title: HCC.ct-184

description: cell-free DNA


title: osk_d0-c_c19

status: Public on Jan 01 2019

type: SRA

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

country: China

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

library_source: transcriptomic

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts and transcripts per million(TPM) were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: Mouse ESCs (mESCs) and iPS cell lines were cultured on feeder layers with mESC medium (high glucose DMEM, 15%FBS, NEAA, GlutaMAX, LIF) plus 2i (1 m PD0325901, 3 m CHIR99021). MEF cells were maintained in 10% FBS medium (high glucose DMEM supplemented with 10% FBS, GlutaMAX and NEAA). The reprogramming cells at different days were cultured in iCD1 medium.

extract_protocol:
For bulk cells, total RNAs were extracted by chloroform-isopropanol method; for single cell, following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).

tag: cell type

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: Stage

tag: strain background


title: HCC.ct-183

city: La Jolla

first: Kang

last: Zhang

address: 9500 Gilman Dr

country: USA

institute: UCSD

description: cell-free DNA

library_source: genomic

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers and methylation frequencies were calculated using custom scripts (BamExtractor, D.Diep, K.Zhang)
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values and numbers of C and T for all samples at all analyzed CpG markers

molecule: genomic DNA

organism: Homo sapiens

source_name: blood serum

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

value: blood serum

tag: group

value: hepatocellular carcinoma patient


title: osk_d0-b_c57


title: HCC.ct-182

description: cell-free DNA


title: osk_d0-c_c42


title: osk_d0-b_c55


title: HCC.ct-180

description: cell-free DNA


title: osk_d0-b_c53


title: osk_d0-b_c51


title: osk_d0-b_c07


title: HCC.ct-181

description: cell-free DNA


title: HCC.ct-179

description: cell-free DNA


title: osk_d0-b_c72


title: HCC.ct-178

description: cell-free DNA


title: osk_d0-c_c49


title: osk_d0-c_c43


title: HCC.ct-177

description: cell-free DNA


title: HCC.ct-176

description: cell-free DNA


title: HCC.ct-185

description: cell-free DNA


title: osk_d0_c29


title: HCC.ct-173

description: cell-free DNA


title: osk_d0_c28


title: osk_d0-b_c59


title: osk_d0-b_c58


title: HCC.ct-175

description: cell-free DNA


title: HCC.ct-174

description: cell-free DNA


title: HCC.ct-172

description: cell-free DNA


title: osk_d0_c27


title: osk_d0-c_c37


title: HCC.ct-171

description: cell-free DNA


title: HCC.ct-169

description: cell-free DNA


title: osk_d0-c_c86


title: osk_d0-c_c35


title: osk_d0-c_c36


title: osk_d0-c_c30


title: osk_d0-c_c32


title: osk_d0-c_c31


title: HCC.ct-166

description: cell-free DNA


title: HCC.ct-165

description: cell-free DNA


title: osk_d0-c_c33


title: HCC.ct-167

description: cell-free DNA


title: osk_d0-c_c38


title: osk_d0-c_c10


title: HCC.ct-164

description: cell-free DNA


title: osk_d0_c47


title: osk_d0-b_c19


title: HCC.ct-170

description: cell-free DNA


title: osk_d0-b_c18


title: HCC.ct-162

description: cell-free DNA


title: osk_d0-b_c15


title: HCC.ct-160

description: cell-free DNA


title: HCC.ct-158

description: cell-free DNA


title: HCC.ct-159

description: cell-free DNA


title: osk_d0-b_c66


title: osk_d0-b_c11


title: osk_d0-b_c67


title: HCC.ct-161

description: cell-free DNA


title: HCC.ct-156

description: cell-free DNA


title: HCC.ct-157

description: cell-free DNA


title: osk_d0-b_c63


title: HCC.ct-155

description: cell-free DNA


title: HCC.ct-168

description: cell-free DNA


title: osk_d0-b_c60


title: HCC.ct-153

description: cell-free DNA


title: osk_d0-b_c65


title: HCC.ct-151

description: cell-free DNA


title: HCC.ct-152

description: cell-free DNA


title: osk_d0_c76


title: mef-b_c65


title: mef-a_c02


title: mef-a_c01


title: HCC.ct-163

description: cell-free DNA


title: HCC.ct-154

description: cell-free DNA


title: HCC.ct-150

description: cell-free DNA


title: HCC.ct-149

description: cell-free DNA


title: HCC.ct-148

description: cell-free DNA


title: mef-a_c06


title: HCC.ct-147

description: cell-free DNA


title: HCC.ct-145

description: cell-free DNA


title: osk_d0-b_c64


title: HCC.ct-146

description: cell-free DNA


title: mef-a_c60


title: mef-b_c62


title: HCC.ct-144

description: cell-free DNA


title: mef-b_c60


title: HCC.ct-142

description: cell-free DNA


title: mef-b_c66


title: mef-b_c67


title: HCC.ct-143

description: cell-free DNA


title: HCC.ct-140

description: cell-free DNA


title: mef-b_c64


title: mef-b_c61


title: mef-a_c08


title: mef-a_c50


title: mef-a_c07


title: HCC.ct-136

description: cell-free DNA


title: HCC.ct-139

description: cell-free DNA


title: HCC.ct-137

description: cell-free DNA


title: HCC.ct-135

description: cell-free DNA


title: HCC.ct-134

description: cell-free DNA


title: mef-b_c13


title: mef-b_c12


title: HCC.ct-138

description: cell-free DNA


title: HCC.ct-132

description: cell-free DNA


title: HCC.ct-131

description: cell-free DNA


title: mef-b_c11


title: mef-b_c70


title: mef-b_c68


title: mef-b_c15


title: HCC.ct-141

description: cell-free DNA


title: HCC.ct-133

description: cell-free DNA


title: HCC.ct-129

description: cell-free DNA


title: mef-b_c23


title: mef-b_c26


title: HCC.ct-127

description: cell-free DNA


title: mef-b_c14


title: HCC.ct-126

description: cell-free DNA


title: HCC.ct-130

description: cell-free DNA


title: HCC.ct-125

description: cell-free DNA


title: HCC.ct-124

description: cell-free DNA


title: mef-b_c21


title: mef-b_c22


title: mef-a_c10


title: HCC.ct-122

description: cell-free DNA


title: mef-a_c12


title: mef-b_c10


title: HCC.ct-121

description: cell-free DNA


title: HCC.ct-120

description: cell-free DNA


title: HCC.ct-119

description: cell-free DNA


title: mef-a_c15


title: mef-a_c14


title: HCC.ct-118

description: cell-free DNA


title: mef-a_c18


title: HCC.ct-128

description: cell-free DNA


title: mef-b_c25


title: mef-a_c03


title: HCC.ct-116

description: cell-free DNA


title: HCC.ct-117

description: cell-free DNA


title: mef-b_c24


title: mef-a_c53


title: HCC.ct-115

description: cell-free DNA


title: mef-a_c54


title: HCC.ct-114

description: cell-free DNA


title: HCC.ct-123

description: cell-free DNA


title: HCC.ct-112

description: cell-free DNA


title: mef-b_c71


title: mef-a_c57


title: mef-a_c51


title: mef-a_c56


title: HCC.ct-111

description: cell-free DNA


title: HCC.ct-109

description: cell-free DNA


title: mef-a_c17


title: mef-b_c72


title: mef-a_c52


title: HCC.ct-108

description: cell-free DNA


title: mef-a_c11


title: mef-a_c59


title: mef-b_c69


title: mef-a_c55


title: mef-a_c66


title: HCC.ct-107

description: cell-free DNA


title: HCC.ct-105

description: cell-free DNA


title: mef-a_c04


title: HCC.ct-102

description: cell-free DNA


title: mef-a_c05


title: mef-b_c51


title: HCC.ct-113

description: cell-free DNA


title: mef-a_c09


title: HCC.ct-110

description: cell-free DNA


title: HCC.ct-100

description: cell-free DNA


title: HCC.ct-103

description: cell-free DNA


title: mef-b_c18


title: mef-b_c17


title: HCC.ct-99

description: cell-free DNA


title: mef-a_c49


title: HCC.ct-96

description: cell-free DNA


title: HCC.ct-98

description: cell-free DNA


title: HCC.ct-106

description: cell-free DNA


title: mef-a_c62


title: HCC.ct-97

description: cell-free DNA


title: mef-b_c49


title: mef-b_c09


title: HCC.ct-95

description: cell-free DNA


title: HCC.ct-93

description: cell-free DNA


title: mef-b_c08


title: mef-b_c05


title: HCC.ct-94

description: cell-free DNA


title: mef-b_c04


title: HCC.ct-92

description: cell-free DNA


title: HCC.ct-91

description: cell-free DNA


title: HCC.ct-90

description: cell-free DNA


title: mef-b_c01


title: HCC.ct-101

description: cell-free DNA


title: HCC.ct-88

description: cell-free DNA


title: mef-b_c52


title: mef-b_c02


title: mef-b_c53


title: mef-b_c50


title: HCC.ct-86

description: cell-free DNA


title: mef-b_c56


title: mef-b_c57


title: HCC.ct-85

description: cell-free DNA


title: mef-b_c55


title: HCC.ct-84

description: cell-free DNA


title: HCC.ct-83

description: cell-free DNA


title: mef-b_c58


title: HCC.ct-82

description: cell-free DNA


title: mef-b_c59


title: HCC.ct-77

description: cell-free DNA


title: HCC.ct-76

description: cell-free DNA


title: HCC.ct-81

description: cell-free DNA


title: HCC.ct-74

description: cell-free DNA


title: HCC.ct-78

description: cell-free DNA


title: HCC.ct-71

description: cell-free DNA


title: HCC.ct-73

description: cell-free DNA


title: HCC.ct-72

description: cell-free DNA


title: HCC.ct-89

description: cell-free DNA


title: HCC.ct-70

description: cell-free DNA


title: HCC.ct-69

description: cell-free DNA


title: HCC.ct-75

description: cell-free DNA


title: HCC.ct-67

description: cell-free DNA


title: HCC.ct-65

description: cell-free DNA


title: HCC.ct-66

description: cell-free DNA


title: HCC.ct-64

description: cell-free DNA


title: HCC.ct-63

description: cell-free DNA


title: HCC.ct-104

description: cell-free DNA


title: HCC.ct-62

description: cell-free DNA


title: HCC.ct-59

description: cell-free DNA


title: HCC.ct-58

description: cell-free DNA


title: HCC.ct-56

description: cell-free DNA


title: HCC.ct-60

description: cell-free DNA


title: HCC.ct-80

description: cell-free DNA


title: HCC.ct-57

description: cell-free DNA


title: HCC.ct-79

description: cell-free DNA


title: HCC.ct-61

description: cell-free DNA


title: HCC.ct-55

description: cell-free DNA


title: HCC.ct-54

description: cell-free DNA


title: HCC.ct-52

description: cell-free DNA


title: HCC.ct-51

description: cell-free DNA


title: HCC.ct-50

description: cell-free DNA


title: HCC.ct-46

description: cell-free DNA


title: HCC.ct-43

description: cell-free DNA


title: HCC.ct-49

description: cell-free DNA


title: HCC.ct-42

description: cell-free DNA


title: HCC.ct-48

description: cell-free DNA


title: HCC.ct-45

description: cell-free DNA


title: HCC.ct-44

description: cell-free DNA


title: HCC.ct-41

description: cell-free DNA


title: HCC.ct-40

description: cell-free DNA


title: HCC.ct-39

description: cell-free DNA


title: HCC.ct-38

description: cell-free DNA


title: HCC.ct-37

description: cell-free DNA


title: HCC.ct-34

description: cell-free DNA


title: HCC.ct-35

description: cell-free DNA


title: HCC.ct-31

description: cell-free DNA


title: HCC.ct-30

description: cell-free DNA


title: HCC.ct-33

description: cell-free DNA


title: HCC.ct-32

description: cell-free DNA


title: HCC.ct-53

description: cell-free DNA


title: HCC.ct-27

description: cell-free DNA


title: HCC.ct-29

description: cell-free DNA


title: HCC.ct-36

description: cell-free DNA


title: HCC.ct-28

description: cell-free DNA


title: HCC.ct-25

description: cell-free DNA


title: HCC.ct-47

description: cell-free DNA


title: HCC.ct-68

description: cell-free DNA


title: HCC.ct-23

description: cell-free DNA


title: HCC.ct-26

description: cell-free DNA


title: HCC.ct-24

description: cell-free DNA


title: HCC.ct-22

description: cell-free DNA


title: HCC.ct-20

description: cell-free DNA


title: HCC.ct-19

description: cell-free DNA


title: HCC.ct-18

description: cell-free DNA


title: HCC.ct-17

description: cell-free DNA


title: HCC.ct-16

description: cell-free DNA


title: HCC.ct-15

description: cell-free DNA


title: HCC.ct-14

description: cell-free DNA


title: HCC.ct-87

description: cell-free DNA


title: HCC.ct-13

description: cell-free DNA


title: HCC.ct-12

description: cell-free DNA


title: HCC.ct-3

description: cell-free DNA


title: HCC.ct-1

description: cell-free DNA


title: HCC.ct-4

description: cell-free DNA


title: HCC.ct-5

description: cell-free DNA


title: HCC.ct-10

description: cell-free DNA


title: HCC.ct-6

description: cell-free DNA


title: HCC.ct-7

description: cell-free DNA


title: HCC.ct-8

description: cell-free DNA


title: HCC.ct-2

description: cell-free DNA


title: HCC.ct-9

description: cell-free DNA


title: DN-MAML-2

city: Charlestown

first: Long

last: Zhao

state: MA

address: 149 13th Street

department: Cardiovascular Research Center

institute: Massachusetts General Hospital

description: maml2 FPKM

data_processing:
Samples were processed using the RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).  After QC of the raw reads with FastQC, adapter sequences and other contaminant sequences were trimmed from the reads using Cutadapt.
Trimmed reads were aligned to UCSC build zv9 of the zebrafish genome (Drier), augmented with transcript information from Ensembl release 79 using STAR.
Alignments were checked for evenness of coverage, rRNA content, genomic context, complexity, etc. using FastQC, Qualimap, MulitQC and custom tools.
Counts of reads aligning to known genes were generated by featureCounts. Differential expression was called using DESeq2.
Genome_build: zv9

organism: Danio rerio

growth_protocol: Adult fish density was mantained at 4 fish per liter.

extract_protocol:
Heart samples were collected and RNA extracted using RNeasy Plus Micro Kit (Qiagen) as per the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hearts of 6-12 months old fish were amputated and following daily 1 hour heat shock (38C) treatment.

tag: strain

value: TU-AB

tag: developmental stage

value: adult; 6-12 months

tag: genotype/variation

tag: time point

value: 5 day post amputation

tag: tissue

value: Heart


title: DN-MAML-1

description: maml1 FPKM


title: DN-MAML-3

description: maml3 FPKM


title: CB-HSPC_ATACseq

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: ATAC-Seq of hematopoietic stem/progenitor cells from cord blood

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
For RNA-Seq, paired-end reads were aligned to the human genome (hg19) with STAR (v2.2.0c) with default parameters.  For ATAC-Seq, single end reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5) with default parameters. Only uniquely alignable reads were used for downstream analysis.
For RNA-Seq, Fragments Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).  ATAC-Seq reads were analyzed for peaks using HOMER by treated the experiments as default ChIP-Seq experiments.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-14) FPKM.

source_name: hematopoietic stem/progenitor cell from cord blood

growth_protocol: iPSCs (passage 11) and ESCs cultured on MEF feeders in human ESC medium were manually dissociated and plated on 8 days old overgrown OP9 feeders to start differentiation. Cells were co-cultured with the OP9 feeders for 12-14 days in OP9 differentiation medium (Alpha MEM containing 10% FBS, 100 μM monothioglycerol and 50 μg/ml ascorbic acid) as described by Vodyanik, M. A. & Slukvin, II. (Curr Protoc Cell Biol 2007). Differentiated cells were dissociated with collagenase and Accutase (Innovative Cell Technologies) and subjected to cell sorting, RNA  isolation and transposition assay. Cord blood CD34+ cells were isolated from donated cord blood units by immnuselection with CD34 magnetic microbeads (Miltenyi biotec).

extract_protocol:
RNA was extracted with Qiagen RNeasy micro kit. ATAC-seq was carried out according to Buenrostro et al (Nat. Methods, 2013).DNA was purified using Zymo ChIP DNA Clean & Concentrator kit (Zymo Research).
The Agilent TapeStation or Bioanalyzer was used to determine RNA integrity (RIN) numbers prior to library preparation. Stranded mRNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA tail was isolated using poly-T oligos conjugated to magnetic beads. mRNA was then fragmented and reverse-transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. dUTP-incorporated second strand was not amplified. cDNA was then end-repaired, index adapter-ligated and PCR amplified. Purification of nucleic acids after each enzymatic steps was achieved by using AMPure XP beads (Beckman Coulter).

treatment_protocol: Wnt inhibitors were added on day 6 of the differentiation protocol. Half of the medium was refreshed every other day with inhibitors until cell harvest

tag: cell surface marker


title: iPSC-HPC-DMSO_RNAseq

description:
RNA-Seq of hematopoietic progenitor cells derived from iPSCs treated with DMSO
fpkm.txt

source_name: hematopoietic progenitor cell derived from iPSC


title: iPSC-HPC-IWR1_ATACseq

description: ATAC-Seq of hematopoietic progenitor cells derived from iPSCs treated with IWR1

value: hematopoietic progenitor cell derived from iPSC


title: WT control-3

description: control 3 FPKM

source_name: WT control_heart

value: Wild type


title: WT control-2

description: control 2 FPKM


title: iPSC-HPC-DMSO_ATACseq

description: ATAC-Seq of hematopoietic progenitor cells derived from iPSCs treated with DMSO


title: iPSC-HPC-RNAseq-r2

description:
RNA-Seq of hematopoietic progenitor cells derived from iPSCs
fpkm.txt


title: CB-HSPC-RNAseq-r2

description:
RNA-Seq of hematopoietic progenitor cells from cord blood
fpkm.txt

value: hematopoietic stem/progenitor cell from cord blood


title: iPSC-HPC-IWR1_RNAseq

description:
RNA-Seq of hematopoietic progenitor cells derived from iPSCs treated with IWR1
fpkm.txt


title: iPSC-HPC-RNAseq-r1


title: CB-HSPC-RNAseq-r1


title: HCC.ct-11

description: cell-free DNA


title: HCC.ct-21

description: cell-free DNA


title: WT control-1

description: control 1 FPKM


title: mRNA transcriptome from 30DAP

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

description: mRNAs

data_processing:
Raw snRNA read data were checked for sequence quality using FastQC. After trimming 3' adapter sequence "ATCTCGTATGCCGTCTTCTGCTTG", snRNA sequence reads were sequentially aligned against annotated B. rapa, B. napus and A. thaliana miRNA mature/star sequences, hairpin sequences curated in miRBase Release 17, A. thaliana small RNA sequences from the Arabidopsis Small RNA Project (ASRP), any known RNA genes in Rfam, and entries in the Brassica Unigene set. Finally, remaining reads were aligned against B. rapa genome scaffolds (v1.1). Uniquely aligned reads against the B. rapa genome scaffolds were further analysed for novel miRNA prediction using miRDeep2. mRNA transcriptome data were also aligned to the annotated B. rapa genome. Alignment results were output in SAM/BAM format to facilitate further analysis. For mRNA alignment, BAM format was converted into a BEDGraph file to extract chromosome coverage information using BEDtools. All alignments were performed using the NovoAlign software.

Files of type *bam_coverage.bg were generated by BEDtools 'genomeCoverageBed' command.
The command used to convert .bam to .bg:
$BEDDIR/genomeCoverageBed -ibam $bamfile -g $genomesize -bga >$bedgraph
Column descriptions:
The first one is the name for chromosomes (e.g. A01) or supercontigs "BGIScaffold000001".
The second column is the start position.
The third column is the end position.
The fourth column is the value for the corresponding region, which is the coverage information.

Files of type *unnormalized_counts.txt were generated with in-house scripts.
Files mRNA_transcripts*unnormalized_counts.txt have two columns. The first column lists all the identified predicted B.rapa mRNA transcripts, and the second column lists all the numbers of maximum depth for the corresponding mRNA transcript, which we used to quantify the expression level for the transcript. Identifiers starting with Bra (e.g. Bra011877) are the predicted mRNA/gene name for the Brassica rapa genome v1.1 (see brad database at http://brassicadb.org/brad/index.php for more information about sequenced B. rapa).
Files small_RNAs*unnormalized_counts.txt have the level of expression (number of reads) for the corresponding annotated small RNAs in Brassica and Arabidopsis. Identifiers starting with ASRP (e.g., ASRP100169) are the annotated small RNAs in Brassica and Arabidopsis (closely related). The names with "ASRP" are those small RNAs identified from the Arabidopsis thaliana small RNA Project (http://asrp.cgrb.oregonstate.edu/). For the process of small RNA deep sequencing data, firstly we tried to identify those matching all annotated small RNA in Brassica and Arabidopsis thaliana, and then aligned the remaining reads to the sequence scaffolds of Brassica rapa. Hence, in these two tables "small_RNAs_unnormalized_counts.txt", you see the first column as the identifier of annotated small RNAs and the second column have the number of reads matching to it.
Genome Build:
30dap_accepted_hits_sorted.bam_coverage.bedGraph: B. rapa v1.1
Expression_profilling_mRNA_transcripts_30DAP_unnormalized_counts.txt: B. rapa v1.1

organism: Brassica rapa

source_name: seed, 30DAP

growth_protocol: Seed of the homozygous Brassica rapa var. trilocularis (yellow sarson) inbred line R-o-18 were sown in 75% peat:12% loam:3% vermiculite:10% grit, and grown under controlled conditions at 18-15oC with 16 hours light at 300 µmol m2s-1.

extract_protocol: Seed was collected at the described time points and frozen in liquid nitrogen. Total RNA including the snRNA fraction was extracted using mirVana™ miRNA Isolation Kit (Ambion) and assessed for quality and quantity (NanodropTM1000, Thermo-Scientific). Library construction of snRNAs was performed using the Illumina Small RNA Sample Prep kit (v1.5) and sequenced using an Illumina Genome Analyser IIx (GAIIx) platform by Source BioScience (Nottingham, UK). For each sample 24-25 million reads (38 bp, single end) were obtained. Total RNA for transcriptome analysis was extracted from the same time points using the Qiagen RNeasy kit, with the extracted RNA assessed for quality and quantity as above. Transcriptome sequencing was performed on the GAIIx platform by the University of Warwick (UK).

treatment_protocol: Seedlings were transplanted in 9cm pots 14-17 days after initial potting. In order to limit dispersal of pollen, inflorescences were enclosed in micro-perforated pollination bags prior to anthesis. Individual flowers were hand pollinated and tagged. Developing seed were collected at the stated days after pollination (DAP).

value: seed

tag: development


title: mRNA transcriptome from 15DAP

description: mRNAs

data_processing:
Raw snRNA read data were checked for sequence quality using FastQC. After trimming 3' adapter sequence "ATCTCGTATGCCGTCTTCTGCTTG", snRNA sequence reads were sequentially aligned against annotated B. rapa, B. napus and A. thaliana miRNA mature/star sequences, hairpin sequences curated in miRBase Release 17, A. thaliana small RNA sequences from the Arabidopsis Small RNA Project (ASRP), any known RNA genes in Rfam, and entries in the Brassica Unigene set. Finally, remaining reads were aligned against B. rapa genome scaffolds (v1.1). Uniquely aligned reads against the B. rapa genome scaffolds were further analysed for novel miRNA prediction using miRDeep2. mRNA transcriptome data were also aligned to the annotated B. rapa genome. Alignment results were output in SAM/BAM format to facilitate further analysis. For mRNA alignment, BAM format was converted into a BEDGraph file to extract chromosome coverage information using BEDtools. All alignments were performed using the NovoAlign software.

Files of type *bam_coverage.bg were generated by BEDtools 'genomeCoverageBed' command.
The command used to convert .bam to .bg:
$BEDDIR/genomeCoverageBed -ibam $bamfile -g $genomesize -bga >$bedgraph
Column descriptions:
The first one is the name for chromosomes (e.g. A01) or supercontigs "BGIScaffold000001".
The second column is the start position.
The third column is the end position.
The fourth column is the value for the corresponding region, which is the coverage information.

Files of type *unnormalized_counts.txt were generated with in-house scripts.
Files mRNA_transcripts*unnormalized_counts.txt have two columns. The first column lists all the identified predicted B.rapa mRNA transcripts, and the second column lists all the numbers of maximum depth for the corresponding mRNA transcript, which we used to quantify the expression level for the transcript. Identifiers starting with Bra (e.g. Bra011877) are the predicted mRNA/gene name for the Brassica rapa genome v1.1 (see brad database at http://brassicadb.org/brad/index.php for more information about sequenced B. rapa).
Files small_RNAs*unnormalized_counts.txt have the level of expression (number of reads) for the corresponding annotated small RNAs in Brassica and Arabidopsis. Identifiers starting with ASRP (e.g., ASRP100169) are the annotated small RNAs in Brassica and Arabidopsis (closely related). The names with "ASRP" are those small RNAs identified from the Arabidopsis thaliana small RNA Project (http://asrp.cgrb.oregonstate.edu/). For the process of small RNA deep sequencing data, firstly we tried to identify those matching all annotated small RNA in Brassica and Arabidopsis thaliana, and then aligned the remaining reads to the sequence scaffolds of Brassica rapa. Hence, in these two tables "small_RNAs_unnormalized_counts.txt", you see the first column as the identifier of annotated small RNAs and the second column have the number of reads matching to it.
Genome Build:
15dap_accepted_hits_sorted.bam_coverage.bedGraph: B. rapa v1.1
Expression_profilling_mRNA_transcripts_15DAP_unnormalized_counts.txt: B. rapa v1.1

source_name: seed, 15DAP


title: small RNAs from 15DAP

description: small RNAs

data_processing:
Raw snRNA read data were checked for sequence quality using FastQC. After trimming 3' adapter sequence "ATCTCGTATGCCGTCTTCTGCTTG", snRNA sequence reads were sequentially aligned against annotated B. rapa, B. napus and A. thaliana miRNA mature/star sequences, hairpin sequences curated in miRBase Release 17, A. thaliana small RNA sequences from the Arabidopsis Small RNA Project (ASRP), any known RNA genes in Rfam, and entries in the Brassica Unigene set. Finally, remaining reads were aligned against B. rapa genome scaffolds (v1.1). Uniquely aligned reads against the B. rapa genome scaffolds were further analysed for novel miRNA prediction using miRDeep2. mRNA transcriptome data were also aligned to the annotated B. rapa genome. Alignment results were output in SAM/BAM format to facilitate further analysis. For mRNA alignment, BAM format was converted into a BEDGraph file to extract chromosome coverage information using BEDtools. All alignments were performed using the NovoAlign software.

Files of type *bam_coverage.bg were generated by BEDtools 'genomeCoverageBed' command.
The command used to convert .bam to .bg:
$BEDDIR/genomeCoverageBed -ibam $bamfile -g $genomesize -bga >$bedgraph
Column descriptions:
The first one is the name for chromosomes (e.g. A01) or supercontigs "BGIScaffold000001".
The second column is the start position.
The third column is the end position.
The fourth column is the value for the corresponding region, which is the coverage information.

Files of type *unnormalized_counts.txt were generated with in-house scripts.
Files mRNA_transcripts*unnormalized_counts.txt have two columns. The first column lists all the identified predicted B.rapa mRNA transcripts, and the second column lists all the numbers of maximum depth for the corresponding mRNA transcript, which we used to quantify the expression level for the transcript. Identifiers starting with Bra (e.g. Bra011877) are the predicted mRNA/gene name for the Brassica rapa genome v1.1 (see brad database at http://brassicadb.org/brad/index.php for more information about sequenced B. rapa).
Files small_RNAs*unnormalized_counts.txt have the level of expression (number of reads) for the corresponding annotated small RNAs in Brassica and Arabidopsis. Identifiers starting with ASRP (e.g., ASRP100169) are the annotated small RNAs in Brassica and Arabidopsis (closely related). The names with "ASRP" are those small RNAs identified from the Arabidopsis thaliana small RNA Project (http://asrp.cgrb.oregonstate.edu/). For the process of small RNA deep sequencing data, firstly we tried to identify those matching all annotated small RNA in Brassica and Arabidopsis thaliana, and then aligned the remaining reads to the sequence scaffolds of Brassica rapa. Hence, in these two tables "small_RNAs_unnormalized_counts.txt", you see the first column as the identifier of annotated small RNAs and the second column have the number of reads matching to it.
Genome Build:
bra_s_4_vs_brapa_scaf_new.bam_sorted.bam_coverage.bedGraph: B. rapa v1.1
Expression_profilling_small_RNAs_15DAP_unnormalized_counts.txt: B. rapa v1.1


title: C74

city: Minneapolis

first: Dong Seong

last: Cho

state: MN

address: 421 Washington Ave S.E.

department: Chemical Engineering and Materials Science

institute: University of Minnesota

description: single cell

data_processing:
Illumina Casava1.8 software used for basecalling.
2 bp of sequenced reads were trimmed for low-quality sequence, then mapped to rn5 whole genome using Tophat2 with parameters -r 240 --mate-std-dev 140 --segment-length 24.
Reads were counted using summarizeOverlaps function in R.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text file include raw counts of sequencing reads for each sample.

organism: Rattus norvegicus

source_name: Converted hypoblast stem cells (cHypoSCs)

growth_protocol: Converted (c) hypoblast stem cells (cHypoSCs) were derived from rat embryonic stem cells (rESCs) by culturing with LIF, PDGF, EGF, and 2% fetal bovine serum. After 7 days of initial plating, the cells were passaged every 2-3 days.

extract_protocol:
RNA was extracted using C1 Single-Cell Auto Prep Kit with the manufacturer's protocol (Fluidigm, PN 100-5950).
RNA libraries were prepared for sequencing with Illumina Nextera XT DNA sample preparation protocol as described in C1 Single-Cell Auto Prep protocol (Fluidigm, PN 100-5950).

treatment_protocol: After 12 days of differentiation of rESCs, cHypoSCs were collected for single-cell RNA-seq.

value: rESC-derived converted hypoblast stem cells

tag: differentiation day

value: 12 days


title: C88

description: single cell


title: C72

description: single cell


title: C94

description: single cell


title: C96

description: single cell


title: C54

description: single cell


title: small RNAs from 30DAP

description: small RNAs

data_processing:
Raw snRNA read data were checked for sequence quality using FastQC. After trimming 3' adapter sequence "ATCTCGTATGCCGTCTTCTGCTTG", snRNA sequence reads were sequentially aligned against annotated B. rapa, B. napus and A. thaliana miRNA mature/star sequences, hairpin sequences curated in miRBase Release 17, A. thaliana small RNA sequences from the Arabidopsis Small RNA Project (ASRP), any known RNA genes in Rfam, and entries in the Brassica Unigene set. Finally, remaining reads were aligned against B. rapa genome scaffolds (v1.1). Uniquely aligned reads against the B. rapa genome scaffolds were further analysed for novel miRNA prediction using miRDeep2. mRNA transcriptome data were also aligned to the annotated B. rapa genome. Alignment results were output in SAM/BAM format to facilitate further analysis. For mRNA alignment, BAM format was converted into a BEDGraph file to extract chromosome coverage information using BEDtools. All alignments were performed using the NovoAlign software.

Files of type *bam_coverage.bg were generated by BEDtools 'genomeCoverageBed' command.
The command used to convert .bam to .bg:
$BEDDIR/genomeCoverageBed -ibam $bamfile -g $genomesize -bga >$bedgraph
Column descriptions:
The first one is the name for chromosomes (e.g. A01) or supercontigs "BGIScaffold000001".
The second column is the start position.
The third column is the end position.
The fourth column is the value for the corresponding region, which is the coverage information.

Files of type *unnormalized_counts.txt were generated with in-house scripts.
Files mRNA_transcripts*unnormalized_counts.txt have two columns. The first column lists all the identified predicted B.rapa mRNA transcripts, and the second column lists all the numbers of maximum depth for the corresponding mRNA transcript, which we used to quantify the expression level for the transcript. Identifiers starting with Bra (e.g. Bra011877) are the predicted mRNA/gene name for the Brassica rapa genome v1.1 (see brad database at http://brassicadb.org/brad/index.php for more information about sequenced B. rapa).
Files small_RNAs*unnormalized_counts.txt have the level of expression (number of reads) for the corresponding annotated small RNAs in Brassica and Arabidopsis. Identifiers starting with ASRP (e.g., ASRP100169) are the annotated small RNAs in Brassica and Arabidopsis (closely related). The names with "ASRP" are those small RNAs identified from the Arabidopsis thaliana small RNA Project (http://asrp.cgrb.oregonstate.edu/). For the process of small RNA deep sequencing data, firstly we tried to identify those matching all annotated small RNA in Brassica and Arabidopsis thaliana, and then aligned the remaining reads to the sequence scaffolds of Brassica rapa. Hence, in these two tables "small_RNAs_unnormalized_counts.txt", you see the first column as the identifier of annotated small RNAs and the second column have the number of reads matching to it.
Genome Build:
bra_s_5_vs_brapa_scaf_new.bam_coverage.bedGraph: B. rapa v1.1
Expression_profilling_small_RNAs_30DAP_unnormalized_counts.txt: B. rapa v1.1


title: C47

description: single cell


title: C46

description: single cell


title: C44

description: single cell


title: C40

description: single cell


title: C39

description: single cell


title: C43

description: single cell


title: C31

description: single cell


title: C38

description: single cell


title: C33

description: single cell


title: C30

description: single cell


title: C37

description: single cell


title: C27

description: single cell


title: C32

description: single cell


title: C26

description: single cell


title: C24

description: single cell


title: pop

description: bulk population control


title: C95

description: single cell


title: C25

description: single cell


title: C80

description: single cell


title: C23

description: single cell


title: C17

description: single cell


title: C10

description: single cell


title: C45

description: single cell


title: C14

description: single cell


title: C15

description: single cell


title: C13

description: single cell


title: C09

description: single cell


title: C05

description: single cell


title: C03

description: single cell


title: Attp2_Saureus_Set3

city: College Park

first: Stephen

middle: M.

last: Mount

state: MD

address: HJP, 4065 Campus Dr.

department: Cell Biol. & Mol. Genetics

institute: Univ. Maryland

data_processing:
Raw reads (51 nucleotides each) were trimmed 13 nucleotides from the 5-prime end using trimmomatic 3
Reads were aligned to the Flybase D. melanogaster November 2014 genome release, FB2014_06 Dmel Release 6.03 (dmel-all-aligned-r6.03.fasta.gz) using Rsubread version 1.18.0.
Genes with at least one count per million (cpm) in 3 (minimum number of biological replicates within a group) or more samples were kept and quantile normalized for library size.
The R voom-limma package was used to carry out differential expression analysis using the linear model gene exprs = factor 1 + factor 2 was fit.  Factor 1 has two levels: mutant and wild type; and factor 2 has 3 levels: PBS, S. aureus, and uninjected.

organism: Drosophila melanogaster

source_name: Wildtype, Attp2, Saureus

growth_protocol: Control flies (w1118; P{UAS-mCD8::GFP.L}LL5, hmlΔGAL4; attP2) expressed the mCD8:GFP fusion protein on the surface of hemocytes and expressed normal levels of A2bp1 in hemocytes.  A2bp1 RNAi flies were generated with the following genotype:  w1118;  P{UAS-mCD8::GFP.L}LL5, hmlΔGAL4; P{HMS0048}attP2. A2bp1 RNAi flies expressed both the mCD8:GFP fusion protein and the 21 bp short RNAi hairpin against A2bp1 in hemocytes. Groups of 60 female flies were injected with equal volumes of S. aureus (OD 5.0) in sterile PBS or PBS (wounding control).  Uninjected flies served as a control.

extract_protocol:
mCD8-positive cells were isolated using Dynabeads Mouse CD8 (Lyt2) (Invitrogen, 11447D)  and resuspended in RLT Buffer from the Qiagen RNeasy Mini Kit.  Total RNA was then isolated according to the manufacturers protocols. Following cDNA library preparation, Illumina adaptors and indexes were added. Sequencing was carried out using an 50 base pair single-end reads on an Illumina HiSeq1000 system.
RNA libraries were prepared for sequencing using Illumina's TruSeq mRNA Sample Preparation Kit following standard Illumina protocols.

treatment_protocol: Groups of 60 female flies were injected with equal volumes of S. aureus (OD 5.0) in sterile PBS or PBS (wounding control).  Uninjected flies served as a control. Flies were incubated at 25°C for 3 hours before sample extraction.

value: Wildtype

value: TRiP Attp2 adult hemocytes


title: Attp2_Uninjected_Set3

source_name: Wildtype, Attp2, uninjected


title: Attp2_PBS_Set3

source_name: Wildtype, Attp2, PBS


title: HMS00478_Uninjected_Set3

source_name: A2bp1 RNAi, HMS00478, uninjected

value: A2bp1 RNAi

value: TRiP HMS00478 adult hemocytes


title: HMS00478_PBS_Set3

source_name: A2bp1 RNAi, HMS00478, PBS


title: HMS00478_PBS_Set2


title: HMS00478_Saureus_Set3

source_name: A2bp1 RNAi, HMS00478, Saureus


title: HMS00478_Saureus_Set2


title: Attp2_PBS_Set2


title: M4

city: Shanghai

first: Ronhua

last: Liu

address: No.138, Yi Xue Yuan Rd.

institute: Department of Immunology, Fudan University

description:
CRC mice at stage T1 induced by AOM and DSS.
small RNA
Processed data file: miRNA_All_Counts.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and mm10_GRCm38 genome.
Count counting.
Genome_build: mm10_GRCm38 / miRBase 21.0
Supplementary_files_format_and_content: miRNA_All_Counts.txt: Tab-delimited text file contains counts for each sample.

source_name: Colorectum, CRC

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by gel electrophoresis.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: Pathogen-free 7-week-old female mice were injected with 10 mg/kg body weight of azoxymethane (AOM) intraperitoneally (for negative control, with 0.9% NaCl solution). After 5 days, 2.5% dextran sodium sulfate (DSS) was given in the drinking water for 7 days, followed by 14 days of regular water, which was repeated three times. Stage T1: Day17 after AOM and DSS induction.

tag: strain/background

value: wild type

tag: gender

value: female

tag: disease status

value: colorectal cancer (CRC)

value: colorectum

tag: mouse id


title: HMS00478_Uninjected_Set2


title: M2

description:
Healthy mice compared to CRC mice at stage T1.
small RNA
Processed data file: miRNA_All_Counts.txt

source_name: Colorectum, healthy

value: healthy


title: HMS00478_PBS_Set1


title: M1b


title: Attp2_Saureus_Set2


title: Attp2_Uninjected_Set2


title: M1a


title: M6


title: M5


title: Attp2_PBS_Set1


title: Attp2_Saureus_Set1


title: Attp2_Uninjected_Set1


title: HMS00478_Uninjected_Set1


title: w_rep1

city: Dresden

first: Holger

last: Brandl

state: Choose One...

address: Pfotenhauerstrasse 108

department: Bioinformatics Service

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description:
control
w_rep1

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped using STAR 2.5.2b (--outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs   RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Abundance estimation was performed STAR (--quantMode GeneCounts)
Genome_build: BDGP6, Ensembl v81
Supplementary_files_format_and_content: FPKM normalized expressoin score table

source_name: w

growth_protocol: Flies were raised on yeast, corn-meal standard food under regular light conditions at 25 °C. Heads of two day old adults were disected for RNA extraction. 50 heads per sample were pooled.

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions. mRNA was isolated from 1ug total RNA by poly-dT enrichment using the   NEBNext Poly(A) mRNA Magnetic Isolation Module according to the   manufacturers instructions. Final elution was done in 15ul 2x first   strand cDNA synthesis buffer (NEBnext, NEB).
After chemical   fragmentation by incubating for 15 min at 94°C the sample was directly   subjected to the workflow for strand specific RNA-Seq library   preparation (Ultra Directional RNA Library Prep, NEB). For ligation   custom adaptors were used (Adaptor-Oligo 1:   5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2:   5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3'). After ligaton   adapters were depleted by an XP bead purification (Beckman Coulter)   adding beads in a ratio of 1:1. Indexing was done during the following   PCR enrichment (15 cycles) using custom amplification primers carring   the index sequence indicated with ‘NNNNNN’. (Primer1: Oligo_Seq    AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, primer2:   GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, primer3: CAAGCAGAAGACGGCATACGAGAT   NNNNNN GTGACTGGAGTT. After two more XP beads purifications (1:1)   libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen).   For Illumina flowcell production, samples were equimolarly pooled and   distributed on one lane for 75bp single end sequencing on Illumina HiSeq   2500 resulting in on average 28 Mio reads per sample.

value: head

tag: age

tag: genotype

value: white


title: Prp31_P18_rep3

description:
homozygous mutant
Prp31_P18_rep3

value: Prp31 homozygous mutant


title: w_rep2

description:
control
w_rep2


title: w_rep3

description:
control
w_rep3


title: Prp31_P18_rep2

description:
homozygous mutant
Prp31_P18_rep2


title: M3


title: NORAD siRNA transfection, HCT116 SAM68 KO cells, rep1

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were aligned to the human genome (hg19 assembly) using STAR Aligner
Read counts for individual genes (defined as overlapping sets of RefSeq transcripts annotated with their Entrez Gene identifier) were counted using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: Read counts for individual genes

molecule: polyA RNA

source_name: HCT116 SAM68 KO_siRNA pool against NORAD

growth_protocol: Human cell lines U2OS and HCT116 were routinely cultured in DMEM containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using TRI reagent (MRC)
Strand-specific mRNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: All transfections were performed using Lipofectamine 3000 reagent (Thermo Fisher Scientific). NORAD plasmid was previously described (Tichon et al. Nature Communications 2016). For SAM68 overexpression we used the pcDNA3-HA-SAM68 plasmid, which encodes the mouse SAM68 gene (a gift from David Shalloway, Addgene #17690). As controls for overexpression experiments, we used pcDNA3.1(+) (Invitrogen). In transfection 100 ng was used per 20,000 cells in 96-well plates for 48 h before cells were harvested.   Knockdowns were performed using siRNAs directed against SAM68 and NORAD (from Dharmacon, Supplementary Table 3), while as control we used the mammalian non-targeting siRNA (Lincode Non-targeting Pool, Dharmacon), at final concentration of 50nM. Cells harvested after 48h for further experimental procedures.

tag: cell line

tag: genotype background

value: SAM68 KO

tag: transfected with

value: siRNA pool against NORAD


title: Prp31_P18_rep1

description:
homozygous mutant
Prp31_P18_rep1


title: KELLY_CYC065_H3K27AC

city: Houston

first: Charles

middle: Yang

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Chromatin IP against H3K27ac in CYC065 KELLY

data_processing:
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

growth_protocol: KELLY cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Tn5 enzyme and amplified using 2x NEBNext HiFi master mix.
ChIPmentation (Schmidl et a., 2015; PMC4589892)

treatment_protocol: CYC065 drug treatment was performed by addition of 1uM CYC065 to growth media for 3hrs

value: KELLY

tag: cell type

value: Neuroblastoma

tag: input

tag: treatment

value: 1uM CYC065 for 3HR

tag: growth protocol

value: 10% FBS, DMEM

tag: barcode

value: TTGACCCT

tag: antibody

tag: antibody maker

value: abcam

tag: antibody catalog number


title: KELLY_DMSO_CDK9

description: Chromatin IP against CDK9 in DMSO KELLY

source_name: Chromatin IP against CDK9 in DMSO KELLY

value: 0.1% DMSO for 3HR

value: TGGTCACA

value: santa-cruz


title: KELLY_DMSO_H3K27AC

description: Chromatin IP against H3K27ac in DMSO KELLY

value: TGGGTTTC


title: KELLY_CYC065_WCE

description: Input for CYC065 KELLY

source_name: Input for CYC065 KELLY

value: GTGTGGTG


title: Control siRNA transfection, HCT116 SAM68 KO cells, rep1

source_name: HCT116 SAM68 KO_Control siRNA

value: Control siRNA


title: KELLY_DMSO_WCE

description: Input for DMSO KELLY

source_name: Input for DMSO KELLY

value: AGGTTGGG


title: KELLY_CYC065_CDK9

description: Chromatin IP against CDK9 in CYC065 KELLY

value: CCACTCCT


title: Control siRNA transfection, HCT116 SAM68 KO cells, rep2


title: NORAD siRNA transfection, HCT116 WT cells, rep1

source_name: HCT116 WT_siRNA pool against NORAD

value: wild type


title: NORAD siRNA transfection, HCT116 WT cells, rep2


title: SAM68 plasmid transfection, rep2

source_name: U2OS_SAM68 plasmid

value: SAM68 plasmid


title: Control siRNA transfection, HCT116 WT cells, rep1

source_name: HCT116 WT_Control siRNA


title: Control siRNA transfection, HCT116 WT cells, rep2


title: HMS00478_Saureus_Set1

tag: genotype/variation

value: A2bp1 RNAi

value: TRiP HMS00478 adult hemocytes


title: SAM68 plasmid transfection, rep1


title: Control plasmid transfection, rep2

source_name: U2OS_Control plasmid

value: Control plasmid


title: Control plasmid transfection, rep1


title: SAM68 siRNA transfection, rep2

source_name: U2OS_siRNA pool against SAM68

value: siRNA pool against SAM68


title: SAM68 siRNA transfection, rep1


title: Control siRNA transfection, rep2

source_name: U2OS_Control siRNA


title: Control siRNA transfection, rep1


title: 5269

city: Toulouse

first: ludovic

last: Martinet

address: 2 av Hubert Curien

department: CRCT

country: France

institute: INSERM U1037

data_processing:
Fastq files were aligned to the Ensembl GRCh38 Homo sapiens reference genome using STAR (version 2.3.0, (Dobin et al., 2013))
Gene expression summary was obtained using the Subread featurecount algorithm (version 1.4.6, (Liao et al., 2014)).
Patient gene expression was then normalized using standard procedure from the limma R package(Ritchie et al., 2015), retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files includes normalized gene espression values retaining only genes expressed (more than 15 aligned reads) in at least 50% of patients.

source_name: non-tumoral CD138- fraction of patient BM aspirate taken at the time of diagnosis

extract_protocol:
RNeasy mini kit (Qiagen)
The RNA-Seq library preparation was performed using TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, Calif) according to the manufacturer’s instructions (High Sample Protocol). The RNA-Seq libraries were checked on the 2200 Tapestation System (Agilent) using the High-Sensitivity DNA 1000 ScreenTape assay. The average fragment size of the final libraries was found to be 230 to 327 bps. Libraries were quantified by qPCR on a LightCycler 480 System (Roche Molecular Diagnostics, Pleasanton, Calif) using KAPA Library Quantification Kit for Illumina platforms (Kapa Biosystems, Boston, Massachusetts). Libraries were then pooled in equal quantities, checked and quantified using same techniques (2200 Tapestation and LightCycler 480).
Paired-end sequencing (2 x 75 bps) of these libraries was performed on a NextSeq 500 Illumina sequencing platform (Illumina) by 5 successive runs using NextSeq 500 High Output kit v2 (Illumina) generating in average 20 million pairs of reads per sample.

tag: disease state

value: MM

tag: tissue

value: CD138 depleted bone marrow

tag: date of sample

tag: sex (male

tag: age at diagnosis (years)

tag: iss stage (1, 2, 3, undetermined (n.d))


title: 5275


title: 5267


title: 5279


title: 5263


title: NORAD siRNA transfection, HCT116 SAM68 KO cells, rep2

tag: cell line

tag: genotype background

value: SAM68 KO

value: siRNA pool against NORAD


title: 5233


title: 5260


title: 5252


title: 5250


title: 5225


title: 5222


title: 5220


title: 5190


title: 5209


title: 5182


title: 5191


title: 5192


title: 5179


title: 5187


title: 5217


title: 5271


title: 5188


title: 5172


title: 5194


title: 5226


title: 5251


title: 5158


title: 5155


title: 5180


title: 5167


title: 5262


title: 5171


title: 5224


title: 5153


title: 5175


title: 5143


title: 5137


title: 5149


title: 5138


title: 5152


title: 5133


title: 5140


title: 5124


title: 5123


title: Pseu_12hA

city: Cambridge

first: Erel

last: Levine

address: 52 Oxford St

institute: Harvard University

description:
Sample D2
Processed data file: FPKM_All.xlsx

data_processing:
TopHat 2.0.7
Cufflinks
Cuffmerge 2.1.1
Genome_build: WS240
Supplementary_files_format_and_content: FPKM_All.xlsx: Excel file includes FPKM confidence interval for each sample (time point on PA14) and negative control (on E. coli OP50).

organism: Caenorhabditis elegans

source_name: whole animal, PA14, 12 hrs

growth_protocol: Standard C. elegans growth on E. coli OP50.

extract_protocol:
Trizol extraction.
Oligo(dT) extraction to enrich eukaryotic mRNA, followed by C. elegans library construction.

treatment_protocol: Slow-killing assay (Man-Wah Tan et al., PNAS 1999).

tag: strain/background

value: whole body

tag: bacteria

value: Pseudomonas aeruginosa PA14

tag: time post infection

value: 12 hrs


title: Pseu_22h

description:
Sample E
Processed data file: FPKM_All.xlsx

source_name: whole animal, PA14, 22 hrs

value: 22 hrs


title: Pseu_22hA

description:
Sample F
Processed data file: FPKM_All.xlsx


title: Pseu_17h

description:
Sample H
Processed data file: FPKM_All.xlsx

source_name: whole animal, PA14, 17 hrs

value: 17 hrs


title: 5122


title: Pseu_8h

description:
Sample C
Processed data file: FPKM_All.xlsx

source_name: whole animal, PA14, 8 hrs

value: 8 hrs


title: 5120


title: OP50_22h

description:
Sample I
Processed data file: FPKM_All.xlsx

source_name: whole animal, OP50, 22 hrs

value: Escherichia coli OP50


title: Pseu_4h

description:
Sample B
Processed data file: FPKM_All.xlsx

source_name: whole animal, PA14, 4 hrs

value: 4 hrs


title: hepatopancreas sur-FKC

city: Minato-ku

first: Sasiwipa

last: Tinwongger

state: Tokyo

address: 4-5-7 Konan

department: Applied marine bioscience

country: Japan

institute: Tokyo university of marine science and technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, then de novo assembled using Trinity
Transcripts in each sample were aligned and estimated abundance using bowtie and RSEM
The transcripts.gene.results of all samples were used to construct a matrix of counts and matrix of normalized expression values by RSEM.
Differential expression was analyzed by perform pairwise comparison among 3 groups in each tissue using edgeR
Supplementary_files_format_and_content: MATRIX;  tab-delimited text files include the raw counts of genes from all 6 samples
Supplementary_files_format_and_content: MATRIX;  tab-delimited text files include TMM-normalized expression values of all 6 samples

organism: Penaeus vannamei

source_name: hepatopancreas of AHPND-resistance L. vannamei which were survived after feeding with FKC-VpAHPND (Rvan-Hp)

extract_protocol:
Total RNA from hepaotpancreas and stomach was isolated using RNAiso reagent (Takara, JApan), treated with RQ1 RNase-free DNase (Promega, USA) and purified with RNeasy Mini Kit (Qiagen, Germany)
The total RNAs of each tissue were pooled by group. Four μg of pooled RNA was used to construct a cDNA library following the protocols of Illumina Truseq Stranded mRNA Library Prep Kit (Illumina, USA)

value: hepatopancreas


title: stomach sur-FKC

source_name: stomach of AHPND-resistance L. vannamei which were survived after feeding with FKC-VpAHPND (Rvan-St)

value: stomach


title: 5154


title: hepatopancreas Vp-inf

source_name: hepatopancreas from L. vannamei after immersed with VpAHPND for 24 h (24h-Hp)


title: 5117


title: stomach Vp-inf

source_name: stomach from L. vannamei after immersed with VpAHPND for 24 h (24h-St)


title: Pseu_12h

description:
Sample D
Processed data file: FPKM_All.xlsx


title: hepatopancreas control

source_name: hepaotpancreas from normal L. vannamei (0h-Hp)


title: 5097


title: 5103


title: 5105


title: 5104


title: 5095


title: 5094


title: RNA-seq_prmt10

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

data_processing:
Two independent CLIP-seq libraries (wild type HLP1 and △RRM) were sequenced on Illumina GAⅡ. 3'-end adaptors and the 5'-end four barcodes were removed using FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Tags less than 14 nt in length or adapter-only were discarded. Tags ranging from 14～19 nt (no mismatch allowed) and tags ≥ 20 nt (two mismatches allowed) were aligned to the Arabidopsis genome (TAIR10) using bowtie (0.12.7) (Langmead et al., 2009). The identical sequences with the same 4 nt random barcodes were regarded as one tag to exclude PCR duplication. The RNA-seq libraries for Col, hlp1-1, atprmt10-1 and double mutants were constructed according to strand-specific mRNA-Seq Sample Preparation Protocol. All the raw RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) by using TopHat (1.3.0) (Trapnell et al., 2009) with no more than six mismatches. PAS-seq tags less than 20 nt were discarded. All tags more than 50nt were trimmed to 50 nt and reversely complemented because the tags were sequenced from 3' end of transcripts (Fu et al., 2011). Then trimmed tags were mapped to the Arabidopsis genome (TAIR10) using bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only unique mapped tags from CLIP-seq/RNA-seq/PAS-seq were kept for downstream analyses and were tranfered into wiggle files which can be displayed in IGV (Robinson et al., 2011).
Genome_build: TAIR10

organism: Arabidopsis thaliana

growth_protocol: All of the Arabidopsis thaliana lines used in this study were in the Col background. Plant growth, flowering time analysis, and plant transformation were performed as reported previously (Pei et al., 2007).

extract_protocol: 12-day-old seedlings (from MS plates containing 3% sucrose grown under LD at 23°C) expressing either CFP-HLP1 or CFP-HLP1ΔRRM were soaked in ice-cold PBS buffer and irradiated twice for 400 mJ/cm2 in the Hoefer UVC 500 Ultraviolet Crosslinker (GE). CLIP experiment was performed as described (Licatalosi et al., 2008; Xue et al., 2009). Poly(A) site sequencing was performed as described (Fu et al., 2011; Shepard et al., 2011). Briefly, poly(A) RNAs were purified using the mRNA purification kit (Invitrogen), and heat fragmented at 95°C for 30 min. Reverse transcription (Superscript Ⅱ, Invitrogen) was performed using our modified HITS-3’ adaptor at 42°C for 30 min, then add the HITS-5’ adaptor (a SMART oligo) and incubated for additional 30 min. The cDNAs were purified using the Qiagen PCR Cleanup kit and the second strand cDNAs were synthesized by 3 cycles PCR using Phusion DNA polymerase (NEB) and the PE1.0 and PE2.0 primers. The PCR products were separated by 2% agarose gel and the 200-300 bp bands were excised and purified. Gel-extracted DNAs were further amplified by a 13-cycle PCR. The PCR products were purified using the Qiagen PCR Cleanup kit. TA-cloning was performed before Illumina GA Ⅱ sequencing.

treatment_protocol: The seedlings were ground into fine power in liquid nitrogen and RNA was extracted by TRNzol reagent (Tiangen).

value: seedlings

tag: tag


title: stomach control

source_name: stomach from normal L. vannamei (0h-St)


title: 5115


title: 5088


title: 4965


title: 4966


title: 5093


title: 5091


title: 5087


title: 4942


title: 5092


title: 4946


title: 4923


title: 4920


title: L3_WT

city: Montréal

first: Claude

last: Perreault

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 1.17.21.3
Samples demultiplexed using Casava 1.8.2
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version M13
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M13 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output (first line identifies the column)

source_name: mTEC lo from WT mice

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Sample Preparation(Illumina)

tag: strain

value: B6.B6CB-Psmb11tm1Smta (Psmb11+/+)

tag: age

value: 6- to 8- week-old

value: thymus

tag: cell type

value: primary MHCII lo medullary thymic epithelial cells


title: 4933

value: MM

value: CD138 depleted bone marrow


title: 4941


title: 5108


title: 4919


title: 4917


title: L2_KO

source_name: mTEC lo from Psmb11-deficient mice

value: B6.B6CB-Psmb11tm1Smta (Psmb11-/-)


title: L1_WT


title: L2_WT


title: L1_KO


title: 5085


title: H3_WT

source_name: mTEC hi from WT mice

value: primary MHCII hi medullary thymic epithelial cells


title: 4971


title: H3_KO


title: ChIP_H3K27ac_Rep1_Input

city: Stanford

first: Mark

middle: A

last: Zarnegar

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description: Native chromatin ChIP-seq using 0.25-0.5 million cells

data_processing:
Sequence reads were generated by Illumina's NextSeq500 platform.
Sequence reads were aligned to the hg19 genome using Bowtie2.2.6.2 using -very-fast-local.
BAM files were then used with Deeptools bamCoverage to produce normalized (RPKM) BigWig signal tracks using 100 bp bins.  Reads were extended 200 bp.
MACS2 was used for peak calling (-nomodel, p=0.01, -broad,cuttoff 0.1, duplicates = auto, extension 200)
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files contain RPKM nnormalized genome-wide signals generated with bamCoverage verison 2.3.6.0.  Scores were calculated using 100 bp bins after extending reads to 200 bp. Peak files are provided in BED format as output by MACS2.

growth_protocol: MDA-MB231 were grown in DMEM (Invitrogen) supplemented with PSA (Life Technologies), 10% FBS (Hyclone), Glutamax (ThermoFisher Scientific) and sodium pyruvate (Life Technologies).

extract_protocol:
For ChIP, unfixed cells were clarified after enzymmatically digesting and lysing cells, then histone-DNA complexes were isolated with antibody.
Libraries were prepared with Illumina's NEXTERA XT DNA library prep kit

treatment_protocol: MDA-MB231 were infected with lentivirus containing EV-control, CDK19 shRNA, or CDK8 shRNA, then grown for 96 hours prior to processing for ChIP

value: breast cancer cells

value: EV-control

tag: chip antibody


title: ChIP_H3K27ac_Rep3_Input

tag: genotype/variation


title: H2_WT


title: ChIP_H3K27ac_Rep2_CDK8KD

value: CDK8 knockdown

value: H3K27ac (Active Motif #39133)


title: H2_KO

source_name: mTEC hi from Psmb11-deficient mice


title: ChIP_H3K27ac_Rep2_Input


title: ChIP_H3K27ac_Rep1_CDK8KD


title: ChIP_H3K27ac_Rep3_CDK19KD

value: CDK19 knockdown


title: L3_KO


title: ChIP_H3K27ac_Rep3_CDK8KD


title: H1_WT


title: H1_KO


title: 8SM_WT2

data_processing:
Basecalls performed using Illumina RTA 1.18.64
Samples demultiplexed using bcl2fastq 2.17
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version M9
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M9 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output (first line identifies the column)

source_name: 8SM thymocytes from WT mice

extract_protocol:
TriZol + RNeasy micro Kit (Qiagen, #74004)
KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: 4 weeks old

value: primary thymocytes


title: ChIP_H3K27ac_Rep1_CDK19KD


title: 8SM_WT3


title: ChIP_H3K27ac_Rep3_Control


title: 8SM_WT1


title: ChIP_H3K27ac_Rep2_Control


title: 5210

source_name: non-tumoral CD138- fraction of patient BM aspirate taken at the time of diagnosis

tag: disease state


title: 8SM_KO2

source_name: 8SM thymocytes from Psmb11-deficient mice

tag: tissue


title: Input

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

institute: University of Manitoba

data_processing:
Alignment to GRCh38 using bowtie2 2.2.4
Peak calling using MACS2 v2.1.0.20140616
Genome_build: GRCh38
Supplementary_files_format_and_content: BAM alignment files and MACS peak files

source_name: D283 Cell line

growth_protocol: D283 tumorspheres were grown in ultra low-attachment plates in Neural Proliferation Media consisting of Dulbecco’s modified Eagle’s medium (DMEM)/F12 supplemented with 1% N2 (Gibco), 1% B27 (Gibco), 20 ng/ml epidermal growth factor (EGF; R&D Systems), and 20 ng/ml basic fibroblast growth factor (bFGF; R&D Systems).

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Kaur et al., Disease Models & Mechanisms, 2015). D283 tumorspheres were crosslinked for 10 minutes in 1% formaldehyde and quenched by 0.125M glycine for 5 minutes. Using 500 μl of sonification buffer [50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% (w/v) Triton X-100, 0.1% (v/v) sodium deoxycholate, 1% (w/v) SDS and protease inhibitors] cell pellets were resuspended and sonicated into ∼400 bp with a bioruptor. Samples were incubated with protein A-Dynabeads ovalbumin and salmon sperm for 1 hour at 4°C to preclear the chromatin. OTX2 antibody was coupled to protein A-Dynabeads with protein A (rabbit antibody) in immunoprecipitation buffer. The precleared-chromatin and antibody bound beads were incubated overnight at 4°C. Unbound chromatin was washed away while the bound fraction was eluted in 400 μl of elution buffer and reverse crosslinked with 5 M NaCl (0.2 M final) and 4 μl of RNAse A (1 mg/ml) overnight at 55°C. Samples were treated with proteinase K (20 μg/μl), DNA was extracted using phenol:chloroform and suspended in 50 μl elution buffer 27
NextFlex Illumina Chip-seq kit

treatment_protocol: none - OTX2+ control tumorspheres

tag: antibody


title: 8SM_KO3


title: 8SM_KO1


title: OTX2

value: ChIP Grade OTX2 - Abcam - ab21990


title: 8M2_WT3

source_name: 8M2 thymocytes from WT mice


title: ChIP_H3K27ac_Rep1_Control


title: 8M2_KO3

source_name: 8M2 thymocytes from Psmb11-deficient mice


title: 8M2_KO2


title: 8M2_WT2


title: cWAS-iMP2

description: human iPSC differentiated on OP9 feeders

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
For RNA-Seq, paired-end reads were aligned to the human genome (hg19) with STAR (v2.2.0c) with default parameters.  Only uniquely alignable reads were used for downstream analysis.
RNA-Seq, Fragments Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression values for each experiment. Columns definition, 1: Entrez Gene ID, 2: RefSeq ID, 3: chr, 4: start(hg19), 5: end(hg19), 6: strand, 7: transcript length, 8: Copies in genome, 9: Annotation/Symbol, 10-14: FPKM values, 15-23: additional annotations

source_name: iPSC

growth_protocol: iPSCs cultured on MEF feeders in human ESC medium were manually dissociated and plated on 8 days old overgrown OP9 feeders to start differentiation. Cells were co-cultured with the OP9 feeders for 12-14 days in OP9 differentiation medium (Alpha MEM containing 10% FBS, 100 μM monothioglycerol and 50 μg/ml ascorbic acid) as described by Vodyanik, M. A. & Slukvin, II. (Curr Protoc Cell Biol 2007). Differentiated cells were dissociated with collagenase and Accutase (Innovative Cell Technologies) and subjected to further differentiation into macrophages using GM-CSF and M-CSF.

extract_protocol:
RNA was extracted with Qiagen RNeasy micro kit.
The Agilent TapeStation or Bioanalyzer was used to determine RNA integrity (RIN) numbers prior to library preparation. Stranded mRNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA tail was isolated using poly-T oligos conjugated to magnetic beads. mRNA was then fragmented and reverse-transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. dUTP-incorporated second strand was not amplified. cDNA was then end-repaired, index adapter-ligated and PCR amplified. Purification of nucleic acids after each enzymatic steps was achieved by using AMPure XP beads (Beckman Coulter).
Strand specific polyA+ RNAseq (PE75)

tag: individual

value: WAS patient 2

value: WAS-iPSC (gene corrected)

tag: genotype

value: wild type

tag: protocol

value: differentiated into macrophages


title: 8M2_KO1


title: ChIP_H3K27ac_Rep2_CDK19KD

tag: cell line


title: WAS-iMP1

value: WAS patient 1

value: WAS-iPSC


title: WAS-iMP2


title: 8M1_WT2

source_name: 8M1 thymocytes from WT mice

value: B6.B6CB-Psmb11tm1Smta (Psmb11+/+)


title: 8M1_WT3


title: 8M1_WT1


title: DF4

city: Graz

first: Ursula

last: Hiden

address: Auenbruggerplatz 14

department: Obstetrics and Gynecology

country: Austria

institute: Medical University of Graz

description: miRNAs

data_processing:
A total of 97 million reads was obtained with an average of 3.4 million reads per sample. Identification of miRNA reads was performed using the CAP-miRSeq v1.1 workflow yielding on average 800,000 miRNA read counts per sample.
Differentially expressed miRNAs were identified based on a negative binomial distribution from raw count data using the R/Bioconductor package edgeR. Only miRNAs with 150 counts in at least 3 samples were further considered (Expression spreadsheet all data).
To test differences between disease states (GDM (D) versus control (C)) a generalized linear model (GLM) was used including disease state as the main factor.
Fetal sex and maternal pre-pregnancy body mass index (BMI) were included as categorical and continuous covariates, respectively, and a likelihood ratio test was performed. To test the interaction between the disease state and fetal sex, a complete GLM was used including both factors and their interaction, and maternal pre-pregnancy BMI was included as covariate (attached file: C vs D spreadsheet).
The analyses were also performed separately for  female (CF vs DF) and male fpEC (CM vs DM ) again accounting for maternal BMI as covariate. P-values were adjusted for multiple testing based on the false discovery rate (FDR) according to the Benjamini-Hochberg method.
Normalized data (counts per million; CPM) were log2-transformed (log2(CPM+1)) for further analyses.
Supplementary_files_format_and_content: Expression spreadsheet all data': Raw data of all samples in an excel file
C vs D spreadsheet': Processed data for comparison between C and D, excel file; cells of male and female progeny were analyzed together, covariates: fetal sex, pre-pregnancy BMI
CM vs DM spreadsheet': Processed data for comparison between CM and DM, excel file; only cells of male progeny were analyzed
CF vs DF spreadsheet': Processed data for comparison between CF and DF, excel file; only cells of female progeny were analyzed, covariates: pre-pregnancy BMI

source_name: GDM female 4

growth_protocol: fpEC were routinely generated by pefusion of chorionic placental arteries and cultured in Endothelial Basal Medium (EBM) medium supplemented with the EGM-BV BulletKit (both from Cambrex). Cells were grown in 75 cm2 flasks to approximately 90% confluency, washed with ice cold Phosphate Buffered Saline (PBS) and harvested.

extract_protocol:
1 ml of TRIzol was added to each flask. Cells were detached by scraping and homogenized by vortexing and RNA extraction was performed according to the manufacturer's protcol, but using 100% ethanol instead of isopropanol for RNA precipitation (-80°C over night).
Total RNA (1 µg) enriched for miRNA was used for generating NGS libraries using Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific). Preparation was performed following the instructions for generating small RNA libraries (Ion Total RNA-Seq Kit v2 for Small RNA Libraries, Thermo Fisher Scientific): Adapters were ligated to total RNA molecules followed by reverse transcription. DNA fragments were purified and size selected to enrich fragments of 94 to 114 base pairs. Libraries were post-amplified for 14 cycles and library concentration was determined using the Ion Library TaqMan™ Quantitation Kit (Thermo Fisher Scientific). Equimolar concentrations of up to 16 barcoded miRNA libraries were pooled and sequenced using the Ion Proton System (Thermo Fisher Scientific) with the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific).

value: feto-placental endothelial cells

tag: pre-pregnancy bmi

tag: fetal sex

value: female

tag: diagnosis

value: GDM pregnancy

tag: developmental stage

value: from third trimester placenta after delivery


title: 8M1_KO3

source_name: 8M1 thymocytes from Psmb11-deficient mice

value: B6.B6CB-Psmb11tm1Smta (Psmb11-/-)


title: 8M1_KO2


title: DF7

description: miRNAs

source_name: GDM female 7


title: DF5

description: miRNAs

source_name: GDM female 5


title: DF2

description: miRNAs

source_name: GDM female 2


title: DF1

description: miRNAs

source_name: GDM female 1


title: 4SM_WT2

source_name: 4SM thymocytes from WT mice


title: DM6

description: miRNAs

source_name: GDM male 6

value: male


title: DM7

description: miRNAs

source_name: GDM male 7


title: 8M2_WT1


title: 4SM_WT3


title: cWAS-iMP1

city: La Jolla


title: CB-MP

description: macrophage differentiated from cord blood progenitor cells

source_name: cord blood

value: cord blood progenitor cell


title: 4SM_KO3

source_name: 4SM thymocytes from Psmb11-deficient mice

value: 4 weeks old


title: 8M1_KO1

value: primary thymocytes


title: DF6

description: miRNAs

source_name: GDM female 6


title: 4M2_WT3

source_name: 4M2 thymocytes from WT mice


title: DM3

description: miRNAs

source_name: GDM male 3


title: 4SM_KO1


title: DF3

description: miRNAs

source_name: GDM female 3


title: 4SM_WT1


title: DM2

description: miRNAs

source_name: GDM male 2


title: 4SM_KO2


title: DM5

description: miRNAs

source_name: GDM male 5


title: 4M2_WT2


title: DM1

description: miRNAs

source_name: GDM male 1


title: CF9

description: miRNAs

source_name: control female 9

value: normal pregnancy


title: 4M2_WT1


title: 4M2_KO3

source_name: 4M2 thymocytes from Psmb11-deficient mice


title: CF8

description: miRNAs

source_name: control female 8


title: CF7

description: miRNAs

source_name: control female 7


title: 4M2_KO2


title: 4M2_KO1


title: 4M1_WT3

source_name: 4M1 thymocytes from WT mice


title: DM4

description: miRNAs

source_name: GDM male 4


title: CF4

description: miRNAs

source_name: control female 4


title: CF3

description: miRNAs

source_name: control female 3


title: CF5

description: miRNAs

source_name: control female 5


title: CF2

description: miRNAs

source_name: control female 2


title: CF1

description: miRNAs

source_name: control female 1


title: CM5

description: miRNAs

source_name: control male 5


title: 4M1_KO1

source_name: 4M1 thymocytes from Psmb11-deficient mice


title: 4M1_KO3


title: 4M1_WT1


title: 4M1_WT2


title: RHD493

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

data_processing:
Data was run on hiSEq2000 with basecalling as per statndard protocol
Reads were mapped with STAR v2.3.3 and Gencode annotation M9
Gene counts were determined with featurecounts.  DEGs were determined with edgeR in R v 3.1.2
Genome_build: mm10
Supplementary_files_format_and_content: processed data consists of raw gene counts in matrix format

extract_protocol:
Adipose tissues were lysed in TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) and RNA was isolated followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific, Waltham, MA, USA) using SMARTSeq v2 protocol  except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA).

tag: agent

value: Mycobacterium tuberculosis str. Erdman

value: murine adipocytes


title: RHD490

tag: strain


title: CM4

description: miRNAs

source_name: control male 4


title: CM2

description: miRNAs

source_name: control male 2


title: RHD492


title: CF6

description: miRNAs

source_name: control female 6


title: RHD489


title: 4M1_KO2

tag: age


title: CM3

description: miRNAs

source_name: control male 3

tag: cell type


title: CM1

description: miRNAs

source_name: control male 1


title: ICR wounded skin 3 day after wound

city: Seoul

first: Eun-Jung

last: Kim

address: 50 Yonsei-ro

department: Department of Oral Biology

country: South Korea

institute: Yonsei Universiry

description: ICR 3days 1ea 160616

data_processing:
Basecalls performed using CASAVA version v2.17.1.14
Data were filtered using the following configurations: 1) Reads contain more than 10% of skipped bases (marked as ‘N’s), 2) Reads contain more than 40% of bases whose quality scores are less than 20, 3) Reads of which average quality scores of each read is less than 20
RNA-seq reads were aligned to the GRCm38.p2 genome assembly using STAR version 2.4.0b with default configurations.
Excel file generated using rsem-1.2.19 with default configurations and cufflinks-2.2.1 with the following configurations: multi-read-correction & frag-bias-correct.
Genome_build: GRCm38.p2
Supplementary_files_format_and_content: gene_unigene_result.xlsx

source_name: ICR wounded skin 3 day after wound

extract_protocol:
Total RNA was extracted from skin wound samples using a TRIZOL reagent (Invitrogen, CA, USA). After DNase I (Roche, Basel, Switzerland) treatment, the RNA was purified with RNeasy kit (Qiagen, Hilden, Germany).
Illumina TruSeq RNA Library Prep Kit

value: ICR

tag: treatment

value: wounding

tag: time

value: 3 days after wound

value: wounded dermis


title: RHD491


title: RHT2477

value: Uninfected


title: RHD488


title: RHT2478


title: LPCO_12

city: Los Angeles

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

description: replicate 1

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.  Bisulfite-converted reads were aligned to aligned to mouse genome (UCSC assembly 10) using using the bisulfite aligner BS Seeker2, which utilizes the short read aligner Bowtie. As bisulfite treatment converted unmethylated cytosines (Cs) to thymines (Ts), we estimated the methylation level at each covered cytosine by methylation percentage which was calculated as NC/(NC + NT), where NC is the number of methylated reads and NT is the number of unmethylated reads
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including the methylation level of cytosines in CpG, CHH and CHG context. The 8 fields in the files are (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T)., (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

source_name: low protein diet (LP)

extract_protocol:
Geome DNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of DNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Qubit RNA assay (Life Technologies, NY, USA) and gel electrophoresis
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications (Chen, P.Y. et al. Physiol Genomics 45, 565-576). Briefly, about 1,000 ng genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters (Illumina Inc, CA, USA). Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 2500 System (Illumina Inc, CA, USA).

value: hypothalamus


title: HFCO_11

description: replicate 1

source_name: high fat diet (HF)


title: LPCO_06

description: replicate 1


title: HFCO_06

description: replicate 1


title: RHT2475


title: COCO_15

description: replicate 1

source_name: normal Chow diet (CO)


title: RHT2474


title: RHT2473


title: LPCO_02

description: replicate 1


title: TG.E6_3

city: Madrid

first: Álvaro

last: Ucero

address: Calle de Melchor Fernández Almagro, 3

department: Grupo de Genes, Desarrollo y Enfermedad

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description:
WT3
Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
Processed data file: ALLsamples.genes.fpkm_table.xls

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits.
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: ALLsamples.genes.fpkm_table.xls: FPKM values calculated with Cufflinks.

source_name: Lung, WT

growth_protocol: Not applicable.

extract_protocol:
Total RNA was purified using RNeasy Mini kit (Qiagen) and digested with DNase (Qiagen).
1 µg of total RNA sample was used as provided by the user. Sample RNA Integrity Numbers were in the range 7.3 to 9 (average 8.3) when assayed on an Agilent 2100 Bioanalyzer.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced).
Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles).
The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Not applicable.

tag: strain/background

tag: genotype/variation

value: WT

value: 6 weeks

value: lung


title: Ofas_egg48-64h_Septic2

city: Leiden

first: Chris

last: Jacobs

state: Zuid-Holland

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

data_processing:
Data trimming using Trimmomatic v0.36 using HEADCROP:10 MINLEN:50 TRAILING:20
Alignment to the genome using Hisat v2.0.5
Collect countdata using featureCounts (v1.5.2)
Count data was analysed using DEseq2 and differential gene expression between either Naive and Sterile or Naive and Septic was tested.
Genome_build: Ofas.scaffolds.fa.gz (downloaded from https://i5k.nal.usda.gov/sites/default/files/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/Current%20Genome%20Assembly/1.Genome%20Assembly/BCM-After-Atlas/Scaffolds/Ofas.scaffolds.fa.gz) and OGS v1.2 from https://i5k.nal.usda.gov/sites/default/files/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/Current%20Genome%20Assembly/2.Official%20or%20Primary%20Gene%20Set/OGS_v1.2/oncfas_OGSv1.2_02192016/oncfas_OGSv1.2_original.gff
Supplementary_files_format_and_content: count_data.txt contains the raw counts per sample for each gene.
Supplementary_files_format_and_content: Naive-vs-Sterile_DESeq2.csv contains the output of the differential expression analysis of DESeq2 when comparing Naive with Sterile injury.
Supplementary_files_format_and_content: Naive-vs-Septic_DESeq2.csv contains the output of the differential expression analysis of DESeq2 when comparing Naive with Septic injury.
Supplementary_files_format_and_content: Ofasciatus_analysis.rmd, Ofasciatus_analysis.html: R markdown documents that include full details of the analysis.

organism: Oncopeltus fasciatus

source_name: Egg

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) followed by DNA digestion and column purification (Qiagen Rneasy)
TruSeq library preparation sequenced on a HiSeq 2000 system.

tag: temp

value: 25 degrees Celcius

value: Septic injury


title: COCO_22

description: replicate 1

tag: tissue


title: COCO_14

description: replicate 1


title: TG.E6_5

description:
Fra22
Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
Processed data file: ALLsamples.genes.fpkm_table.xls

source_name: Lung, Fra-2tg

value: Fra-2tg (mutant)


title: Ofas_egg48-64h_Sterile3

value: Sterile injury


title: TG.E6_2

description:
WT2
Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
Processed data file: ALLsamples.genes.fpkm_table.xls


title: Ofas_egg48-64h_Septic1


title: Ofas_egg48-64h_Sterile1


title: p21KO_24h_fasted_liver_replicate2

first: Elena

last: López-Guadamillas

state: Madrid

address: Calle Melchor Fdez Almagro

department: Molecular Oncology

institute: CNIO

data_processing:
RNA-seq processing:
Read files were quality-checked with FastQC.
Reads were aligned to the mouse genome (mm10) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Mus musculus mm10 transcript annotations from the UCSC Genome Browser were used
Genome_build: mm10
Supplementary_files_format_and_content: tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values

extract_protocol:
For RNA-seq Total RNA was extracted using the RNeasy kit (Qiagen)
For RNA-seq 1 µg of total RNA sample was used. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: mice were fed ad libitum or fasted for 24 hours

tag: genotype

tag: diet

value: 24h fasted

value: liver

tag: background strain


title: Ofas_egg48-64h_Septic3


title: TG.E6_6

description:
Fra23
Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
Processed data file: ALLsamples.genes.fpkm_table.xls


title: Ofas_egg48-64h_Sterile2


title: TG.E6_1

description:
WT1
Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
Processed data file: ALLsamples.genes.fpkm_table.xls


title: Ofas_egg48-64h_Naive3

value: Naive


title: p21KO_24h_fasted_liver_replicate1


title: p21KO_fed_liver_replicate2

value: ad libitum fed


title: WT_24h_fasted_liver_replicate2


title: Ofas_egg48-64h_Naive2


title: p21KO_fed_liver_replicate1


title: WT_fed_liver_replicate3


title: Ofas_egg48-64h_Naive1


title: WT_24h_fasted_liver_replicate1


title: WT_fed_liver_replicate1


title: TG.E6_4

description:
Fra21
Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
Processed data file: ALLsamples.genes.fpkm_table.xls


title: RHT2476

value: murine adipocytes


title: poly-1

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

data_processing:
Illumina Casava software used for basecalling.
The sequencing raw reads were mapped onto the P. gulae draft genome using Bowtie 2. Uniquely and properly mapped read pairs were used for further analysis.
Expression levels of genes, the RPKM (reads per kilobase of exon per million mapped reads) measure was calculated.
Genome_build: GCA_000378065.1_ASM37806v1_assembly
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Porphyromonas gulae

source_name: mRNA from polyP3 treatment

growth_protocol: The bacteria were grown on either brucella agar vontaining 5% laked sheep blood, 5 mg/L heamin, and 1 mg/L vitamin K1 (B-HK agar) or brucella broth (Becton, Dickinson and Company) containing 5 mg/L heamin and 1 mg/L vitamin K1 (B-HK) at 37°C anaerobically (80% N2, 10% H2, 10% CO2).

extract_protocol:
Total RNA from bacteria was extracted using TRIZOL and bacterial rRNA was revmoved by Ribo-Zero rRNA Removal Kit.
Poly(A) mRNA was isolated and fragmented using Illumina TruSeq Stranded Total RNA Sample Prep Kit.

treatment_protocol: Various concentrations of polyP3 were prepared and added to B-HK agar. The final concentrations of polyP3 ranged from 125 mg/L to 1000 mg/L (corresponding to 0.0125-0.1%). The agar plates were inoculated with an inoculum of approximately 10^5 CFU/spot and incubated at 37°C anaerobically for 3 days.

tag: treated with


title: poly-2


title: control-1

source_name: mRNA from no treatment

value: none (no treatment)


title: control-2


title: shSFRP2 D17 pre-osteoblasts, 2

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
sFRP2 KD D17 pre-osteoblasts derived from LFS iPSCs
S32

data_processing:
Sequence reads were aligned to human transcript reference (RefSeq Genes, hg19) for the expression analysis at gene levels using TopHat (Trapnell et al., 2009) and HTSeq softwares (Anders et al., 2015). The rawcount of reads aligned to each gene was further normalized by Reads Per Kilobase of transcript per Million (RPKM) as gene expression abundance measurement.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including RPKM values of each gene
Supplementary_files_format_and_content: log2 transformed RPKM

source_name: sFRP2 Knockdown in LFS pre-osteoblasts

extract_protocol:
Total RNA (1-3μg/sample) extracted from MSCs or pre-osteoblasts in vitro culture were submitted to Novogene for quality control analysis. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and double stranded cDNA synthesized using random hexamers
cDNA was synthesized using random hexamers, M-MuLV Reverse Transcriptase (RNase H), and DNA Polymerase I. NEBNext Adaptor with hairpin loop structure were ligated to the cDNA in preparation for hybridization. The library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA)

value: sFRP2 knockdown osteoblasts derived from LFS iPSCs


title: LFS D17 pre-osteoblasts, 1

description:
LFS D17 pre-osteoblasts derived from LFS iPSCs
S23

source_name: LFS Pre-osteoblasts

value: pre-osteoblasts derived from LFS iPSCs


title: shSFRP2 D0 MSCs, 1

description:
sFRP2 KD in mesenchymal stem cells derived from LFS iPSCs
S25

source_name: sFRP2 Knockdown in LFS mesenchymal stem cells

value: sFRP2 knockdown MSCs derived from LFS iPSCs


title: shSFRP2 D0 MSCs, 2

description:
sFRP2 KD in mesenchymal stem cells derived from LFS iPSCs
S26


title: shSFRP2 D14 pre-osteoblasts, 2

description:
sFRP2 KD D14 pre-osteoblasts derived from LFS iPSCs
S30


title: shSFRP2 D14 pre-osteoblasts, 1

description:
sFRP2 KD D14 pre-osteoblasts derived from LFS iPSCs
S29


title: LFS D14 pre-osteoblasts, 1

description:
LFS D14 pre-osteoblasts derived from LFS iPSCs
S21


title: shSFRP2 D7 pre-osteoblasts, 1

description:
sFRP2 KD D7 pre-osteoblasts derived from LFS iPSCs
S27


title: LFS D7 pre-osteoblasts, 2

description:
LFS D7 pre-osteoblasts derived from LFS iPSCs
S20


title: shSFRP2 D7 pre-osteoblasts, 2

description:
sFRP2 KD D7 pre-osteoblasts derived from LFS iPSCs
S28


title: LFS D14 pre-osteoblasts, 2

description:
LFS D14 pre-osteoblasts derived from LFS iPSCs
S22


title: LFS D0 MSCs, 1

description:
LFS mesenchymal stem cells derived from LFS iPSCs
S17

source_name: LFS mesenchymal stem cells

value: MSCs derived from LFS iPSCs


title: WT_fed_liver_replicate2

value: WT


title: LFS D7 pre-osteoblasts, 1

description:
LFS D7 pre-osteoblasts derived from LFS iPSCs
S19


title: sFRP2OE D14 pre-osteoblasts, 1

description:
sFRP2OE D14 pre-osteoblasts derived from WT iPSCs
S13

source_name: sFRP2 overexpression in WT osteoblasts

value: sFRP2OE osteoblasts derived from WT iPSCs


title: HFCO_03

description: replicate 1

value: hypothalamus


title: EpiLC_tol_rep3

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

description:
EPI_tol_3_0
Processed data file: EPI_genes.fpkm_table.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm10 reference assembly (GRCm38) by the Tophat2 software (Kim et al., 2013). We used default parameters except that we reduced maximum insertion and deletion length to 2bp, and kept only uniquely mapping, “no mixed” and “no discordant” reads.
We quantified gene expression levels in each sample by cuffnorm (Trapnell et al., 2012) with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_genes.fpkm_table.txt: Tab-delimited text files include FPKM values for each replicate.

source_name: EpiLC, total

growth_protocol: mESCs (E14) were cultured in serum-free N2B27 medium containing 2i (MEK and GSK inhibitor, PD0325901 and CHIR99021) and LIF. The nESC-to-EpiLC transition was conducted as described (Hayashi et al., 2011) with minor modifications. Briefly, mouse nESCs cells were plated at a density of 1x10e4 per cm2 in gelatin-coated plates with N2B27 medium containing activin A (20 ng/ml) and bFGF (12 ng/ml). The medium was changed every day. The converted EpiLCs were collected at day 3.

extract_protocol:
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HiSeq system (lllumina).

treatment_protocol: Cellular fractionation was prepared as described (Pandya-Jones and Black, 2009), with minor changes. 1x10e7 cells (E14) were gently trypsinized from plate and centrifugation. As for isolation of nuclei, the lysate was layered on to 500 ul cold sucrose buffer.

tag: originating cell line

value: EpiLC

tag: subcellular fraction

value: total


title: EpiLC_tol_rep2

description:
EPI_tol_2_0
Processed data file: EPI_genes.fpkm_table.txt


title: LFS D0 MSCs, 2

description:
LFS mesenchymal stem cells derived from LFS iPSCs
S18


title: sFRP2OE D7 pre-osteoblasts, 2

description:
sFRP2OE D7 pre-osteoblasts derived from WT iPSCs
S12


title: sFRP2OE D17 pre-osteoblasts, 2

description:
sFRP2OE D17 pre-osteoblasts derived from WT iPSCs
S16


title: shSFRP2 D17 pre-osteoblasts, 1

description:
sFRP2 KD D17 pre-osteoblasts derived from LFS iPSCs
S31


title: sFRP2OE D17 pre-osteoblasts, 1

description:
sFRP2OE D17 pre-osteoblasts derived from WT iPSCs
S15


title: EpiLC_tol_rep1

description:
EPI_tol_1_0
Processed data file: EPI_genes.fpkm_table.txt


title: sFRP2OE D14 pre-osteoblasts, 2

description:
sFRP2OE D14 pre-osteoblasts derived from WT iPSCs
S14


title: sFRP2OE D7 pre-osteoblasts, 1

description:
sFRP2OE D7 pre-osteoblasts derived from WT iPSCs
S11


title: sFRP2OE D0 MSCs, 2

description:
sFRP2 overexpression in mesenchymal stem cells derived from WT iPSCs
S10

source_name: sFRP2 overexpression in WT mesenchymal stem cells

value: sFRP2OE MSCs derived from WT iPSCs


title: EpiLC_cyt_rep3

description:
EPI_cyt_3_0
Processed data file: EPI_genes.fpkm_table.txt

source_name: EpiLC, cytoplasmic

value: cytoplasmic