, end of night_2

value: psp RNAi line 18


title: psp RNAi line 18, end of night_3


title: psp RNAi line 17, end of night_2


title: psp RNAi line 18, end of night_1


title: psp RNAi line 17, beginning of day_3

value: beginning of day

value: end of day


title: M3_P3

source_name: Human milk cells_month 3_participant 3


title: psp RNAi line 18, beginning of day_2


title: psp RNAi line 18, beginning of day_3


title: psp RNAi line 17, beginning of day_1


title: psp RNAi line 18, beginning of day_1


title: umbilical cord artery 1

city: chongqing

first: Jia

last: Luo

state: chongqing

address: tiansheng road

institute: Southwest University

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the dataset was further processed with an in-house program called ACGT101-miR (LC Sciences, Houston, TX) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats. Unique sequences with lengths of 18-26 nts were subsequently mapped to specific-species precursors in miRBase 21.0 by BLAST searching to identify known miRNAs and novel 3p- and 5p-derived miRNAs. Lengths varying at both 3’- and 5’-ends and one mismatch inside of the sequence were allowed in the alignment.
MiRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test. The significance threshold was set to be 0.01 and 0.05 in each test.
Genome_build: Genome database:Sus scrofa (Sscrofa10.2); miRbase version: V21.0
Supplementary_files_format_and_content: identified miRNAs with details (reads,location,length,etc)

organism: Sus scrofa

source_name: umbilical cord blood

extract_protocol:
In brief, dilute plasma ﬂuid with an equal volume of PBS and centrifuge 30 min at 2,000 × g, 4◦C, to remove cell. Then, carefully transfer supernatant to ultracentrifuge tubes or bottles without pellet contamination, centrifuge 45 min at 12,000 × g, 4◦C. Next, filter the suspension through a 0.22-µm ﬁlter, and collect in a fresh ultracentrifuge tube or bottle, centrifuge 2h at 160,000 × g, 4◦C. Pour off the supernatant. Resuspend the pellet in 250µl PBS and Store at −80◦C until use.
Three normal and three IUGR piglets were pooled, respectively, used for library construction. Approximately 1 μg of total RNA was used to prepare the small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina). Single-end sequencing (36 bp) on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) was performed following the recommended protocol.

treatment_protocol: Ready to concentration 15% EDTA anticoagulant solution, join 2 drops in the 5 ml syringe every time before collecting umbilical cord blood. When piglet was born, puts it under the heat lamp, a man picked up the umbilical cord, another discerned the UA and UV in light quickly, with syringe in draw blood vessels. After, upside down to make them blending fully timely, packing in 2 ml centrifuge tube, 1 ml per tube, for the next step.

tag: tissues

value: umbilical cord artery

tag: content

value: exosome

tag: breed

value: Yorkshire


title: umbilical cord artery 2


title: umbilical cord vein 2

value: umbilical cord vein


title: 2972R

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Fusion  transcripts were detected using three different approaches: tophat-fusion, defuse, and EASANA fusion (GenoSplice technology)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2014_2 were also provide

source_name: Brain

extract_protocol:
Total RNA from cryopreserved tumour samples was extracted using the iPrep Trizol® Plus RNA kit (Life Technologies)
Library was prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology) with an input total RNA of 1µg

value: CD 20+ DLBCL


title: 3004R


title: 3002R


title: 2764R


title: 3024R


title: 2763R


title: psp RNAi line 17, end of night_1


title: METTL14_2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: METTL14 siRNA-transfected cells after 48 hrs.

data_processing:
Illumina Casava v1.8.2 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b.
Gene count measurements were obtained using HTSeq-count.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count.

source_name: MDA-MB-231, METTL14 siRNA

growth_protocol: Human breast cancer cell line MDA-MB-231 was purchased from American Type Culture Collection (ATCC) and cultured in standard growth medium according to their guidelines. The cell lines were authenticated annually by using PCR for short tandem repeats.

extract_protocol:
Qiagen miRNeasy kit following manufacturer's protocol.
Total RNA samples about 1-2 g were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was barcoded and then pooled for cluster generation and sequencing run with 100bp single-end (SE) sequencing protocol.

treatment_protocol: METTL14-siRNA (siRNA ID: SASI_Hs01_00179440, Sigma_Aldrich, St. Louis, MO) and transfection by using ThermoFisher Lipofectamine RNAi MAX following manufacturer's protocol.

value: human breast cancer cell line

tag: treatment

value: METTL14 siRNA


title: CON_2

source_name: MDA-MB-231, control siRNA

value: Scrambled siRNA


title: Conditioned_3

city: Bern

first: Andrew

middle: J.

last: Macpherson

state: Bern

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Basecalling software for Illumina HiSeq 2500
Sequence quality control with fastqc 0.11.2
Adaptor trimming with trimmomatic 0.33
Sequence alignment with tophat 2.0.13
Sequence counting with HTSeq 0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPG (read counts per gene) values for each Sample;
Supplementary_files_format_and_content: Row counts with HTSeq
Supplementary_files_format_and_content: Normalized counts with DEseq2

source_name: Conditioned_Small intestinal (Jejunum) tissue

extract_protocol:
Small intestinal (Jejunum) tissues were removed, placed in Trizol solution, and flash frozon in liquid nitrogen. RNA was harvested using Trizol reagent and subsequent Rnsasy MinElute kit (Qiagen). Ribosomal DNA was removed with Ribominus Transcriptome Isolation Kit (Invitrogen). RNA libraries were prepared with TruSeq RNA sample preparation v2 kit (TruSeq Stranded mRNA Sample Preparation, Illumina).
RNA libraries were prepared for Illumina HiSeq 2500 sequencing using standard Illumina protocols.

tag: strain background

tag: mouse status

value: HA107-conditioned mouse

tag: tissue

value: Small intestinal (Jejunum) tissue


title: Unconditioned_3

source_name: Unconditioned_Small intestinal (Jejunum) tissue

value: unconditioned


title: Unconditioned_2


title: psp RNAi line 17, beginning of day_2


title: Conditioned_1


title: Unconditioned_1


title: Conditioned_2


title: umbilical cord vein 1


title: METTL14_1

tag: cell type


title: SUM1315_DN_Rep1

city: Philadelphia

first: Rumela

last: Chakrabarti

address: 380 S University Ave, 411 Hill Pavilion

department: Department of Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

data_processing:
Reads were mapped to the Homo Sapiens genome (GRCH37 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the Ensembl GRCH37 build were quantified with featureCounts (v1.5.0) and subsequently converted Transcripts per Million (TPM) values location.
Genome_build: GRCH37
Supplementary_files_format_and_content: TPM

extract_protocol:
Total RNA was isolated from the cell lines using the Invitrogen RNA extraction kit in accordance with the manufacturer’s instructions.
RNA-Sequencing libraries were prepared using the Kapa Stranded mRNA-Seq Kit Illumina Librabry Prep Kit, multiplexed and sequenced on the Illumina NextSeq 500.

tag: shRNA


title: HCC1806RR_DN_Rep1


title: SUM1315_Vec_Rep1

value: Vector


title: SstRed-3

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Bascalling performed using RTA 1.18.64.0
The strand specific reads were screened for ribosomal RNA by aligning with BWA (0.7.12) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were subjected to single-end transcript abundance quantification with Kallisto (0.43.0) with an estimated fragment length of 200 and standard deviation of 20. Transcript sequences are derived via UCSC refFlat (downloaded on 2015_02_20) and the mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: Standard output file of Kallisto (abundance.txt) as tab separated text files

source_name: CEA (both sides) punched out of acute brain slice (mouse 7)

growth_protocol: PKCδ::Cre or SST::Cre mice were crossed to Cre-dependent Rosa::td-Tomato lines, and the offspring used for neural population sequencing.

extract_protocol:
Mice were decapitated, brains extracted on ice and 1mm thick brain section cut in ice-cold Hibernate A Low Fluorescence solution (BrainBits). The central amygdala was extracted using biopsy punchers (1mm diameter; Integra Miltex) and enzymatically dissociated (Papain Dissociation System, Worthington Biochem). Approximately 1000 td-Tomato+ cells were retrieved with subsequent FACS sorting.
Libraries were prepared with the SMARTer® smRNA-Seq Kit for Illumina® (Clontech, 78100 Saint-Germain-en-Laye, France) and submitted to deep sequencing on a HiSeq 2500 system (Illumina, San Diego, USA).

tag: strain/genotype

value: SST::Cre (Jackson #013044) X Rosa::loxP-STOP-loxP-td-Tomato (Jackson #007905)

tag: age

value: 20-week old

tag: Sex

value: male

value: central amygdala


title: PkcdRed-2

source_name: CEA (both sides) punched out of acute brain slice (mouse 2)

value: PKC delta-type::Cre (mmrrc #11559) X Rosa::loxP-STOP-loxP-td-Tomato (Jackson #007905)

value: 9-week old


title: SstRed-4

source_name: CEA (both sides) punched out of acute brain slice (mouse 8)


title: PkcdRed-1

source_name: CEA (both sides) punched out of acute brain slice (mouse 1)


title: SstRed-1

source_name: CEA (both sides) punched out of acute brain slice (mouse 5)

value: 8-week old


title: SstRed-2

source_name: CEA (both sides) punched out of acute brain slice (mouse 6)