title: PBScontrol_2

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Data preprocessing and transcript abundance calculation (RPKM: fragments per kilo bases of exons for per million mapped reads) were performed using TopHat and Cufflinks software.
Genome_build: rn4
Supplementary_files_format_and_content: gct files include normalized expression values for each sample.

source_name: Liver tissue

extract_protocol: Liver was harvested and snap-frozen until RNA isolation. Total RNA was extracted using Trizol reagent. Two animals were pooled together. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 200ng of total RNA for the construction of sequencing libraries following manufacturer's protocols.

tag: model

value: PBS-injected control

tag: drug treatment


title: PBScontrol_1

status: Public on Dec 16 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus


title: OBC_Wnt5a_11

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

data_processing:
For Smart-seq2 libraries: Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)  Demultiplexed reads were aligned to the mouse genome mm10 and ERCC reference using NextGenMap (Sedlazeck et al., 2013)  Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCm38.74)
For UMI-seq libraries: Reads were tagged with UMI and sample barcode using the Drop-seq pipeline (Macosko et al., 2015). Reads were aligned to the mouse genome mm10 using STAR (Dobin et al., 2013). Unique gene-wise counts were generated using the Drop-seq pipeline. Sample-barcode annotation can be found in additional file "UMIseq_niche_cells_barcode_annotation.txt". For data deposition, samples were demultiplexed using bamtools filter command.
Genome_build: mm10
Supplementary_files_format_and_content: sample- and gene-wise expression tables

organism: Mus musculus

source_name: OBC niche cell

extract_protocol:
cDNA was synthesized, barcoded, pooled and pre-amplified according to Soumillon et al. 2014. 800 pg of the cDNA pool was used for library preparation using the Nextera XT Kit (Illumina)
Lineage-negative, Sca-1+, Kit+ (LSK) and niche cells were FACS sorted according to Istvanffy et al. 2011. Cells were sorted into lysis buffer composed of 0.2 % Triton-X100 and 0.5 U/µl RNAse Inhibitor

tag: niche genotype

tag: strain

tag: library protocol

value: UMI-seq


title: lowdoseDEN_1

value: low-dose DEN

value: vehicle


title: MSC_Wnt5a_5

source_name: MSC niche cell


title: lowdoseDEN_2

source_name: Liver


title: EC_Wnt5a_16

source_name: EC niche cell


title: MSC_Wnt5a_4


title: lowdoseDEN_AM095_2

extract_protocol: Liver was harvested and snap-frozen until RNA isolation. Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 200ng of total RNA for the construction of sequencing libraries following manufacturer's protocols.

value: low-dose DEN rat


title: lowdoseDEN_AM063_1


title: EC_WT_15

value: WT


title: OBC_WT_9


title: OBC_Wnt5a_10


title: lowdoseDEN_AM063_2


title: MSC_WT_3


title: EC_WT_14


title: GEP_106

city: Redwood city

first: Anne

last: Chang

state: CA

address: 450 Broadway street, Pavilion C

department: Dermatology

institute: Stanford University School of Medicine

data_processing:
Basecalls performed using  CASAVA v1.8.2
The raw reads from 3’-sequencing were aligned to human genome reference (hg19) using Bowtie 2 (version 2.1.0) (Langmead et al., 2009) with default parameters (-D 15 -R 2 -N 0 -L 22 -i S,1,1,15).
Reads, which aligned concordantly to the genome were counted according to the RefGene annotation from UCSC using DEGseq (v0.50.1).
The longest isoform were selected when there are multiple isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with normalized reads count for each gene across all samples

organism: Homo sapiens

source_name: sun-protected skin from healthy volunteer

extract_protocol:
Total RNA from full thickness skin biopsies of the sun protected upper inner arm skin was extracted using RNAeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD).
The 3′ -end sequencing for expression quantification (3’-end seq) was performed as  described in Beck et al. (2010).

treatment_protocol: Skin biopsies by punch technique were performed after infiltration of the subcutaneous skin with 1% lidocaine with epinephrine diluted 1:1,000,000 for local anesthesia. The skin biopsies were 4 mm in diameter and included both dermis and epidermis. The samples were bisected, and half was preserved in formalin solution for staining with hematoxylin and eosin while the other half was preserved in RNAlater

tag: subject status

value: healthy volunteer

tag: ethnic background

value: European descent

tag: age

tag: gender

value: female

tag: tissue

value: skin biopsie from sun protected upper inner arm


title: MSC_WT_2


title: OBC_WT_7


title: EC_WT_13


title: MSC_WT_1


title: MSC_Wnt5a_6


title: 611Tx_Wnt5a

source_name: LSK progenitor cell

extract_protocol:
cDNA was synthesized and pre-amplified according to Picelli et al 2013. 500 pg of cDNA was used for library preparation using the Nextera XT Kit (Illumina)
Lineage-negative, Sca-1+, Kit+ (LSK) and niche cells were FACS sorted according to Istvanffy et al. 2011. Cells were sorted into lysis buffer composed of 0.2 % Triton-X100 and 0.5 U/µl RNAse Inhibitor


title: 641Tx_Wnt5a


title: 8581Tx_WT


title: 8471Tx_Wnt5a


title: 8491Tx_Wnt5a


title: 8541Tx_Wnt5a


title: 8571Tx_WT


title: 8551Tx_WT


title: lowdoseDEN_AM095_1

data_processing:
Data preprocessing and transcript abundance calculation (RPKM: fragments per kilo bases of exons for per million mapped reads) were performed using TopHat and Cufflinks software.
Genome_build: rn4
Supplementary_files_format_and_content: gct files include normalized expression values for each sample


title: OBC_WT_8


title: 3Cr-P5-4

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r 50. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 50.  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mouse brain cells

growth_protocol: We developed a mouse model of malignant glioma, one that utilizes E16.5 IUE approaches in combination with CRISPR mediated gene editing, where we use IUE to introduce gRNA vectors to delete NFI, PTEN, and p53, CAS9, and a GFP reporter, resulting in the generation of malignant glioma at P70. Using the GFP label to distinguish tumor from normal brain tissue, along with FACS-based selection against the glioma stem cell (GSC) and endothelial cells (see methods), we screened our tumor models for the presence of these prospective astroglial populations in the non-GSC fractions of these tumors.

extract_protocol:
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

tag: cell type

value: astrocyte


title: 3Cr-P2-4


title: 8531Tx_WT


title: 3Cr-P2-3


title: 3Cr-P1-1


title: 3Cr-P1-4


title: 3Cr-Bulk-4


title: Vm_S_3

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

country: China

institute: Yangzhou University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality sequence and the percentage of unknown bases (N) is greater than 10%. These “clean bases” were used  for further de novo assembly by Trinity software (Grabherr et al., 2011), and then the assembled unigenes were obtained.
All clean reads of each sample were mapped to unigenes for quantifying the gene expression level.
The FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of genes were calculated using RSEM software (Li et al., 2011)
Supplementary_files_format_and_content: tab-delimited text files include readcounts and normalized FPKM values for each Sample

organism: Viburnum macrocephalum f. keteleeri

source_name: Sterile flowers

growth_protocol: Adult V. macrocephalum f. keteleeri (15 years old) used in this study was grown in the campus of Yangzhou University under natural condition

extract_protocol:
The fertile and sterile flowers were collected from V. macrocephalum f. keteleeri in 31 March, 2015 (rapid flowering stage), and then were frozen in liquid nitrogen immediately after harvest and stored at -80°C until use. The total RNAs were extracted from fertile and sterile flowers using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liao-ning, China) according to the manufacturer’s protocol, respectively, and then treated with genomic DNA (gDNA) Eraser (TaKaRa, Dalian, China) to eliminate any DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adult - 15 years old

tag: Stage

value: Rapid flowering stage

value: Sterile flowers

tag: location

value: centre of an inflorescence

tag: forma

value: keteleeri


title: Vm_S_2


title: Vm_S_1


title: Root_col_with Al

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

data_processing:
The gene expression level is calculated by using RPKM (Mortazavi et al., 2008) method (Reads Per kb per Million reads).
Statistical analysis of differentially expressed genes (DEGs) was conducted using the probability (P) value and FDR (False Discovery Rate).
Genome_build: n/a

organism: Arabidopsis thaliana

source_name: Wild type roots_with Al

growth_protocol: The seedlings were pre-grown in 2% modified MGRL solution for 6 d at pH 5.0 in a growth chamber with a 16/8 h light/dark cycle at 22 oC.

extract_protocol:
Total RNA was isolated using the RNeasy® Plant Mini Kit (QIAGEN GmbH, Qiagen, GmbH, Hilden, Germany) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Approximately 500 seedlings (6-d-old) of both the wild-type Col and arf10/16 double mutant line were exposed to a 2% MGRL solution containing 0 or 10 μM AlCl3 (pH 5.0). After 24 h, the roots were sampled for RNA isolation.

value: Roots

tag: treatment

tag: genotype

value: wild type

tag: genetic background


title: Vm_F_3

source_name: Fertile flowers

value: Fertile flowers

value: outer ring of an inflorescence


title: Root_arf_with Al

source_name: arf10/arf16 double mutant roots_with Al

value: arf10/arf16 double mutant


title: Root_col_without Al

source_name: Wild type roots_without Al

value: control


title: Root_arf_without Al

source_name: arf10/arf16 double mutant roots_without Al


title: 3Cr-Bulk-2


title: 3Cr-Neg-3


title: Vm_F_2


title: 3Cr-Neg-1


title: 8561Tx_WT

value: WT


title: Vm_F_1


title: 8481Tx_WT


title: bovine_SOX9_ChIPseq_2

status: Public on Dec 15 2016

city: Montpellier

first: Francis

last: Poulat

address: 141 rue de la Cardonille

department: Genetic and Development

country: France

institute: IGH CNRS-UM UMR9002

description: processed data file: Bovine_SOX9_ChIPseq.bed

library_source: genomic

data_processing:
The base calling software name version and parameters are OLB-1.9.4/bin/setupBclToQseq.py --input-dir Data/Intensities/BaseCalls --output-dir --use-bases-mask Y*,Y*,Y*
ChIP-seq reads were aligned to the mouse mm9 or bovine Bostau6 (UMD3.1) genome assembly using SOAP2.21
For peaks calling, the number of reads being twice in the inputs than in the ChIP-seq experiments, we generated from the inputs a random sampling of 20 million reads each, using a homemade script which respects the proportion of reads per chromosome of the initial input. With this method we generated ten input samples for each ChIP-seq analysis that were used for ten rounds of peaks calling with the MACS software (1.4) (Zhang et al. 2008)( bw=250, mfold=10 et p value=1e-5). Peaks common to the ten  operations with FDR<0.05  were kept for further analysis.  Script is available upon request
Genome_build: mm9 or BosTau6
Supplementary_files_format_and_content: bed with peaks coordinate in mm9 for mouse and BosTau6 for bovine

molecule: genomic DNA

organism: Bos taurus

source_name: fetal testis

growth_protocol: Animal care and handling were conformed to the “Réseau des Animaleries de Montpellier” (RAM). For bovine fetus production and collection, experiments reported in this work were in agreement with the ethical guidelines of the French National Institute for Agricultural Research (INRA). Fetuses were produced by artificial insemination of Holstein females with semen of Holstein males (day 0), then collected at 90 days post-fertilization at the INRA slaughterhouse (France). The protocol (N°: 12/046) was approved by the local ethical committee (COMETHEA) and Eric Pailhoux is the recipient of an official authorization for animal experimentation (N°: B91-649).

extract_protocol:
Upon collection, gonads were crushed in liquid nitrogen using a mortar. Tissue powders were immediately fixed with PBS containing 2mM of Disuccinimidyl glutarate (DSG: PIERCE ref 20693) initially solubilized in DMSO as described previously (Nowak et al. 2005). Samples were then incubated for 30 minutes on a rotating wheel at room temperature. After three washes with PBS, samples were subsequently fixed with PBS 1% formaldehyde for 30 minutes at room temperature
Libraries were prepared according to Illumina's instructions. 10-300ng DNA is combined with End Repair Mix, and incubate at 20°C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37°C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20°C for 15 min. Purify the Adapter-ligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN).

value: testis

value: Holstein

tag: developmental stage

tag: antibody

value: rabbit anti SOX9 homemade (ref Gasca et al, PNAS 2002, vol 99, 11199-11204)


title: bovine_input_DNA


title: bovine_SOX9_ChIPseq_1


title: DS23114

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

institute: UMass Medical School

data_processing:
Basecalls performed using CASAVA
HiC data sets were aligned against hg19, binned and normalized using the methods described in "The Hitchhiker's guide to Hi-C analysis: practical guidelines", Methods, 2015, Lajoie et.al.
Binning, normalization and further downstream analysis of the data was done using the method in "Structural organization of the inactive X  chromosome in the mouse", Nature, 2016, by Giorgetti et. Al
Genome_build: hg19
Supplementary_files_format_and_content: tar archive containing raw and normalized interactions

source_name: immortalized cell line

growth_protocol: This is an adherent cell line and was passaged according to ATCC protocols, except that cells were dispersed using Accutase (Sigma A-6964) rather than Trypsin

extract_protocol:
Hi-C experiment were conducted according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).)
Libraries were prepared according to Illumina's protocol for Truseq library construction, with the following modifications:  Volumes and primers were scaled down to accommodate low input material.

tag: cell line

value: Human large cell lung carcinoma

tag: restriction enzyme

value: HindIII


title: 3Cr-P5-1

value: astrocyte


title: DS23107


title: PD_28day

city: Beijing

first: Weidong

last: Han

address: #28 Fuxing Road, HaiDian District

department: School of Life Sciences

institute: Chinese PLA General Hospital

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads.
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin.
The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned
Genome_build: mirbase 21
Supplementary_files_format_and_content: tab-delimited text files for each Sample

source_name: Plasma

extract_protocol:
Plasma was collected on day 0 and 28 of cycle 1. RNA was harvested using Trizol reagent
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).

value: Plasma

tag: cancer type

value: Colorectal cancer

tag: clinical response

value: progressive disease (PD)

tag: collection day


title: PD_0day


title: PR-2_28day

value: Gastic cancer

value: partial response (PR)


title: iWT_CPC_rep1_atac

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

data_processing:
Library strategy: ATAC-Seq
Basecalls performed using Hiseq Control Software
Nextera adaptor sequences were trimmed using cutadapt (version 1.8.1; custom parameters: (-O 5, -m 30 –q 15))
Aligned to the hg19 genome using bowtie (version 1.1.1; custom parameters: (-X 2000, -m 1))
Duplicate reads were filtered using Picard MarkDuplicates (version 1.92) and reads in repetitive regions (ENCODE Blacklist) were filtered using samtools (version 0.1.19)
Genome_build: hg19
Supplementary_files_format_and_content: Peaks were called using MACS2 (version 2.1.0; custom parameters: (--nomodel –shift -100 –extsize 200). Peak files are in ENCODE narrowPeak format.

source_name: cardiac progenitor isogenic WT

growth_protocol: ES and iPS cells were cultured in mTeSR® on hESC-qualified (BDsciences) matrigel-coated plates. For human cardiac differentiation into cardiac progenitors we modified the protocols originally developed by Lian et al. to achieve high yield, high-purity, tripotential cardiac progenitors in vitro (Lian et al., 2012).

extract_protocol:
Similar to Buenrostro et al., 50,000 CPCs were lyzed, transposed via Tagmentation (Nextara kit), column purified and amplified for 15 cycles.
Barcoded ATAC-seq libraries were made from transposed and amplified DNA using the Nextera Sample Prep Kit, checked for adapter artifacts by Agilent Bioanalyzer using DNA high sensitivity reagents and chips.

value: iPS-derived cardiac progenitor cells

tag: passages

tag: differentiation stage

value: Differentiation D7


title: iWT_CPC_rep2_atac


title: G296S_CPC_rep2_atac

source_name: cardiac progenitor isogenic G296S mutant


title: MUT_Tbx5_chip

data_processing:
Basecalls performed using Hiseq Control Software
Contaminants were removed and raw reads were trimmed for low quality reads using the default settings of fastq-mcf from ea-utils 1.1.2-537
Trimmed reads were then aligned to the hg19 genome using default settings of bowtie 2.1.0 (Langmead et al., 2012).
Low quality alignments were removed using samtools 0.1.19 (Li et al., 2009) with a MAPQ score cutoff of 30 (“-q 30”)
PCR duplicates were removed using the default settings of MarkDuplicates from picard-tools 1.98
Genome_build: hg19
Supplementary_files_format_and_content: Peaks were called using MACS2 (version 2.1.0; custom parameters: (--keep-dup 1 –g 2.7e9 –q 0.01 –bw 498). All peaks reported passed an FDR threshold of 1%.  Peak files are in ENCODE narrowPeak format.

source_name: purified cardiomyocyte G296S mutants

growth_protocol: ES and iPS cells were cultured in mTeSR® on hESC-qualified (BDsciences) matrigel-coated plates. For human cardiac differentiation into cardiomyocytes, we modified the protocols originally developed by Lian et al. and Tohyama et al. to achieve high yield, high-purity cardiac commitment in vitro (Lian et al., 2012; Tohyama et al., 2013).

extract_protocol:
Cross-linked cell pellets were lyzed, nuclei extracted, sonicated, immunoprecipitated, washed, reverse cross-link and column purified.
Barcoded ChIP-seq libraries were made from ChIP DNA using the NuGen Ovation Ultralow DR or Diagenode Microplex Kit, checked for adapter artifacts by Agilent Bioanalyzer using DNA high sensitivity reagents and chips, and quantified by qPCR using an Illumina Library Quantification kit (KAPA Biosystems)

value: iPS-derived cardiomyocytes

value: Differentiation D32

tag: chip antibody


title: MUT_H3K4me3_chip

tag: cell type


title: G296S_CPC_rep1_atac


title: MUT_Med1.sorted_chip


title: C3_input_d15_chip

value: Differentiation D15

value: Input


title: MUT_input_chip


title: MUT_H3K27me3_chip


title: MUT_Gata4_chip


title: MUT_H3K36me3_chip


title: MUT_H3K27ac_chip


title: 3_2_input_chip


title: C3_Hdac2_d15_chip


title: 3_2_H3K4me3_chip


title: 3_2_H3K36me3_chip


title: 4_2_Med1_chip


title: 4_2_H3K4me3_chip


title: 3_2_H3K27me3_chip


title: 4_2_Tbx5_chip


title: 3_2_H3K27ac_chip


title: 4_2_input_chip


title: PR-2_0day

tag: tissue


title: 4_2_H3K27me3_chip


title: 4_2_Gata4_chip


title: 4_2_H3K27ac_chip


title: PR-1_0day

value: esopheageal cancer


title: PR-1_28day


title: 2_6_Tbx5_chip


title: 2_6_H3K27me3_chip


title: 2_6_H3K4me3_chip


title: 2_6_H3K36me3_chip


title: 2_6_H3K27ac_chip


title: 2_6_input_chip


title: WT_Med1_chip

source_name: purified cardiomyocyte WT


title: 2_6_Gata4_chip


title: 2_6_Med1_chip


title: WT_H3K27me3_chip


title: WT_H3K27ac_chip


title: WT_Gata4_chip


title: WT_H3K36me3_chip


title: 4_2_H3K36me3_chip


title: WT_input_chip


title: 7_2_H3K27ac_chip


title: 7_2_input_chip


title: C19_input_d15_chip

description: iWT


title: C19_Hdac2_d15_chip

description: iWT


title: 7_2_H3K36me3_chip


title: 7_2_H3K4me3_chip


title: 7_2_H3K27me3_chip


title: 6_1_input_chip


title: 6_1_H3K36me3_chip


title: 6_1_H3K27me3_chip


title: 6_1_H3K27ac_chip


title: 6_1_H3K4me3_chip


title: H7_Tbx5_chip


title: WT_H3K4me3_chip


title: H7_H3K4me3_chip


title: WT_Tbx5_chip


title: H7_H3K36me3_chip


title: H7_input_chip


title: H7_H3K27ac_chip


title: H7_H3K27me3_chip


title: 5_6_input_chip


title: 5_6_Tbx5_chip


title: 5_6_H3K27me3_chip


title: 5_6_Med1_chip


title: 5_6_Gata4_chip


title: 5_6_H3K27ac_chip


title: 1_8_Tbx5_chip


title: 5_6_H3K36me3_chip


title: 1_8_Med1_chip


title: 1_8_H3K4me3_chip


title: Chow-chow, rep2 (ChIP-Seq)

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Aligment to mm9 using STAR
Differential gene expression and H3K27ac binding identified using DESeq2.
Gene ontology analysis using PANTHER.
To quantify exon and intron RNA reads the iRNA pipeline was used (Madsen, J. G. et al. iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic acids research, doi:10.1093/nar/gku1365 (2015).
Pathway analysis of intron-regulated genes using the curated reactome database (Croft, D. et al. The Reactome pathway knowledgebase. Nucleic acids research 42, D472-477, doi:10.1093/nar/gkt1102 (2014).Fabregat, A. et al. The Reactome pathway Knowledgebase. Nucleic acids research 44, D481-487, doi:10.1093/nar/gkv1351 (2016)).
H3K27ac ChIP-seq binding sites identified using HOMER
Enriched motif analysis using DNA motifs for TFs curated by HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Chow-chow, liver

extract_protocol:
ChIP-seq libraries of H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Purified RNA was subjected to either polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq and libraries of H3K27ac-enriched DNA and DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: C57BL/6J mice (Jackson Laboratory) were fed either a HFD (D12327, Research Diet, 40% fat by calories) or chow diet (NIH-31, Zeigler Brothers Inc., 8% fat by calories) for seven weeks from 12 weeks of age (groups termed HFD and Chow, respectively). After seven weeks, half of the mice where sacrificed by CO2 narcosis followed by cervical dislocation, livers were dissected and processed for RNA purification, nuclei isolation or frozen in liquid nitrogen for subsequent studies. Blood samples were taken as indicated and processed for metabolic measurements. The other half of the animals continued on a chow diet (termed HFD-chow and Chow-chow) for an additional five weeks

tag: strain

value: chow-chow

tag: age

value: 24 weeks


title: HFD-chow, rep3 (ChIP-Seq)

source_name: HFD-chow, liver

tag: treatment

value: HFD-chow


title: 1_8_H3K36me3_chip


title: HFD-chow, rep2 (ChIP-Seq)


title: Chow-chow, rep3 (ChIP-Seq)


title: Chow-chow, rep1 (ChIP-Seq)


title: HFD-chow, rep1 (ChIP-Seq)


title: 1_8_input_chip


title: HFD, rep3 (ChIP-Seq)

source_name: HFD, liver

value: HFD

value: 19 weeks


title: 1_8_H3K27me3_chip


title: 1_8_H3K27ac_chip


title: H7_Med1_chip


title: H7_Gata4_chip


title: HFD, rep2 (ChIP-Seq)


title: HFD, rep1 (ChIP-Seq)


title: 1_8_Gata4_chip


title: 5_6_H3K4me3_chip


title: Chow, rep3 (ChIP-Seq)

source_name: Chow, liver

value: chow


title: iWT_CM_D32_rep2_rna

data_processing:
Basecalls performed using Hiseq Control Software
Contaminants were removed and raw reads were trimmed for low quality reads using the default settings of fastq-mcf from ea-utils 1.1.2-537
Trimmed reads were aligned to the hg19 genome assembly using Tophat with the following settings: “--segment-mismatches 2 -m 2 -r 192 --mate-std-dev 200 --microexon-search”.
Unmapped reads (“-F 0x4”), non-primary aligned reads (“-F 0x100”), and low quality reads (MAPQ less than 30, “-q 30”) were filtered using samtools 0.1.19
PCR duplicates were removed using the default settings of MarkDuplicates from picard-tools 1.98
Genome_build: hg19
Supplementary_files_format_and_content: USeq application DefinedRegionDifferentialSeq (Nix et al., 2008) was used to normalize raw read counts and calculate FPKM (counts/ exonicBasesPerKB/ millionTotalMappedReadsToGeneTable). Each row is a unique gene identified that was significantly detected (counts >5). Each column is raw counts or FPKM for each sample belonging to the same experiment.

source_name: purified cardiomyocyte isogenic WT

growth_protocol: ES and iPS cells were cultured in mTeSR® on hESC-qualified (BDsciences) matrigel-coated plates. For human cardiac differentiation into CPC and CM, we modified the protocols originally developed by Lian et al. and Tohyama et al. to achieve stage-specific, high yield, high-purity cardiac commitment in vitro (Lian et al., 2012; Tohyama et al., 2013).

extract_protocol:
Total RNA was Trizol-extracted (Invitrogen) and further purified using the Qiagen RNAeasy Micro Kit with DnaseI in-column treatment.
cDNA was prepared with the NuGen Ovation RNA-seq System V2 Kit. Total RNA (50 ng) was reverse transcribed to synthesize the first-strand cDNA using a combination of random hexamers and a poly-T chimeric primer. The RNA template was then partially degraded by heating, and the second strand cDNA was synthesized using DNA polymerase. The double-stranded DNA was then amplified using single primer isothermal amplification (SPIA). In this linear cDNA amplification process, RNase H degraded RNA in DNA/RNA heteroduplex at the 5′-end of the double-stranded DNA, after which the SPIA primer bound to the cDNA and the polymerase started replication at the 3′-end of the primer by displacement of the existing forward strand. Random hexamers were then used to amplify the second-strand cDNA linearly. Finally, libraries from the SPIA amplified cDNA were made using the NuGen Ovation Ultralow DR Kit. The mRNA-seq libraries were analyzed by Agilent Bioanalyzer and quantified using an Illumina Library Quantification Kit (KAPA Biosystems). Four mRNA-seq libraries were pooled per lane of paired-end 100 bp sequencing (High output) on an Illumina HiSeq 2500 instrument.


title: G296S_CM_D32_rep1_rna

source_name: purified cardiomyocyte isogenic G296S mutant


title: G296S_CM_D15_rep2_rna

source_name: unpurified cardiomyocyte isogenic G296S mutant


title: G296S_CM_D15_rep1_rna


title: HFD 40U, rep1 (DHS-Seq)

source_name: HFD 40U, liver

extract_protocol:
Livers were isolated from mice and nuclei were immediately purified. DNase digestions were performed by adding digestion buffer containing 40U of DNase I (Sigma). DNase I digestion efficiency was evaluated by quantitative PCR53 and samples with optimal digestion efficiency were incubated RNase A (Sigma) before 50–500 bp DNA fragments were purified using ultracentrifugation. DNase-seq libraries were constructed according to manufacturer´s (Illumina) instructions as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Purified RNA was subjected to either polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq and libraries of H3K27ac-enriched DNA and DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).


title: HFD 40U, rep2 (DHS-Seq)


title: Chow 40U, rep1 (DHS-Seq)

source_name: Chow 40U, liver


title: iWT_CM_D15_rep2_rna

source_name: unpurified cardiomyocyte isogenic WT


title: Chow 40U, rep2 (DHS-Seq)


title: HFD-chow, rep3 (RNA-Seq)

extract_protocol:
5 mg of liver tissue were homogenized using UltraThorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) according to manufacturer’s instructions. Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
Purified RNA was subjected to either polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq and libraries of H3K27ac-enriched DNA and DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).


title: G296S_CPC_rep2_rna


title: HFD-chow, rep1 (RNA-Seq)


title: HFD-chow, rep2 (RNA-Seq)


title: G296S_CPC_rep1_rna


title: HFD, rep3 (RNA-Seq)


title: G296S_CM_D32_rep2_rna


title: iWT_CPC_rep1_rna


title: HFD, rep2 (RNA-Seq)


title: H7_CM_rep2_rna

source_name: cardiomyocyte H7-derived

value: ES-derived cardiomyocyte

value: Differentiation D30


title: HFD, rep1 (RNA-Seq)


title: H7_CPC_GATA4si_rep2_rna

source_name: cardiac progenitor H7-derived

value: ES-derived cardiac progenitor

value: Differentiation D7+ GATA4si


title: Chow-chow, rep2 (RNA-Seq)


title: H7_CM_rep1_rna


title: H7_CPC_GATA4si_rep1_rna


title: Chow-chow, rep3 (RNA-Seq)


title: Chow, rep2 (ChIP-Seq)


title: Chow, rep1 (ChIP-Seq)


title: iWT_CM_D32_rep1_rna


title: Chow-chow, rep1 (RNA-Seq)


title: Chow, rep3 (RNA-Seq)


title: H7_CPC_rep1_rna


title: H7_MES_rep2_rna

source_name: mesoderm H7-derived

value: ES-derived mesoderm

value: Differentiation D3


title: iWT_CM_D15_rep1_rna

value: iPS-derived cardiomyocytes


title: Chow, rep2 (RNA-Seq)


title: Chow, rep1 (RNA-Seq)


title: H7_CPC_rep2_rna

value: Differentiation D7


title: iPS_4_rna

source_name: induced pluripotent stem cell 4.2

value: induced pluripotent stem cell

value: undifferentiated


title: iPS_2_rna

source_name: induced pluripotent stem cell 2.6


title: iPS_5_rna

source_name: induced pluripotent stem cell 5.6


title: H7_MES_rep1_rna


title: XY-WT rep2

data_processing:
Trimmomatic (version 0.30)
Tophat2 (version 2.0.8)
HTSeq-count (version 0.6.1p1)
voom' from ‘limma’ R package (version 3.24.0)
Genome_build: Mus_musculus.GRCm38.77
Supplementary_files_format_and_content: Voom output of all differentially expressed genes

source_name: testis

growth_protocol: All animal work was performed under Monash Medical Centre Animal Ethics approval (MMCB/2012/23). Microdissected gonads were separated from mesonephros of E13.5 embryos, snap frozen and stored at −80°C.

extract_protocol:
RNA was extracted using the RNeasy kit (QIAGEN GmbH, D-40725 Germany).
Libraries were generated using NuGEN Mondrian Technology, utilising SPIA amplification methodology (which specifically selects and linearly reverse transcribes nonribosomal RNA).  6pM of bar-coded libraries per lane were sequenced using the Illumina HiSeq1500. Paired-end RNA sequencing chemistry, using 150 nt read lengths, at 50 million reads per sample was performed.

value: testis

tag: genotype

value: XY Sox9flox/flox wildtype


title: XY-WT rep3


title: XY-WT rep1


title: XY-KO rep3

value: XY AMH-Cre; Sox9flox/flox


title: iPS_1_rna

source_name: induced pluripotent stem cell 1.8


title: XY-KO rep1


title: iPS_3_rna

source_name: induced pluripotent stem cell 3.2


title: XX-WT rep2

source_name: ovary

value: ovary

value: XX Sox9flox/flox wildtype


title: XX-WT rep1


title: XY-KO rep2


title: ES_H7_rna

source_name: H7 embryonic stem cell

value: embryonic stem cell


title: XX-WT rep3


title: wt rep 1

city: Turku

first: Emilia

last: Peuhu

address: Medisiina D5, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of turku

data_processing:
The base calling was done using bcl2fastq (v1.8.4)
Read alignment was done using TopHat (v2.0.10) to mm10 mouse genome reference
Genewise read counts were calculated using HTSeq (v0.5.4p3)
Genome_build: mm10
Supplementary_files_format_and_content: files are tab delimited text filse containing the genewise read counts for each sample

source_name: Mammary gland stromal fibroblasts

growth_protocol: Cells were isolated from collagenase digested mouse mammary glands (3 mice pooled per sample) by differential centrifugation and grown in vitro in full serum containing medium until confluent. Floating cells were removed.

extract_protocol:
RNA was isolated using NucleoSpin kit (Macherey-Nagel).
Library preparation was done according to Illumina TruSeq® RNA Sample Preparation v2 Guide

treatment_protocol: Samples collected from 6-well plate, lysed in RLT lysis buffer (Qiagen)

value: Mammary gland

value: 7 weeks old

value: wt/wt

tag: passage


title: Gata6 WT3

city: Ithaca

first: Alex

last: Wang

state: NY

address: 260 Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Sequenced reads were trimmed and filtered to remove low quality reads using FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), then mapped to mm10 assembly using Tophat2 with the following parameters: "--segment-length 22 --segment-mismatches 0 --no-novel-juncs"
Gene level read counts wre measured using htseq-counts (http://www-huber.embl.de/HTSeq/) using default parameters.
DESeq2 package for R was used to normalize gene level read counts and analyze differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table and DESeq output

source_name: epidermal keratinocytes

growth_protocol: Cells were grown in low calcium E media

extract_protocol:
RNA was isolated by TRIzol and purified with Qiagen RNeasy mini spin columns
Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare libraries from 2 ug of total RNA

treatment_protocol: Passage 8-10, cells were treated with 1 uM 4-hydroxytamoxifen for 6 hours

value: WT (K14CreERT2-;Gata6 fl/fl)

value: tamoxifen 6 hours


title: wt rep 2


title: wt rep 3


title: Sharpincpdm rep 2

value: cpdm/cpdm (Sharpin deficient)


title: Sharpincpdm rep 1


title: Sharpincpdm rep 3


title: T2_ko_2

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

institute: CNRS, Université Claude Bernard Lyon 1

data_processing:
Raw RNA-seq reads were aligned on the mouse mm10 genome assembly using TopHat 2.0.9. Parameters: intron size between 40bp and 1Mb, anchor size 8, library-type fr-firststrand.
Gene expression computations were performed using uniquely mapping reads extracted from TopHat alignments and genomic annotations from Ensembl release 82.
BedGraph files were generated for the unique RNA-seq read coverage, separately for each strand.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files containing per base unique RNA-seq read coverage for each sample.

molecule: polyA RNA

source_name: trunk segment T2

extract_protocol:
Total RNA was extracted from tissues using QIAGEN RNeasy Plus Micro Kit after disruption and homogenization. RNA quality was assessed using an Agilent 2100 Bioanalyser.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina HiSeq 2500 sequencer. Single-end, 100bp reads were produced.

value: CBA / C57BL/6 mix

value: trunk segment T2

value: Del(Hotair) homozygous

tag: developmental stage


title: H2B_IP_MNase_800U_Replicate_2

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: Biological replicate 2

data_processing:
Sequences were aligned to the yeast genome (sacCer3) using Bowtie2 with default settings.
Reads were size selected, and we kept all reads with the lengths between 50 and 200bp.
Genome-wide coverage profiles were computed in MATLAB, and they were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: Cells were grown to mid-log phase in Synthetic Complete (SC) medium.

extract_protocol:
Nuclei were prepared from cross-linked cells and digested with different amounts of MNase (units given in filenames). For IP we used a monoclonal anti-HA antibody (see Methods for details).
The DNA was repaired using the DNA PreCR kit from New England Biolabs. Paired-end libraries were constructed and indexed using Illumina kits from NEB (E7370 and E7335).

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 15 min at room temperature and then treated with 0.5M glycine for 5 min. Stored as pellets at -80C.

tag: strain name

value: MATa can1-100 his3-11 leu2-3,112 lys2delta trp1-1 ura3-1 hta2-htb2delta::TRP1 HA-6His-HTB1::HIS3


title: HL_ko_2

source_name: hindlimb

value: hindlimb


title: H2B_Input_MNase_800U_Replicate_2

description: Biological replicate 2


title: T1_ko_2

source_name: trunk segment T1

value: trunk segment T1


title: T3_ko_2

source_name: trunk segment T3

value: trunk segment T3


title: H2B_Input_MNase_500U_Replicate_2

description: Biological replicate 2


title: FL_ko_2

source_name: forelimb

value: forelimb


title: T3_wt_2

value: wild type


title: H2B_Input_MNase_600U_Replicate_2

description: Biological replicate 2


title: GT_ko_2

source_name: genital tubercule

value: genital tubercule


title: H2B_Input_MNase_400U_Replicate_2

description: Biological replicate 2


title: Gata6 iKO2

value: iKO (K14CreERT2+;Gata6 fl/fl)


title: T2_wt_2


title: H2B_IP_MNase_200U_Replicate_2

description: Biological replicate 2


title: T1_wt_2


title: H2B_Input_MNase_100U_Replicate_2

description: Biological replicate 2


title: iWT_CPC_rep2_rna

source_name: cardiac progenitor isogenic WT

value: iPS-derived cardiac progenitor cells

value: Differentiation D7


title: HL_wt_2


title: H2B_Input_MNase_200U_Replicate_2

description: Biological replicate 2


title: H2B_Input_MNase_50U_Replicate_1

description: Biological replicate 1


title: H2B_IP_MNase_50U_Replicate_1

description: Biological replicate 1


title: GT_wt_2


title: FL_wt_2


title: H2B_IP_MNase_400U_Replicate_1

description: Biological replicate 1


title: T3_wt_1


title: H2B_Input_MNase_300U_Replicate_1

description: Biological replicate 1


title: H2B_Input_MNase_400U_Replicate_1

description: Biological replicate 1


title: T2_wt_1


title: T1_wt_1


title: H2B_Input_MNase_200U_Replicate_1

description: Biological replicate 1


title: H2B_Input_MNase_100U_Replicate_1

description: Biological replicate 1


title: T3_ko_1


title: GT_wt_1


title: H4_Input_MNase_300U_Replicate_1

description: Biological replicate 1

value: MATa ade2-1 leu2-3,112 trp1-1 ura3-1 hht1-hhf1delta::LEU2 URA3::HHT2-HA-HHF2


title: HL_wt_1


title: H4_Input_MNase_50U_Replicate_1

description: Biological replicate 1


title: T2_ko_1


title: T1_ko_1


title: H4_Input_MNase_25U_Replicate_1

description: Biological replicate 1


title: H4_Input_MNase_200U_Replicate_1

description: Biological replicate 1


title: H4_IP_MNase_200U_Replicate_1

description: Biological replicate 1


title: H4_Input_MNase_100U_Replicate_1

description: Biological replicate 1


title: HL_ko_1


title: FL_ko_1


title: H4_IP_MNase_25U_Replicate_2

description: Biological replicate 2


title: GT_ko_1


title: H4_IP_MNase_200U_Replicate_2

description: Biological replicate 2


title: Min6-ARX clone 17, no dox

city: Boston

first: Jin

last: Li

address: Blackfan 3

institute: BIDMC

data_processing:
Aligned with Tophat 2.0
Quantified with Tophat 2.0
Genome_build: mm10
Supplementary_files_format_and_content: The processed files contain all the samples' RPKM in tab-delimited format

source_name: mouse beta cell line

growth_protocol: alpha-TC1 cells are cultured with low glucose DMEM medium with 10% FBS and 1% Pen/Strep. Min6_ARX cells are cultured with high glucose DMEM medium with 10% FBS and 1%Pen/Strep.

extract_protocol:
Qiagen rneasy kit
illumina RNA-seq 2.0 kit

treatment_protocol: The cells are treated with 10uM Artemether disovled in DMSO

value: Min6-ARX inducible cells with different induction time of Dox


title: Min6-ARX clone 17, 3 day dox


title: PG rep2

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

description:
Okazaki fragments
Embryos contain ~1-30 cells

data_processing:
Sequencing reads were mapped to the WS220 genome using Bowtie2 with –local function. Reads with q<30 were removed using Samtools.
Reads were binned in 100bp intervals using Bedtools, maintaining strand identity. Data was partially smoothed by calculating the median with a sliding window of 1.5kb for each strand.
Data was normalized (such that the sum of Watson and Crick reads = 1) and positions of origins were mapped using a 12kb window
Genome_build: Ws220
Supplementary_files_format_and_content: wig file

organism: Caenorhabditis elegans

source_name: Pre-gastrula embryos

growth_protocol: To collect synchronous L1 population, 10,000 worms were grown on NGM plates. Their progeny were washed with M9 buffer and passed through 11 µM nylon net filters (Millipore Ltd. NY1104700). Approximately 150,000 synchronized L1 stage worms were grown in liquid media supplemented with OP50 bacteria until reaching L3 stage. Synchronized L3 staged worms were collected by centrifugation, followed with 3 times washing with M9 buffer containing 50 µg/ml Ampicillin.

extract_protocol:
Samples were resuspended in 480 µl Lysis buffer (50 mM Tris-HCL, pH 8.0, 50mM EDTA, 100 mM NaCl, 1.5% Sarkosyl, 1% SDS) and incubated with 200 µg proteinase K at 42 degree overnight. Digested proteins and peptides were precipitated by addition of 200 µl 5M KOAc and centrifugation at 16,000g for 30 minutes at 4˚C. Genomic DNA was precipitated by adding 500 µl isopropanol and spinning at 16,000 g at 4˚C for 10 minutes. Genomic DNA pellets were washed with 70% ethanol and then resuspended in 300 µl STE (10mM Tris-HCL, PH8.0, 1 mM EDTA, 100mM NaCl). Residual RNA was digested by addition of 5U RiboShredder RNase Blend (Epicentre) at 37˚C overnight. Genomic DNA was precipitated with 30 µl 3M NaOAc and 1.7 ml ethanol pelleted at 10,000g for 10 minutes at 4˚C. DNA pellets were washed with 70% ethanol and resuspended in 30 µl TE (10mM Tris-HCl pH 7.5, 0.1 mM EDTA) and stored over night at 4˚C to allow complete resuspension of genomic DNA. Samples were stored at -80˚C.
Three hundred ng purified Okazaki fragments were used to generate sequencing library similar to the previously optimized protocol . Following fragment ligation the total reaction was loaded on a 2% agarose gel; fragments corresponding to ~200-700 bp were purified from the gel using QiAquick gel extraction kit (Qiagen). Purified ligated fragments were amplified by (PCR 16) cycles using custom Illumina or Ion Torrent sequencing oligos

treatment_protocol: lig-1 (Ahringer laboratory) and control (empty vector) RNAi-expressing bacteria were grown overnight at 37˚C in LB medium supplemented with 50 µg/ml Ampicillin and 10µg/ ml tetracycline. Bacterial cultures were transferred to fresh LB medium supplemented with 50 µg/ml Ampicillin and were grown at 37˚C until reaching OD 1.0. RNAi expression was induced with 1mM IPTG for 1 hour at room temperature. lig-1 RNAi expressing bacteria was diluted 1:10 with control (empty vector) bacteria to a final volume of 500ml. Diluted bacteria were harvested by centrifugation and added to C. elegans S-Basal liquid media containing 150,000-200,000 well synchronized early L3 staged N2 worms (see below). N2 worms were grown in S-Basal liquid culture containing diluted lig-1 RNAi at 20˚C until adulthood.

value: N2 Bristol egl-30

tag: Stage

value: Pre-gastrula embryos

tag: RNAi

value: Ligase 1 depletion


title: Min6-ARX clone 16, 6 day dox


title: Mixed Early rep2

description:
Okazaki fragments
Embryos contain ~1-200 cells

source_name: Mixed early embryos

value: N2 Bristol WT

value: Mixed early


title: H4_Input_MNase_25U_Replicate_2

description: Biological replicate 2


title: Late rep2

description:
Okazaki fragments
Embryos contain ~200-500 cells

source_name: Late embryos

value: Late embryos


title: Lib153OverExpressTRUB2rep3_input

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Reads were aligned to the human genome (hg19) using STAR aligner with default parameters
An in house script was used to merge left and right reads into a single bam file spanning the full interval from the beginning of the 'left' read to the end of the 'right' read
Strand specific bedgraph files were generated quantifying the number of reads beginning at each position, using bedtools genomecov (activating the '-5' and '-strand' flags
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

growth_protocol: Human HEK293 cells were plated in 6-well plates at 20% confluence.

extract_protocol:
Enrichment of polyadenylated RNA (polyA+ RNA) from total RNA was performed using one round of enrichment using Oligo(dT) dynabeads (Invitrogen) according to the manufacturer’s protocol. CMC-treatment was performed essentially as described in (Schwartz et al, Cell, 2014).
The mRNA was chemically fragmented into ~80-150 nt-long fragments by performing a short fragmentation (30 seconds) using RNA fragmentation reagent and stop solution (Ambion). RNA was subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3’ ligation of an RNA adapter using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed using AffinityScript Multiple Temperature Reverse Transcriptase (Agilent) or SuperScript III (Life Technologies), and the cDNA was subjected to a 3’ ligation with a second adapter using T4 ligase. The single-stranded cDNA product was then amplified for 9-12 cycles in a PCR reaction. Libraries were sequenced on Illumina HiSeq 2500 platforms generating paired end reads.

treatment_protocol: siRNAs targeting TRUB1, TRUB2, and PUS7 (catalog numbers: s4111 and s4112) were transfected using Lipofectamine RNAiMAX (Life Technologies) following the manufacturer’s protocols, with two siRNA boosts at 48 and 96 hours following transfection; As negative controls, we used Ambion® In Vivo Negative Control #1 siRNA (catalog number: 4457287). Cells were harvested at 144 hours. For overexpression, plasmids encoding full length TRUB1 and TRUB2 were obtained from DNASU (HsCD00039729 and HsCD00041101, respectively) and cloned into a Gateway destination vector, downstream of an EF1ɑpromoter. The plasmids were transfected into HEK293 cell using either Lipofectamine LTX reagent (Life technologies) or polyJet (signagen) with one boost of the plasmid at 24 hours. Cells were harvested 48 hours following transfection.

value: input

tag: cell line


title: Min6-ARX clone 17, 6 day dox


title: H4_IP_MNase_25U_Replicate_1

description: Biological replicate 1


title: FL_wt_1

value: CBA / C57BL/6 mix


title: Lib153OverExpressTRUB2rep3_Treat

value: Treat


title: Min6-ARX clone 9, 6 day dox


title: Min6-ARX clone 9, 3 day dox


title: Lib153OverExpressTRUB2rep1_input


title: Lib153OverExpressTRUB2rep2_Treat


title: Min6-ARX clone 9, no dox


title: Lib153OverExpressTRUB1rep3_input


title: Second repeat of Artemether

source_name: mouse alpha cell line


title: First repeat of Artemether


title: Lib153OverExpressTRUB1rep2_input


title: H4_Input_MNase_200U_Replicate_2

description: Biological replicate 2


title: Lib153OverExpressTRUB1rep3_Treat


title: Second repeat of DMSO


title: Lib153OverExpressTRUB1rep2_Treat


title: First repeat of DMSO


title: mouse_SOX9_ChIPseq_2

description: processed data file: Mouse_SOX9_ChIPseq.bed

source_name: fetal testis

extract_protocol:
Upon collection, gonads were crushed in liquid nitrogen using a mortar. Tissue powders were immediately fixed with PBS containing 2mM of Disuccinimidyl glutarate (DSG: PIERCE ref 20693) initially solubilized in DMSO as described previously (Nowak et al. 2005). Samples were then incubated for 30 minutes on a rotating wheel at room temperature. After three washes with PBS, samples were subsequently fixed with PBS 1% formaldehyde for 30 minutes at room temperature
Libraries were prepared according to Illumina's instructions. 10-300ng DNA is combined with End Repair Mix, and incubate at 20°C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37°C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20°C for 15 min. Purify the Adapter-ligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN).

value: testis

value: swiss OF1

tag: antibody

value: rabbit anti SOX9 homemade (ref Gasca et al, PNAS 2002, vol 99, 11199-11204)


title: Embryo

city: Cambridge

first: Donald

middle: M

last: Bryant

state: MA

address: 65 Landsdowne Stree

department: Biological and Biomedical Sciences

institute: Harvard University

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Trinity version trinityrnaseq_r2013-02-25 was used for de novo transcriptome assembly and analysis as follows. The combined set of 1.3 billion RNA-Seq reads spanning all sampled tissues were combined into a single pair of fastq files, quality trimmed using Trimmomatic (Bolger et al., Bioinformatics, 2014) (parameters LEADING:5 TRAILING:5 MINLEN:36) and subsequently normalized using the in silico normalization step incorporated into Trinity ($TRINTY_HOME/util/normalize_by_kmer_coverage.pl --seqType fq --JM 100G --left ALL_AXOLOTL_READS.left.fq.P.qtrim.fq --right ALL_AXOLOTL_READS.right.fq.P.qtrim.fq --pairs_together --JELLY_CPU 10 --PARALLEL_STATS --max_cov 50). The resulting normalized reads were then assembled using Trinity (Trinity.pl --left left.fq --right right.fq --seqType fq --JM 100G --CPU 10).
Counts of RNA-Seq fragments mapping to transcripts in our assembly were determined for each tissue type using RSEM (Li B and Dewey C.N., BMC Bioinformatics, 2011) (http://deweylab.github.io/RSEM/) with default options.
Genome_build: The axolotl genome has not been fully sequenced; We generated a transcriptome from our RNA-seq data using Trinity and deposited it in TSA (GFBM000000000)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TMM-normalized FPKMs for the combined embryo samples as well as the other samples in the study

organism: Ambystoma mexicanum

source_name: Whole embryo from an embryonic stage between the egg and end of neurula

extract_protocol:
RNA was harvested using Trizol reagent. The Illumina TruSeq v2 protocol was used throughout to generate barcoded sequencing libraries. Paired-end, 100-bp sequencing was performed using the Illumina HiSeq 2500.
RNA libraries were prepared for sequencing using the Illumina TruSeq v2 protocol

value: whole embryo

value: wild-type

value: leucistic


title: Min6-ARX clone 16, 3 day dox


title: Bone_255_AR005_ACAGTG

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Trinity version trinityrnaseq_r2013-02-25 was used for de novo transcriptome assembly and analysis as follows. The combined set of 1.3 billion RNA-Seq reads spanning all sampled tissues were combined into a single pair of fastq files, quality trimmed using Trimmomatic (Bolger et al., Bioinformatics, 2014) (parameters LEADING:5 TRAILING:5 MINLEN:36) and subsequently normalized using the in silico normalization step incorporated into Trinity ($TRINTY_HOME/util/normalize_by_kmer_coverage.pl --seqType fq --JM 100G --left ALL_AXOLOTL_READS.left.fq.P.qtrim.fq --right ALL_AXOLOTL_READS.right.fq.P.qtrim.fq --pairs_together --JELLY_CPU 10 --PARALLEL_STATS --max_cov 50). The resulting normalized reads were then assembled using Trinity (Trinity.pl --left left.fq --right right.fq --seqType fq --JM 100G --CPU 10).
Counts of RNA-Seq fragments mapping to transcripts in our assembly were determined for each tissue type using RSEM (Li B and Dewey C.N., BMC Bioinformatics, 2011) (http://deweylab.github.io/RSEM/) with default options.
Genome_build: The axolotl genome has not been fully sequenced; We generated a transcriptome from our RNA-seq data using Trinity and deposited it in TSA (GFBM000000000)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TMM-normalized FPKMs for each Sample

source_name: Bone

extract_protocol:
RNA was harvested using either Trizol reagent or the Qiagen Rneasy columns.The Illumina TruSeq v2 protocol was used throughout to generate barcoded sequencing libraries. Paired-end, 100-bp sequencing was performed on the Illumina HiSeq 2500 at Harvard Medical School’s Biopolymers facility.
RNA libraries were prepared for sequencing using the Illumina TruSeq v2 protocol

value: Bone


title: Gata6 iKO4

source_name: epidermal keratinocytes

value: iKO (K14CreERT2+;Gata6 fl/fl)

value: tamoxifen 6 hours


title: mouse_input_DNA

data_processing:
The base calling software name version and parameters are OLB-1.9.4/bin/setupBclToQseq.py --input-dir Data/Intensities/BaseCalls --output-dir --use-bases-mask Y*,Y*,Y*
ChIP-seq reads were aligned to the mouse mm9 or bovine Bostau6 (UMD3.1) genome assembly using SOAP2.21
For peaks calling, the number of reads being twice in the inputs than in the ChIP-seq experiments, we generated from the inputs a random sampling of 20 million reads each, using a homemade script which respects the proportion of reads per chromosome of the initial input. With this method we generated ten input samples for each ChIP-seq analysis that were used for ten rounds of peaks calling with the MACS software (1.4) (Zhang et al. 2008)( bw=250, mfold=10 et p value=1e-5). Peaks common to the ten  operations with FDR<0.05  were kept for further analysis.  Script is available upon request
Genome_build: mm9 or BosTau6
Supplementary_files_format_and_content: bed with peaks coordinate in mm9 for mouse and BosTau6 for bovine


title: Lib147siTruB2Rep2_Treat


title: Min6-ARX clone 16, no dox

value: Min6-ARX inducible cells with different induction time of Dox


title: Bone_256_AR006_GCCAAT


title: Lib153OverExpressTRUB2rep2_input


title: Lib153OverExpressTRUB2rep1_Treat


title: Gata6 iKO3


title: Lib153OverExpressTRUB1rep1_Treat


title: Bone_257_AR012_CTTGTA


title: Lib147siTruB1Rep2_Treat


title: Lib147siTruB1Rep1_Treat


title: Lib147siTruB2Rep1_Treat


title: Gata6 WT4

value: WT (K14CreERT2-;Gata6 fl/fl)


title: Lib153OverExpressTRUB1rep1_input


title: CartLong_258_AR002_CGATGT

source_name: Cartilage from long bones

value: Cartilage from long bones


title: Lib147siControlRep2_Treat

source_name: siControl


title: Gata6 WT2


title: Lib147siControlRep1_Treat


title: CartLong_260_AR014_AGTTCC


title: CartLong_259_AR004_TGACCA


title: CartWrist_261_AR007_CAGATC

source_name: Cartilage from wrist

value: Cartilage from wrist


title: MAF9 stable cells + PRDM16mut sample1

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

description: Processed data file: FPKM_MAF9_stable_PR16.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm9 whole genome using Bowtie2 version 2.0.0.7 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Tophat2 version 2.0.3
Differential expression analysis was performed using Tophat2-Cuffdiff module
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Bone marrow cells transduced with MLL-AF9

growth_protocol: Bone marrow cells cultured in IMDM medium with 15%FBS and IL3(10ng/ml),IL6(10ng/ml) and SCF(10ng/ml)

extract_protocol:
The RNA was extracted with Trizol reagent and further purified by Qiagen RNasy Mini kit.
TruSeq RNA Sample Prep Kit v2 used in library construction. Oligo(dT) was used in reversse transcription.

value: BM cells transduced with MLL-AF9

tag: cotransducation

tag: cell collection

value: cells collected after 10 days puromycin selection transduction


title: MAF9 stable cells + PRDM16mut sample2


title: MAF9 stable cells + PRDM16 sample2


title: CartWrist_262_AR015_ATGTCA


title: E2A-HLF+PRDM16mut cotransduction sample2

description: Processed data file: FPKM_E2A_PR16.txt

source_name: Lin- bone marrow cells

value: Lin- BM cells

value: E2A-HLF+PRDM16mut cotransduction

value: cells collected after 10 days G418 and puromycin selection following the cotransduction


title: Lib142siTRUB1rep1_Treat

value: Treat


title: MAF9 stable cells + PRDM16 sample1


title: Ovaries_218_AR016_CCGTCC

source_name: Ovaries

value: Ovaries


title: CartWrist_263_AR018_GTCCGC


title: E2A-HLF+PRDM16mut cotransduction sample1

description: Processed data file: FPKM_E2A_PR16.txt


title: Lib142siPUS7rep3_Treat


title: Lib142siPUS7rep1_Treat


title: Lib142siPUS7rep2_Treat


title: E2A-HLF+PRDM16  cotransduction sample2

description: Processed data file: FPKM_E2A_PR16.txt

value: E2A-HLF+PRDM16  cotransduction


title: E2A-HLF+PRDM16  cotransduction sample1

description: Processed data file: FPKM_E2A_PR16.txt


title: Testes_250_AR002_CGATGT

source_name: Testes

value: Testes

value: wild-type


title: mouse_SOX9_ChIPseq_1

value: testis

value: swiss OF1

value: rabbit anti SOX9 homemade (ref Gasca et al, PNAS 2002, vol 99, 11199-11204)


title: Ovaries_219_AR018_GTCCGC

value: leucistic


title: Ovaries_220_AR019_GTGAAA


title: Lib142siControlrep1_input

value: input


title: Lib142siControlrep1_Treat


title: Lib142siTRUB1rep3_Treat


title: Testes_253_AR007_CAGATC


title: Lib142siTRUB1rep2_Treat


title: Testes_254_AR013_AGTCAA


title: Testes_251_AR004_TGACCA


title: MAF9+PRDM16 cotransduction sample2

description: Processed data file: FPKM_MAF9_PR16.txt

value: MAF9+PRDM16 cotransducation


title: blood_vessel_904_CAGATC

source_name: Blood Vessel

value: Blood Vessel


title: MAF9+PRDM16 cotransduction sample1

description: Processed data file: FPKM_MAF9_PR16.txt


title: blood_vessel_905_CTTGTA


title: distal_CGATGT_L008

source_name: Blastema from distal amputation

value: Blastema from distal amputation


title: blood_vessel_906_AGTCAA


title: elbow_10325_AGTTCC

source_name: Elbow

value: Elbow


title: elbow_10328_GTCCGC


title: distal_GCCAAT_L006


title: Lib142siControlrep2_Treat


title: gillfilament_10319_ACAGTG

source_name: Gill Filament

value: Gill Filament


title: forearm_10324_AGTCAA

source_name: Forearm

value: Forearm


title: MAF9+PRDM16mut cotransduction sample2

description: Processed data file: FPKM_MAF9_PR16.txt

value: Lin- BM cells

value: MAF9+PRDM16mut cotransduction

value: cells collected after 10 days G418 and puromycin selection following the cotransduction


title: hand_10327_CCGTCC

source_name: Hand

value: Hand


title: hand_10320_CGATGT


title: OCILY13.2_THZ1_6H_R1

first: Tharu

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads that passed filter were aligned to hg19 using STAR (Dobin et al., 2012).
Gene expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/ HTSeq/).
Differentially expressed genes between paired samples were identified with the edgeR package using the generalized linear model likelihood ratio test (Robinson et al., 2010). Genes with a FDR<0.05 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count is provided as a .txt file. The EdgeR outputs are also provided as .txt files.

source_name: OCI-LY13.2 cells

growth_protocol: Cells were grown in RPMI 1640 medium with 10% FBS, 2mM glutamine, and pen/strep.

extract_protocol:
Total RNA was harvested using the Rneasy Micro Kit (Qiagen).
Genomic DNA was eliminate with Dnase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.

treatment_protocol: Cells were treated with vehicle (0.005%DMSO) or 500nM THZ1 for 3 h or 6 h.

value: 500nM THZ1

tag: time of treatment

value: 6 h


title: OCILY13.2_THZ1_6H_R3


title: OCILY13.2_THZ1_6H_R2


title: OCILY13.2_VEH_6H_R3


title: heart_908_ATGTCA

source_name: Heart

value: Heart

value: wild-type


title: OCILY13.2_VEH_6H_R2


title: heart_909_CCGTCC


title: MAF9+PRDM16mut cotransduction sample1

description: Processed data file: FPKM_MAF9_PR16.txt


title: OCILY13.2_VEH_6H_R1


title: OCILY13.2_THZ1_3H_R3

value: 3 h


title: proximal_CAGATC_L006

source_name: Blastema from proximal amputation

value: Blastema from proximal amputation

value: leucistic


title: proximal_TGACCA_L008


title: forearm_10321_TGACCA


title: OCILY13.2_THZ1_3H_R2


title: OCILY13.2_THZ1_3H_R1


title: skeletal_901_TGACCA

source_name: Skeletal Muscle

value: Skeletal Muscle


title: skeletal_900_CGATGT


title: OCILY13.2_VEH_3H_R3


title: OCILY13.2_VEH_3H_R2


title: skeletal_902_ACAGTG


title: hand_10323_CTTGTA


title: skeletal_903_GCCAAT


title: heart_907_AGTTCC


title: upperarm_10322_CAGATC

source_name: Upper arm

value: Upper arm


title: OCILY13.2_VEH_3H_R1


title: upperarm_10326_ATGTCA


title: Late rep1

source_name: Late embryos

value: N2 Bristol WT

value: Late embryos

value: Ligase 1 depletion


title: PG rep1

source_name: Pre-gastrula embryos

value: N2 Bristol egl-30

value: Pre-gastrula embryos


title: fk068_Ldon_nooxctrl1

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

data_processing:
Pull down libraries were sequenced on an Illumina MiSeq with a read length of 151 bp. Reads were trimmed to remove adapters and low quality 3’ ends using cutadapt version 1.7. Trimmed reads were then aligned to the reference genome using bwa mem version 0.7.10. Only primary alignments with mapping quality of 10 or more were retained for further analyses. Alignment filtering and manipulations were performed with samtools version 1.1. See Additional file 1, Table S4 for a summary of the mapping step. Peaks of read enrichment were detected using macs version 2.1.0.20140616. Further analyses were performed by means of bedtools, deepTools,  DREME, and custom bash, R and python scripts. Detailed protocols for bioinformatics analysis including statistical analysis are available from the github repository (https://github.com/sblab-bioinformatics/mapping-5hmU-in-Leishmania).
Genome_build: Reference genome for L. major: ftp://ftp.sanger.ac.uk/pub/project/pathogens/Leishmania/major/Current/LmjF_v6.1_20131105/fasta/LmjF_v6.1_all_20131105.fa
Genome_build: Reference genome for L. donovani: ftp://ftp.sanger.ac.uk/pub/project/pathogens/Leishmania/infantum/V5210211/Linfantum.fa
Supplementary_files_format_and_content: Output of MACS2 peak caller in “txt” format reporting positions of enriched regions and their statistical significance

organism: Leishmania donovani

extract_protocol:
The genomic DNA samples for Leishmania major (ATCC 30012D, lot 60685413, lot 63717803, lot ATCC-CUST-30012D) and the RNA sample for Leishmania major (lot ATCC-CUST-30012R) were obtained from ATCC. The genomic DNA sample for Leishmania donovani GR383WT1 (single batch) was provided courtesy of Prof. Charles L. Jaffe (National Center for Leishmaniasis, Kuvin Centre for Study of Tropical & Infectious Diseases, Jerusalem).
5hmU DNA immune-precipitation (DIP)
Fragmented DNA samples were subjected to adapter ligation using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) and TruSeq sequence adapter solutions (Illumina). For generating 5hmU-enriched library by DIP, the adapter ligated DNA (in 20 uL) was heated to 95  C for 10 min and then immediately cooled on ice to denature. A mixture of the denatured DNA, anti-5-hydroxymethyluridine antibody ab19735 (5 uL, Abcam, RRID:AB_722498), and rabbit anti-goat IgG H&L ab6697 (10  L, Abcam, RRID:AB_955988), and 0.1% (v/v) tween 20 in PBS was incubated with rotation at 4  C, then added to Dynabeads Protein G (Life Technologies). The beads were washed 3 times with 0.1% (v/v) tween 20 in PBS (200 uL), re-suspended in 0.1% (v/v) tween 20 in PBS and treated with proteinase K (20 ug/uL, 1.75 uL) at 50  C for 2 h. The supernatant containing the eluted DNA was collected and purified. The obtained 5hmU enriched libraries were amplified by amplified by PCR. The libraries were sequenced on Illumina MiSeq with single-end read (length of 150bp) or paired-end read (length of 75bp x 2).
5hmU chemical enrichment
DNA samples were ligated with chemically modified Truseq adapters prior to the biotin tagging. The adapter ligated DNA sample was oxidised using the oxidant solution provided in the TrueMethyl kit (Cambridge Epigenetics) followed by desalting with Micro Bio-Spin P-6 Gel Columns (Bio-Rad). The sample was biotinylated by treatment with (+)-biotinamidohexanoic acid hydrazide followed by purification, and used immediately for enrichment.
The biotinylated DNA was bound to Dynabeads MyOne Streptavidin C1 (Life Technologies) by gentle mixing. The beads were placed on a magnetic rack and the supernatant was removed. The beads were washed 5 times and the DNA was eluted by incubating the beads in elution buffer (0.05% (v/v), 5 mM anisidine, 0.1% (v/v) tween 20 in 50 mM sodium phosphate buffer pH 6). The elution process was repeated once more. The obtained 5hmU enriched libraries were purified and amplified by PCR. The libraries were sequenced on Illumina MiSeq (single-end read with length of 150bp).
Base J chemical enrichment
Fragmented DNA sample was treated with NaIO4 in sodium acetate buffer (pH 5.5) at 40  C followed by purification of DNA. The resultant DNA was biotinylated by treatment with (+)-biotinamidohexanoic acid hydrazide followed by purification. The biotinylated DNA was subjected to NGS adapter ligation using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) and TruSeq sequence adapter solutions (Illumina). Downstream procedures for base J enrichment were carried out as described in 5hmU chemical enrichment sequencing except the PCR was carried out while base J modified DNA fragments were bound to the magnetic beads. The libraries were sequenced on Illumina MiSeq (single-end read with length of 150bp).
Total RNA library preparation
Total RNA (1 ug) was fragmented by incubating in a fragmentation buffer (40 mM Tris-HCl pH 8.2, 100 mMLiCl, and 30 mM MgCl2) followed by purification. The RNA was treated in T4 PNK (Thermo Fisher Scientific) in absence of ATP and purified to remove phosphate group at 3 -end. The adapter (5 - 5rApp AGATCGGAAGAGCACACGTCTG-SpC3- 3 ) was ligated to the RNA by T4 RNA ligase 2 K227Q (New England BioLabs), followed by purification. Reverse transcription was carried out using the reverse primer (5 -CAGACGTGTGCTCTTCCGATCT-3 ) and SuperScript III Reverse Transcriptase (Thermo Fisher Scientific) followed by RNA degradation by heating up samples at 95 C in presence of NaO and purification. ssDNA adapter was ligated to the resulted single-stranded DNA, by following literature protocols [1] The obtained samples were amplified by PCR using primers (5 -CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3  and 5 -AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3 ). The libraries were sequenced on Illumina MiSeq with paired-end read length 75bp.
Kwok, C. K. & Balasubramanian, S. Targeted Detection of G-Quadruplexes in Cellular RNAs. Angew Chem Int Edit 54, 6751-6754, doi:10.1002/anie.201500891 (2015).

value: No oxidation control pull-down

value: Chemical tagging


title: fk067_Ldon_chem2


title: fk070_Ldon_input

value: Input


title: PP-m33

first: Jeffrey

last: Zhao

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
The outputs data (FASTQ files) are mapped to the target genome using the rnaStar aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions.
We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done.
After mapping we compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases.
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: reads per gene for each sample

source_name: hESC-derived cells

growth_protocol: hESCs were cultured on iMEF feeder and then differentiated into early pancreatic progenitor stage. At the pancreatic progenitor stage, the cells were cultured in DMEM medium containing 1X GlutaMAX and 1% B27.

extract_protocol:
Cells were lysed using TRIzol and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, #217004).
RNA libraries were prepared for sequencing using standard Illumina protocols by the MSKCC Integrated Genomics Operation Core

treatment_protocol: The medium also contained 50 ng/ml FGF10, 0.25 uM SANT-1, 2 uM retinoic acid and 250 nM LDN-193189 for directed differentiation into early pancreatic progenitor cells.

value: ESCs

tag: genotype/variation


title: PP-wt1

tag: cell type

value: wild type


title: Mixed Early rep1

source_name: Mixed early embryos

value: Mixed early


title: fk069_Ldon_nooxctrl2


title: PP-wt5


title: PP-m32


title: fk066_Ldon_chem1


title: fk048_Ldon_DIP2

value: Antibody (DIP)

tag: antibody info.

value: polyclonal anti-5-hydroxymethyluridine (Abcam, ab19735, RRID:AB_722498)


title: fk047_Ldon_DIP1

tag: strain


title: fk096_Lmaj_totalrna3

organism: Leishmania major

tag: strain lot #


title: y61

city: Durham

first: Rachel

middle: A

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

data_processing:
Reads were filtered with Trim Galore v.0.3.1 with the following parameters: --q 20 --l 25 --s 3
Reads were mapped to the Ficedula albicollis genome (Ensembl version 1.4.74, unmasked) using Tophat2. Tophat2 parameters were: read-mismatches 16, read-gap-length 10, read-edit-dist 28, splice-mismatches 1, max-insertion-length 12, max-deletion-length 12, max-multihits 5, b2-D 15, b2-N 1, b2-L 20, b2-i S,1,0.50.
The expression level of each gene was quantified using the union mode of the python script htseq-count (HTSeq).
Genes were filtered to only include protein-coding genes.
We used conditional quantile normalization (cqn package in R) to normalize for sequencing depth (TMM), GC-content, and gene length (averaged from the transcripts in the ficalb1.4.74 gtf file).
Genome_build: FicAlb_1.4
Supplementary_files_format_and_content: Tab-delimited text file containing gene transcript abundance measurements. The unit of measure is the log2 transformed read counts controlling for library size, GC content, and gene length, as produced by CQN (R package) and analagous to RPKM.

organism: Catharus ustulatus

source_name: brain (hypothalamus + optic chiasma)

extract_protocol:
Brain tissue was flash frozen on dry ice. mRNA was extracted using the Trizol Plus RNA Purification Kit, with DNAse treatment with the Ambion RNAse-Free DNAse Set and column cleanup with the PureLink RNA Mini Kit (Invitrogen, Carlsbad, CA USA).
cDNA libraries were synthesized using the TruSeq RNA Sample Preparationv2 kit (Illumina) with TruSeq Indexes.

treatment_protocol: Birds were kept in captivity under constant conditions except photoperiod, which was adjusted weekly to mimic natural daylength. Samples were collected 10 weeks apart-- half were collected during the non-migratory period (summer) and half were collected during the migratory period (fall).

tag: migration status

value: Migratory

tag: ecotype

value: Coastal

tag: Sex

value: Male

tag: tissue

value: brain (hypothalamus + optic chiasma)

tag: time of tissue collection (hours after lights on)

tag: date of tissue collection


title: fk094_Lmaj_totalrna1


title: r192

value: Inland


title: t20


title: y57

value: Non-migratory

value: Female


title: fk095_Lmaj_totalrna2


title: fk116_Lmaj_baseJ2

value: Base J


title: y52


title: fk117_Lmaj_baseJ3


title: y60


title: upperarm_10329_GTGAAA

value: Upper arm

tag: genotype

value: wild-type

value: leucistic


title: t21


title: t18


title: y66


title: fk056_Lmaj_nooxctrl3

value: No oxidation control pull-down

value: Chemical tagging


title: fk059_ox_NPD_spiked

value: Input


title: y53


title: fk057_Lmaj_nooxctrl4


title: t26


title: r197


title: fk054_Lmaj_chem3


title: r187


title: y64


title: y69


title: y68


title: A2_Seed_BBCH 05_Apera_spica_venti

city: Slagelse

first: Khalid

last: Mahmood

address: Forsøgsvej 1

department: Agro-ecology

institute: Aarhus University

data_processing:
The raw reads were quality-clipped before performing the assembly using the software Trimmomatic
De novo transcriptome assembly was performed using Trinity assembler. The assembly method was a composite of different methods in order to reduce transcripts redundancy. . First the de novo Trinity pipeline (version 2.1.1) was used with a minimum contig length of 200 bp and a minimum kmer covariance of 2. The longest isoform for each gene was selected (perl script by Brian Haas on trinityrnaseq-users google group), then contigs were merged according to a similarity criterion of 90% in CD-HIT-EST (version 4.6.3
The contigs were then translated to coding protein sequences using Transdecoder (version 2.0.1).]) following identification of the longest ORFs. This pipeline was performed for each of the seven tissue- and growth stage- specific libraries. Non-redundant assemblies were used in downstream functional annotation KEGG, and GO enrichment analysis.
Genome_build: De novo assembly
Supplementary_files_format_and_content: txt files include annotation and RPKM values for each Sample

organism: Apera spica-venti

source_name: Seed

growth_protocol: Seeds from six herbicide susceptible populations of Apera spica-venti originating at six different locations in Denmark, were mixed together to create a meta-population encompassing a range of genetic variations possible within the species. Each of these six populations were previously tested between 2007 and 2010 with ALS and ACCase inhibitor herbicides and found to be susceptible (Mathiassen, pers. comm). Seeds were sown under greenhouse conditions on table with an automatic watering system. Leaf, stem, and root material from individual plant were harvested once the plants were at BBCH stage 34 to 36 (stem elongation). Tissues were cut in small pieces and immediately put in liquid nitrogen and then stored at -80°C. These tissues were kept separated by individual plant. Seeds from this meta-population were sown in 9 cm petri dishes with four filter papers and grown in a climate cabinet (Termaks Series KB8000L) at night/day temperatures of 10ºC /17ºC for 10h/14h, and imbibed with 5 mL of demineralized water. Germinated seeds were harvested at stage BBCH 05 (radicle emerges from seed), 07 (coleoptile emerges from caryopsis), 08 (coleoptile elongation), and 09 (Emergence: coleoptile breaks through soil surface). A total of 0.5 g of frozen tissue from leaf, stem, and root was grounded separately using a 2010 Geno/Grinder (SPEX Sample prep, Stanmore, UK) for 45 sec at 1,500 hertz and then soaked in liquid nitrogen. A total of 0.7 g of germinated seeds were grounded using the same method but for 2 cycles of 45 seconds at 1,500 hertz and were not soaked in liquid nitrogen. The RNA mini plant kit (Qiagen, Hilsen, Germany) was used for RNA extraction following the manufacturer protocol, three wash steps were performed. RNA quality was verified using a spectrophotometer (Nanodrop 3300, Wilmington, USA) and bioanalyzer (Agilent 2100, Santa Clara, USA). Samples that showed a RIN value of 6.0 and more were treated with DNAse 1 according to the protocol (Qiagen, Hilsen, Germany) and suspended in a final volume of 14 μL. RNA quality was verified again with spectrophotometer (NanoDrop-1000 v.3.1.0) and bioanalyzer using the RNA 6000 Plant Nano program (Agilent 2100). Samples with a RIN value higher than 6 were selected for cDNA library construction. The lower than recommended (>8) RIN value threshold selected here is because of difficulties in extracting high quality RNA from germinated seed samples. Nine libraries were created; seven for each of the individual tissues/growth stage samples, and two more libraries for leaf and root respectively to be sequenced by both 5’ and 3’ end for analysis of transcript start site because we believe they have the most important number of expressed genes of interest for future study. Samples of mRNA were selected and fragmentedand  transformed to 150-400 bp  short insert, strand specific cDNA libraries for sequencing on Illumina HiSeq 2500 with chemistry version 3 (Eurofins MGW, Germany)

extract_protocol:
A total of 0.5 g of frozen tissue from leaf, stem, and root was grounded separately using a 2010 Geno/Grinder (SPEX Sample prep, Stanmore, UK) for 45 sec at 1,500 hertz and then soaked in liquid nitrogen. A total of 0.7 g of germinated seeds were grounded using the same method but for 2 cycles of 45 seconds at 1,500 hertz and were not soaked in liquid nitrogen. The RNA mini plant kit (Qiagen, Hilsen, Germany) was used for RNA extraction following the manufacturer protocol, three wash steps were performed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: BBCH stage 05

value: radicle emerges from seed


title: fk046_Lmaj_nooxctrl2


title: A5_Seed_BBCH 09_Apera_spica_venti

value: BBCH stage 09

value: Emergence:coleoptile breaks through soil surface


title: A6_Leaf_Apera_spica_venti

source_name: Leaf

value: BBCH stage 34 to 36

value: stem elongation


title: t28

value: Male

value: brain (hypothalamus + optic chiasma)


title: fk043_Lmaj_DIP2

value: Antibody (DIP)

value: polyclonal anti-5-hydroxymethyluridine (Abcam, ab19735, RRID:AB_722498)


title: A3_Seed_BBCH 07_Apera_spica_venti

value: BBCH stage 07

value: coleoptile emerges from caryopsis


title: fk050_Lmaj_chem1


title: fk045_Lmaj_nooxctrl1


title: fk051_Lmaj_chem2


title: fk113_Lmaj_baseJ1

value: Base J


title: y62

value: Non-migratory

value: Coastal


title: A7_Root_Apera_spica_venti

source_name: Root


title: A8_Stem_Apera_spica_venti

source_name: Stem


title: A4_Seed_BBCH 08_Apera_spica_venti

value: BBCH stage 08

value: coleoptile elongation


title: fk052_Lmaj_DIP3


title: fk041_Lmaj_DIP1


title: NRDE-3-associated small RNAs in eri-1;dpy-13 after dpy-13 RNAi

status: Public on Dec 14 2016

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

institute: University of Science & Technology of China

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 20 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
Genome_build: WS243
Supplementary_files_format_and_content: .txt files. Basically, the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script.

source_name: embryo

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated dpy-13 RNAi plate (approximately 3000 L1s per plate).

extract_protocol:
NRDE-3-associated siRNAs were isolated from embryo lysates as described (Zhou, X et al, Genetics 197, 121-32 (2014)). Briefly, the animals were sonicated in lysis buffer (20 mM Tris-HCl [pH 7.5], 200 mM NaCl, 2.5 mM MgCl2, and 0.5% NP-40); the lysate was pre-cleared with protein G-agarose beads (Roche), and incubated with anti-FLAG M2 agarose (Sigma) beads. The beads were washed extensively, and FLAG::GFP::NRDE-3 and associated RNA were eluted with 100 μg/ml 3xFLAG peptide (Sigma). The eluates were incubated with TRIzol reagent (Invitrogen), followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by the Beijing Genomics Institute (BGI Shenzhen). sRNAs ranging from 20 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

tag: temperature

tag: chip antibody

value: anti-FLAG M2 antibody (Sigma)

tag: molecule subtype

value: IPed small RNA


title: NRDE-3-associated small RNA in wild type N2 animals

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).


title: e11.5_forelimb_distal_wt_mRNA_rep1

city: montreal

first: Rushikesh

last: Sheth

address: 110 avenue des pins ouest

department: Genetics and Development

country: Canada

institute: IRCM

data_processing:
Paired-end reads were aligned to the mm9 reference genome and to the Mus Musculus transcriptome (iGenome refGene GTF) using TopHat v2.0.13 (PMID: 23618408). The option --no-coverage-search was specified, while all the other parameters were left to default.
Transcripts abundance were quantified using Cufflinks v2.1.1 (PMID: 20436464).
Gene-wise counts were calculated using htseq-count, considering the same GTF as reference and only reads with a unique match to the genome (samtools view -q1).
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63.
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM) (refer to http://cole-trapnell-lab.github.io/cufflinks/ for details).

source_name: embryonic forelmb bud

growth_protocol: The Hoxa13 loss of function allele was generated by insertion of neomycine cassette in Hoxa13 coding region (PMID: 8898214). In Hoxd13 loss of function allele, a lacZ reporter transgene is inserted in the first exon of Hoxd13 (PMID: 10652274). The Hoxa13 and Hoxd13 mutant lines were maintained in a mixed background. Noon of the day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5). Mice and embryos were genotyped by PCR using genomic DNA extracted from tail biopsies and yolk sacs, respectively.

extract_protocol:
Micro-dissected E11.5 forelimb ZAPs from wild type and mutant embryos were stored at -80 C in Qiagen RNA later solution until genotyped. For each genotype, RNA was extracted from pools of micro-dissected tissue samples (N=4) with Qiagen Rneasy micro kit following manufacturer's protocol.
The quality of total RNA from two independent pools of limb tissue for each genotype was analyzed on RNA 6000 Pico kit (Agilent 2100 bioanalyzer), followed by ribosomal RNA depletion using Ribo-Zero Magnetic Gold Kit (Epicentre). Strand-specific RNA-Seq libraries were produced using Illumina TruSeq Stranded Total RNA - low sample protocol. The resulting cDNA was subjected to 8 cycles of PCR amplification and sequenced on a HiSeq 2000 instrument with a paired-end 50 cycles protocol.

value: Mixed C57BL/6 - CD1

tag: developmental stage

value: gestational day e11.5

value: forelimb bud

tag: library type

value: Stranded (first-strand synthesis)


title: e11.5_forelimb_distal_wt_mRNA_rep2


title: e11.5_forelimb_distal_ko_mRNA_rep2

value: Mixed C57BL/6 - CD1 Hoxa13-/-;Hoxd13-/-


title: e10.5_forelimb_H3K27me3_input

description: Input DNA

data_processing:
Reads were mapped to the mouse mm9 genome using Bowtie v0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS v1.4 (PMID: 18798982) with default parameters and --nomodel. Each IP was compared to experiment-matched input DNA.
In the case of e10.5 forelimb H3K27me3 sample, trimming of 56 bases at the 3' was performed before alignment. All the other samples were trimmed by 6 bases at their 3'.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

source_name: embryonic forelmb bud, ChIP input

growth_protocol: The Hoxa13 loss of function allele was generated by insertion of neomycine cassette in Hoxa13 coding region (PMID: 8898214). In Hoxd13 loss of function allele, a lacZ reporter transgene is inserted in the first exon of Hoxd13 (PMID: 10652274). The Hoxa13 and Hoxd13 mutant lines were maintained in a mixed background. Noon of the day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5). Mice and embryos were genotyped by PCR using genomic DNA extracted from tail biopsies and yolk sacs, respectively

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 16630818) with some modifications. Briefly, E11.5 ZAP cells from wild type and mutant limbs were cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was cross-linked using formaldehyde as previously described except for HOXA13 ChIP for which we performed the cross-linking using a dual method using disuccinimidyl glutarate (DSG) and formaldehyde (PMID: 21123453). Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp. Protein A and G Dynabeads (Invitrogen) were incubated 6h at 4 C with 5 µg of antibody. The chromatin was then incubated with the beads overnight at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 65 C overnight. Samples were treated for 15 min RT with RNase A and then with Proteinase K for one hour at 55 C. Finally, the DNA was purified on QIAquick columns (Qiagen) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared by the IRCM functional genomics core facility using Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2000.

value: gestational day e10.5

tag: antibody


title: e10.5_forelimb_mRNA


title: r182

value: Migratory

value: Inland

value: Male

value: brain (hypothalamus + optic chiasma)


title: e11.5_forelimb_distal_wt_HoxD13_input

description: Input DNA


title: e11.5_forelimb_distal_wt_H3K27ac

description: Chromatin IP against H3K27ac

source_name: embryonic forelmb bud, H3K27ac ChIP

value: anti-H3K27ac (Abcam, ab4729)


title: e11.5_forelimb_distal_wt_HoxA13_input

description: Input DNA


title: e11.5_forelimb_distal_wt_H3K27me3

description: Chromatin IP against H3K27me3

source_name: embryonic forelmb bud, H3K27me3 ChIP

value: anti-H3K27me3 (Millipore, 07-449)


title: e11.5_forelimb_distal_ko_H3K27ac_input

description: Input DNA


title: BCondition3

first: Lucas

last: Carey

state: Bejijng

address: 5 Yiheyuan Road

department: Center for Quantitative Biology

institute: Peking University

description:
AMPLICON
exp_log2_cond3 & cv2_log2_cond3 in expression_all_constructs.tab

data_processing:
Sequencing reads are from PCR amplicons of barcodes attached to promoters. Each read has two barcodes, an expression bin barcode (added via PCR after sorting cells by FACS) and a promoter-specific barcode. The first step is to build a matrix of the number of times each promoter barcode bin is seen, containing each condition-specific & expression level (FACS sorting) bin.
This matrix is N rows (# of promoters) by M columns (# of expression bins). One matrix per experiment. Rows are normalized to compute the relative counts per bin of each promoter.
The expression level of each promoter is then computed from these matricies. Details are in the paper, and in Sharon et al 2012.
Promoter-specific barcodes are in Sharon et al. 2012.
Supplementary_files_format_and_content: Tab files of calculated expression levels and promoter annotations.
expression_all_constructs.tab is a tab file with computed expression data for each of the barcoded promoter in each condition. Column exp reports expression level, cv2 reports the squared coefficient of variation.
annotation_all_constructs.tab is a tab file with annotation for each barcoded promoter

molecule: other

source_name: Yeast grown in media w/ 1/9 amino acid concentration. Biological replicate B

growth_protocol: yeast were grown in synthetic media with varying amino acid concentrations

extract_protocol:
DNA barcodes were PCR amplified with condition-specific and expression-bin specific barcoded primers
PCR amplicons were used to prepare standard Illumina libraries by adding sequencing adapters via PCR

treatment_protocol: cells were sorted by YFP/mCherry expression ratios

tag: growth protocol

value: media w/ 1/9 amino acid concentration


title: BCondition6

description:
AMPLICON
exp_log2_cond6 & cv2_log2_cond6 in expression_all_constructs.tab

source_name: Yeast grown in media w/ 1/2048 amino acid concentration. Biological replicate B

tag: strain


title: e11.5_forelimb_distal_wt_H3K27ac_input

description: Input DNA


title: ACondition4

description:
AMPLICON
exp_log2_cond4 & cv2_log2_cond4 in expression_all_constructs.tab

source_name: Yeast grown in media w/ 1/16 amino acid concentration. Biological replicate A

value: media w/ 1/16 amino acid concentration


title: e11.5_forelimb_distal_ko_H3K27me3

description: Chromatin IP against H3K27me3


title: e11.5_forelimb_distal_ko_H3K27ac

description: Chromatin IP against H3K27ac


title: BCondition4

source_name: Yeast grown in media w/ 1/16 amino acid concentration. Biological replicate B


title: ACondition5

description:
AMPLICON
exp_log2_cond5 & cv2_log2_cond5 in expression_all_constructs.tab

source_name: Yeast grown in media w/ 1/64 amino acid concentration. Biological replicate A

value: media w/ 1/64 amino acid concentration


title: BCondition5

source_name: Yeast grown in media w/ 1/64 amino acid concentration. Biological replicate B


title: ACondition3

source_name: Yeast grown in media w/ 1/9 amino acid concentration. Biological replicate A


title: BCondition1

description:
AMPLICON
exp_log2_cond1 & cv2_log2_cond1 in expression_all_constructs.tab

source_name: Yeast grown w/ normal amino acid concentration. Biological replicate B

value: normal amino acid concentration


title: e11.5_forelimb_distal_ko_mRNA_rep1


title: ACondition6

source_name: Yeast grown in media w/ 1/2048 amino acid concentration. Biological replicate A


title: ACondition1

source_name: Yeast grown w/ normal amino acid concentration. Biological replicate A