title: constituitive_ko_control_P0_No_70

value: neonatal


title: E10.14_p1

status: Public on Mar 14 2018

type: SRA

city: Munich

first: Ilaria

last: Lavagi

address: Feodor Lynen Strasse 25

country: Germany

institute: Ludwid Maximilian University

library_source: transcriptomic

data_processing:
SCRB-Seq libraries were demultiplexed from Nextera barcodes and cell barcodes
Alignments were calculated using STAR 2.5.2b using all default Parameters.
UMI tables were generated using the published Drop-seq pipeline (Macosko et al., 2015. Cell 161, 1202-1214)
Genome_build: Bos tau7 (NCBI) and ERCC spike-in reference
Supplementary_files_format_and_content: The 'umi_bosTau_ERCC.txt' contains the endogenous and ERCC UMI counts. These count has been performed after running Drop-seqAll reads were mapped to Bos tau7 (NCBI) and ERCC spike-in reference. Alignments were calculated using STAR 2.5.2b using all default parameters. UMI tables were generated using the published Drop-seq pipeline.
Supplementary_files_format_and_content: The normalized_UMI.txt:  Data were then normalized in the following way, to account for differences in efficiency of transcript recovery between wells: UMI counts were divided by the total number of UMI counts per cell and then multiplied by the median of total UMI counts across all cells.

molecule: total RNA

organism: Bos taurus

source_name: Day3_16-cell stage

growth_protocol: Embryos were produced in vitro according to a standard procedure including in vitro maturation (IVM) and fertilization (IVF) (Reichenbach et al., 2010, Transgenic Research 19, 549-556). Briefly, follicles from slaughterhouse ovaries were aspirated and obtained cumulus-oocyte- complexes (COCs) matured for 23 h in MPM supplemented with LH and FSH and 5% estrous cow serum (ECS). Matured COCs were co-incubated with frozen-thawed sperm, prepared by the swim-up method. For IVM and IVF, COCs were incubated at 39°C in a maximum humidified atmosphere of 5% CO 2 in air. After 20 h of co-incubation, presumptive zygotes were vortexed to remove remaining cumulus cells and transferred to synthetic Oviductal fluid (SOF) supplemented with 5% ECS, 400 μl BME, 100 μl MEM under mineral oil and cultured at 5% CO 2 , 5% O 2 , 90% N 2 and 39°C in humidified air.

extract_protocol:
The zona pellucida was removed by treatment with 5 mg/ml pronase for 1 min. nzyme reaction was stopped by washing embryos in THP supplemented with 10% fetal calf serum (FCS) and dissolved ZP was completely removed by gentle pipetting. Embryos were incubated in drops of PBS without Mg 2+ and Cl 2+ supplemented with 4 mg/ml polyvinylpyrrolidone under oil for 5-10 min and blastomeres were subsequently disaggregated by gentle pipetting (Simmet et al., 2015). Single cells were transferred individually to 0.5 μl drops of Buffer A under mineral oil (Prelude Direct Lysis Module, NuGEN), collected in a 384-well plate and stored at -80 °C
Single Cell RNA Barcoding and Sequencing (SCRB-Seq) libraries were prepared (Soumillon et al., 2014). Briefly, the plate was thawed and 0.1 μl (1:10 6) ERCC RNA Spike-In Mix (Life Technologies) was added to each well; the addition of exogenous molecules in equal amount enabled us to later perform quality control. Cell barcode are reported in section “samples”.
Subsequently, the construct, which contains cell barcodes (6 nt), the Unique Molecular Identifiers (UMIs; 10 nt) and a polyT with the anchor, was incorporated to the sequence through the template switching reaction while RNA was reverse transcribed; Maxima H Minus Reverse Transcriptase (Thermo Scientific) was used. After this step, the samples were pooled. Not-incorporated barcode primers were removed through digestion with Exonuclease I (New England Biolabs). Full-length cDNA amplification was performed with the KAPA HiFi HotStart polymerase (KAPA Biosystems). Nextera XT libraries were constructed from 1 ng of pre-amplified cDNA with a custom P5 primer (IDT). The libraries were sequenced paired-end with 16 cycles to decode cell barcodes and UMI from read 1 and 45 cycles into the cDNA fragment.

tag: developemental stage

value: 16-cell stage

tag: embryo source

tag: cell barcode

value: TCCCGC


title: 007A

city: Madison

first: Rozalyn

last: Anderson

state: WI

address: 2500 Overlook Terrace

department: Department of Medicine

country: USA

institute: University of Wisconsin-Madison

description: expression.xlsx

data_processing:
Trimming-Sequencing reads were trimmed using the Skewer trimming program to remove sequencing adapters and bases with quality scores lower than Q20 (Jiang et al., 2014) Version 0.1.123: -q 20 -k 15 -l 25
Aligning-Trimmed reads were subsequently aligned to the Macaca mulatta reference genome (Zimin et al., 2014) using the STAR aligner(Dobin et al., 2013). Version 2.5.0a\n
Read count quantification-Quantification of expected read counts for each gene and isoform was calculated by RSEM (Li and Dewey, 2011). Version v1.2.31
Filtering-Transcripts were removed from the analysis if they had fewer than 5 reads in half of the samples.
Differential gene expression analysis-The remaining read counts were used for differential gene expression analysis using DESeq2 (Love et al., 2014), with the results used for pathway analysis via GSEA (Mootha et al., 2003; Subramanian et al., 2005).
Genome_build: Mmul_8.0.1 (rheMac8)
Supplementary_files_format_and_content: RNA_RawExpression_ReadCounts.xlsx; Single matrix file containing read counts for all transcripts and samples

organism: Macaca mulatta

source_name: Liver biopsy

extract_protocol:
Liver samples were homogenized in 1 mL TRIzol per 50 mg wet weight. Manual grinding with a pestle was used to pulverize the tissue, following which the sample was incubated for 5 min at room temperature. RNA extraction proceeded using a Direct-zol RNA kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. RNA was then submitted to the University of Wisconsin-Madison Biotechnology Center Sequencing Facility for high throughput RNA-Seq.
Each RNA library is generated following Illumina “TruSeq RNA Sample Preparation Guide and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, California, USA). Quality and quantity of finished libraries are assessed using an Agilent DNA1000 series chip assay (Agilent Technologies, Santa Clara, CA) and Invitrogen Qubit HS Kit (Invitrogen, Carlsbad, California, USA), respectively. Each library is standardized to 2μM. Cluster generation is performed using a TruSeq Paired End Cluster Kit (v3) and the Illumina cBot, with libraries multiplexed for 2x100bp sequencing using the TruSeq 100bp SBS kit (v3) on an Illumina HiSeq2000. Images are analyzed using CASAVA 1.8.2.

tag: sample year

value: 0 year

tag: diet

value: CR


title: 006B

description: expression.xlsx

value: 2 year

value: Control


title: constituitive_ko_6_wk_No_380

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

data_processing:
Basecalling was performed using RTA 1.18.61
bcl files were converted to fastq using CASAVA 1.8.2
fastq files were aligned to the mouse genome (Gencode M10) using the Star aligner (version STAR_2.5.2b)
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1)
Prior to differential gene expression analysis low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis was performed using the limma/voom pipeline (limma version 3.28.21).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files with raw transcript counts ("counts.txt"), counts per million ("cpm.txt") and normalized counts ("Voom_Matrix.txt").

organism: Mus musculus

source_name: FACS sorted Microglia

growth_protocol: All animals were maintained in SPF condition

extract_protocol:
Embryos and P0 pups were killed by decapitation. Other animals were killed by transcardial perfusion in anasthesia. Microglia cells were isolated from the brain by FACS sorting. Total RNA was extracted from sorted microglia by Pico Pure RNA extraction kit (Life Technologies) according to manufacturer’s protocol.
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).

treatment_protocol: For constituitive knockout mice and controls no treatment prior to cell isolation was performed. For Tamoxifen induction in inducible knockout animals and controls Pregnant females were injected with 3 mg Tamoxifen (20 mg/ml Tamoxifen + 10 mg/ml Progesterone; Sigma‐Aldrich) intra peritonially at E13 to induce Hdac1 and 2 knock out at embryonic stage.

tag: genotype

value: HDAC1/2-loxP/loxP CX3CR1-Cre

tag: treatment

value: no treatment

tag: age

value: 45 days


title: constituitive_ko_6_wk_No_379


title: 009B

description: expression.xlsx


title: constituitive_ko_control_6_wk_No_377


title: constituitive_ko_P0_No_68


title: constituitive_ko_control_6_wk_No_376


title: 006A

description: expression.xlsx


title: E16.6_p1

value: ACAATA


title: 005A

description: expression.xlsx


title: E10.13_p1

value: GTGCGC


title: 005B

description: expression.xlsx


title: constituitive_ko_control_2_wk_No_83

value: 14 days


title: constituitive_ko_2_wk_No_89


title: 004B

description: expression.xlsx


title: E10.11_p1

value: GGGTCG


title: 004A

description: expression.xlsx


title: E10.12_p1

value: GGTGGC


title: constituitive_ko_6_wk_No_398


title: 008A

description: expression.xlsx


title: 001B

description: expression.xlsx


title: E10.9_p1

value: GGGCAG


title: constituitive_ko_control_6_wk_No_396


title: constituitive_ko_control_2_wk_No_81


title: E10.10_p1

value: GGGGAC


title: E10.7_p1

value: GGCCAC


title: E10.6_p1

value: 16-cell stage

value: GGAGCC


title: E10.4_p1

value: GCGGTC


title: E10.1_p1

value: GCCGTG


title: E10.2_p1

value: GCGAGC


title: E3.16_p1

value: GCCCTC


title: E10.8_p1

value: GGCGTC


title: E3.15_p1

value: GCCAGG


title: E3.14_p1

value: GCACGG


title: constituitive_ko_control_2_wk_No_77

value: no treatment


title: constituitive_ko_control_2_wk_No_78


title: 001A

description: expression.xlsx

value: 0 year

value: Control


title: E10.5_p1

value: GCTCGC


title: E10.3_p1

value: GCGCTG


title: E3.12_p1

value: GACCGC


title: E3.13_p1

value: GAGCGG


title: E3.9_p1

value: CGGTGG


title: E3.8_p1

value: 16-cell stage

value: CGGGCT


title: E3.7_p1

value: CGGCCA


title: E3.6_p1

value: CGCTGC


title: 35S:TCP5 8H-2

city: Wageningen

first: Sam

middle: Wijnand

last: van Es

address: Droevendaalsesteeg

department: Plant Developmental Systems

country: Netherlands

institute: Wageningen University and Research

description:
K2
PolyA mRNA

data_processing:
FastQC
Bowtie2, standard parameters
Cufflinks, multiread correct
Genome_build: TAIR10
Supplementary_files_format_and_content: *_gene_expression.tabular.txt: Tab-delimited text files with FPKM values for each sample.

organism: Arabidopsis thaliana

source_name: inflorescence, TCP5 induction, 8hr

extract_protocol:
InviTrap® Spin Plant RNA Mini Kit.
Illumina TruSeq Library Preparation Kit.

tag: ecotype/background

tag: tissue

value: inflorescence

tag: genotype/variation

value: 35S:TCP5 induction

tag: time after induction


title: 35S:TCP5 8H-3

description:
K3
PolyA mRNA


title: constituitive_ko_2_wk_No_80

value: HDAC1/2-loxP/loxP CX3CR1-Cre

value: 14 days


title: 35S:TCP5 2H-1

description:
J1
PolyA mRNA

source_name: inflorescence, TCP5 induction, 2hr


title: E3.4_p1

value: CGCCCT


title: 35S:TCP5 2H-2

description:
J2
PolyA mRNA


title: 35S:TCP5 2H-3

description:
J3
PolyA mRNA


title: 35S:TCP5 8H-1

description:
K1
PolyA mRNA


title: E3.3_p1

value: CGAGGC


title: E3.5_p1

value: CGCGCA


title: 35S:TCP5 0H-2

description:
I2
PolyA mRNA

source_name: inflorescence, TCP5 induction, 0hr


title: 35S:TCP5 0H-3

description:
I3
PolyA mRNA


title: E3.1_p1

value: CCGTCG


title: E3.2_p1

value: CCTGGC


title: 35S:TCP5 0H-1

description:
I1
PolyA mRNA


title: E2.13_p1

value: CCCCGT


title: E2.14_p1

value: CCCTGG


title: Col0 8H-2

description:
H2
PolyA mRNA

source_name: inflorescence, control for induction, 8hr

value: control for induction


title: E2.15_p1

value: CCGGAC


title: E3.10_p1

value: 16-cell stage

value: CGTGGG


title: E3.11_p1

value: CTGCGG


title: E2.11_p1

value: CAGGGG


title: E2.12_p1

value: CCCACG


title: Col0 2H-2

description:
G2
PolyA mRNA

source_name: inflorescence, control for induction, 2hr

value: inflorescence


title: Col0 2H-1

description:
G1
PolyA mRNA


title: E2.9_p1

value: AGGGGC


title: Col0 0H-3

description:
F3
PolyA mRNA

source_name: inflorescence, control for induction, 0hr


title: E2.8_p1

value: AGCGGG


title: E2.10_p1

value: CACGGC


title: E2.7_p1

value: ACGGGG


title: Col0 0H-2

description:
F2
PolyA mRNA


title: pATML1:TCP5 o.e.-3

description:
E3
PolyA mRNA

source_name: stage 12 petals, TCP5 overexpression

value: stage 12 petals

value: pATML1:TCP5 overexpression


title: Col0 0H-1

description:
F1
PolyA mRNA


title: pATML1:TCP5 o.e.-2

description:
E2
PolyA mRNA


title: E2.5_p1

value: GTACCG


title: Col0 control for o.e.-3

description:
D3
PolyA mRNA

source_name: stage 12 petals, control for overexpression

value: control for overexpression


title: Col0 8H-3

description:
H3
PolyA mRNA


title: E2.3_p1

value: TCTGCA


title: E2.4_p1

value: CCAACC


title: Col0 control for o.e.-2

description:
D2
PolyA mRNA


title: E2.1_p1

value: GGGATT


title: E2.2_p1

value: 16-cell stage

value: GTTCGA


title: pATML1:TCP5 o.e.-1

description:
E1
PolyA mRNA


title: E15.6_p2

source_name: Day2_8-cell stage

value: 8-cell stage

value: GCTAGA


title: E15.5_p2

value: CTAGTG


title: Col0 control for o.e.-1

description:
D1
PolyA mRNA


title: Col0 8H-1

description:
H1
PolyA mRNA

value: inflorescence

value: control for induction


title: Col0 2H-3

description:
G3
PolyA mRNA


title: tcp5tcp13tcp17 k.o.-2

description:
C2
PolyA mRNA

source_name: stage 12 petals, Tcp5Tcp13Tcp17 KO

value: Tcp5Tcp13Tcp17 KO


title: tcp5 k.o.-3

description:
B3
PolyA mRNA

source_name: stage 12 petals, Tcp5 KO

value: Tcp5 KO


title: E15.2_p2

value: AGACCT


title: E15.4_p2

value: CCACAT


title: E15.3_p2

value: CACCAA


title: E14.8_p2

value: TTTCTT


title: tcp5 k.o.-2

description:
B2
PolyA mRNA

value: stage 12 petals


title: Col0 control for k.o.-3

description:
A3
PolyA mRNA

source_name: stage 12 petals, control for KO

value: control for KO


title: Col0 control for k.o.-2

description:
A2
PolyA mRNA


title: E2.6_p1

value: ACCGGC


title: E14.7_p2

value: TTTACA


title: E14.6_p2

value: TTGAAA


title: E15.1_p2

value: TTTTGA


title: Col0 control for k.o.-1

description:
A1
PolyA mRNA


title: tcp5 k.o.-1

description:
B1
PolyA mRNA


title: E14.3_p2

value: 8-cell stage

value: TTAATC


title: E14.5_p2

value: TTATTG


title: tcp5tcp13tcp17 k.o.-1

description:
C1
PolyA mRNA


title: E14.4_p2

value: TTAGTT


title: E14.1_p2

value: TGATTT


title: E14.2_p2

value: TGTTTA


title: E11.8_p3

value: TCTTAA


title: E11.6_p3

value: TATTGT


title: E11.7_p3

value: TCATAT


title: E11.2_p3

value: TACTAT


title: E11.1_p3

value: TAATGA


title: E11.4_p3

value: TATAGA


title: E11.3_p3

value: TAGTAA


title: E16.9_p3

value: TAAAGT


title: k4m2_aILC2_4

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

library_source: genomic

data_processing:
Reads were aligned using bowtie2 (ChIPmentation) or HISAT (RNA-seq) with default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization
ChIPmentation: HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
RNA-seq: Sample scaling and statistical analysis were performed using the R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: HOMER peak calling (ChIPmentation) or RPKM expression values (RNA-Seq)

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: Only for aILC2: 7 days of culture (no feeders) in Yssel's medium supplemented with IL-2, IL-7, IL-25 and IL-33. See Lim et al. Journal of Experimental Medicine (2016)

extract_protocol:
Murine ILC2s were obtained from Gata3-YFP/YFP mice with airway inflammation, human ILC2s from peripheral blood. Cells were FACS-sorted using specific antibodies (and YFP for murine cells) as described in detail in the manuscript.
ChIPmentation: Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015); RNA-Seq: Smart-seq2library construction (as described in Picelli et al. Nature Methods (2013)

tag: cell type

value: FACS-purified lymphocytes; short-term culture

tag: antibody

value: anti-H3K4Me2, Abcam ab32356


title: E16.8_p3

value: GTTTAT


title: k4m2_aILC2_2


title: E16.7_p3

value: 8-cell stage

value: GTAATA


title: k4m2_aILC2_3


title: k4m2_aILC2_1


title: 3Amk-12-2

city: Emeryville

first: Taek Soon

last: Lee

state: CA

address: 5885 Hollis Street

institute: Joint BioEnergy Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed and quality filtered using Bbduk.
Trimmed and filtered reads were mapped to Escherichia coli DH1 reference genome using bwa-mem.
Transcript counts were quantified using featureCounts.
Differential gene expression analysis was done using DESeq2.
Genome_build: NC_017638.1
Supplementary_files_format_and_content: a tab-delimited text file that includes FPKM values for all samples

organism: Escherichia coli DH1

source_name: E. coli cells

extract_protocol:
RNA sample were taken at 0, 1, and 12 hours after induction. Volumes corresponding to 1E9 CFU/mL were immediately quenched in 2 volumes of RNAlater (Ambion) and left to stabilize for 5 minutes at room temperature. Samples were then pelleted at 5000 g for 15 minutes, decanted and stored at -80°C. Total RNA was isolated using the Qiagen RNeasy minikit (Qiagen) according to Protocol 2. Manufacturer’s instructions were followed exactly. RNA was eluted in one step in 45 µL of RNase free water. Total RNA was then treated with TURBO DNase(Ambion) according to manufacturer’s instructions. DNase was then removed with the DNase inactivation reagent and removed from the sample at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Vincent J. Coates Genomics Sequencing Laboratory at the California Institute for Quantitative Biosciences where rRNA was depleted using RiboZero.

tag: strain

value: DH1 harboring pJBEI-6829 and pJBEI-6833

tag: hour

value: 12 hour post induction


title: E16.4_p3

value: CTATAT


title: E16.5_p3

value: CTTTAA


title: U937-9-CL68

city: Bethesda

first: Zhijie

last: Wu

state: MD

address: 10 Center Drive

department: NHLBI

institute: NIH

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).
RPKM-1 through RPKM_9 means RPKM value for U937-1 through U937-9.
Three comparisons were made for gene expression.
edgeR-WTvsMT.csv means comparison of WT group (U937-1, U937-2 and U937-3) with Mutation group (U937-4 through U937-9).
edgeR-WTvsHet.csv means comparison of WT group (U937-1, U937-2 and U937-3) with heterozygous+- group (U937-4, U937-5 and U937-6).
edgeR_WTvsHomozygousmutant.csv means comparison of WT group (U937-1, U937-2 and U937-3) with homozygous-- group (U937-7, U937-8 and U937-9).

source_name: Pleura/pleural effusion of patients with lymphoma

growth_protocol: All cell lines were cultured in RPMI 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 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

tag: cell line

value: Myeloid

value: Homozygous -- (ASXL1 mutated)


title: U937-8-CL13


title: U937-7-CL11


title: 3Amk-12-1


title: U937-6-CL96

value: Heterozygous+- (ASXL1 mutated)


title: U937-5-CL78


title: 3Amk-1-1

value: 1 hour post induction


title: E16.2_p3

tag: developemental stage

value: CAAATA


title: E11.5_p3

tag: embryo source

value: TATGAA


title: 3Amk-1-2


title: 3Amk-0-2

value: 0 hour post induction


title: E16.1_p3

tag: cell barcode

value: ATTTCA


title: U937-3-CL3

value: WT (ASXL1 wild type_transfected)


title: E14.9_p3

value: ATTCTA


title: E16.3_p3

value: CATTAT


title: U937-4-CL15


title: E14.7_p3

value: 8-cell stage

value: ATGAAT


title: 3A-12-1

value: DH1 harboring pJBEI-6829 and pJBEI-6833


title: E14.8_p3

value: ATTACT


title: E16.6_p3

value: GATAAT


title: 3A-12-2

value: 12 hour post induction


title: 3Amk-0-1


title: U937-1-CL0

value: Myeloid

value: WT (ASXL1 wild type_blk)


title: E14.5_p3

value: ATATAG


title: 3A-1-1

value: 1 hour post induction


title: 3A-1-2


title: 3A-0-2


title: E14.2_p3

value: AGATTA


title: E14.3_p3

value: ATAAAC


title: E14.1_p3

value: ACTTAT


title: WT-0-2

value: DH1 harboring pBbA5c and pTrc99A

value: 0 hour post induction


title: WT-12-2


title: 3A-0-1


title: U937-2-CL2

value: WT (ASXL1 wild type_transfected)


title: WT-1-2


title: E1.5_p3

value: AATCTT


title: E1.6_p3

value: 8-cell stage

value: AATTCT


title: WT-0-1


title: WT-12-1


title: E1.7_p3

value: ACAATA


title: WT-1-1


title: E1.3_p3

value: AAGATT


title: E1.4_p3

value: AATACA


title: pleb

city: tianjin

first: liu

last: jingui

address: jinnan district yanguanroad tianjin univercity

country: China

institute: tianjin univvercity

description: pleb-VS-pYthA.GeneDiffExpFilter.xls

data_processing:
RTA2.7.3 and bcl2fastq2-v2.16 softwares used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to F44 whole genome using SOAPaligner/SOAP2 with the parameters:-m 0 -x 10000 -s 48 -l 35 -v 5 -r 2 -p 3.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al.,Nature Methods. 2008.
Genome_build: F44
Supplementary_files_format_and_content: xls files include RPKM values for each Sample.

organism: Lactococcus lactis

source_name: cell

growth_protocol: overexpressing ythA strain and the control were cultivated in the seed medium and taken at mid-log phase.

extract_protocol:
Total RNA of the strains was isolated by using Quick-RNA™ MicroPrepkit (ZYMO, Research, USA) and treated with DNAse I (NEB) as per manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type with empty plasmid


title: E1.2_p3

value: AAAGTT


title: E14.6_p3

value: ATCAAA


title: E1.1_p3

value: AAAACT


title: pYthA

description: pleb-VS-pYthA.GeneDiffExp.xls

value: overexpressing strain


title: E14.4_p3

value: ATACAA


title: Sox2 NSC 1k 4

status: Public on Mar 13 2018

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

data_processing:
Library strategy: DamID-seq
Read quality was checked using FastQC (version 0.11.5) and adapters were trimmed using cutadapt (version 1.13).
Reads were aligned to the UCSC mm10 assembly of the mouse genome [3] using bwa mem [4] (version 0.7.15).
Unmapped, secondary, and supplementary alignments were filtered using SAMtools [5] (version 1.4).
Reads mapped to ENCODE blacklist regions [6], alternate, unplaced, and mitochondrial contigs were filtered using BEDtools [7] (version 2.26.0).
Reads were counted into fragments using the featureCounts command from Subread [8] (version 1.5.0).
Fragments with 10 read counts or lower in equivalent average log count-per-million (aveLogCPM) values were removed.
Normalisation factors were calculated with the normOffsets function from the csaw package (version 1.8.1). The type argument was set to “scaling”.
Using these normalisation factors, log count-per-million (logCPM) values were calculated and smooth quantile normalised using the qsmooth package (version 0.0.1)
Differentially bound fragments were identified by testing for differential abundance between the Dam-POI (Protein-of-Interest) and Dam-only samples. The normOffsets/qsmooth normalised count matrix was used with limma-trend from the limma package (3.30.13). The trend and robust arguments were set to TRUE.
Fragments were then combined into differentially-bound regions using the mergeWindows and combineTests function from the csaw package. The tol and max.width arguments were set to 260 (median GATC fragment size for the mm10 assembly)  and 10,000, respectively.
Peaks were defined as regions with a false discovery rate (FDR) smaller than 0.1 and a log fold-change (logFC) greater than 0.5.
Read coverage across the genome was calculated with the genomecov command from BEDtools (version 2.26.0). Coverage for each sample was scaled using the normalisation factors calculated previously.
The bedGraph files were converted into bigWig files with the UCSC bedGraphToBigWig tool [11] (version 4). Subtracted bigWig files were generated using the diff command from WiggleTools [12] (version 1.2).
Genome_build: mm10
Supplementary_files_format_and_content: Peak calls are in narrowPeak file format
Supplementary_files_format_and_content: Read coverage is in bigWig file format

source_name: Neural Stem Cell

growth_protocol: Neural Stem Cells were routinely maintained in EGF (10 ng/mL), FGF2 (10 ng/mL), Laminin (1 μg/mL)-supplemented NSC complete medium and passaged every 3-4 days at 1:6/1:8 density. Cells were kept at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
Genomic DNA was extracted with the Quick-gDNA™ MicroPrep (ZymoResearch) kit according to the manufacturer's instruction.
Extracted gDNA was digested with DpnI (NEB, R0176S) and DamID adapter were then ligated using T4 DNA Ligase (M0202L). After ligation, the DNA was digested with DpnII (R0543S) and the DamID fragments of interest were amplified with the KAPA HiFi Polymerase (Roche, 07958935001). DNA was then purified using homemade SPRI magnetic beads and 50 ng of DNA were used as input for DamID-seq library preparation by using the Nextera® DNA Sample Preparation Kit (according to manufacturer's instructions). The libraries were quantitated using the The Qubit® 2.0 Fluorometer (Thermo Fisher). The DNA size distribution of the library was measured by an Agilent Bioanalyzer. Each sample was prepared in 3 or 4 biological replicates.

tag: fusion protein

value: ES-derived Neural Stem Cells (NSC)

tag: cell number

tag: replicate number


title: Sox2 NSC 1k 2


title: Sox2 NSC 1k 3


title: Sox2 NSC 1k 1


title: Dam NSC 1k 2

value: Dam


title: Sox2 NSC 10k 4


title: Sox2 NSC 10k 2


title: Dam NSC 10k 4


title: Sox2 NSC 10k 1


title: Sox2 NSC 10k 3


title: Dam NSC 1M 2


title: Dam NSC 1M 3


title: Dam NSC 1M 4


title: Dam NSC 10k 1


title: Sox2 NSC 1M 1


title: Dam NSC 10k 2


title: Dam NSC 1k 1


title: Dam NSC 10k 3


title: Sox2 NSC 1M 3


title: Dam NSC 1k 4


title: Dam NSC 1M 1


title: Dam NSC 1k 3


title: High-Low_1

city: Changsha

first: Kang

last: Xu

state: Hunan

address: 644 Yuanda 2 Road

institute: Institute of Subtropical Agriculture, Chinese Academy of Sciences

description: Sow feed by  High-Low methods

data_processing:
Illumina Casava1.7 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: susScr3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: High-Low, liver

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

treatment_protocol: the sow in 2×Trp group feed by diets containing 0.26% Trp two times at 07:00 and 14:30, the sow in High-Low group feed by diet containing 0.39% Trp at 07:00 and diet containing 0.13% Trp at 14:30

tag: maternal diet

value: High-Low

tag: breed

value: Landrace x Yorkshire

value: newborn liver


title: High-Low_2

description: Sow feed by  High-Low methods


title: 2×Trp_1

description: Sow feed by  2×Trp methods

source_name: 2×Trp, liver


title: 2×Trp_3

description: Sow feed by  2×Trp methods


title: 2×Trp_2

description: Sow feed by 2×Trp methods


title: Oct4 E75 LSEB 5

source_name: Late Streak, Early Bud Embryo

growth_protocol: Epiblast samples were dissected from 7.5 dpc embryos classified by morphological criteria.

value: Embryonic Day 7.5 (E75) - Late Streak, Early Bud (LSEB) Embryo


title: Oct4 E75 LSEB 6


title: Oct4 E75 LSEB 4


title: Sox2 NSC 1M 2


title: Sox2 NSC 1M 4


title: Oct4 E75 LSEB 3


title: Oct4 E75 LSEB 2


title: Dam E75 LSEB 3


title: High-Low_3

description: Sow feed by  High-Low methods


title: Dam E75 LSEB 6


title: Dam E75 LSEB 4


title: Dam E75 LSEB 2


title: Dam ESC 1k 3

source_name: Embryonic Stem Cell

growth_protocol: Embryonic Stem Cells cells were routinely grown on FBS supplemented GMEM with LIF, Pen/Strep, Beta-mercaptoethanol, Glutamine/Pyruvate and Non-essential Amino Acids. Cells were kept on gelatin-coated plates at 37 ºC in a humidified incubator with 5% CO2. Medium was changed every other day and cells were split when 70-80% confluent.

value: Embryonic Stem Cells (ESC)


title: Dam ESC 1k 4


title: Oct4 ESC 1k 1


title: Oct4 ESC 1k 2


title: Dam ESC 1k 2


title: Dam ESC 1k 1


title: Oct4 ESC 10k 2


title: Oct4 ESC 10k 3


title: Dam ESC 10k 4


title: Oct4 ESC 10k 1


title: Dam ESC 10k 3


title: Dam ESC 10k 2


title: Oct4 ESC 1M 2


title: Oct4 E75 LSEB 1


title: Dam E75 LSEB 5


title: Oct4 ESC 1M 3


title: Dam E75 LSEB 1


title: Oct4 ESC 1M 1


title: Dam ESC 1M 3


title: Dam ESC 10k 1


title: Oct4 ESC 1k 3


title: Oct4 ESC 1k 4


title: Dam ESC 1M 1


title: Dam ESC 1M 2


title: JK CD47Flow 2

first: Sukhbir

last: Kaur

department: NCI

description:
not captured using conjugated MNPs to CD47Antibody
AB2346-L1_JK_CD47flow_HLT7JBGXY_S13_R1_001
Slxg-HLT7JBGXY-L1-D701-D502

data_processing:
RNA sequencing reads were aligned by DNASTAR version 14 SeqMan NGen to either small coding/noncoding RNAs (CDS, rRNA, tRNA, ncRNA, tmRNA and miscRNA) or to miRNA reference (mature and precursors) evaluate small RNAs. DNASTAR version 14.1 ArrayStar was used for differential expression analysis.
Genome_build: miRbase 2.1, GRCh38

source_name: Jurkat cell line un-bound exosomes

growth_protocol: The Jurkat T cell line (E6.1) was purchased from ATCC. The cells were maintained using RPMI 1640 containing 10% FBS, glutamine, penicillin, and streptomycin (Gibco). The Jurkat and JinB8 T cells used for experiments were maintained less than 6 weeks in culture.

extract_protocol:
Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.
Small RNA sequencing libraries were size selected (<150bp) using the Agencourt AMPure beads. KAPA qPCR Library Quantification Kit was applied prior to pooling for the final libraries validation and normalization. The sequencing was done with 12.5 million reads per sample with 75 bp reads. (Multiplexing 32 samples on a 400 million read flow cell).

treatment_protocol: The cultured Jurkat were washed with IXPBs followed by a second wash with HITES medium (DMEM/F12 supplemented with, bovine serum albumin, hydrocortisone, insulin, transferrin, and trace elements). EVs were isolated from Jurkat T cells were cultured overnight using HITES medium. The conditioned media from Jurkat T cells were collected, and cell debris were removed using centrifugation at 300 g for 5 minutes and 2500 g for 10 minutes respectively. Centrifuged media were concentrated using Ultra-4 centrifugal filters to about 1 ml volume and further centrifuged at 10,000 rpm for 10 minutes. EVs were isolated using an Exo-Quick kit (SBI)  and CD63, CD47 and MHC1 positive EVs were captured using conjugating MNPs (15nM)  with respective antibodies. The uncaptured samples (not bonded) used as Flow  samples.

value: Jurkat T cell line

tag: tissue source

value: myeloid

tag: sample type

value: Exosome not  bound by CD47


title: Oct4 ESC 10k 4


title: JK CD47Flow 1

description:
not captured using conjugated MNPs to CD47Antibody
AB2345-L1_JK_CD47flow_HLT7JBGXY_S12_R1_001
Slxg-HLT7JBGXY-L1-D712-D501

value: Exosome not bound by CD47


title: JK CD47Cap 3

description:
captured using conjugated MNPs to CD47Antibody
AB2344-L1_JK_CD47Cap_HLT7JBGXY_S11_R1_001
Slxg-HLT7JBGXY-L1-D711-D501

source_name: Jurkat cell line exosomes bound by CD47

value: Exosome bound by CD47


title: JK CD47Cap 2

description:
captured using conjugated MNPs to CD47Antibody
AB2343-L1_JK_CD47Cap_HLT7JBGXY_S10_R1_001
Slxg-HLT7JBGXY-L1-D710-D501


title: JK CD47Cap 1

description:
captured using conjugated MNPs to CD47Antibody
AB2342-L1_JK_CD47Cap_HLT7JBGXY_S9_R1_001
Slxg-HLT7JBGXY-L1-D707-D504


title: JK MHC1Flow 1

description:
not captured using conjugated MNPs to MHC1 Antibody
AB2340-L1_JK_MHCflow_HLT7JBGXY_S7_R1_001
Slxg-HLT7JBGXY-L1-D705-D504

value: Exosome not bound by MHC1


title: JK MHC1Flow 2

description:
not captured using conjugated MNPs to MHC1 Antibody
AB2341-L1_JK_MHCflow_HLT7JBGXY_S8_R1_001
Slxg-HLT7JBGXY-L1-D706-D504


title: JK MHC1Cap 1

description:
captured using conjugated MNPs to MHC1 Antibody
AB2338-L1_JK_MHCCap_HLT7JBGXY_S5_R1_001
Slxg-HLT7JBGXY-L1-D705-D501

source_name: Jurkat cell line exosomes bound by MHC1

value: Exosome bound by MHC1


title: JK CD63Flow 2

description:
not captured using conjugated MNPs to CD63 Antibody
AB2337-L1_JK_CD63Flow_HLT7JBGXY_S4_R1_001
Slxg-HLT7JBGXY-L1-D704-D504

value: Exosome Not bound by CD63


title: JK MHC1Cap 2

description:
captured using conjugated MNPs to MHC1 Antibody
AB2339-L1_JK_MHCCap_HLT7JBGXY_S6_R1_001
Slxg-HLT7JBGXY-L1-D706-D501


title: JK CD63Cap 2

description:
captured using conjugated MNPs to CD63 Antibody
AB2335-L1_JK_CD63Cap_HLT7JBGXY_S2_R1_001
Slxg-HLT7JBGXY-L1-D702-D504

source_name: Jurkat cell line exosomes bound by CD63

value: Exosome bound by CD63


title: JK CD63Flow 1

description:
not captured using conjugated MNPs to CD63 Antibody
AB2336-L1_JK_CD63Flow_HLT7JBGXY_S3_R1_001
Slxg-HLT7JBGXY-L1-D703-D504


title: JK CD63Cap 1

description:
captured using conjugated MNPs to CD63 Antibody
AB2334-L1_JK_CD63Cap_HLT7JBGXY_S1_R1_001
Slxg-HLT7JBGXY-L1-D701-D504


title: JK CD47Flow 3

description:
not captured using conjugated MNPs to CD47Antibody
AB2347-L1_JK_CD47flow_HLT7JBGXY_S14_R1_001
Slxg-HLT7JBGXY-L1-D702-D502


title: untreated CTLL2 cells 8 hr rep 3

city: Morgantown

first: David

middle: John

last: Klinke

state: WV

department: Chemical Engineering

institute: West Virginia University

description:
Set2_8hr_2
Batch 2
RNAseq_All_normalized_counts.csv

data_processing:
Demultiplexing of samples and conversion from Illumina's bcl format to standard fastq format was performed using CASAVA 1.8.4 (Illumina).
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mus musculus assembly GRCm38.p2 whole genome using STAR aligner v2.4.2
The number of reads associated with a transcript was determined using featureCounts v.1.5.0 with the parameters specified to ignore duplicates, use base pair ends to avoid counting each end twice, only count fragments that had both ends present.
Transcript abundance was determined using the DESeq2 package in R v3.3.2 and reported as variance stabilized normalized counts.
Genome_build: GRCm38.p2
Supplementary_files_format_and_content: comma separated values file include normalized count values determined using DEseq2 for each Sample ...

source_name: CTLL2 cytotoxic T cells

growth_protocol: CTLL2 cells were grown in complete media for 24 hrs prior to the start of the experiment.

extract_protocol:
Total RNA was isolated from CTLL2 cells by TRIzol reagent extraction (Thermo Fisher Scientific). Prior to RNA-Seq library preparation, RNA quality and integrity was determined using the Agillent Bioanalyzer 2100. Only RNA with RIN values >8.0 were used for the experiment.
RNA-Seq libraries were built with Illumina's TruSeq RNA Kit V2 (RS-122-2001) as per manufacturers protocol. All libraries were indexed in such a way as to ensure only one index/lane on the HiSeq. Finished libraries were quality checked with a High Sensitivity DNA chip on the Bioanalyzer to determine average size and quantified on a Qubit with high sensitivity DNA reagents. The libraries were then sent to the Marshall Genomics Core Facility where they were pooled in equimolar ratios and run on three lanes of an Illumina HiSeq1500 in a 2 x 50 base paired end design yielding a minimum of 49.1 million reads per sample.

treatment_protocol: Following the addition of fresh complete media, CTLL2 cells were either unstimulated or treated with fresh B16F0 exosomes resuspended in PBS, to a final exosome concentration of 0.2 mg/ml. The transcriptome was assayed at the indicated time points.

tag: treatment

value: untreated


title: B16F0 exosome-treated CTLL2 cells 8 hr rep 1

description:
Set1_8hr_9
Batch 1
RNAseq_All_normalized_counts.csv

value: B16F0 exosome-treated


title: B16F0 exosome-treated CTLL2 cells 8 hr rep 2

description:
Set2_8hr_4
Batch 2
RNAseq_All_normalized_counts.csv


title: H3K4me3 GIC-20 shScramble

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

description: H3K4me3 ChIP-seq, in GIC-20 cells exposed to shScramble

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
ChIP-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 1.1.2.  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.
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.

source_name: Glioma Initiating Cells

growth_protocol: GICs grown in DMEM/F12 media with B27 and N2 supplements, Glutamax, Pen/Strep, EGF, bFGF, and LIF as neurospheres.

extract_protocol:
cells per sample were fixed with 1% formaldehyde and ChIP-seq was performed according to previous studies (Chen et al., 2015; doi: 10.1016/j.cell.2015.07.042 and Chen et al. 2015; doi: 10.1101/gad.246173.114)
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.

treatment_protocol: Cells treated with lentivirus with either shScramble or two independent shIDH1 sequences.

tag: shRNA sequence

value: shScramble (SHC016)

tag: chip antibody


title: H3K4me3 GIC-387 shScramble-1

description: H3K4me3 ChIP-seq, in GIC-387 cells exposed to shScramble1


title: H3K4me3 GIC-387 shScramble-2

description: H3K4me3 ChIP-seq, in GIC-387 cells exposed to shScramble2


title: H3K4me3 GIC-387 shIDH1-89

description: H3K4me3 ChIP-seq, in GIC-387 cells exposed to shIDH1-89


title: H3K4me3 GIC-20 shIDH1-98

description: H3K4me3 ChIP-seq, in GIC-20 cells exposed to shIDH1-98


title: B16F0 exosome-treated CTLL2 cells 8 hr rep 3

description:
Set2_8hr_6
Batch 2
RNAseq_All_normalized_counts.csv


title: H3K4me3 GIC-20 shIDH1-89

description: H3K4me3 ChIP-seq, in GIC-20 cells exposed to shIDH1-89


title: untreated CTLL2 cells 8 hr rep 2

description:
Set2_8hr_1
Batch 2
RNAseq_All_normalized_counts.csv


title: H3K4me3 GIC-387 shIDH1-98

description: H3K4me3 ChIP-seq, in GIC-387 cells exposed to shIDH1-98


title: untreated CTLL2 cells 8 hr rep 1

description:
Set1_8hr_1
Batch 1
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 4 hr rep 2

description:
Set1_4hr_7
Batch 1
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 4 hr rep 2

description:
Set1_4hr_1
Batch 1
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 4 hr rep 3

description:
Set2_4hr_1
Batch 2
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 4 hr rep 1

description:
Set2_4hr_4
Batch 2
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 2 hr rep 3

description:
Set2_2hr_4
Batch 2
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 2 hr rep 1

description:
Set2_2hr_5
Batch 2
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 2 hr rep 2

description:
Set1_2hr_9
Batch 1
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 2 hr rep 1

description:
Set1_2hr_2
Batch 1
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 0.5 hr rep 3

description:
Set2_05hr_4
Batch 2
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 0.5 hr rep 2

description:
Set2_05hr_6
Batch 2
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 2 hr rep 2

description:
Set2_2hr_1
Batch 2
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 0.5 hr rep 1

description:
Set1_05hr_8
Batch 1
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 0.5 hr rep 3

description:
Set2_05hr_2
Batch 2
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 0.5 hr rep 1

description:
Set1_05hr_2
Batch 1
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 0 hr rep 3

description:
Set2_0hr_2
Batch 2
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 0 hr rep 4

description:
Set2_0hr_3
Batch 2
RNAseq_All_normalized_counts.csv


title: B16F0 exosome-treated CTLL2 cells 4 hr rep 3

description:
Set2_4hr_5
Batch 2
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 0.5 hr rep 2

description:
Set2_05hr_1
Batch 2
RNAseq_All_normalized_counts.csv


title: untreated CTLL2 cells 0 hr rep 2

description:
Set2_0hr_1
Batch 2
RNAseq_All_normalized_counts.csv


city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

description:
S
Macrophages from acute myeloid leukemia with high level sM-CSF

data_processing:
Base calling was done by BGIseq-500
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5)
Alignment was performed against RefSeq by bowtie2 (version 2.2.5) with parameters as: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200
FPKM values of each gene for each sample was measured via RSEM
Supplementary_files_format_and_content: text file with gene_id, transcript_id(s),  length, expected_count,  and FPKM

source_name: Macrophage

extract_protocol:
sorted Macrophages were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGIseq-500

treatment_protocol: GFP+BFP+ leukemia cells with high level mM-CSF or sM-CSF or none were transplanted into 6-8 weeks old C57BL/6J mice (8×10^5 cells/mouse) without irradiation. All mice suffered AML with a survival time of 30-40 days. GR1-CD115intF4/80+ macrophages were sorted from spleen of leukemia mice at day18

tag: disease state

value: acute myeloid leukemia

tag: tissue

value: Spleen

tag: cell type

value: macrophage

tag: age

value: 6-8 week


title: MCF7_CD24+_2

status: Public on Mar 12 2018

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description: MCF7 24+ significant MCF7 Parental vs. MCF7 24+ significant list

data_processing:
CLC genomic workbench 7.0
Illumina adapter sequences and sequences tags of length less than 17 and more than 27 were removed
miRNA sequences were aligned to human genome (homo sapiens GRCh 37.57) and known miRNA database (miRBase-19)
Statistical analysis: Bonferroni and FDR corrected
Filtering: Significant, above 2; Kalz test: FDR pvalue <0.05; Kalz test: FC abs value>2
Genome_build: miRBase 19
Supplementary_files_format_and_content: Excel files xlsx containing expression values  of miRNAs of monolayer and sorted cd24+ spheroid cells

source_name: MDA Spheroid (Replicate 2)

growth_protocol: The monolayer and sorted CD24+ spheroid cells were cultured in tissue culture-treated flasks and as suspension spheroid respectively. Both are maintained in 5% CO2 humidified incubator.

extract_protocol:
Total RNA with retention of small RNAs from the cells were extracted using miRNAeasy
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina Tru-seq small RNA

tag: cell source

value: Estrogen-dependent human breast adenocarcinoma

tag: culture condition

value: Sorted CD24+ spheroid

tag: culture dimension

tag: cell line


title: untreated CTLL2 cells 0 hr rep 1

description:
Set1_0hr_2
Batch 1
RNAseq_All_normalized_counts.csv

tag: strain


title: MCF7_CD24+_1

source_name: MDA Spheroid (Replicate 1)


title: Macrophages form acute myeloid leukemia

description:
V
Macrophages form acute myeloid leukemia


title: MCF7_P_3

description: mcf7 parental matureSmall RNA sample-1  mcf7 parental size grouped on mature

source_name: MDA Monolayer (Replicate 3)

value: Monolayer


title: untreated CTLL2 cells 2 hr rep 3

description:
Set2_2hr_3
Batch 2
RNAseq_All_normalized_counts.csv


title: DKO_Dnmt1KD_TKO-like_RRBS

city: Cambridge

first: Jocelyn

last: Charlton

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
WGBS : 10 bp were clipped from the WGBS raw sequencing reads at either end. The reads were then aligned to the mm9 build of the mouse genome using BSmap.  DNA methylation calling for individual CpG sites was performed using mcall from the MOABS package.
RRBS: Sequenced reads were aligned to the mm9 of hg19 reference genome using BSmap for WGBS. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files. WGBS: chrom, start, end, ratio, totalC, methC, strand, next, Plus, totalC, methC, Minus, totalC, methC, localSeq   RRBS: chr, start, end, methC/totalC, ratio (out of 1000). RNAseq text files contain headers

source_name: mESCs

growth_protocol: ES cells were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF

extract_protocol:
genomic DNA was purified using Phenol/Chloroform extraction
WGBS: 100-200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 10; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research), eluting in 15 µl low TE buffer. To minimize loss during storage, bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences). The libraries were sequenced for 100-bp paired-end reads on an Illumina HiSeq 2500 sequencer. RRBS: Genomic DNA was quantified using a Qubit® 2.0 Fluorometer, and quality-assessed on an Agilient 2200 TapeStation D1000 ScreenTape.  RRBS was performed on 20ng of each sample using the NuGen Ovation® RRBS Methyl-Seq System.  Barcoded samples were pooled in groups of 8 immediately prior to Bisulfite Conversion with the Qiagen EpiTect® Fast Bisulfite Conversion kit.  Library pools were purified with a 1X Agencourt RNA XP bead clean-up and sequenced on an Illumina HiSeq® 2500 Sequencing System. All protocols were carried out according to manufacturer's recommendations except where specified.
Bisulfite-seq and bisulfite-seq reduced representation

treatment_protocol: Doxycycline was used induce expression of dCas9 or Dnmt3a/b

value: mESCs

tag: genotype/variation

value: DKO


title: untreated CTLL2 cells 4 hr rep 1

description:
Set2_4hr_3
Batch 2
RNAseq_All_normalized_counts.csv


title: MCF7_P_1

source_name: MDA Monolayer (Replicate 1)


title: mESC_V6.5_WT_dCas9_Dnmt3acat_Nodox_RRBS

description: bisulfite converted DNA

data_processing:
WGBS : 10 bp were clipped from the WGBS raw sequencing reads at either end. The reads were then aligned to the mm9 build of the mouse genome using BSmap.  DNA methylation calling for individual CpG sites was performed using mcall from the MOABS package.
RRBS: Sequenced reads were aligned to the mm9 of hg19 reference genome using BSmap for WGBS. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files.  RRBS: chr, start, end, methC/totalC, ratio (out of 1000).

extract_protocol:
genomic DNA was purified using Phenol/Chloroform extraction
WGBS: 100-200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 10; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research), eluting in 15 µl low TE buffer. To minimize loss during storage, bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences). The libraries were sequenced for 100-bp paired-end reads on an Illumina HiSeq 2500 sequencer. RRBS: Genomic DNA was quantified using a Qubit® 2.0 Fluorometer, and quality-assessed on an Agilient 2200 TapeStation D1000 ScreenTape.  RRBS was performed on 20ng of each sample using the NuGen Ovation® RRBS Methyl-Seq System.  Barcoded samples were pooled in groups of 8 immediately prior to Bisulfite Conversion with the Qiagen EpiTect® Fast Bisulfite Conversion kit.  Library pools were purified with a 1X Agencourt RNA XP bead clean-up and sequenced on an Illumina HiSeq® 2500 Sequencing System. All protocols were carried out according to manufacturer's recommendations except where specified.

value: wildtype


title: mESC_V6.5_WT_dCas9_Dnmt3acat_dox_RRBS

description: bisulfite converted DNA


title: MCF7_P_2

source_name: MDA Monolayer (Replicate 2)


title: MCF7_CD24+_3

source_name: MDA Spheroid (Replicate 3)


title: DKO_dCas9-Cat3a_noGuide_Nodox_3w_RRBS

description: bisulfite converted DNA

data_processing:
WGBS : 10 bp were clipped from the WGBS raw sequencing reads at either end. The reads were then aligned to the mm9 build of the mouse genome using BSmap.  DNA methylation calling for individual CpG sites was performed using mcall from the MOABS package.
RRBS: Sequenced reads were aligned to the mm9 of hg19 reference genome using BSmap for WGBS. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: Bed files. WGBS: chrom, start, end, ratio, totalC, methC, strand, next, Plus, totalC, methC, Minus, totalC, methC, localSeq   RRBS: chr, start, end, methC/totalC, ratio (out of 1000). RNAseq text files contain headers


title: DKOzero_transient_dCas9-Cat3a_ANV_DazlGuide_3day_RRBS

description: bisulfite converted DNA

tag: transfection

value: dCas9-cat3a constructs


title: DKOzero_transient_dCas9-Cat3a_DazlGuide_3day_RRBS

description: bisulfite converted DNA


title: mESC_DKOzero_Dnmt3acat_RRBS

description: bisulfite converted DNA

data_processing:
Sequenced reads were aligned to the mm9 reference genome using BSmap for WGBS. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files. RRBS: chr, start, end, methC/totalC, ratio (out of 1000)

growth_protocol: ES cells were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 10^5 U LIF

extract_protocol:
genomic DNA was purified using Phenol/Chloroform extraction
Genomic DNA was quantified using a Qubit® 2.0 Fluorometer, and quality-assessed on an Agilient 2200 TapeStation D1000 ScreenTape.  RRBS was performed on 20ng of each sample using the NuGen Ovation® RRBS Methyl-Seq System.  Barcoded samples were pooled in groups of 8 immediately prior to Bisulfite Conversion with the Qiagen EpiTect® Fast Bisulfite Conversion kit.  Library pools were purified with a 1X Agencourt RNA XP bead clean-up and sequenced on an Illumina HiSeq® 2500 Sequencing System. All protocols were carried out according to manufacturer's recommendations except where specified.


title: mESC_DKOzero_passage10_RRBS

description: bisulfite converted DNA

value: DKOzero


title: mESC_DKOzero_RRBS

description: bisulfite converted DNA

data_processing:
Sequenced reads were aligned to the mm9 reference genome using BSmap for WGBS. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence.
genome build: mm9
processed data files format and content:  Bed files. RRBS: chr, start, end, methC/totalC, ratio (out of 1000)

extract_protocol:
Genomic DNA was quantified using a Qubit® 2.0 Fluorometer, and quality-assessed on an Agilient 2200 TapeStation D1000 ScreenTape.  RRBS was performed on 20ng of each sample using the NuGen Ovation® RRBS Methyl-Seq System.  Barcoded samples were pooled in groups of 8 immediately prior to Bisulfite Conversion with the Qiagen EpiTect® Fast Bisulfite Conversion kit.  Library pools were purified with a 1X Agencourt RNA XP bead clean-up and sequenced on an Illumina HiSeq® 2500 Sequencing System. All protocols were carried out according to manufacturer's recommendations except where specified.
genomic DNA was purified using Phenol/Chloroform extraction


title: mESC_DKOzero_Dnmt3AOE_RRBS

description: bisulfite converted DNA


title: mESC_KH2_WT_RRBS

description: bisulfite converted DNA


description:
M
Macrophages from acute myeloid leukemia with high level mM-CSF


title: mESC_dCas9_Dnmt3acat_WGBS

description: bisulfite converted DNA

data_processing:
10 bp were clipped from the WGBS raw sequencing reads at either end. The reads were then aligned to the mm9 build of the mouse genome using BSmap.  DNA methylation calling for individual CpG sites was performed using mcall from the MOABS package.
genome build: mm9
processed data files format and content: Bed files. WGBS: chrom, start, end, ratio, totalC, methC, strand, next, Plus, totalC, methC, Minus, totalC, methC, localSeq

extract_protocol:
100-200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 10; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research), eluting in 15 µl low TE buffer. To minimize loss during storage, bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences). The libraries were sequenced for 100-bp paired-end reads on an Illumina HiSeq 2500 sequencer.
genomic DNA was purified using Phenol/Chloroform extraction


title: 293T_transient_dCas9-Cat3a_ANV_Bach2Guide_3day_RNAseq_r2


title: 293T_transient_dCas9-cat3a_Bach2Guide_3day_RNAseq_r2


title: 293T_WT_RNAseq_r2

value: WT


title: 293T_transient_dCas9-cat3a_ANV_Bach2Guide_15day_RRBS

description: bisulfite converted DNA


title: 293T_transient_dCas9-Cat3a_ANV_Bach2Guide_3day_RNAseq_r1


title: 293T_transient_dCas9-cat3a_ANV_Bach2Guide_7day_RRBS

description: bisulfite converted DNA


title: 293T_transient_dCas9-Cat3a_ANV_Bach2Guide_3day_RRBS_r2

description: bisulfite converted DNA


title: 293T_transient_dCas9-cat3a_Bach2Guide_3day_RRBS_r2

description: bisulfite converted DNA


title: 293T_transient_dCas9-cat3a_Bach2Guide_7day_RRBS

description: bisulfite converted DNA


title: HCT116_WT_AllCells_16hArrest_bulk

data_processing:
Raw sequencing reads were aligned using BSMAP, Custom Perl scripts were used to remove read pairs that aligned to different chromosomes.
Methylation calls were made by observing the bisulfite conversion of unmethylated cytosines in sequenced reads compared to the reference genome using custom Perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited bed files contain the number of methylated and unmethylated reads for every CpG captured. Column contents for 6 column files are: chromosome, start, end, methylated CpGs, total CpGs, methylation percentage [0-1]. Column contents for 5 column files are: chr, start, end, 'methylated CpGs/total CpGs', methylation percentage [0-1000]

source_name: Cancer cell line

growth_protocol: Human ESC lines were grown in feeder free culture system using mTeSR1 medium and Geltrex ECM coating. BJ fibroblast line was grown in MEM-Alpha basal medium (Gibco) supplemented with 10% FBS, 1% PenStrep and bFBF. BJ fibroblasts were also cultured under hygromycin resistance. HCT116 and HCT116ΔPBD were cultured in McCoy's 5A medium with 10% FBS and 1% PenStrep with 0.05mg/ml hygromycin B.

extract_protocol:
Genomic DNA was isolated from cell lysates by phenol-chloroform extraction.
Genomic DNA was sonicated, heat denatured, and immunoprecipitated for BrdU. DNA was bisulfite converted and bisulfite libraries were prepared using Accel-NGS Methyl-seq DNA library kit by Swift Biosciences.

treatment_protocol: All cells (where indicated) were pulsed with 50 µM concentration of BrdU. Cells arrested in G2/M were treated with Nocodazole (2µg/ml) for 16 hours.

tag: dna

value: All

tag: chase time

value: Nocodazole


title: 293T_transient_dCas9-cat3a_Bach2Guide_15day_RRBS

description: bisulfite converted DNA


title: 293T_WT_RNAseq_r1


title: siNC

city: Guangzhou

first: yinghui

last: wang

state: Guangdong

address: No.1023 Shatai South Road，Baiyun District,

department: radiation medicine

institute: southern medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for poly-N or low-qualitysequence.Reference genome and gene model annotation files were downloaded from genome website  (human assembly GRCh37/hg19 ) directly. Index of the reference genome was built using Bowtie v2.0.6 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: human assembly GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: skin/epidermis

growth_protocol: A431 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum  and maintained at 37℃ with 5% CO2 in a humidified atmosphere.

extract_protocol:
Culture medium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
1 μg of total RNA was subjected to library synthesis for sequencing using standard Illumina protocols

value: skin/epidermis

value: 85 years

tag: sirna

value: siNC


title: mESC_DKOzero_passage2_RRBS

description: bisulfite converted DNA


title: HCT116_WT_AllCells_bulk

tag: treatment


title: HUES64_DKO_AllCells_1hBrdU_1hChase_nascent_rep1

source_name: Embryonic stem cell line

growth_protocol: Human ESC lines were grown in feeder free culture system using mTeSR1 medium and Geltrex ECM coating. BJ fibroblast line was grown in MEM-Alpha basal medium (Gibco) supplemented with 10% FBS, 1% PenStrep and bFBF. BJ fibroblasts were also cultured under hygromycin resistance.

extract_protocol:
Genomic DNA was isolated from cell lysates by phenol-chloroform extraction.
Genomic DNA was soniaticated, heat denatured, and immunoprecipitated for BrdU. DNA was bisulfite converted and bisulfite libraries were prepared using Accel-NGS Methyl-seq DNA library kit by Swift Biosciences.

value: HUES64 DNMT3A-/-/DNMT3B-/-

value: Nascent

value: 1 hour


title: HUES64_DKO_AllCells_1hBrdU_0Chase_nascent_rep2


title: HUES64_DKO_AllCells_1hBrdU_4hChase_nascent_rep2

value: 4 hour


title: HUES64_DKO_AllCells_1hBrdU_0Chase_nascent_rep1


title: HUES64_WT_AllCells_1hBrdU_16hChase_nascent_rep1

value: HUES64 WT

value: 16 hours


title: HUES64_WT_AllCells_1hBrdU_16hChase_nascent_rep2


title: HUES64_WT_AllCells_1hBrdU_4hChase_nascent_rep2

value: 4 hours


title: HUES64_DKO_AllCells_1hBrdU_4hChase_nascent_rep1


title: mESC_DKOzero_WGBS

description: bisulfite converted DNA

value: mESCs


title: HUES64_WT_AllCells_1hBrdU_4hChase_nascent_rep1


title: HUES64_WT_AllCells_1hBrdU_1hChase_nascent_rep2


title: HUES64_WT_AllCells_1hBrdU_1hChase_nascent_rep1


title: 293T_transient_dCas9-cat3a_Bach2Guide_3day_RNAseq_r1


title: mESC_V6.5_WT_WGBS

description: bisulfite converted DNA

value: wildtype


title: 293T_WT_RRBS_r2

description: bisulfite converted DNA


title: HUES64_WT_AllCells_1hBrdu_16hArrest_bulk


title: siHOXA9_02


title: HUES64_WT_S6fraction_1hBrdu_0Chase_nascent


title: HUES64_WT_AllCells_1hBrdu_16hArrest_nascent


title: HUES64_WT_S3fraction_1hBrdu_0Chase_nascent


title: HUES64_WT_S5fraction_1hBrdu_0Chase_nascent


title: HUES64_WT_S4fraction_1hBrdu_0Chase_nascent


title: MeDIP-HEK293-rep2

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

description: somatic cell

data_processing:
Basecalls performed by BGI, Shenzhen
Data were filtered using samtools rmdup to remove potential PCR duplicates
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantitified by Cuffdiff.
Genome_build: hg38 (RNA-seq)
Genome_build: hg19 (MeDIP-seq)
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 250 bp

source_name: HEK 293 transfected with reporter construct

extract_protocol:
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were sythesised using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT.
MeDIP-seq were performed as previously described (Xiong et al, Molecular Cell 64, 913-925). Mouse monoclonal anti-5-methylcytidine (BI-MECY-000) for MeDIP was purchased from Eurogentec.
The MeDIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).
The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.

value: Human embryonic kidney

tag: antibody

value: BI-MECY-000, Eurogentec


title: HUES64_WT_S1fraction_1hBrdu_0Chase_nascent

growth_protocol: Human ESC lines were grown in feeder free culture system using mTeSR1 medium and Geltrex ECM coating. HCT116 cells were grown in McCoy’s 5A (modified) medium supplemented with 10% FBS and 1% PEN/STREP.

treatment_protocol: All cells indicated as "nascent" were pulsed with 50 µM BrdU. Repli-BS was then performed using an antibody against BrdU to enrich for nascent DNA. "Treatment" refers to whether cells were arrested or not: all arrested cells were treated with nocodazole (2µg/ml) for 16 hours to induce G2/M arrest.


title: MeDIP-HEK293-rep1

description: somatic cell

value: HEK 293 transfected with reporter construct

value: WT


title: HUES64_WT_S2fraction_1hBrdu_0Chase_nascent


title: HUES64_DKO_AllCells_1hBrdU_1hChase_nascent_rep2


title: input-HEK293-rep1

description: somatic cell


title: input-HEK293-rep2

description: somatic cell


title: 293T_transient_dCas9-cat3a_Bach2Guide_3day_RRBS_r1

description: bisulfite converted DNA

value: dCas9-cat3a constructs


title: 293T_WT_RRBS_r1

description: bisulfite converted DNA


title: MCF7_WT_RRBS

description: bisulfite converted DNA


title: MCF7_transient_dCas9-Cat3a_ANV_BACH2Guide_3day_RRBS

description: bisulfite converted DNA


title: WT_mESCs_targeted_BSseq


title: MCF7_transient_dCas9-cat3a_Bach2Guide_3day_RRBS_rep2

description: bisulfite converted DNA


title: HUES64_WT_AllCells_1hBrdU_0Chase_nascent_rep3


title: HUES64_WT_AllCells_1hBrdU_16hChase_nascent_rep3


title: HUES64_WT_AllCells_1hBrdU_8hChase_nascent_rep3

value: 8 hours


title: HUES64_WT_AllCells_1hBrdU_1hChase_nascent_rep3


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone6_3day_targeted_BSseq

value: DKO


title: HUES64_WT_AllCells_1hBrdU_4hChase_nascent_rep3


title: HUES64_WT_AllCells_1hBrdU_2hChase_nascent_rep3

value: 2 hours


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone6_1day_targeted_BSseq


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone6_0day_targeted_BSseq


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone3_3day_targeted_BSseq


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone6_2day_targeted_BSseq


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone3_1day_targeted_BSseq


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone1_3day_targeted_BSseq


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone1_0day_targeted_BSseq


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone1_2day_targeted_BSseq


title: 293T_transient_dCas9-Cat3a_ANV_Bach2Guide_3day_RRBS_r1

description: bisulfite converted DNA


title: RG108-treat-RNAseq-rep2

description:
somatic cell
RG108-treat-RNAseq-RPKM.txt.gz

value: RG109 treated


title: RG108-treat-RNAseq-rep1

value: RG108 treated


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone1_1day_targeted_BSseq


title: No7-compound-treat-RNAseq-rep2

description:
somatic cell
No7-compound-treat-RNAseq-RPKM.txt.gz

value: No7-compound treated


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone3_0day_targeted_BSseq


title: No6-compound-treat-RNAseq-rep1

description:
somatic cell
No6-compound-treat-RNAseq-RPKM.txt.gz

value: No6-compound treated


title: No6-compound-treat-RNAseq-rep2


title: No5-compound-treat-RNAseq-rep1

description:
somatic cell
No5-compound-treat-RNAseq-RPKM.txt.gz

value: No5-compound treated


title: No5-compound-treat-RNAseq-rep2


title: No4-compound-treat-RNAseq-rep2

description:
somatic cell
No4-compound-treat-RNAseq-RPKM.txt.gz

value: No4-compound treated


title: No3-compound-treat-RNAseq-rep2

description:
somatic cell
No3-compound-treat-RNAseq-RPKM.txt.gz

value: No3-compound treated


title: No4-compound-treat-RNAseq-rep1


title: No1-compound-treat-RNAseq-rep1

description:
somatic cell
No1-compound-treat-RNAseq-RPKM.txt.gz

value: No1-compound treated


title: No3-compound-treat-RNAseq-rep1


title: No1-compound-treat-RNAseq-rep2


title: DMSO-treat-RNAseq-rep2

description:
somatic cell
DMSO-treat-RNAseq-RPKM.txt.gz

value: DMSO-treated


title: 5Aza-dC-treat-RNAseq-rep1

description:
somatic cell
5azadC-treat-RNAseq-RPKM.txt.gz

value: Human embryonic kidney

value: 5Aza-dC treated


title: 5Aza-dC-treat-RNAseq-rep2

value: HEK 293 transfected with reporter construct


title: DMSO-treat-RNAseq-rep1


title: DKO_dCas9-Cat3a_multiple_sgRNA_clone3_2day_targeted_BSseq

value: mESCs


title: mESC_dCas9-Cat3a_noGuide_dox_7d_WGBS

data_processing:
WGBS : 10 bp were clipped from the WGBS raw sequencing reads at either end. The reads were then aligned to the mm9 build of the mouse genome using BSmap.  DNA methylation calling for individual CpG sites was performed using mcall from the MOABS package.
RRBS: Sequenced reads were aligned to the mm9 of hg19 reference genome using BSmap for WGBS. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: Bed files. WGBS: chrom, start, end, ratio, totalC, methC, strand, next, Plus, totalC, methC, Minus, totalC, methC, localSeq   RRBS: chr, start, end, methC/totalC, ratio (out of 1000)

tag: molecule subtype

value: bisulfite converted DNA


title: No7-compound-treat-RNAseq-rep1


title: KAP1_deficient_Treg_rep2

status: Public on Mar 11 2018

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

description:
KO2
KO-Treg2_S21

data_processing:
Sequenced reads were trimmed for adaptor sequence, and low quality reads were removed. Rest of the reads were then mapped to mm10 using TopHat2 (ver 2.1.1).
Tag counts were obtained with HT-seq (ver 0.7.2).
Differentially expressed genes were determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts generated by HT-seq and DESeq2 output result txt file

source_name: KAP1 deficient Treg

extract_protocol:
CD4+ T cells were purified with CD4+ T cell Isolation Kit (Miltenyi) and Treg (YFP+) were further purified by FACS Aria II. Total RNA was extracted using NucleoSpin RNA kit (Clontech).
RNA libraries were prepared for sequencing using TruSeq RNA library Prep Kit v2 (Illumina) according to the protocol.

tag: strain background

value: KAP1 deficient

value: Spleen

value: Treg (YFP+)


title: Input_KO

description: readcountsaroundtss.txt

data_processing:
First three bases of sequenced reads were trimmed according to the library protocol and low quality sequences were removed. Rest of the reads were aligned to mm10 by using Bowtie2 (ver.2.2.9) in a default setting.
Uniquely mapped reads were selected and the dupulicated reads were discarded by using Picard Tools (ver.2.1.1)
The number of reads which were aligned between -1kb to +1kb of TSS was counted using 'intersect' command of bedtools software (ver 2.26.0)
Genome_build: mm10
Supplementary_files_format_and_content: txt file [gene ID, read counts around TSS (WT), read counts around TSS (KO)]

extract_protocol:
Nuclear lysates were sonicated and histone-DNA complexes were isolated with antibody.
Libraries were prepared by using DNA SMART ChIP-Seq kit (Clontech) according to the protocol. 150-400bp products were selected and subjected to the analysis.

tag: tissue


title: H3K9me3_WT

description: readcountsaroundtss.txt

source_name: wild type Treg


title: KAP1_deficient_Treg_rep1

description:
KO1
KO-Treg1_S20

tag: cell type


title: KAP1_deficient_Treg_rep3

description:
KO3
KO-Treg3_S22


title: KAP1_sufficient_Treg_rep3

description:
WT3
WT-Treg3_S19

source_name: WT Treg

value: wild type; KAP1 sufficient


title: KAP1_sufficient_Treg_rep2

description:
WT2
WT-Treg2_S18


title: KAP1_rep2

data_processing:
First three bases of sequenced reads were trimmed according to the library protocol and low quality sequences were removed. Rest of the reads were aligned to mm10 by using Bowtie2 (ver.2.2.9) in a default setting.
Uniquely mapped reads were selected and the dupulicated reads were discarded by using Picard Tools (ver.2.1.1)
Peaks were called using MACS2 (ver.2.2.1) in a default setting.
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: Regulatory T cells

value: KAP1(active motif, 1Tb-A9)


title: Input_rep2


title: Input_rep1


title: KAP1_rep1


title: No2-compound-treat-RNAseq-rep1

description:
somatic cell
No2-compound-treat-RNAseq-RPKM.txt.gz

value: No2-compound treated


title: Puf3-PTP-Input

city: State College

first: Liwang

last: Cui

state: PA

address: 553 ASI bldg

institute: Penn State

data_processing:
Basecalls performed using CASAVA version 1.8.4
Adapter sequence removal and quality trimming of reads were performed using Trimmomatic version 0.35
Data were mapped to Plasmodium falciparum reference genome (Pf3D7_01_v3) with Tophat version v2.1.1
Reads mapped to genes were then counted using featureCounts  version 1.5.3 with parameters -M -O -s 2
Reads counts were normalized using DESeq1
Genome_build: Pf3D7_01_v3
Supplementary_files_format_and_content: tab delimited file with raw read counts for each gene in each sample.

organism: Plasmodium falciparum

growth_protocol: Culturing of 3D7 wild type strain with complete medium everyday.Complete medium (Hepes, sodium bicarbonate, gentamycin RPMI1640)

extract_protocol:
Tandem affinity purification (TAP) of PfPuf3 was performed using the  PfPuf3-PTP parasite line and 3D7 as control.  Parasite pellet was lysed with five-fold volume of pre-cooled PA150 buffer containing a protease inhibitor cocktail. Then the parasites were manually lysed by 60-100 strokes in a Dounce homogenizer with a tight pestle and centrifuged at 16,000 g for 20 min at 4°C. Take 100ul supernatant and labeled as Input, add 1 ml Trizol for future RNA extraction. The rest of supernatant was incubated with 100 ul (settled volume) of IgG agarose beads (GE Healthcare) at 4°C for 2 h. The beads were washed three times with pre-cooled PA150 and equilibrated twice with the TEV buffer. Then the beads were incubated 2 h with 2 ml of TEV buffer containing 100-150 U of TEV protease with gentle rotation at 4°C. The supernatant was obtained by centrifugation at 500 xg for 5 min at 4°C. Add Trizol into the supernatant and then do RNA extraction according to ambion TRIzol Reagent instrction.
Libraries were made according to KAPABIOSYSTEMS KAPA Stranded mRNA-seq kit instrction.

treatment_protocol: Culturing of Puf3-PTP trangenic strain with complete medium everyday.Complete medium (Hepes, sodium bicarbonate, gentamycin RPMI1640)

tag: genotype

tag: background strain


title: 3D7-IP

value: wildtype


title: 3D7-Input


title: KAP1_sufficient_Treg_rep1

description:
WT1
WT-Treg1_S17


title: NPC_PCGF5_input

status: Public on Mar 10 2018

first: Jiajian

last: Zhou

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads by ChIP-seq were mapped to mm9 genome using Bowtie2 with default parameters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
For histone modification chipseq, peaks were called using MACS2 (v2.1.0), a q-value of 10^-2 was used as the cutoff; For PCGF5 chipseq, peaks were called using MACS2 (v2.1.0), a p-value of 10^-4 was used as the cutoff;
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation. Overlapping analysis was performed using bedtools.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS in bed format (https://github.com/taoliu/MACS#output-files).

source_name: in-vitro differentiated neural cells

growth_protocol:
sample1-6:Sox1-GFP ESC lines were cultured on mitomycin C-inactivated mouse embryo fibroblasts in DMEM high-glucose media containing 15% FBS (Gibco), 1mM sodium pyruvate (Gibco), 1mM non-essential amino acids (Gibco), 1 x GlutaMAX (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), and the 2i inhibitors (3 μM CHIR99021, and 1 μM PD0325901).
sample7-14:For neural differentiation in suspension as described in (Watanabe, K. et al., 2005) , the dissociated ESCs were suspended in the Petri dish and cultured in GMEM (Gibco) supplemented with 8% knockout serum replacement (Gibco), 1 mM Glutamine, 1 mM pyruvate, 0.1 mM nonessential amino acids and 0.1 mM b-mercaptoethanol (Gibco).

extract_protocol:
cells were crosslinked with 2mM EGS [ethylene glycol bis(succinimidylsuccinate)] and crosslink it again with 1％formaldehyde. The cells were sonicated to achieve a chromatin sized of 200-500 bp in SDS lysis buffer containing 1 × protease inhibitor cocktails and 1 mM PMSF. Then the sonicated chromatin was dialyzed with TE buffer containing 150 mM Nacl and incubated with M2-Magnetic beads overnight at 4°C with rotation. Wash twice with TBS-T (Tween-20 at 0.05%), and wash four times with TBS at 4°C. For H2AK119ub1 and H3K27me3, chromatin was extracted in buffer A (10mM Tris-HCL PH=7.9, 1.5mM Mgcl2, 10mM KCL, 0.1% TritonX-100, protease inhibitors). The resultant chromatin was re-suspended in 200ul Buffer B (50 mM Tris–HCl, pH 7.9, 3.5mM MgCl2, 2 mM CaCl2, protease inhibitors) and digested into nucleosomes fragments at 37℃ by adding 5ul 200U/ml MNase. After that, nucleosomes fragments were crosslinked with 0.5% formaldehyde immediately. Magnetic protein A/G beads were washed and added with the recommended antibody for overnight. Immune complexes were washed and Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for either ChIP-Seq. The amounts of immunoprecipitated DNA were normalized to the input.
About 10 ng IP DNA and input DNA measured by Qubit Fluorometer (Invitrogen) were used to construct DNA library by using ChIP-Seq Sample Prep Kit (Illumina).

value: in-vitro differentiated neural cells

tag: chip/antibody

value: Wild type


title: Input_WT

description: readcountsaroundtss.txt


title: NPC_PCGF5


title: NPC_input


title: PCGF5-depleted_NPC_input


title: NPC_H2AK119ub1

value: Anti-h2ak119ub1(Cell signaling:#8240)


title: Lung_cDC_CD11c_cre+_MyD88 fx_6h_OVA_stFLA

city: RTP

first: Seddon

last: Thomas

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: Sorted cDC

data_processing:
Library strategy: ATAC-seq
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
Cleaned reads were aligned to mm9 using Bowtie with the parameters -m1, -v2 and –X1500; duplicates were removed using Picard;
Two biology replicates for each condition were merged into one sample;
we adjusted the read start sites to represent the center of the transposon binding event; all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the – strand were offset −5 bp;
PeaKDEck (Version 1.1)was used to call all reported ATAC-seq peaks;with a window size of 300 bp and probabilityValue –sig0.0001.
Genome_build: mm9

source_name: Lung cDC CD11c cre+ MyD88 fx/fx-6h OVA/stFLA

extract_protocol:
Genomic DNA was isolated from 25,000 sorted cells were lysed in cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) for 5 min.
The ATAC-seq tagmentation reaction was performed as previously described (Buenrostro, 2013) with the following modifications. Nuclei were incubated with 2.5 μl of Tn5 Transposase in 25 μl of reaction buffer. Purified DNA fragments were amplified with 9 cycles of PCR, and PCR products were purified by using AMPure XP beads (1:3 ratio of sample to beads, Beckman Coulter). The libraries were sequenced on NextSeq 500 (Illumina) in 50 bp paired-end format. The data was highly reproducible since the number of peaks observed was almost completely the same between biological replicates with similar read depth

treatment_protocol: Mice were either untreated or sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 6 hours in vivo.  After this time, lungs were isolated and digested with collagenease, DNase, hyaluronidase, and Liberase TM to generate a single cell suspension. Cells were stained for flow cytometry and sorted for autofluorescence-, CD11c+, I-A(b) hi, CD88-, Ly6C- cells to include cDCs but not alveolar macrophages, moDCs, or inflammatory DCs.

tag: background

tag: gender

value: male

value: Lung

value: Sorted cDC

tag: timepoint

value: OVA/ stFLA

value: MyD88 fx/fx; Itgax-cre+/Tg


title: NPC_H3K27me3

tag: genotype/variation


title: Lung_cDC_WT_MyD88 fx_6h_OVA_stFLA

description: Sorted cDC

source_name: Lung cDC WT MyD88 fx/fx-6h OVA/stFLA

value: MyD88 fx/fx


title: Lung_cDC_SPC_cre+_MyD88 fx_6h_OVA_stFLA

description: Sorted cDC

source_name: Lung cDC SPC cre+ MyD88 fx/fx-6h OVA/stFLA

value: MyD88 fx/fx; Sftpc-cre+/Tg


title: PCGF5-depleted_NPC_H3K27me3


title: Lung_cDC_MyD88_KO_6h_OVA_stFLA

description: Sorted cDC

source_name: Lung cDC MyD88 KO-6h OVA/stFLA


title: Lung_cDC_SPC_cre+_MyD88 fx_0h

description: Sorted cDC

source_name: Lung cDC SPC cre+ MyD88 fx/fx-0h


title: Puf3-PTP-IP


title: Lung_cDC_WT_MyD88 fx_0h

description: Sorted cDC

source_name: Lung cDC WT MyD88 fx/fx-0h


title: Lung_cDC_MyD88_KO_0h

description: Sorted cDC

source_name: Lung cDC MyD88 KO-0h


title: PCGF5-depleted_NPC_H2AK119ub1


title: Lung_cDC_CD11c_cre+_MyD88 fx_0h

description: Sorted cDC

source_name: Lung cDC CD11c cre+ MyD88 fx/fx-0h


title: PCGF5-depleted_ES_input

source_name: 46C mES

value: embryonic stem cells (ES)


title: PCGF5-depleted_ES_H2AK119ub1


title: PCGF5-depleted_ES_H3K27me3


title: ES_input


title: ES_H3K27me3


title: WT_day6-#2

description: PolyA+ selected

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were first aligned to the mm9 genome using TopHat (v2.0.4), then gene expression level quantification was conducted using Cufflinks (v2.1.1).
Genes with fold change greater than 1.5 were determined as differentially express genes (DGEs) between Pcgf5-/- KO and WT.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM Gene quantification result generated by Cufflinks

molecule: polyA RNA

growth_protocol: MPI-II cell line were cultured on feeders-coated plates in DMEM high-glucose media containing 15% FBS, 1mM sodium pyruvate, 1mM non-essential amino acids, 1 3 MPI-II cell lineGlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF) (Millipore), and the 2i inhibitors, 3 mM CHIR99021 (Selleck), and 1 mM PD0325901.

extract_protocol:
Purified RNA was fragmented and the cDNA was synthesized by reverse transcription. The resulting double-stranded DNA fragments were en-repaired and A-nucleotide overhangs were added.
After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

treatment_protocol: MPI-II cell line were induced to differentiate by culturing in differentiation N2B27 medium.

tag: cell line

value: MPI-II cell line

value: WT

value: mES

tag: time point

value: Differentiation 6 days


title: WT_day6-#1

description: PolyA+ selected


title: WT_day0-#1

description: PolyA+ selected

value: Differentiation 0 day


title: ES_H2AK119ub1


title: WT_day0-#2

description: PolyA+ selected


title: Pcgf5-/-_day6-#2

description: PolyA+ selected


title: H3K9me3_KO

description: readcountsaroundtss.txt

tag: strain

value: Spleen


title: Pcgf5-/-_day6-#1

description: PolyA+ selected


title: Pcgf5-/-_day0-#1

description: PolyA+ selected


title: Cell 175

city: Cincinnati

first: Harinder

last: Singh

state: OH

address: 333 Burnet Avenue

department: Immunobiology

institute: CCHMC

description: cells were sorted by flow based on surface phenotype (B220+ Fashi GL7hi NP+)

data_processing:
Reads were aligned to mm10 mouse genome assembly by using Tophat v2.0.
Aligned reads were then used to build transcript model using cuffdiff from cufflinks v2.2.
The quantile normalization was used to reduce technical variation and batch effects.
Genome_build: mm10
Supplementary_files_format_and_content: normalized FPKM values

source_name: NP+ GC B cells

extract_protocol:
Flow-sorted cells were resuspended at a concentration of 3×105 cells/ml then loaded onto a primed C1 Fluidic Chip for mRNA-Seq (5-10 μm). Cell separation was visually scored. Cells were lysed on chip and reverse transcription was performed using Clontech SMARTer® Kit using the mRNA Seq: RT + Amp (1771x) according to the manual. After the steps of reverse transcriptase, cDNAs were transferred to a 96 well plate and diluted with C1TM DNA Dilution Reagent. Quant-iTTM PicoGreen® dsDNA Assay Kit (Life Technologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit (Agilent Technologies (Santa Clara, CA) were used to quantify cDNAs.
Libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA) on cDNAs with an initial concentration>200 pg/μl that were then diluted to 100 pg/μl. In each single-cell library preparation, a total of 125pg cDNA was tagmented at 55 °C for 20 minutes. Libraries were pooled and purified on AMPure® bead-based magnetic separation before a final quality control using Qubit® dsDNA HS Assay Kit (Life Tecnologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit.

tag: days post immunization

value: 13 days


title: Cell 180


title: Cell 179


title: Cell 177


title: Cell 176


title: Cell 181


title: Cell 182


title: Cell 170


title: Cell 174


title: Cell 167


title: Cell 165


title: Cell 164


title: Cell 172


title: Cell 173


title: Cell 169


title: Cell 162


title: Cell 166


title: Cell 168


title: No2-compound-treat-RNAseq-rep2

value: Human embryonic kidney

value: HEK 293 transfected with reporter construct

tag: treatment

value: No2-compound treated


title: Cell 160


title: Pcgf5-/-_day0-#2

description: PolyA+ selected


title: Cell 178


title: Cell 171


title: Cell 156


title: Cell 155


title: Cell 152


title: Cell 153


title: Cell 151


title: Cell 150


title: Cell 149


title: Cell 148


title: Cell 147


title: Cell 146


title: Cell 145


title: Cell 142


title: Cell 143


title: Cell 144


title: Cell 139


title: Cell 158


title: Cell 159


title: Cell 163


title: Cell 136


title: Cell 138


title: Cell 135


title: Cell 157


title: Cell 133


title: Cell 141


title: Cell 154


title: Cell 132


title: Cell 131


title: Cell 129


title: Cell 130


title: Cell 161


title: Cell 128


title: Cell 127


title: Cell 134


title: Cell 124


title: Cell 140


title: Cell 137


title: Cell 126


title: Cell 125


title: Cell 122


title: Cell 123


title: Cell 116


title: Cell 115


title: Cell 117


title: Cell 119


title: Cell 111


title: Cell 109


title: Cell 120


title: Cell 110


title: Cell 113


title: Cell 112


title: Cell 114


title: Cell 118


title: Cell 108


title: Cell 106


title: Cell 107


title: Cell 105


title: Cell 102


title: Cell 104


title: Cell 100


title: Cell 97


title: Cell 99


title: Cell 94


title: Cell 121


title: Cell 96


title: Cell 103


title: Cell 95


title: Cell 91


title: Cell 98


title: Cell 89


title: Cell 86


title: Cell 87


title: Cell 88


title: Cell 90


title: Cell 101


title: Cell 82


title: Cell 81


title: Cell 84


title: Cell 79


title: Cell 83


title: Cell 80


title: Cell 93


title: Cell 78


title: Cell 76


title: Cell 75


title: Cell 77


title: Cell 73


title: Cell 74


title: Cell 92


title: Cell 71


title: Cell 70


title: Cell 68


title: Cell 69


title: Cell 85


title: Cell 67


title: Cell 65


title: Cell 66


title: Cell 64


title: Cell 60


title: Cell 62


title: Cell 59


title: Cell 61


title: Cell 57


title: Cell 53


title: Cell 54


title: Cell 55


title: Cell 51


title: Cell 50


title: Cell 58


title: Cell 52


title: Cell 47


title: Cell 45


title: Cell 48


title: Cell 49


title: Cell 46


title: Cell 43


title: Cell 44


title: Cell 42


title: Cell 39


title: Cell 37


title: Cell 38


title: Cell 40


title: Cell 41


title: Cell 63


title: Cell 36


title: Cell 35


title: Cell 33


title: Cell 34


title: Cell 32


title: Cell 31


title: Cell 26


title: Cell 28


title: Cell 27


title: Cell 56


title: Cell 30


title: Cell 29


title: Cell 24


title: Cell 72


title: Cell 19


title: Cell 20


title: Cell 22


title: Cell 21


title: Cell 16


title: Cell 15


title: Cell 14


title: Cell 11


title: Cell 10


title: Cell 9


title: Cell 18


title: Cell 7


title: Cell 13


title: Cell 12


title: Cell 8


title: Cell 17


title: Cell 25


title: Cell 4


title: Cell 6


title: Cell 5


title: Cell 23


title: Cell 1


title: Adelman_Bl6_mESC_C2cells_2i_4sU-RNA-seq_control_rep2

status: Public on Mar 09 2018

city: Boston

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
4-thiouridine labeled RNA from C2 embryonic stem cells
processed data file:
Adelman_mESC_C2cells_2i_4sU-RNA-seq_control_rep1and2_mean_normalized_coverage_plus.bw
Adelman_mESC_C2cells_2i_4sU-RNA-seq_control_rep1and2_mean_normalized_coverage_minus.bw

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
4sU read pairs containing one or more members with mean quality score <20 filtered; start-seq trimmed for adapter using cutadapt 1.9.1, pairs containing reads trimmed shorter than 20 nt filtered
4sU mapped to reference using tophat 2.0.4, in a strand-specific manner, with bowtie1 as the underlying aligner, also to index of ERCC spikes using bowtie 0.12.8; start-seq mapped to index composed of annotated rRNA/tRNA and spike-in sequences, successfully aligned pairs filtered, remaining mapped to reference using bowtie 0.12.8 retaining uniquely mappable pairs only, allowing 2 mismatches; ChIP-seq mapped using bowtie 0.12.8 retaining uniquely mapped pairs only, allowing 2 mismatches
4sU strand-specific coverage tracks were generated using genomeCoverageBed, normalized with custom scripts using factors determined by DESeq 1.12.2 based on ERCC spike counts and combined with unionBedGraphs and custom scripts (mean count); start-seq strand-specific bedGraphs generated using custom scripts based on 5' mapping location of end 1 reads only, with all replicates combined; ChIP-seq bedGraphs were generated by removing duplicate fragments, filtering fragments of length <50 and >400, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts
Genome_build: dm3 (ChIP-seq, start-seq), mm9 (4sU)
Supplementary_files_format_and_content: 4sU: bigWig containing mean normalized coverage of all replicates; start-seq: bedGraph containing combined count of end 1 5' mapping locations for all replicates; ChIP-seq: bedGraph containing combined count of fragment centers for all replicates

growth_protocol: Drosophila S2 cells from the DGRC were grown in M3 media supplemented with bactopeptone, yeast extract and 10% FBS. For all experiments, cells were harvested at a consistent cell density of 4-6x10^6 cells/ml. mESC culture was conducted at 37°C in 5% CO2. NELF-BFl/Fl, CreER+/- ESCs were maintained without feeders in 2i media (knockout DMEM (KO-DMEM), 15% knockout serum replacement (KOSR, Invitrogen), 1 mM NaPyruvate (Millipore), 1% NEAA, 1% BME, 1% Pen/Strep, 1% Glutamax, 1000 U/ml ESGRO, 1 µM MEK inhibitor (PD0325901, Stemgent), and 3 µM GSK3 inhibitor (CHIR99021, Stemgent)) and passaged every 2 days.

extract_protocol:
4sU experiments: metabolically labeled RNA was extracted with Trizol. Equal amounts of total RNA were biotinylated and pulled down with streptavidin beads. 4-thiouridine labeled RNA was eluted with DTT, ethanol precipitated and resuspended in RNAse-free H2O. Start-seq experiments: nascent RNA was isolated from nuclei. ChIP-seq experiments: Sonicated genomic DNA was extracted after IP with respective antibody, Phenol-Chloform extracted and ethanol precipitated.
4sU experiments: TruSeq Stranded Total RNA, with Ribozero Gold and ERCC spikes. Start-seq experiments: TruSeq Small RNA, with homemade spike-in RNAs. ChIP-seq experiments: NextFlex Rapid DNA-seq on IPed or digested genomic DNA

treatment_protocol: 4sU experiments: Two independent biological replicates were generated for Control and 4OHT treated C2 embryonic stem cells to ablate NELF-KO where RNA was metabolically labeled for 10minutes using 500 μM 4-thiouridine. To activate Cre recombinase and recombine out the floxed NELF-B allele, NELF-BFl/Fl, CreER+/- ESCs were treated with 100 nM 4OHT (Sigma) for 5 days. ESCs were then grown in 2i media without 4OHT for the completion of the experiment. Start-seq experiments: Start-RNA libraries were prepared as described in (Nechaev et al., Science 2010 and Henriques et al. 2013). ChIP-seq experiments: ChIP-seq libraries were prepared as described in (Muse et al., Nat Genetics 2007 and Henriques et al. 2013).

value: embryonic stem cell

tag: source gender

value: male

value: control

value: nascent RNA


title: Adelman_Bl6_mESC_C2cells_2i_4sU-RNA-seq_control_rep1

tag: molecule subtype


title: Adelman_Bl6_mESC_C2cells_2i_4sU-RNA-seq_NELF-KO_rep2

description:
4-thiouridine labeled RNA from C2 embryonic stem cells
processed data file:
Adelman_mESC_C2cells_2i_4sU-RNA-seq_NELF-KO_rep1and2_mean_normalized_coverage_plus.bw
Adelman_mESC_C2cells_2i_4sU-RNA-seq_NELF-KO_rep1and2_mean_normalized_coverage_minus.bw

value: NELF-KO


title: Cell 3


title: OMA_3_mp

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: Processed data file: RSEMNormExpectedCounts.txt

data_processing:
Libraries sequenced using Illumina HiSeq 2500.
Base-calling was produced by Illumina RTA Software v 1.13.48.
Demultiplexed fastq files were generated from the bcl files using bclToFastq v1.18 from Illumina.
Sequencing adaptor contaminations were removed using cutadapt.
Reads were mapped and gene expression quantified using rsem v1.17.
Counts were normalized using voom from Limma R package.
Genome_build: GRCm38 v70
Supplementary_files_format_and_content: RSEMNormExpectedCounts.txt: Tab-separated text file. Contains expected counts per gene aligned with RSEM. Samples in columns, Genes in rows.

source_name: Heart, OMA1 KO, isoproterenol

extract_protocol:
Mice were killed by cervical decapitation, and heart tissue were dissected and immediately frozen in liquid nitrogen.
Total RNA was extracted with TRIzol reagent and then purified on RNeasy spin columns (Qiagen).
RNA libraries were prepared for sequencing using TruSeq RNASeq kit from Illumina.

treatment_protocol: Isoproterenol (ISO; 10 mg/kg/day, Sigma) was chronically administered with minipumps (Mini-Osmotiz Pump Model 2004, Alzet) for 7 days before sample collection for RNA.

tag: strain/background

value: OMA1 KO

tag: age

value: 12 weeks

tag: Sex

value: Heart

value: Isoproterenol


title: Cell 2


title: Adelman_Bl6_mESC_C2cells_2i_4sU-RNA-seq_NELF-KO_rep1

tag: cell type


title: OMA_2_mp

tag: tissue


title: OMA_3

source_name: Heart, OMA1 KO, non-treated


title: C57_1_mp

source_name: Heart, WT, isoproterenol

value: wild type


title: OMA_1_mp


title: C57_3_mp