title: wildtype_without_sComS_smallRNA-seq

description:
small RNAs
Table 3.xls

extract_protocol:
Small RNA libraries were prepped through the SMARTer smRNA-Seq kit for Illumina (Clontech Laboratories). Library PCR was executed for 12 cycles. Fragments ranging from 150bp to 400bp were selected using an Egel EX 2% gel (Invitrogen).Quality of the libraries was evaluated with the use of a High sensitivity DNA chip (Agilent technologies) and concentrations were determined through qPCR according to Illumina protocol. Both Libraries were equimolar pooled for sequencing on a NextSeq 500 high-throughput run with 76bp single reads. 2.3 pM of the library pool was loaded on the flowcell with a Phix spike-in of 5%.
S. salivarius WT, ∆comR and ∆comX strains were overnight precultivated in CDMG at 37°C. They were resuspended in 50 ml of fresh pre-warmed CDMG at a final OD600=0.05 and grown for approximately 2h30 (OD600=0.2) at 37°C. We then supplemented the medium with either DMSO (negative control) or 1µM sComS and incubated for 30 min at 37°C. Cells were harvested by centrifugation (10 min; 4.000 rpm), the supernatant were discarded and the cell pellets were frozen with liquid nitrogen. Finally, RNAs were extract using the RiboPure bacteria kit (Ambion-Life Technologies) and follow the protocol as provided by the manufacturer, with exception of cell lysis and RNA precipitation. For Lysis, cells were resuspended in RNAwiz buffer supplemented with Zirconia beads and shaked for 40 sec (4 times) in a fastPrep homogenizer device (MP biomedicals). For RNA precipitation, a 1.25-ethanol volume (instead of 0.5) was added to partially purified RNAs. Total RNA was checked for quality on a RNA Nano chip (Agilent technologies) and concentration was measured using Ribogreen assay (Life technologies). rRNA depletion was performed on 2 µg total RNA with the Ribo-Zero rRNA removal kit for Gram Positive Bacteria (Illumina) according to manufacturer’s instructions

value: WT

value: DMSO


title: MDA-MB-231-shCtrl-R1

status: Public on Jan 10 2018

type: SRA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Cells treated with non-targeting dsRNA

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

tag: cell line

tag: passages

value: Low passages (6-10)

tag: shRNA


title: 2_E_TH_65

city: Austin

first: Emma

last: Erickson

state: TX

address: 2500 Speedway MBB 1.124

department: Neuroscience

institute: University of Texas at Austin

data_processing:
Base-calling was performed with BCL2fastq (version 2.17)
Samples were trimmed with FASTX Toolkit (version 0.0.14) and adapter sequences removed with Cutadapt (version 1.8)
Alignment was performed using Bowtie2 (version 2.2.5) against the mouse reference genome (UCSC, mm10)
Duplicate reads were filtered with Picard (version 1.141)
Raw counts were obtained with HTSeq (version 0.5.3p9)
Normalized counts and differential expression results were obtained with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: text files including raw read counts

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 5% of the suspension was taken as the total homogenate, spun at 1000 x g and flash frozen in liquid nitrogren.
RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the HiSeq 4000 (Illumina, San Diego, CA) using (150 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.

treatment_protocol: Mice were allowed to voluntary drink 15% (v/v) ethanol every other day for 72 days. Only water was available on off days. Mice were sacrificed 24hrs after their last drinking day

tag: strain

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: treatment

value: Ethanol

tag: cell type

value: total homogenate


title: wildtype_sComS_smallRNA-seq

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

country: Switzerland

institute: UNIL

description:
small RNAs
Table 3.xls

data_processing:
Sequenced mRNAs or sRNAs generated several million reads that were mapped on the WT S. salivarius chromosome and processed through both bowties V0.12.9 and samtools V0.1.18 algorithms to yield BAM files encompassing the read coordinates. In regard to RNAseq, we imported these files into SeqMonk V0.23.0 (www.bioinformatics.babraham.ac.uk/projects/) to assess the total number of reads for each coding sequence (CDS). The dataset was exported into an excel file for further analyses. First, the dataset was standardized to CDS-mapped reads per million overall reads count. Then, we estimated a normalized ratio of CDS-mapped reads in mutants vs WT. The implemented file was used to generate a regulatory network scheme from the Cytoscape software (www.cytoscape.org/). Concerning smRNAseq, the genome was subdivided into 50 bp-probes and, for every probe, we calculated a value that represents the number of reads which occur within the probe
Genome_build: Streptococcus salivarius HSISS4: CP013216
Supplementary_files_format_and_content: the xls files reporting RNAseq were generated by SeqMonk sofware.The sheet is organized in columns as follows:   column 1 : gene name  column 2 : genome unit   column 3 : probe start  column 4 : probe end   column 5 : gene function  column 6 : locus tag  column 7 : old locus tag assigned in the previous genome sequencing  column 8 : orientation of the probe in regard to the associated gene  column 9 : It is reported here the absolute value of reads per probe in the WT  column 10 : It is reported here the absolute value of reads per probe in the comR mutant  column 11 : It is reported here the absolute value of reads per probe in the comX mutant  column 12 : Ratio of Normalized abundance of reads per probe in comR mutant versus WT background  column 13 : Ratio of normalized abundance of reads per probe in comX mutant versus WT background  column 14 : log10 transformation of column 12  column 15 : log10 transformation of column 13
Supplementary_files_format_and_content: the xls files reporting smRNAseq were generated by SeqMonk sofware.The sheet is organized in columns as follows:   column 1: probe name  column 2 : genome unit   column 3 : probe start  column 4 : probe end   column 5 : closest gene   column 6 : probe location from the closest gene   column 7 : probe distance, the distance of the probe from ORF  column 8 : It is reported here the absolute value of reads per probe in the WT (+DMSO)  column 9 : It is reported here the absolute value of reads per probe in the WT activated with the pheromone  column 10 : normalized abundance of reads per probe in mock condition (DMSO)  column 11 : normalized abundance of reads per probe in pheromone-activated WT  column 12 : ratio of normalized abundance of reads per probe in pheromone-activated WT versus mock condition (DMSO)

organism: Streptococcus salivarius

growth_protocol: Streptococcus salivarius and derivatives were grown at 37°C in chemically defined medium supplemented with glucose (CDMG) without shaking

tag: genotype

tag: medium supplemented with

value: sComS


title: Rap1-AA+rapa rep2

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor is clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert is quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Genome_build: R64
Supplementary_files_format_and_content: Wig files providing coverage for all samples. All wigs are normalized to 10,000,000 reads.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae culture

growth_protocol: For all datasets, 2L of yeast cells expressing Rpb1-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) . For Anchor Away strains, rapamycin was added at OD600=0.4 for two hours to a final concentration of 1µg/ml. For rna15 experiment, cells were grown at 25°C to OD600=0.6. 1 volume of media preheated at 30 or 37°C was added and cultures were incubated at 30 or 37°C for 1 hour and half.

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20’ at 20000g at 4°C.IgG and nickel purification steps were performed as previously described in the original protocol (granneman et al., 2009) with minor changes: i) IgG purification steps has been realized using M-280 tosylactivated dynabeads (15mg per samples) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol). Eluates were concentrated in Vivacon® ultrafiltration spin columns 30 KDa MWCO to a final volume of 120 µl. A protein fractionation step was performed using the Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree) system from Expedeon. RNA pol II containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol. RNA were reverse transcribed using the Reverse transcriptase IV (Invitrogen)
Between half to ¾ of the cDNA solution was used to performed multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of ech primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per milliliter of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

treatment_protocol: Cells were submitted to UV crosslink in a UV lamp system (Megatron) for 50 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume / g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

value: 1h Rapamycin

value: as w303, Rpb1-HTP::Ura, Rap1-FRB-Rap1::LEU tor1-1 fpr1::NAT, RPL13A-2xFKBP12::TRP1


title: 2_E_TH_75


title: 2_E_TH_78


title: 2_E_TH_76


title: 2_E_TH_63


title: Wild Type

value: as BMA, RPB1-HTP::TRP1kl


title: 2_E_TH_60


title: 2_E_TH_62


title: 2_E_TH_61


title: 2_E_TH_59


title: 2_E_TH_64


title: Rap1-AA-rapa rep2


title: 2_E_AS_77

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 5% of the suspension was removed and the remaining cells were manually dissociated in Neural Tissue Dissociation Buffer (P) (Miltenyi Biotec). Myelin was removed using a 25% percoll gradient and astrocytes were captured using ACSA2 microbeads (Miltenyi Biotec). Cells were spun at 1,000 x g and flash frozen in liquid nitrogen.
RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the HiSeq 4000 (Illumina, San Diego, CA) using (150 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.

value: astrocyte


title: 2_E_TH_66


title: ∆comX_sComS_RNA-seq

description:
mRNAs
Table 2.xls

extract_protocol:
Total stranded mRNA libraries were prepped with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs). Library PCR was executed for 15 cycles. Quality of the libraries was evaluated with the use of a High sensitivity DNA chip (Agilent technologies) and concentrations were determined through qPCR according to Illumina protocol.
S. salivarius WT, ∆comR and ∆comX strains were overnight precultivated in CDMG at 37°C. They were resuspended in 50 ml of fresh pre-warmed CDMG at a final OD600=0.05 and grown for approximately 2h30 (OD600=0.2) at 37°C. We then supplemented the medium with either DMSO (negative control) or 1µM sComS and incubated for 30 min at 37°C. Cells were harvested by centrifugation (10 min; 4.000 rpm), the supernatant were discarded and the cell pellets were frozen with liquid nitrogen. Finally, RNAs were extract using the RiboPure bacteria kit (Ambion-Life Technologies) and follow the protocol as provided by the manufacturer, with exception of cell lysis and RNA precipitation. For Lysis, cells were resuspended in RNAwiz buffer supplemented with Zirconia beads and shaked for 40 sec (4 times) in a fastPrep homogenizer device (MP biomedicals). For RNA precipitation, a 1.25-ethanol volume (instead of 0.5) was added to partially purified RNAs. Total RNA was checked for quality on a RNA Nano chip (Agilent technologies) and concentration was measured using Ribogreen assay (Life technologies). rRNA depletion was performed on 2 µg total RNA with the Ribo-Zero rRNA removal kit for Gram Positive Bacteria (Illumina) according to manufacturer’s instructions


title: SOCa

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

country: India

institute: National Institute of Technology

data_processing:
bcl2fastq software (Illumina) was used for converting image file to FASTq format.
Sequenced reads were trimmed for adaptor sequence using srna Work bench and Quality check of the generated data was done using the FASTqc software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of annotated piRNAs predicted for each Sample.

source_name: ovary

extract_protocol:
The tissue samples from two ovarian cancer patients and one healthy donor was surgically resected and immediately placed into RNAlater solution (Invitrogen) at room temperature. These samples were collected from the neighbouring hospitals in the state. The median age of the donors was 60 years. All patients provided written informed consent. The IEC approval has been taken to carry out this work. The resected ovarian cancer tissues were characterized as endometrioid and serous type from the tissue biopsy. The samples were stored at -80°C until next-generation sequencing and other experiments were performed. Total RNA was extracted from all three tissue samples (ENOCa, SOCa, and normal ovary) with the use of RNeasy Mini kit (Qiagen, USA) according to the manufacturer’s instructions. The purity of isolated RNA was evaluated using NanoDrop spectrophotometer (Thermo Scientific) by measuring absorbance at 260 nm and 280 nm. An aliquot of each the samples of ENOCa, SOCa, and normal ovary was also run on an Agilent RNA Bioanalyzer chip to check for RNA integrity number (RIN) and was found to be 7.7, 7 and 6.3 respectively.
The RNA libraries were constructed for sequencing following Illumina TruSeq Small RNA library protocol outlined in “TruSeq Small RNA Sample Preparation Guide” (Part # 15004197; Rev. F; February 2014) and using TruSeq Small RNA sample preparation kit (Illumina, # RS-200-0012). The library was size selected in the range of 145 – 165 bp.

value: serous ovarian cancer

tag: disease

value: ovarian cancer


title: ENOCa

value: endometrioid ovarian cancer


title: NO

value: normal ovary

value: normal


title: 2_E_AS_76


title: 2_E_AS_78


title: 2_C_TH_82

treatment_protocol: Mice had access to water for 72 days

value: Control (water)


title: 2_E_AS_60


title: 2_C_TH_81


title: 2_E_AS_61


title: 2_E_AS_65


title: 2_E_AS_59


title: 2_C_TH_69


title: 2_C_TH_74


title: 2_C_TH_73


title: 2_C_TH_80


title: 2_C_TH_72


title: 2_C_TH_71


title: 2_E_AS_62


title: 2_C_TH_68


title: 2_C_TH_70


title: 2_C_TH_67


title: 2_C_AS_81


title: 2_C_AS_79


title: 2_C_AS_82


title: 2_C_AS_74


title: 2_E_AS_75


title: CRE RNA-seq

city: New Orleans

first: Jinqiang

last: Zhang

address: 1430 Tulane Ave

department: Pathology

institute: Tulane University

data_processing:
Illumina Casava1.7 software used for basecalling.
Cufflink 2.0.1 was used for FPKM files
Genome_build: mm9 (NCBIM37.66)
Supplementary_files_format_and_content: fpkm_tracking file including FPKM values for both samples

source_name: IHCs infected with Cre-adenovirus

extract_protocol:
Total RNAs were isolated from these frozen tissues with Qiagen RNeasy Mini kit
Poly A RNA libraries were prepared for sequencing using standard Illumina protocols (Directional_mRNA-Seq_SamplePrep_Guide_15018460_A).

value: Initiated hepatocytes (IHCs) infected with Cre-adenovirus

value: Tgfbr2 flox/flox


title: 2_C_AS_73

value: brain


title: 2_E_AS_66

value: prefrontal cortex


title: GFP RNA-seq

source_name: IHCs infected with GFP-adenovirus

value: Initiated hepatocytes (IHCs) infected with GFP-adenovirus


title: 2_C_TH_79

value: total homogenate


title: 2_C_AS_72


title: 2_C_AS_71


title: 2_C_AS_69


title: 2_C_AS_70


title: ChIP_WT_Rad21_rep1

status: Public on Jan 09 2018

city: Kowloon

first: Jian

last: Yan

address: 83 Tat Chee Ave

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

library_source: genomic

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2
Genome_build: mm9

molecule: genomic DNA

source_name: E14 embryonic stem cell

extract_protocol: All libraries were constructed using standard illumina TruSeq LT library prep.

tag: antibody

value: wild type

value: E14 embryonic stem cell


title: 2_C_AS_68


title: ChIP_dCD_Rad21_rep2

value: MLL3/4 enzymatically dead


title: 4C_E14_TSSBait2

description: 4C-seq for E14 cells

data_processing:
Library strategy: 4C-Seq
base-calling use bcl2fastq version 2.17
alignment was performed using 4cseqpipe
Genome_build: mm9

source_name: E14, mouse embryonic stem cell line

growth_protocol: Mouse embryonic stem cell lines F123 and Sox2 super-enhancer knockout DEL were cultured in mouse ES cell media: DMEM 85%, 15% fetal bovine serum (Hyclone), penicillin/streptomycin, 1× non-essential amino acids (Gibco), 1× GlutaMax, 1000 U/ml LIF (Millipore), 0.4 mM β-mercaptoethanol. Mouse ES cells were initially cultured on 0.1% gelatin-coated petridish with CF-1 irradiated mouse embryonic fibroblasts (GlobalStem) and were passaged twice on 0.1% gelatin-coated feeder-free plates before harvesting.

extract_protocol:
4C-seq: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n.
All libraries were constructed using standard illumina TruSeq LT library prep.

value: wild type, E14 strain


title: ChIP_WT_Rad21_rep2


title: 2_C_AS_80

value: astrocyte


title: ChIP_SET_Rad21

source_name: DKO cell, E14 embryonic stem cell with MLL3/4 double knock out

value: MLL3/4 double knock out


title: ChIP_WT_H3K4me1_rep2


title: ChIP_dCD_Rad21_rep1


title: ChIP_SET_H3K27ac


title: 4C_dCD_TSSBait2

description: 4C-seq for dCD cells

source_name: dCD, mouse embryonic stem cell line

value: dCD

value: Mll3/4, enzymatically dead


title: ChIP_dCD_H3K4me1_rep2


title: 4C_E14_SEBait2

description: 4C-seq for E14 cells


title: 4C_D0_E14_Car2SE

description: 4C, E14, D0, Car2 super-enhancer

data_processing:
Library strategy: 4C-seq
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, bwa for Hi-C, Tophat for RNA-seq, 4cseqpipe for 4C-seq
Genome_build: mm9

growth_protocol: Mouse embryonic stem cell lines E14 and Mll3/4 double knockout were cultured in mouse ES cell media: DMEM 85%, 15% fetal bovine serum (Hyclone), penicillin/streptomycin, 1× non-essential amino acids (Gibco), 1× GlutaMax, 1000 U/ml LIF (Millipore), 0.4 mM β-mercaptoethanol. Mouse ES cells were initially cultured on 0.1% gelatin-coated petridish with CF-1 irradiated mouse embryonic fibroblasts (GlobalStem) and were passaged twice on 0.1% gelatin-coated feeder-free plates before harvesting.

extract_protocol:
ChIP-seq: Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (details see Yan et al). Hi-C and 4C-seq: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n.
All libraries were constructed using standard illumina TruSeq LT library prep.


title: ChIP_WT_H3K4me1_rep1


title: HiC_D2.5_DKO

description: Hi-C, Day 2.5

data_processing:
Library strategy: HiC-seq
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, bwa for Hi-C, Tophat for RNA-seq, 4cseqpipe for 4C-seq
Genome_build: mm9

value: Mll3/4 double knock out


title: ChIP_dCas9_H3K4me1


title: ChIP_SET_CTCF

value: CTCF


title: ChIP_SET_H3K4me1


title: ChIP_dCD_H3K4me1_rep1


title: ChIP_dCas9_Rad21


title: ChIP_dCas9_CTCF


title: HiC_D0_E14

description: Hi-C, Day 0


title: ChIP_dCas9_H3K27ac


title: HiC_D1.5_DKO

description: Hi-C, Day 1.5


title: 4C_D0_DKO_Car2SE

description: 4C, DKO, D0, Car2 super-enhancer


title: 4C_dCD_SEBait2

description: 4C-seq for dCD cells


title: HiC_D0_DKO

description: Hi-C, Day 0


title: HiC_D1.5_E14

description: Hi-C, Day 1.5


title: ChIP_D1.5_DKO_Input

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, bwa for Hi-C, Tophat for RNA-seq, 4cseqpipe for 4C-seq
Genome_build: mm9


title: ChIP_D2.5_DKO_Input


title: ChIP_D0_DKO_Input


title: ChIP_D1_DKO_Input


title: ChIP_D2_E14_Input


title: ChIP_D3_E14_Input


title: ChIP_D2.5_E14_Input


title: ChIP_D1_E14_Input


title: HiC_D2.5_E14

description: Hi-C, Day 2.5


title: ChIP_D3_DKO_H3K27ac


title: ChIP_D2.5_DKO_H3K27ac


title: ChIP_D0_E14_Input


title: ChIP_D2_DKO_H3K27ac


title: ChIP_D1.5_DKO_H3K27ac


title: ChIP_D1_DKO_H3K27ac


title: ChIP_D2_DKO_Input


title: ChIP_D2_E14_H3K27ac


title: ChIP_D3_DKO_Input


title: ChIP_D1.5_E14_H3K27ac


title: ChIP_D0_DKO_H3K27ac


title: ChIP_D3_E14_H3K27ac


title: ChIP_D1.5_E14_Input


title: ChIP_D1_E14_H3K27ac


title: ChIP_D0_E14_H3K27ac


title: ChIP_D2_5_DKO_Rad21


title: ChIP_D3_0_DKO_Rad21


title: ChIP_D3_0_DKO_H3K4me1


title: ChIP_D3_0_DKO_Med12


title: ChIP_D2_0_DKO_H3K4me1


title: ChIP_D2_0_DKO_input

value: input


title: ChIP_D2_5_DKO_H3K4me1


title: ChIP_D2_5_DKO_input


title: ChIP_D3_0_DKO_input


title: ChIP_D2_0_DKO_Med12


title: ChIP_D2_0_DKO_Rad21


title: ChIP_D2_5_DKO_Med12


title: ChIP_D1_5_DKO_H3K4me1


title: ChIP_D1_DKO_Rad21


title: ChIP_D1_5_DKO_input


title: ChIP_D1_DKO_H3K4me1


title: ChIP_D1_5_DKO_Rad21


title: ChIP_D1_DKO_Med12


title: ChIP_D1_5_DKO_Med12


title: ChIP_D2.5_E14_H3K27ac


title: ChIP_D0_DKO_input


title: ChIP_D0_DKO_H3K4me1


title: ChIP_D0_DKO_Rad21


title: ChIP_D1_DKO_input


title: ChIP_D3_0_E14_Med12


title: ChIP_D3_0_E14_H3K4me1


title: ChIP_D3_0_E14_input


title: ChIP_D2_5_E14_Med12


title: ChIP_D3_0_E14_Rad21


title: ChIP_D2_0_E14_Rad21


title: ChIP_D2_5_E14_H3K4me1


title: ChIP_D2_0_E14_Med12


title: ChIP_D2_5_E14_Rad21


title: ChIP_D1_5_E14_Med12


title: ChIP_D1_5_E14_input


title: ChIP_D1_5_E14_H3K4me1


title: ChIP_D1_5_E14_Rad21


title: ChIP_D1_E14_input


title: ChIP_D1_E14_Rad21


title: ChIP_D2_0_E14_H3K4me1


title: ChIP_D2_5_E14_input


title: DKO_RNA_D2


title: ChIP_D1_E14_Med12


title: ChIP_D0_E14_H3K4me1


title: DKO_RNA_D3


title: ChIP_D0_E14_Med12


title: ChIP_D0_E14_Rad21


title: ChIP_D0_DKO_Med12


title: ChIP_D2_0_E14_input


title: DKO_RNA_D1.5


title: DKO_RNA_D0


title: ChIP_D0_E14_input


title: E14_RNA_D3


title: E14_RNA_D2.5


title: E14_RNA_D1.5


title: E14_RNA_D2


title: E14_RNA_D1


title: E14_RNA_D0


title: DKO_RNA_D1


title: 4C_F123

description: 4C-seq for F123 cells

data_processing:
Library strategy: 4C-seq
base-calling use bcl2fastq version 2.17
alignment was performed using 4cseqpipe
Genome_build: mm9

source_name: F123 mouse embryonic stem cell line, control


title: 4C_DEL

description: 4C-seq for DEL cells

source_name: F123 mouse embryonic stem cell line, DEL

value: Sox2 Super-enhancer Knock-out


title: ChIPseq-H3K4me1_shGFP_0928

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, Tophat for RNA-seq, bwa for Hi-C
Genome_build: mm9
Supplementary_files_format_and_content: bigWig for ChIP-Seq; normalized fpkm for all genes for RNA-Seq; matrix for HiC; normalized counts for 4C

source_name: embryonic stem cell

extract_protocol:
The ChIP-seq has been carried out as previously described6,7. Briefly, 2 million cells were crosslinked with 1% formadehyde for 10 min at RT. The reaction was quenched by adding 125 mM of Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated with antibodies to pull down the specific DNA bound TFs or histones. After intensive wash, DNA was purified and prepared as sequencing library using illumina Truseq LT kit.
TruSeq


title: ChIPseq-H3K4me1_shRad21_0928


title: ChIPseq-input_shRad21_0928


title: HiC-E14_0915

data_processing:
Library strategy: Hi-C
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, Tophat for RNA-seq, bwa for Hi-C
Genome_build: mm9
Supplementary_files_format_and_content: bigWig for ChIP-Seq; normalized fpkm for all genes for RNA-Seq; matrix for HiC; normalized counts for 4C

extract_protocol:
A new Hi-C pipeline was applied according to the recent development3. Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. The single strand overhang was filled with biotinylated-14-ATP (Life Tech.) using Klenow DNA polymerase (NEB). Different from tradition Hi-C, with in situ protocol the ligation was performed when the nuclear membrane was still intact. DNA was ligated for 4h at 16 °C using T4 ligase (NEB). Protein was degraded by proteinase K (NEB) treatment at 55 °C for 30 min. The crosslinking was reversed with 500 mM of NaCl and heat at 68 °C o/n. DNA was purified and sonicated to 300-700 bp small fragments. Biotinylated DNA was selected with Dynabeads My One T1 Streptavidin beads (Life Tech.). Sequencing library was prepared on beads and intensive wash was performed between different reactions.
TruSeq


title: ChIP_D1_E14_H3K4me1


title: HiC-DKO_0915


title: DKO_RNA_D2.5


title: DKO_TSSbait3

data_processing:
Library strategy: 4C-seq
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, Tophat for RNA-seq, bwa for Hi-C
Genome_build: mm9
Supplementary_files_format_and_content: bigWig for ChIP-Seq; normalized fpkm for all genes for RNA-Seq; matrix for HiC; normalized counts for 4C

extract_protocol:
4C-seq experiments and analysis was performed as described previously1. Briefly, 5 million cells were cross-linked with 2% formaldehyde for 10 min at room temperature (RT) and quenched by adding 125 mM Glycine with 5 min additional incubation at RT. Cells were lysed and nuclei were isolated and digested with Csp6I (Thermo Scientific) over night (o/n). Enzyme was inactivated by heat at 65 °C for 20 min. The digested chromatin was subjected for ligation for 16 h with T4 ligase (Life Technologies). DNA was then purified with phenol/chloroform extraction and ethanol precipitation before the second digestion with NlaIII (NEB) at 37 °C o/n.  After enzyme inactivation, a second ligation was performed at 16 °C for 4 h and DNA was purified, of which 4.8 μg in total was used for PCR amplification using 4 different pairs of primers
TruSeq


title: E14_TSSbait3


title: DKO_SEbait2


title: E14_SEbait2


title: RNAseq-DKO_0921


title: RNAseq-E14_0921


title: E14_SEbait3


title: RNAseq-DKO_0810


title: RNAseq-E14_0810


title: ChIPseq-Input_E14_rep2


title: ChIPseq-Med12_E14_rep2


title: ChIPseq-Med23_DKO


title: ChIPseq-Input_DKO_rep3


title: ChIPseq-Med12_DKO_rep3


title: ChIPseq-Input_DKO_rep2


title: E14_SEbait1


title: ChIPseq-Med1_DKO_rep3


title: wildtype_sComS_RNA-seq

description:
mRNAs
Table 2.xls

value: WT

value: sComS


title: ChIPseq-Med1_E14_rep2


title: ChIPseq-Input_DKO_0803


title: ChIPseq-Smc3_DKO_rep2


title: ChIPseq-Smc3_E14_rep2


title: ChIPseq-H3K4me1_DKO_0803


title: ChIPseq-Input_E14_0803


title: DKO_SEbait1


title: ChIPseq-H3K27ac_E14_0803


title: ChIPseq-Input_DKO_0831


title: ChIPseq-Input_E14_0831


title: ChIPseq-H3K4me1_E14_0831


title: ChIPseq-H3K4me1_E14_0803


title: ChIPseq-H3K4me1_DKO_0831


title: HGC27SeV1

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

country: China

institute: Shanghai Institutes of Biological Sciences

data_processing:
Before read mapping, clean reads were obtained from the raw reads by rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Clean reads after filtering were aligned to human genome (hg38) by Tophat v2.0.9(1).
The differentially expressed genes were achieved by EBSeq algorithms.
Genes were considered significantly differentially expressed under the following criteria: (1) fold change > 1.5 or < 0.667; (2) FDR < 0.05 (2).
Genome_build: hg38
Supplementary_files_format_and_content: xls file includes RPKM and raw read count values for each Sample.

source_name: gastric cancer cells

growth_protocol: HGC-27 cells were maintained in culture supplemented with 10% heat-inactivated fetal calf serum (FCS), 100 µg ml-1 of penicillin, and 100 µg ml-1 of streptomycin at 37°C with 5% CO2 in a humidified incubator (Thermo, MA, USA). The cells were passaged for ≤ 3 months from the frozen early-passage stocks that had been received from the indicated sources.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with PBS or LPS (1ug/ml) for 48 h.

value: derived from metastatic lymph node of gastric cancer

value: SeV treatment for 48 h


title: ChIPseq-Med23_E14_rep4


title: HGC27SeV2


title: HGC27ctrl2

value: PBS treatment for 48 h


title: HGC27ctrl1


title: MS49_PD17_Day8

city: Madison

first: David

last: Vereide

state: WI

address: 330 North Orchard Street

department: Regenerative Biology

institute: Morgridge Institute for Research

data_processing:
Basecalls/demuxxing performed using Illumina bcl2fastq v1.8.4.
Reads were filtered and trimmed for adapters and quality. Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab-delimited file containing RSEM's calculated Expected Counts gene expression estimates.

source_name: expandable arterial endothelial precursors (eAEPs)

extract_protocol:
from RLT+ cell lysates using the RNeasy Plus Micro Kit (Qiagen) with genomic DNA elimination (gDNA Eliminator Spin Columns)
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.

value: eAEP line MS49 matured for four days in the absence of doxycycline after exposure to PD173074 for four days

tag: culture medium

value: EGM2 (Lonza) supplemented with 10 mM HEPES

tag: tissue of origin

value: adult bone marrow


title: MS53_PD17_Day4

value: eAEP line MS53 cultured in the presence of 100 nM PD173074 for four days

value: EGM2 (Lonza) supplemented with 10 mM HEPES, 100 ng/mL doxycycline, and 100 nM PD173074 (Stemgent)


title: MS53_Control_Day4

value: eAEP line MS53 cultured without exposure to PD173074, as a negative control for sample MS53_PD17_Day4

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline


title: MS53_PD17_Day8

value: eAEP line MS53 matured for four days in the absence of doxycycline after exposure to PD173074 for four days


title: MS49_PD17_Day4

value: eAEP line MS49 cultured in the presence of 100 nM PD173074 for four days


title: MS49_Control_Day8

value: eAEP line MS49 matured for four days in the absence of doxycycline, as a negative control for sample MS49_PD17_Day8


title: MS49_Control_Day4

value: eAEP line MS49 cultured without exposure to PD173074, as a negative control for sample MS49_PD17_Day4


title: MS15_Control_Day8

data_processing:
Basecalls/demuxxing performed using Illumina bc2fastq2, v2.17.1.14
Reads were filtered and trimmed for adapters and quality. Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab-delimited file containing RSEM's calculated Expected Counts gene expression estimates.

value: eAEP line MS15 matured for four days in the absence of doxycycline, as a negative control for sample MS15_PD17_Day8

value: cord blood


title: MS15_PD17_Day4

value: eAEP line MS15 cultured in the presence of 100 nM PD173074 for four days


title: MS15_PECAM1_Mid

value: Mature progeny of line MS15 sorted by FACS for mid expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS15_PECAM1_High

value: Mature progeny of line MS15 sorted by FACS for high expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS15_transit

value: eAEP line MS15, spontaneously undergoing an EndoMT


title: MS53_Control_Day8

value: eAEP line MS53 matured for four days in the absence of doxycycline, as a negative control for sample MS53_PD17_Day8


title: MS4_0ng

source_name: expandable mesenchymal precursors (eMPs)

value: mature mesenchymal progeny of eMP line MS4, obtained by the downregulation of MYCN and SOX17 for three days

value: EGM2 (Lonza) supplemented with 10 mM HEPES


title: MS13_100ng

value: eMP line MS13, maintained in culture with the ectopic expression of MYCN and SOX17


title: MS5_0ng

value: mature mesenchymal progeny of eMP line MS5, obtained by the downregulation of MYCN and SOX17 for three days


title: MS51_100ng

value: eMP line MS51, maintained in culture with the ectopic expression of MYCN and SOX17

value: adult bone marrow


title: MS4_100ng

value: eMP line MS4, maintained in culture with the ectopic expression of MYCN and SOX17

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline


title: MS51_0ng

value: mature mesenchymal progeny of eMP line MS51, obtained by the downregulation of MYCN and SOX17 for three days


title: MS13_0ng

value: mature mesenchymal progeny of eMP line MS13, obtained by the downregulation of MYCN and SOX17 for three days


title: MS55_0ng

value: mature endothelial progeny of eAEP line MS55, obtained by the downregulation of MYCN and SOX17 for four days


title: MS5_100ng

value: eMP line MS5, maintained in culture with the ectopic expression of MYCN and SOX17

value: cord blood


title: MS53_10ng

value: mature endothelial progeny of eAEP line MS53, obtained by the downregulation of MYCN and SOX17 for four days

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 10 ng/mL doxycycline


title: MS53_100ng

value: eAEP line MS53, maintained in culture with the ectopic expression of MYCN and SOX17


title: DKO_SEbait3


title: ChIPseq-H3K27ac_DKO_0803


title: MS49_0ng

value: mature endothelial progeny of eAEP line MS49, obtained by the downregulation of MYCN and SOX17 for four days


title: MS49_100ng

value: eAEP line MS49, maintained in culture with the ectopic expression of MYCN and SOX17


title: MS15_PD17_Day8

value: eAEP line MS15 matured for four days in the absence of doxycycline after exposure to PD173074 for four days

value: EGM2 (Lonza) supplemented with 10 mM HEPES


title: MS15_PECAM1_Low

value: Mature progeny of line MS15 sorted by FACS for low expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS15_Control_Day4

value: eAEP line MS15 cultured without exposure to PD173074, as a negative control for sample MS15_PD17_Day4


title: MS55_10ng

value: adult bone marrow


title: MS42_0ng

value: mature endothelial progeny of eAEP line MS42, obtained by the downregulation of MYCN and SOX17 for four days


title: MS42_10ng


title: MS42_100ng

value: eAEP line MS42, maintained in culture with the ectopic expression of MYCN and SOX17

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline


title: MS49_10ng


title: MS15_100ng

value: eAEP line MS15, maintained in culture with the ectopic expression of MYCN and SOX17


title: MS15_10ng

value: mature endothelial progeny of eAEP line MS15, obtained by the downregulation of MYCN and SOX17 for four days


title: HCAEC

source_name: human coronary artery endothelial cells

value: human coronary artery endothelial cells

value: EGM-MV (Lonza)

value: coronary artery


title: HAEC

source_name: human aortic endothelial cells

value: human aortic endothelial cells

value: aorta


title: MS55_100ng

value: eAEP line MS55, maintained in culture with the ectopic expression of MYCN and SOX17


title: HUVEC_1

source_name: human umbilical vein endothelial cells

value: human umbilical vein endothelial cells

value: umbilical vein


title: HUVEC_2

value: EGM2 (Lonza) supplemented with 10 mM HEPES


title: HBVP

data_processing:
Basecalls/demuxxing performed using Illumina bcl2fastq v1.8.4
Reads were filtered and trimmed for adapters and quality. Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab-delimited file containing RSEM's calculated Expected Counts gene expression estimates.

source_name: human brain vascular pericytes

extract_protocol:
Total RNA purchased from ScienCell (product number 1205)
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.

value: human brain vascular pericytes

value: see ScienCell (product number 1205)

value: brain vasculature


title: MS55_PD17_Day4

data_processing:
Basecalls/demuxxing performed using Illumina bcl2fastq2, v2.17.1.14
Reads were filtered and trimmed for adapters and quality. Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab-delimited file containing RSEM's calculated Expected Counts gene expression estimates.

value: eAEP line MS55 cultured in the presence of 100 nM PD173074 for four days

value: EGM2 (Lonza) supplemented with 10 mM HEPES, 100 ng/mL doxycycline, and 100 nM PD173074 (Stemgent)

value: adult bone marrow


title: MS55_Control_Day4

value: eAEP line MS55 cultured without exposure to PD173074, as a negative control for sample MS55_PD17_Day4

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline


title: MS64_Control_Day8

value: eAEP line MS64 matured for four days in the absence of doxycycline, as a negative control for sample MS64_PD17_Day8

value: cord blood


title: MS64_PD17_Day8

value: eAEP line MS64 matured for four days in the absence of doxycycline after exposure to PD173074 for four days


title: MS55_PD17_Day8

value: eAEP line MS55 matured for four days in the absence of doxycycline after exposure to PD173074 for four days


title: MS53_0ng

value: mature endothelial progeny of eAEP line MS53, obtained by the downregulation of MYCN and SOX17 for four days


title: MS58_Control_Day8

value: eAEP line MS58 matured for four days in the absence of doxycycline, as a negative control for sample MS58_PD17_Day8


title: MS55_Control_Day8

value: eAEP line MS55 matured for four days in the absence of doxycycline, as a negative control for sample MS55_PD17_Day8


title: MS58_Control_Day4

value: eAEP line MS58 cultured without exposure to PD173074, as a negative control for sample MS58_PD17_Day4


title: MS69_PECAM1_Mid

value: Mature progeny of line MS69 sorted by FACS for mid expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT

value: EGM2 (Lonza) supplemented with 10 mM HEPES


title: MS64_PD17_Day4

value: eAEP line MS64 cultured in the presence of 100 nM PD173074 for four days


title: MS68_PECAM1_Mid

value: Mature progeny of line MS68 sorted by FACS for mid expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS68_PECAM1_High

value: Mature progeny of line MS68 sorted by FACS for high expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS58_PD17_Day8

value: eAEP line MS58 matured for four days in the absence of doxycycline after exposure to PD173074 for four days


title: MS42_PECAM1_Low

value: Mature progeny of line MS42 sorted by FACS for low expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS58_PD17_Day4

value: eAEP line MS58 cultured in the presence of 100 nM PD173074 for four days

value: EGM2 (Lonza) supplemented with 10 mM HEPES, 100 ng/mL doxycycline, and 100 nM PD173074 (Stemgent)


title: MS42_PECAM1_High

value: Mature progeny of line MS42 sorted by FACS for high expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS42_transit

value: eAEP line MS42, spontaneously undergoing an EndoMT at very late passage

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline

value: cord blood


title: MS69_PECAM1_Low

value: Mature progeny of line MS69 sorted by FACS for low expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT

value: adult bone marrow


title: MS64_Control_Day4

value: eAEP line MS64 cultured without exposure to PD173074, as a negative control for sample MS64_PD17_Day4


title: morula ctrl 1

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v1.3.3 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.2.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.

source_name: Mouse embryo

extract_protocol:
For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB，the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.For epiblast (Epi) and extraembryonic ectoderm (Exe) isolation, embryos were cuttted at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle whose inner diameter is silghtly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the epiblast or extraembryonic ectoderm were then incubated in Ca2+-free CZB for 10 min. Single cells were separated by gentle pipetting using a fire-polished glass needle with an inner diameter of 15-20 μm.200 cells were washed three times in 0.5% BSA-PBS solution per reaction.
Libraries were prepared according to Ovation® RNA‑Seq System V2 (NuGEN, 7102) following the manufacturer’s instructions.

treatment_protocol: For gene knockdown，small interference RNAs (siRNAs) against mouse Rrp9 and negative control were diluted in nuclease-free water to 20 μM. The siRNAs for a given gene were mixed for knock-down, with a working concentration of 5 μM. Oocytes were injected with approximately 10 pL of siRNAs using a Piezo-driven micromanipulator. Allow oocytes to recover for at least 1 h in the incubator prior to Intracytoplasmic sperm injection (ICSI). The sperm head was then injected into the oocyte according to the method described previously (Kimura and Yanagimachi, 1995). The injected embryos were collected in morula stage.

tag: development stage

value: morula embryo


title: MS69_PECAM1_High

value: Mature progeny of line MS69 sorted by FACS for high expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: HAAF

source_name: human aortic adventitial fibroblasts

extract_protocol:
Total RNA purchased from ScienCell (product number 6125)
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.

value: human aortic adventitial fibroblasts

value: see ScienCell (product number 6125)

value: aortic adventitia


title: MS15_0ng

value: mature endothelial progeny of eAEP line MS15, obtained by the downregulation of MYCN and SOX17 for four days

value: EGM2 (Lonza) supplemented with 10 mM HEPES


title: POOL4_9

city: Sheffield

first: Rachel

last: Waller

state: Outside U.S. & Canada

address: SITraN, The University of Sheffield, 385A Glossop Road

country: United Kingdom

institute: University of Sheffield

data_processing:
Basecalls performed using HiSeq Control Software (HCS) v1.5
Initial quality control (QC) testing of post-sequencing data was carried out using the Illumina Sequencing Analysis Viewer to identify the Illumina Phred quality score (>Q30) and pass filter (PF) reads.
Sequence data were converted from the generated image .bcl files to raw, de-multiplexed sequencing data in the .fastq text file format using the Illumina developed bcl2fastq pipeline.
QC testing of the raw data was completed using Chimira, the 3’ adapter sequences were trimmed (Illumina TruSeq 3’ adapter TGGAATTCTCGGGTGCCAAGG sequence)  and the overall miRNA reads counted. Samples POOL1_1, POOL1_11,  POOL2_7, POOL2_9, POOL3_4, POOL4_10 were classed as outliers and removed from subseqeunt data processing.
Individual sample data was uploaded into two independent online software packages; Oasis 2.0 (Capece et al., 2015, Love et al., 2014) and Genboree (Riehle et al., 2012, Coarfa et al., 2014, Subramanian et al., 2015). Specific trimming tools in each of these packages enabled the removal of the Illumina TruSeq 3’ adapter sequence from each sample’s .fastq file and the read size filtered (15-32nt) with low abundance reads (<5 reads) discarded.
Genome_build: The Human genome (Oasis 2.0: hg38, Genboree: Hg19) and miRBase_v21.
Supplementary_files_format_and_content: Both Oasis and Genobroee processed data files are presented as a matrix table, .xlsx file type

source_name: Cerebrospinal fluid (CSF)

extract_protocol:
CSF samples were obtained by lumbar puncture, held on ice and processed within one hour by centrifugation at 800g for 5 minutes to pellet cellular debris. The supernatant was removed, snap frozen and stored in liquid nitrogen. Total RNA was extracted using the miRVana PARIS kit (Thermo Fisher Scientific).
Illumina TruSeq Small RNA library preparation kit  was used with 5ul of extracted RNA for construction  of small RNA sequencing libraries.

tag: subjects

value: sporadic amyotrophic lateral sclerosis (sALS)


title: POOL4_8


title: MS69_transit

value: eAEP line MS69, spontaneously undergoing an EndoMT


title: MS42_PECAM1_Mid

value: Mature progeny of line MS42 sorted by FACS for mid expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS64_0ng

value: mature endothelial progeny of eAEP line MS64, obtained by the downregulation of MYCN and SOX17 for four days


title: POOL4_5


title: MS68_PECAM1_Low

value: Mature progeny of line MS68 sorted by FACS for low expression of PECAM1 from a population of cells spontaneously undergoing an EndoMT


title: MS64_10ng

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 10 ng/mL doxycycline


title: POOL3_11

value: Control


title: morula siRrp9 2


title: MS64_100ng

value: eAEP line MS64, maintained in culture with the ectopic expression of MYCN and SOX17

value: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline

value: cord blood


title: morula siRrp9 1

value: morula embryo


title: morula ctrl 2


title: POOL4_12


title: POOL4_7


title: IFN_24hrs_HIRA_Input

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

description: IMR90 cells at 24hr IFN treatment

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
RNA-seq reads were mapped to hg19 whole genome using tophat 2.0.9 with parameters –solexa-quals, -p 12, --segment-length 18, -M, -G Homo_sapiens.GRCh37.73.gtf
ChIP-seq reads were mapped to hg19 whole genome using bowtie 2.1.0 with parameters -p 12
Aligned reads normalised by library size (number of fragments) and subsequent reads piledup and converted to bigWig format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.

growth_protocol: IMR90 cells were cultured in DMEM supplemented with 20% (v/v) FBS, 2 mM L-Glutamine and incubated at 37°C in a humidified 5% CO2 and 3% O2 atmosphere. Cell Growth media were supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin.

extract_protocol:
Native ChIP was performed for HIRA and HA-H3.3 as described previously (Rai et al. 2014). Antibodies used for ChIP were: Cocktail of mouse mAbs to HIRA (approximately equimolar mixture of WC15, WC19, WC117, WC 119 (Hall et al. 2001)), HA (Millipore 05904) (for anti-HA-H3.3 ChIP). Mouse mAb to HA tag (Covance, MMS-101R) was used as species/class-matched negative control Abs.
ChIP libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: IMR90 cells were treated with 2000U/ml recombinant  human  IFN-β (PBL-11410-2)


title: IFN_0hrs_HIRA_Input

description: IMR90 cells at 0hr IFN treatment


title: POOL4_6


title: MS68_transit

value: eAEP line MS68, spontaneously undergoing an EndoMT

value: adult bone marrow


title: POOL3_5


title: POOL4_4


title: POOL4_1


title: POOL3_12


title: POOL4_2

value: multiple sclerosis control (MS control)


title: POOL3_3


title: POOL3_1


title: shLUC_1_IFN_0hrs_Replicate2

description: IMR90 cells without HIRA KD at 0hr IFN treatment

extract_protocol:
Total RNA was prepared using the RNeasy kit (Qiagen catalog no. 74104), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ChIPseq-input_shGFP_0928

value: wild type


title: shLUC_1_IFN_0hrs_Replicate1


title: POOL3_10


title: IFN_0hrs_HIRA_ChIP

description: IMR90 cells at 0hr IFN treatment


title: POOL4_10


title: IFN_24hrs_HIRA_ChIP

description: IMR90 cells at 24hr IFN treatment


title: POOL3_9


title: POOL4_11


title: POOL2_11


title: POOL3_4


title: POOL4_3


title: S16

city: Bethesda

first: Valentina

last: Giudice

state: MD

address: 10 Center Drive

department: Hematology Branch

institute: NHLBI

description:
S16
S06_SEmiso_vs_S16_SEmiso.miso_bf

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality at the ends. Remaining sequence reads were then aligned to the human reference genome (hg19) using Tophat2.
Gene read counts were measured using FeatureCounts and FPKM values were calculated with cufflinks. edgeR was used to identify differentially expressed genes between conditions, and topGO was used for annotation (Alexa, Rahnenfuhrer, and Lengauer, 2006). Sample comparison for differential gene expression was as follows: WTblk and WT1 versus MT2, MT3, MT4, and MT5. Gene enrichment set analysis (GSEA) was conducted with KEGG, Biocarta, and Reactome pathway datasets (Subramanian et al., 2005).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: WT_0*bf and WT_1*bf: We combined the WT as sample 1 and compared the data with combined KO samples (sample 2).

source_name: K562 cell line

growth_protocol: All cell lines were cultured in IMDM medium supplemented with 10% fetal bovine serum and antibiotics and were incubated at 37°C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Plus Mini kit at cells in the logarithmic and plateau stages of growth. Library construction and sequencing were performed by GeneWiz (South Plainfield, NJ, USA).
Paired-end libraries were generated using the Illumina TruSeq RNA sample preparation kit

value: Bone Marrow

value: DNMT3A mutated


title: ShHIRA_2_IFN_24hrs_Replicate1

description: IMR90 cells with HIRA KD at 24hr IFN treatment


title: POOL2_9


title: POOL3_8


title: S15

description:
S15
S05_SEmiso_vs_S15_SEmiso.miso_bf


title: POOL3_7

value: sporadic amyotrophic lateral sclerosis (sALS)


title: shLUC_1_IFN_24hrs_Replicate2

description: IMR90 cells without HIRA KD at 24hr IFN treatment


title: ShHIRA_2_IFN_6hrs_Replicate2

description: IMR90 cells with HIRA KD at 6hr IFN treatment


title: POOL3_6


title: shLUC_1_IFN_24hrs_Replicate1


title: S13

description:
S13
S03_SEmiso_vs_S13_SEmiso.miso_bf


title: ShHIRA_2_IFN_24hrs_Replicate2


title: shLUC_1_IFN_6hrs_Replicate1

description: IMR90 cells without HIRA KD at 6hr IFN treatment


title: shLUC_1_IFN_6hrs_Replicate2


title: POOL2_12


title: S18

description:
S18
S08_SEmiso_vs_S18_SEmiso.miso_bf


title: POOL2_10


title: shHIRA_1_IFN_24hrs_Replicate2


title: S14

description:
S14
S04_SEmiso_vs_S14_SEmiso.miso_bf


title: POOL2_8


title: ShHIRA_2_IFN_0hrs_Replicate2

description: IMR90 cells with HIRA KD at 0hr IFN treatment


title: POOL2_3


title: S05

description:
S05
S05_SEmiso_vs_S15_SEmiso.miso_bf


title: POOL2_7


title: ShHIRA_2_IFN_0hrs_Replicate1


title: ShHIRA_2_IFN_6hrs_Replicate1


title: POOL2_1


title: S11

description:
S11
S01_SEmiso_vs_S11_SEmiso.miso_bf


title: shHIRA_1_IFN_6hrs_Replicate1


title: S08

description:
S08
S08_SEmiso_vs_S18_SEmiso.miso_bf


title: POOL2_6


title: POOL1_12


title: POOL2_5


title: shHIRA_1_IFN_24hrs_Replicate1


title: S06

description:
S06
S06_SEmiso_vs_S16_SEmiso.miso_bf


title: POOL2_4


title: MT4 [exome]

data_processing:
Library strategy: Exome-seq
The data sets have been analyzed with BWA mapping + GATK SNP/Indel pipeline followed by snpEff annotation against reference genome hg19.
Then BAM files were analyzed for DNMT3A mutations
Genome_build: hg19
Supplementary_files_format_and_content: excel file for variants called (VCF)

extract_protocol:
Whole-exome sequencing of extracted DNA was performed to confirm DNMT3A mutations. Library construction, exon capture, and sequencing was performed by Otogenetics (Atlanta, GA, USA).
In brief, paired-end libraries were generated using the Illumina TruSeq DNA sample preparation kit. Exons were enriched using the Agilent Human All Exon V5 (51 Mb) capture system. Illumina HiSeq2500 was used for sequencing with a paired-end sequencing length of 100-125 bp and approximately 70 million reads per sample.


title: shHIRA_1_IFN_6hrs_Replicate2


title: POOL2_2


title: MT2 [exome]


title: CELL_3

city: Worcester

first: Travis

last: Thomson

state: Massachusetts

address: UMMS, 364 Plantation, LRB 760B

department: Neurobiology

institute: Umass Medical School

data_processing:
Genic reads were mapped to the Drosophila genome using TOPHAT2
Transcripts were assembled using CUFFLINKS
Transposon reads were mapped to Drosophila transposons using eXpress
Deseq2 was used to compare data sets and create graphs
Genome_build: D.melanogaster Apr. 2006 (BDGP R5/dm3);  for transposon the Drosophila transposons transposon_sequence_set.V9.42 was used
Supplementary_files_format_and_content: genes.tsv contains FPKM from cufflinks. Transposons.txt contains FPKM from eXpress.

organism: Drosophila melanogaster

source_name: S2 cells

extract_protocol:
Exosomes were isolated, RNA was isolated using a Qiagen micro kit.
Libraries were prepared as outlined in the NEB instructions in kit, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina

tag: rna source

value: total cellular mRNA


title: POOL1_8


title: WT transfected [exome]

tag: cell line


title: S04

description:
S04
S04_SEmiso_vs_S14_SEmiso.miso_bf


title: S03

description:
S03
S03_SEmiso_vs_S13_SEmiso.miso_bf


title: shHIRA_1_IFN_0hrs_Replicate1


title: S01

description:
S01
S01_SEmiso_vs_S11_SEmiso.miso_bf


title: shHIRA_1_IFN_0hrs_Replicate2


title: CELL_2


title: WT bulkm [exome]


title: POOL1_11


title: Ag55 cells rep3

city: Athens

first: Ruchir

last: Mishra

state: Georgia

address: 103 college station road, B108

department: Entomology

institute: University of Georgia

description: gene_exp.diff, isoform_exp.diff, isoforms.count_tracking

data_processing:
Base calling, de-multiplexing and adapter removal were performed using Illumina BaseSpace. The encoding version is Illumina 1.9
Due to high sequencing base quality at both 3' and 5' ends according to FastQC output and availability of reference genome, preprocessing steps were not performed
The 7 data sets (paired-end reads, including replicates were independently mapped onto the Anopheles gambiae genome ((Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz (downloaded from Vectorbase)) by using Tophat v2.0.13 with parameters -p 4 -r 50 (for Ag55 cells) or -r 100 (for BFAdult)and --mate-std-dev 25 (for BFAdult replicates only)
After the alignment, Cufflinks v2.2.1 was used to estimate the expression values of the transcripts in FPKM (Fragments Per Kilobase per Million mapped reads) with the cuffdiff2 default geometric normalization
Genome_build: Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz downloaded from vectorbase (https://www.vectorbase.org/downloads)
Supplementary_files_format_and_content: tab-delimited files gene_exp.diff and isoform_exp.diff from cuffdiff output containing FPKM values and differentially expressed genes and transcripts, respectively
Supplementary_files_format_and_content: tab-delimited file isoforms.count_tracking containing  transcripts counts

organism: Anopheles gambiae

source_name: cell line

extract_protocol:
RNA was extracted from Ag55 cells using  TRIzol (Ambion). Approximately, 1 × 107 cells (1 flask of 25 cm2) were homogenized in  TRIzol reagent (200 μl) and further processed for RNA extraction following the instructions given in the Ambion kit. Extraction of RNA from Ag55 cells was replicated three times.
RNA libraries were prepared for sequencing using KAPA Stranded mRNA-seq Kit (KK8420) protocol

tag: confluency

value: 80% confluent cells


title: POOL1_5


title: MT5 [exome]


title: MT4

data_processing:
Raw reads were aligned to the human reference genome (hg19) using Bowtie (version 1.1.1). ngs.plot was used to create genome overviews of binding at gene bodies (Shen et al., 2014). Model-based Analysis of ChIP-Seq (MACS) was used to predict highly methylated regions, and these regions were annotated using PAVIS as previously described (Huang et al., 2013).
For differential analysis, the reference genome was divided into non-overlapping 1000-bp windows, and reads in each window for each sample were counted. Differential analysis was then performed between conditions using edgeR in bioconductor. Only windows with a combined coverage of 10 or more reads were included in the analysis. Windows that showed a 4-fold or greater difference (edgeR logFC >2) and p-value < 0.0001 were retained and annotated to the nearest or overlapping gene using ChIPpeakAnno[4] (version 3.2.2) or refseq for 5’ upstream and 5’UTR regions.
Supplementary_files_format_and_content: BED for peaks

extract_protocol:
Methylated DNA immunoprecipitation (MeDIP) was used to detect regional differences in DNA methylation between DNMT3A WT and MT clones. DNA extraction of WTblk, WT1, MT1, MT2, and MT4 cell lines was performed as previously described. 5-mC profiling, fragmentation, library preparation and sequencing were performed by Otogenetics (Atlanta, GA, USA).
In brief, paired-end libraries were generated using the Illumina TruSeq DNA sample preparation kit. Illumina HiSeq2500 was used for sequencing with a paired-end sequencing length of 100-125 bp and approximately 40 million reads per sample.


title: MT2


title: POOL1_4


title: MT3 [exome]


title: POOL1_9


title: MT1


title: Ag55 cells rep2


title: Ag55 cells rep1


title: CELL_4


title: POOL1_3


title: POOL1_7


title: POOL1_1


title: EXO_4

source_name: S2 exosomes

value: exosomal mRNA


title: ATM-/- NSPC_c-myc_rep2

status: Public on Jan 08 2018

city: Boston

first: Rohit

middle: A

last: Panchakshari

state: MA

address: One Blackfan Circle, KARP building

department: PCMM

institute: Children's Hospital Boston

data_processing:
Library strategy: HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: Neural stem/progenitor cells

extract_protocol:
DNA was extracted overnight at 55 degree Celcius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using HTGTS.

treatment_protocol: Purified B cells were stimulated with either aCD40/IL4 for 96 hrs; CH12F3 cell lines were cultured in lymphocyte medium R15 and stimulated with anti-CD40+IL4+TGF-β for 72 hrs.

value: ATM-/-

tag: activation

value: c-myc gRNA/Cas9

tag: treatment protocol

tag: target locus

value: c-myc gRNA/Cas9 induced bait DSB

tag: growth conditions

value: Neurobasal A, 1:50 B27 minus vitamin A, 1:400 Glutamax, 10 microgram/uL Gentamycin; 10 ng/mL each human EGF, mouse FGFb, mouse PDGF-BB


title: Lig4-/- clone #2_c-myc_5'BE_rep3

source_name: CH12F3 murine lymphoma cells

value: Lig4-/- CH12F3 clone #2

value: cytokine stimulation + c-myc gRNA/Cas9


title: ATM-/- NSPC_c-myc_rep3


title: POOL1_10


title: EXO_2


title: CELL_1


title: Lig4-/- clone #1_c-myc_5'BE_rep1

value: Lig4-/- CH12F3 clone #1


title: Lig4-/- clone #2_c-myc_5'BE_rep2


title: POOL1_2


title: EXO_1


title: POOL1_6


title: 53BP1-/- clone #1_c-myc_5'BE_rep1


title: ATM-/- clone #1_c-myc_5'BE_rep3

value: ATM-/- CH12F3 clone #1


title: WT transfected

tag: tissue


title: WT bulk


title: Lig4-/- clone #1_c-myc_5'BE_rep3


title: Lig4-/- clone #1_c-myc_5'BE_rep2


title: Lig4-/- clone #2_c-myc_5'BE_rep1


title: WT CH12F3_c-myc_5'BE_rep3

value: WT CH12F3 cells


title: WT CH12F3_c-myc_5'BE_rep2


title: Lig4-/- NCDel #2_5'Sm_rep3

value: Lig4-/- NCDel cells clone #2

value: cytokine stimulation

value: non-coding IgH Sm-Sa deletion


title: Lig4-/- NCDel #2_5'Sm_rep2


title: EXO_3


title: 53BP1-/- clone #2_c-myc_5'BE_rep1


title: Lig4-/- NCDel #2_5'Sm_rep1


title: 53BP1-/- clone #2_c-myc_5'BE_rep3


title: ATM-/- clone #2_c-myc_5'BE_rep3

value: ATM-/- CH12F3 clone #2


title: Lig4-/- NCDel #1_5'Sm_rep1

value: Lig4-/- NCDel cells clone #1


title: 53BP1-/- clone #1_c-myc_5'BE_rep3


title: ATM-/- clone #2_c-myc_5'BE_rep2


title: 53BP1-/- clone #1_c-myc_5'BE_rep2


title: ATM-/- clone #2_c-myc_5'BE_rep1


title: ATM-/- NSPC_c-myc_rep1


title: 53BP1-/- NCDel #2_5'Sm_rep1

value: 53BP1-/- NCDel cells clone #2


title: ATM-/- clone #1_c-myc_5'BE_rep2


title: 53BP1-/- NCDel #1_5'Sm_rep2

value: 53BP1-/- NCDel cells clone #1


title: ATM-/- NCDel #2_5'Sm_rep3

value: ATM-/- NCDel cells clone #2


title: ATM-/- NCDel #1_5'Sm_rep2

value: ATM-/- NCDel cells clone #1


title: ATM-/- clone #1_c-myc_5'BE_rep1


title: 53BP1-/- clone #2_c-myc_5'BE_rep2


title: ATM-/- NCDel #1_5'Sm_rep3


title: ATM-/- NCDel #1_5'Sm_rep1


title: 53BP1-/- NCDel #2_5'Sm_rep3


title: Lig4-/- NCDel #1_5'Sm_rep3


title: Lig4-/- NCDel #1_5'Sm_rep2


title: 53BP1-/- NCDel #2_5'Sm_rep2


title: WT CH12F3_c-myc_5'BE_rep1


title: 53BP1-/- NCDel #1_5'Sm_rep3


title: WT-NCDel #2_5'Sm_rep1

value: WT NCDel cells clone #2


title: YK

city: West Lafayette

first: Jie

last: Yin

state: Indiana

address: 170 S UNIVERSITY ST

department: Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
Raw sequences were trimmed to remove adaptor sequences, and an initial quality trimming was performed using GS De Novo Newbler (v2.5.3; default parameters) [71]. Trimmed reads were further trimmed using the FASTX-Toolkit with a minimum quality value of 12 and minimum read length of 50 bp.
Trimmed reads were aligned to the Joint Genome Institute (JGI) E. salsugineum genome using the splice-aware aligner GMAP v2012-11-27 with default parameters Only uniquely mapped reads were used for transcript abundance estimates.
Genes were identified via a reference annotation-based transcript assembly method using the Cufflinks package.Reads from SH and YK were assembled separately and then merged using the cuffmerge command. The intersect function within BEDTools v2.17.0 was used to identify genes not annotated in the JGI E. salsugineum genome (newly annotated genes). Same-strandedness was not enforced when identifying newly annotated genes because of the non-strand-specific protocol for 454 library preparation.
The number of reads uniquely aligned to each gene was determined with htseq-count within HTSeq v0.5.4p5 using union mode. The bioconductor package “DESeq” v.1.14.0 was used to identify genes likely to be differentially expressed between SH and YK without biological replicates. Gene expression was normalized, and the significance threshold for differential expression was based on a 0.2 false discovery rate.
Genome_build: Joint Genome Institute (JGI) E. salsugineum genome (http://www.phytozome.net/search.php?show=blast&method=Org_Thalophila)
Supplementary_files_format_and_content: excel file include raw read counts for all samples

organism: Eutrema salsugineum

source_name: YK

growth_protocol: Seeds were stratified in the dark for 10 days at 4°C then sown in a 4:1 mix of Fafard 52 Mix (transcriptome and first metabolome experiments) or Fafard 2 Mix (second metabolome experiment) soilless media (Conrad Fafard, Inc., Agawam, MA, USA) and Turface calcined clay (Profile Products LLC., Buffalo Grove, IL, USA). Plants were grown in 50 mL conical tubes (USA Scientific, Inc., Ocala, FL, USA). A 0.5 cm hole was drilled at the bottom of each tube where seeds were sown. Tubes were then closed with a mesh cap and placed cap-side-down to allow for sub-irrigation. Tubes were placed in a mist room for 12 days, at which point seedlings had reached the 4-leaf stage. Plants were then grown in a growth chamber (E15; Conviron, Pembina, ND, USA) set at 60% relative humidity under a 12 h photoperiod (approximately 230 μmol quantum/m2/s. provided by both fluorescent and incandescent bulbs) with light and dark temperatures of 22 and 20°C, respectively.

extract_protocol:
Four biological replicates consisting of five plants each were collected. whole rosettes of 4-week-old plants were frozen in liquid nitrogen and stored at −80°C. Tissue was finely ground in liquid nitrogen using a mortar and pestle. Approximately 800 mg ground tissue was combined with 1 ml of TRIzol reagent (Gibco/BRL Life Technologies, Invitrogen, Carlsbad, CA, USA) and RNA was extracted according to the manufacturer’s instructions. Quality of RNA was estimated by the ratio of absorbance at 260 to 280 nm and 260 to 230 nm by spectrophotometer (DU 730; Beckman Coulter, Inc., Indianapolis, IN, USA) with both ratios between 1.8 and 2.2.
RNA was reverse-transcribed into cDNA using the Poly(A) Purist protocol (Ambion, Austin, TX, USA). The cDNA samples were fragmented into 300–500 bp molecules and sequencing libraries were constructed for the 454 GS-FLX instrument (454 Life Sciences, Roche Company, Branford, CT, USA) at the Purdue University Genomics Facility (West Lafayette, IN, USA). One sequencing run was performed. Non-strand-specific protocol was used for 454 library preparation.

treatment_protocol: Tissue was collected in the middle of the dark period (1:00 am).

tag: accession from

value: Yukon (YK)

tag: age

value: 4-week old

tag: growth condition

value: 12-hour photoperiod, well-watered

tag: biomass

value: More rosette biomass (dry weight)

tag: tissue thickness

value: thinner leaves

tag: drought tolerance

value: more drought tolerant

value: whole rosette


title: 53BP1-/- NCDel #1_5'Sm_rep1

tag: genotype


title: ATM-/- NCDel #2_5'Sm_rep2


title: NH_FLI_skin_109

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava v1.8.0 software used for extraction of FASTQ files
Reads were mapped using Tophat (v2.0.6) to the genome taken the annotation into account:  tophat2 -p 24 -o OUTPUTDIR -g 1 --no-coverage-search --transcriptome-index=transcriptome_data/Danio_rerio.Zv9.73 Danio_rerio.Zv9.73
Counting of reads per gene was done using htseq-count: htseq-count --quiet --stranded=no --idattr=gene_id --mode=union SAMFILE Danio_rerio.Zv9.73.gtf > OUTPUTFILE
Counts were normalized to RPKM values as described in Mortazavi et al. (2008). Gene were excluded from dataset if at least one sample has a RPKM of 0.
Genome_build: Ensemble Zv9.73
Supplementary_files_format_and_content: Excel file includes raw counts and RPKM values for each sample

organism: Danio rerio

source_name: total RNA extracted from skin

extract_protocol:
Total RNA from was extracted as described (Baumgart et al., 2012; PMID:22487494)
Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.

tag: strain

value: AB JxTu Tg(wt1a:GFP)

value: 42 months

tag: age category

value: skin


title: NH_FLI_skin_108


title: NH_FLI_skin_106


title: WT-NCDel #2_5'Sm_rep3

value: cytokine stimulation

value: non-coding IgH Sm-Sa deletion


title: NH_FLI_skin_147

value: AB JxTu Tg(pu.1:GFP)

value: 36 months


title: WT-NCDel #1_5'Sm_rep3

value: WT NCDel cells clone #1


title: NH_FLI_skin_146


title: NH_FLI_skin_145


title: NH_FLI_skin_134

value: AB JxTu

value: 24 months


title: NH_FLI_skin_137


title: NH_FLI_skin_125

value: AB JxTu Tg(flk:mCherry)

value: 12 months


title: WT-NCDel #1_5'Sm_rep2


title: WT-NCDel #2_5'Sm_rep2

value: WT NCDel cells clone #2


title: WT-NCDel #1_5'Sm_rep1


title: NH_FLI_skin_121


title: SH

source_name: SH

value: Shandong (SH)

value: 4-week old

value: 12-hour photoperiod, well-watered

value: Less rosette biomass (dry weight)

value: thicker leaves

value: less drought tolerant


title: NH_FLI_skin_111

value: AB JxTu Tg(wt1a:GFP)

value: 42 months

value: skin


title: NH_FLI_skin_124

description:
NH_FLI_skin_124
Dre_counts_RPKMs_add_samples.xls

value: liver


title: NH_FLI_skin_119


title: NH_FLI_skin_98

value: 6 months

value: young


title: NH_FLI_skin_94

value: AB JxTu


title: NH_FLI_skin_107


title: NH_FLI_liver_109

source_name: total RNA extracted from liver


title: NH_FLI_skin_150

value: AB JxTu Tg(pu.1:GFP)

value: 36 months


title: NH_FLI_liver_107


title: intestinal_ILC2_rep1

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
The mouse reference genome (mm10) and RefSeq gene annotation were downloaded from UCSC Genome Browser. The bowtie2 index was created based on the RefSeq gene annotation, then read alignment and expression quantification were performed using RSEM 1.3.0 with parameters: --bowtie2 --calc-ci --ci-memory 1024. The calculated TPM (transcript per million) values were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by RSEM with TPM and FPKM values for each gene.

source_name: ILC2 cell from small intestine lamina propria of naïve mice

extract_protocol:
Total RNA was isolated by using QIAGEN miRNeasy Micro Kit (#217084).
RNA-Seq libraries were prepared by using NuGEN Ovation RNA-Seq System V2 (#7102) and KAPA LTP Library Preparation Kit (KK8232)

treatment_protocol: No treatment

value: small intestine lamina propria

tag: cell type


title: NH_FLI_skin_149


title: NH_FLI_skin_136

value: 24 months


title: NH_FLI_skin_120

value: AB JxTu Tg(flk:mCherry)

value: 12 months


title: NH_FLI_liver_150


title: NH_FLI_liver_93+94

description:
NH_FLI_liver_93+94
Dre_counts_RPKMs_add_samples.xls


title: NH_FLI_skin_133


title: NH_FLI_liver_146


title: NH_FLI_skin_122


title: activated_lung_nILC2_rep1

source_name: ILC2 cell from IL-33 treated mouse lungs

treatment_protocol: Mice were intranasally treated with IL-33 daily for 3 days

value: lung


title: NH_FLI_skin_96


title: NH_FLI_skin_85


title: NH_FLI_skin_86


title: NH_FLI_liver_134


title: NH_FLI_liver_133


title: NH_FLI_liver_112


title: MG_UKJ_02_984_liver

description:
MG_UKJ_02_984_liver
counts_RPKMs_add_samples.xls

data_processing:
Illumina's bcl2fastq v1.8.3/ v1.8.4 or CASAVA v1.7 software used for extraction of FASTQ files
Reads were mapped using Tophat (v2.0.6) to the genome taken the annotation into account:  tophat2 -p 24 -o OUTPUTDIR -g 1 --no-coverage-search --transcriptome-index=/transcriptome_data/transcriptome.GRCm38.69 GRCm38.69
Counting of reads per gene was done using either htseq-count v0.5.3p9 (htseq-count --quiet --stranded=no --idattr=gene_id --mode=union SAMFILE Mmu.gtf > OUTPUTFILE) or featureCounts v1.4.3-p1 (featureCounts -T 8 -a Mmu.gtf -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: Ensembl GRCm38.69
Supplementary_files_format_and_content: Excel file contains raw counts and RPKM values of each sample

extract_protocol:
Total RNA from was extracted as described (Baumgart et al., 2012; PMID:22487494)
Preparation of libraries was done using either Illumina’s TruSeq RNA sample prep kit or Illumina’s TruSeq RNA sample prep kit v2 following the manufacturer’s instruction.


title: NH_FLI_skin_135


title: MG_UKJ_24_60314_6HS_brain

description:
MG_UKJ_24_60314_6HS_brain
counts_RPKMs_add_samples.xls

source_name: total RNA extracted from brain (complete hemisphaere)

value: brain


title: intestinal_ILC2_rep2


title: NH_FLI_liver_106


title: NH_FLI_liver_122


title: NH_FLI_liver_110


title: NH_FLI_liver_152


title: NH_FLI_liver_120


title: NH_FLI_liver_98


title: NH_FLI_liver_151


title: ATM-/- NCDel #2_5'Sm_rep1

value: ATM-/- NCDel cells clone #2

value: cytokine stimulation

value: non-coding IgH Sm-Sa deletion


title: NH_FLI_liver_147


title: NH_FLI_liver_96


title: mLN_ILC2_rep1

source_name: ILC2 cell from IL-25 treated mouse menseteric lymph nodes

treatment_protocol: Mice were intraperitoneally treated with IL-25 daily for 3 days

value: mesenteric lymph nodes


title: NH_FLI_liver_86


title: NH_FLI_liver_136


title: lung_iILC2_rep1

source_name: ILC2 cell from IL-25 treated mouse lungs


title: NH_FLI_liver_135


title: lung_nILC2_rep1

source_name: ILC2 cell from the lung of naïve mice


title: NH_FLI_liver_85


title: NH_FLI_brain_111

source_name: total RNA extracted from brain

value: AB JxTu Tg(wt1a:GFP)

value: 42 months


title: NH_FLI_liver_126

value: liver


title: Sample 9_shBruce FM Replicate3

city: Wien

first: Fumiyo

last: Ikeda

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

data_processing:
Base calling was done following the HiSeq2500 instrument manufacturer's base calling software.
Reads were aligned against the Drosophila melanogaster reference genome (UCSC mm10 release) using STAR version 2.4.0d
After alignment reads were associated with known genes based on annotations derived from UCSC and number of reads aligned with each gene was counted using Htseq tool version 0.5.4p3.
Data were normalized using TMM normalisation method of the edgeR R/Bioconductor package (R version 3.2.0, Biocunductor version 3.1)
For statistical testing data were log transformed using voom approach in the limma package.
Genome_build: UCSC mm10 release
Supplementary_files_format_and_content: tab delimited text file including count values for each sample

source_name: MEFs_shBruce_full medium

growth_protocol: Cells were grown in full medium or starved for 2 hours in serum-free amino acid-free medium

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 hours starvation

value: mouse embryonic fibroblasts (MEFs)

value: shBruce

value: full medium


title: NH_FLI_brain_149

value: AB JxTu Tg(pu.1:GFP)

value: 36 months


title: NH_FLI_liver_138

value: AB JxTu

value: 24 months


title: NH_FLI_brain_148


title: MG_UKJ_24_1058_blood

description:
MG_UKJ_24_1058_blood
counts_RPKMs_add_samples.xls

source_name: total RNA extracted from whole blood

value: blood


title: NH_FLI_liver_125

value: AB JxTu Tg(flk:mCherry)

value: 12 months


title: Sample 7_shBruce FM Replicate1


title: Sample 12_shBruce Starv Replicate3

source_name: MEFs_shBruce_starvation medium

value: starvation medium


title: Human AEP cells Pt 2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the hg19 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: hg19
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: Lung epithelium

extract_protocol: Distal lung lobule dissociation with dispase, collagenase, and DNAse, followed by single cell suspension and magnetic bead sorting. Isolated cells were frozen in trizol, and RNA was prepared using standard methods and cleaned up over a column followed by library preparation

value: lung

value: epithelium

tag: patient id

tag: gender

value: F

tag: ethnicity

value: AA


title: NH_FLI_brain_116

value: AB JxTu Tg(wt1a:GFP)

value: 42 months

value: brain


title: NH_FLI_brain_117


title: Human AEP cells Pt 4

value: W


title: Human AEP cells Pt 1


title: NH_FLI_brain_145


title: NH_FLI_brain_113


title: NH_FLI_brain_134


title: Sample 10_shBruce Starv Replicate1

value: mouse embryonic fibroblasts (MEFs)

value: shBruce


title: Sample 8_shBruce FM Replicate2

value: full medium


title: NH_FLI_brain_147

value: AB JxTu Tg(pu.1:GFP)

value: 36 months


title: NH_FLI_brain_112


title: NH_FLI_brain_133

value: AB JxTu

value: 24 months


title: Sample 11_shBruce Starv Replicate2


title: Human AEP-depleted AT2 Pt 1


title: Sample 3_shRenilla FM Replicate3

source_name: MEFs_shRenilla_full medium

value: shRenilla


title: NH_FLI_brain_146


title: NH_FLI_brain_122

value: AB JxTu Tg(flk:mCherry)

value: 12 months


title: Sample 6_shRenilla Starv Replicate3

source_name: MEFs_shRenilla_starvation medium

value: starvation medium


title: NH_FLI_brain_121


title: Sample 5_shRenilla Starv Replicate2


title: NH_FLI_brain_124


title: NH_FLI_brain_132


title: NH_FLI_brain_136


title: Human AEP-depleted AT2 Pt 2

value: lung

value: epithelium

value: F


title: NH_FLI_brain_120


title: Human AEP-depleted AT2 Pt 4


title: Sample 2_shRenilla FM Replicate2


title: NH_FLI_brain_119


title: NH_FLI_brain_99+100

value: 6 months

value: young


title: NH_FLI_brain_97+98

value: brain


title: Human AT2 cells Pt 4

value: W


title: Human AT2 cells Pt 2

value: AA


title: In Vitro Aortic Endothelial Cells (eGFP+)

city: Farmington

first: Patrick

last: Murphy

state: CT

address: 263 Farmington Ave

department: Center for Vascular Biology

institute: University of Connecticut Health Center

description:
100bp PE
From collagenase intimal flush, FACs sorted

data_processing:
reads were mapped with STAR 2.5.1b and options --runThreadN 8 --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM [https://www.ncbi.nlm.nih.gov/pubmed/23104886]
RSEM v.1.2.15 (options --paired-end --calc-ci  -bam -p 8  ) was used to calculate transcript levels [https://www.ncbi.nlm.nih.gov/pubmed/21816040]
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated text file with RSEM output (ENSID, length, effective length, counts, TPM, FPKMs) for each sample, header contains original sequencing run descriptions and data processing details

source_name: Sorted aortic endothelial cells (Cdh5(PAC)CreERT2; mTmG+)

extract_protocol:
RNA from cultured aortic endothelial cells was isolated after one week in culture by sorting 1-2K endothelial cells (by CD31+ and Icam2+) from BD Aria directly into cold Trizol solution.
RNA isolated byQiagen RNAeasy microcolumns.  Pools of RNA were created and then DNAse-treated in solution, before concentrating on RNAeasy columns with elution in minimal volume.  RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit, and samples were sequenced on Illumina HiSeq 2000 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.
RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit
Samples were sequenced on Illumina HiSeq 2000, 2500 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.

tag: sample type

value: Static

tag: time

value: 5 days in culture

tag: genetic background

value: C57 background

tag: treatment

value: No treatment


title: NH_FLI_brain_101+102

value: AB JxTu

tag: tissue


title: NH_FLI_brain_95+96

tag: age


title: Sample 4_shRenilla Starv Replicate1

value: mouse embryonic fibroblasts (MEFs)

value: shRenilla

tag: growth condition


title: NH_FLI_brain_103+104


title: Low Flow Carotid Intima + PBS Liposomes

description:
100bp PE
Pool of 3-5 arterial flushes

source_name: Carotid intimal flush

extract_protocol:
Briefly, vessels were isolated and imaged from euthanized mice, flushed with PBS solution and then 150uL Trizol.
RNA isolated byQiagen RNAeasy microcolumns.  Pools of RNA were created and then DNAse-treated in solution, before concentrating on RNAeasy columns with elution in minimal volume.  RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit, and samples were sequenced on Illumina HiSeq 2000 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.
RNA quality was assessed by Agilent Bioanalyzer or Advanced Analytical, library preparation was performed using the Clontech SMARTer Universal Low Input RNA Kit
Samples were sequenced on Illumina HiSeq 2000, 2500 or NextSeq 500 using 80bp paired-end (PE) reads (triplicates of low-flow, sham and high-flow), 100bp PE reads (re-sequencing of triplicates of low-flow, sham and high-flow, and cultured aortic endothelial cells) or 150bp PE reads (hematopoeitic cell depletions with controls and endothelial Rbfox2 deletion with controls in vivo and in vitro). Base calls were performed using the Offline Base Caller (Illumina) v. 1.9.4 and quality control/assessment was performed using custom scripts.

value: Low flow

value: C57BL/6J (Jax)

value: PBS liposomes


title: Low Flow Carotid Intima + Clodronate Liposomes

description:
100bp PE
Pool of 3-5 arterial flushes

value: Clodronate liposomes


title: CSF1R-81_L16

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

institute: F. Hoffmann-La Roche Ltd.

data_processing:
Raw read data was aligned against mouse transcriptome (MouseEnsembl release 61) using Bowtie2 (Langmead and Salzberg, 2012). Splice junctions were defined as available in Ensembl v75. Read mappings were then mapped to genes and transcripts based on the transcript models annotated in Ensembl v75 using in-house tools and, again using in-house software, RPKM values were computed as described previously (Mortazavi et al., 2008).
Genome_build: MouseEnsembl release 61
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Tumors from C57BL/6N mice subcutaneously inoculated with MC38 cells

extract_protocol:
Tumors were excised and single cell suspensions obtained by mechanical processing and enzymatical digestion (DNAse 0.01%, Dispase 1mg/ml, Collagenase IV 1mg/ml) 16 hrs after treatment. TAM (CD11b+F4/80hiLy6ClowLy6Gneg), monocytic MDSC (CD11b+F4/80-/lowLy6ChiLy6Gneg) were sorted using flow cytometry.  RNA was extracted from multiple FACS-sorted cells or from whole tumor.
1 ng of amplified cDNA was subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 50 cycles using version 4 cluster generation kits and version 4 sequencing reagents (Illumina).

treatment_protocol: 4 mice/group were treated with 30 mg/kg IgG1 isotype control antibody clone MOPC-21 (BioXCell), 4 mg/kg anti-CD40 rat IgG2a antibody clone FGK45 (BioXCell), 30mg/kg anti-CSF-1R antibody clone 2G2, 4 mg/kg rat IgG2a control clone 2A3 (BioXCell). For depletion experiments 4mg/kg mouse anti-CD4 antibody clone GK1.5 (Biolegend), 4mg/kg anti-NK1.1 antibody clone PK136 (BioXCell) and 4mg/kg anti-CD8α antibody clone 53-6.7 (BioXCell) were administered when tumor size reached 190mm3 in average. Antibodies were given every second day for four times. In between doses two and three of the depleting antibodies, animals were further treated with vehicle control (0,9% sodium saline), MOPC21, FGK45, 2G2 or combination of FGK45 and 2G2. The anti-CSF-1R antibody or respective IgG1 control antibody were administered weekly until tumors regressed completely or animals reached termination criteria, while the anti-CD40 antibody was only administered once at day 11 simultaneously with the anti-CSF-1R antibody. All antibodies were given intraperitoneally. All procedures were performed in accordance with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and European Union directives and guidelines.

value: whole tumor


title: CSF1R-80_L24


title: CSF1R-82_L1


title: CSF1R-83_L4.N702


title: Sample 1_shRenilla FM Replicate1

value: full medium


title: CSF1R-79_L1.N703

value: IgG controls


title: CSF1R-57_L23

value: Ly6Cpos MDSC

value: a-CSF-1R + a-CD40


title: CSF1R-58_L3.N711


title: CSF1R-77_L2.N710


title: CSF1R-59_L4.N708


title: CSF1R-78_L3.N704


title: CSF1R-76_L2.N708


title: CSF1R-56_L12


title: Human AT2 cells Pt 1

value: lung

value: epithelium

value: F

value: AA


title: CSF1R-55_L5.N711


title: CSF1R-54_L6.N712


title: CSF1R-51_L5.N710


title: CSF1R-53_L1.N702


title: CSF1R-44_L20


title: CSF1R-46_L36


title: CSF1R-47_L28


title: CSF1R-49_L5


title: CSF1R-48_L5.N708


title: CSF1R-43_L1.N705

value: Ly6ClowLy6Gneg TAM


title: CSF1R-42_L5.N706


title: CSF1R-41_L25


title: CSF1R-39_L8.N704


title: CSF1R-40_L11


title: CSF1R-50_L3.N706


title: NH_FLI_brain_135

value: AB JxTu

value: 24 months

value: brain


title: CSF1R-37_L13


title: CSF1R-52_L3.N712


title: CSF1R-38_L1.N706


title: CSF1R-36_L10


title: CSF1R-35_L7


title: CSF1R-33_L3