title: RNA-Seq-mES-EPOP-KO


title: GFP120613

status: Public on Nov 17 2016

type: SRA

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

country: USA

institute: Morgridge Institute for Research

library_source: transcriptomic

data_processing:
alignment: bowtie
quantification: RSEM
normalization: median-by-ratio
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq values for all genes AdGFP AdNfatc1 and AdNfatc2 with posterior probabilities for DE

molecule: total RNA

organism: Mus musculus

source_name: GFP

extract_protocol: Total RNA was isolated from mouse islets using RNeasy spin columns according to the manufacturer’s directions (Qiagen). RNA quantity was determined using a Nanodrop (Thermo Scientific) and the quality assessed by a Bioanalyzer (Agilent). Total mouse RNA was used for RNA-sequencing on an Illumina HiSeq 2000.

tag: tissue

value: whole pancreatic islets

tag: strain

tag: transduction

value: GFP


title: orc1-161 BrdU ChIP IP HU IP rep1

city: Seattle

first: Laura

last: Lee

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

library_source: genomic

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Mapped reads were filtered (-F 256)
Per-base coverage file was generated from mapped reads
Coverage files were normalized such that the average value at a genomic position of 1
Genome_build: Saccharomyces_cerevisiae.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized per-base coverage

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to OD660 0.2. G1 cells were arrested with alpha-factor (5ug/ml final for BAR1+ strains; 1ug/mL final for bar1- strains). G2/M cells were arrested with nocodazole (15ug/ml final). For cells in S phase, G1-arrested cells were filtered and washed, and released into fresh YPD alone or in YPD containing 200mM HU.

extract_protocol:
Cells were disrupted with glass beads, then crosslinked DNA was sonicated to generate ~350bp fragments
Libraries were constructed using NuGEN Ovation UltraLow Library systems

treatment_protocol: Cells were fixed with 1% formaldehyde for 20 min.

tag: genotype

tag: treatment

value: BrdU

tag: temperature


title: EIP1_OX_7-2-1

city: Shanghai

first: He

last: zuhua

state: Shanghai

address: 300 Fenglin Road

department: SIBS

country: China

institute: Institute of Plant Physiology and Ecology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the rice reference genome Nipponbare genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

organism: Oryza sativa Japonica Group

source_name: leaf

growth_protocol: The RNA samples were isolated from the leafs of the variety ZH11, ebr1 and EIP1_OX plants  grown in the isolated paddy field in our research station (Shanghai) during natural growing seasons.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: booting stage

value: leaf

tag: age

value: two month old plants


title: ebr1-1


title: ChIP-Seq-mES-ElonginB Control Repl1

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 or human genome hg19 using bowtie 1.0 with n = 1 and m = 3
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
RNA-Seq data were aligned by Tophat v0.9 to mm10, using the Galaxy Platform. Normalized Values were derived using Cuffdiff v2.2.1 using a gffread filtered gencode.vM6.basic.annotation.gtf file as template
Supplementary_files_format_and_content: bigwig, txt

source_name: Embryonic stem cells

growth_protocol: E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptomycin (Invitrogen) and LIF (Millipore) on gelatin-coated plates, SH-SY5Y cells were cultured in DMEM, 10% FCS, 1 x Penicillin/Streptomycin

extract_protocol:
Genomic DNA were extracted using antibodies for EPOP, H3K4me3, Elongin B, RNA Polymerase II S5, USP7 or H2Bub. RNA-Seq samples were prepared by isolating total RNA using Trizol, mRNA Isolation, heat fractionation, reverse transcription and second strand synthesis
Libraries were constructed of 10-50 ng of DNA following Illumina’s® protocol

treatment_protocol: For ChIP cells were crosslinked with 1% formaldehyd for 10 min and sonicated to 200 bps.

tag: cell type

value: Control

tag: chip antibody

value: Elongin B; abcam, ab168836


title: orc1-161 BrdU ChIP IP HU IP rep2


title: ebr1-2


title: orc1-161 BrdU ChIP HU Input rep2


title: ZH11-2

value: WT


title: Ahr+/+ B cells replicate 2

status: Public on Nov 16 2016

city: London

first: Brigitta

last: Stockinger

address: Ridgeway

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Libraries were sequenced by Hiseq 2000 in 80bp single-end reads
Basecalling was done using Illumina default pipeline
Reads were mapped using Tophat (version 2) to the mm10 mouse assembly
Read counts for each gene were generated in htseq-count: transcripts from the same gene were collapsed into a single transcript containing all exons
Differences in the abundance of transcripts between KO and WT control samples were calculated in the R/Bioconductor program DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised read counts for each sample and output from DESeq analysis.

molecule: polyA RNA

source_name: B lymphocytes

growth_protocol: B cells were isolated from spleen. B cells were cultured in IMDM 5% FCS, in presence of anti-IgM (10 ug/ml) and IL-4 (20 ng/ml), for 8h. In the last 4h of culture, FICZ (250 nM) was added to the culture.

extract_protocol:
RNA was extracted using the RNAeasy mini kit (Qiagen) and following manufacturer instructions. 1 µg RNA was used for further analysis.
Library generation was performed according manufacturer instructions using the TruSeq stranded mRNA library prep kit (Illumina).

value: Spleen

tag: background strain

value: Ahr+/+

value: B lymphocytes


title: orc1-161 BrdU ChIP HU Input rep1


title: Ahr-/- B cells replicate 1

value: Ahr-/-


title: Ahr-/- B cells replicate 2


title: Ahr-/- B cells replicate 3


title: Ahr+/+ B cells replicate 1


title: ChIP-Seq-mES-EPOP Ab1 Control

growth_protocol: E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptomycin (Invitrogen) and LIF (Millipore) on gelatin-coated plates, SH-SY5Y cells were cultured in DMEM, 10% FCS, 1 x Penicillin/Streptmycin

value: EPOP (Ab1)


title: inputs-Rap1 (2)

city: Madrid

first: Gonzalo

last: Gomez-Lopez

state: Madrid

address: Calle Melchor Fdez Almagro 3

department: Structural Biology

country: Spain

institute: CNIO

description:
genomic DNA
G0_WTvsKO_InputCleaned.147.bed
G1_WTvsKO_InputCleaned.894.bed
G3_WTvsKO_InputCleaned.2266.bed

data_processing:
RNA-seq processing:
Read files were quality-checked with FastQC.
Reads were aligned to the mouse genome (mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Mus musculus mm10 transcript annotations from the UCSC Genome Browser were used
Genome_build: mm10
Supplementary_files_format_and_content: tables were generated with Cufflinks 2.2.1 and contain transcripts abundance measured in FPKM values
ChIP-seq processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA
WT peaks were called using MACS2 with the KO as a control for G0, G1 and G3, pooling the two replicas for each condition
Input peaks were called using MACS2 with random control, pooling the two replicas as treatment
Input peak regions were removed from G0, G1 and G3 peaks using bedtools (reciprocal overlap bigger than 50%)
Genome_build: mm9
Supplementary_files_format_and_content: BED output of called peaks contains chrom, start, end

source_name: inputs Rap1

extract_protocol:
For RNA-seq Total RNA was extracted using the RNeasy kit (Qiagen)
For ChIP-seq assays were performed according to the Millipore protocol. Cells were fixed using 1% formaldehyde, harvested, resuspended in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using Bioruptor Pico (Diagenode) to generate fragments of 150 to 300 bp. Soluble chromatin was diluted 8 fold in ChIP RIPA buffer (10mMTris–HCl, pH 7.5, 140mMNaCl, 1mMEDTA, 0.5mMEGTA,1%Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated with Dynabeads Protein A (Invitrogen) coupled to H3K36me2 antibody ab9049 from Abcam. After incubation, the immunocomplexes were washed sequentially with Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1) and TE. Immunocomplexes were eluted in ChIP elution buffer (1%SDS, 0.1M NaHCO3) and the crosslinking was reverted overnight at 65 ºC. Samples were treated with Proteinase K and RNase A and DNA was extracted using the QIAGEN PCR purification kit. Purified chromatin was used for library construction.
For RNA-seq 1 µg of total RNA sample was used . PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
For ChIP-seq the amount of DNA used was 15ng from each sample. Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEXTflex ChIP Sequencing kit" from Bioo Scientific (part # 5143). Adapter-ligated libraries were completed by limited-cycle PCR (13 cycles) and extracted with a double double-sided SPRI size selection. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: embryonic fibroblast

tag: chip ab

value: input


title: inputs-RAP1

source_name: inputs RAP1


title: G3-Rap1-KO1

description:
genomic DNA
G3_WTvsKO_InputCleaned.2266.bed

source_name: G3 Rap1 KO1


title: G3-Rap1-wt1

source_name: G3 Rap1 wt1


title: Hi-C_NT_25_Rep2_re-analyzed

city: Atlanta

first: Victor

middle: G

last: Corces

state: GA

address: 1510 Clifton Rd

department: Biology

institute: Emory University

description: HiC Library digested with DpnII

data_processing:
Library strategy: Hi-C
Raw HiC data from this submission and the four normal temperature HiC biological replicates digested with DpnII from GSE63515 (GSM1551441, GSM1551442, GSM1551443, GSM1551444) were combined and processed through the Juicer pipeline (Rao et al. 2014. Cell. 159:1665-80) to generate the .hic file.
To identify the significant genomic interactions, the .hic file was further processed through ICE and Fit-Hi-C (Imakaev, et al. 2012. Nature. 9:999-1003; Ay et al. 2014. Genome Research. 24:999-1011)
Genome_build: dm6
Supplementary_files_format_and_content: The .hic file contains the HiC contact matrix. The Fithic .txt file contains the genomic coordinates of the interactions anchors in columns 1-3 and 4-6. The p value and q value for each interaction are reported in column 7 and 8, respectively.

organism: Drosophila melanogaster

source_name: Kc167 _DpnII

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were incubated with HindIII or DpnII. Fragment ends were filled with biotinylated nucleotides, ligated. After reversion of crosslinks, DNA was purified, sonicated and used to make Illumina libraries
To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

tag: cell line

value: Drosophila Embryonic Cell Line


title: Hi-C_NT5_Rep1_re-analyzed

description: HiC Library digested with DpnII


title: G1-Rap1-ko2

description:
genomic DNA
G1_WTvsKO_InputCleaned.894.bed

source_name: G1 Rap1 ko2


title: HinfI_HiC

description: HiC Library digested with HinfI

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. Nuclear lysates were digested with DpnII or Hinf1 and  fragment ends were filled with biotinylated nucleotides prior to ligatation. Ligated fragments were reverse crosslinked, purified, and sonicated prior to generation of Illumina libraries.
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligated at room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.


title: G1-Rap1-ko1

source_name: G1 Rap1 ko1


title: d6_48h

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

data_processing:
The RNA-Seq Pipeline Tophat v13 - available  at RAP (https://bioinformatics.cineca.it/rap/) and including quality controls, adaptor trimming and masking of low quality sequences, tophat 2, bowtie, Cufflinks 2.2 - was used to obtain transcript reconstruction, alignment to reference genome (hg19), and expression. Transcript levels were calculated as FPKM (Fragments Per Kilobase of exon per Million fragments mapped).
Differential expression was computed through CuffDiif 2 (as well as by DEseq)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix in tab-delimited text format, including FPKM values for each Sample

organism: Homo sapiens

source_name: BT168FO (Glioblastoma stem cells)

growth_protocol: Glioblastoma stem cells BT168 (De Bacco et al., Cancer Res. 2012) carrying a Dox inducible FLAG-Omomyc (BT168FO) were grown as neurospheres in serum free neural stem cell medium supplemented with EGF and bFGF.

extract_protocol:
RNA was isolated using TRIzol reagent
Libraries were prepared at the Istituto di Genomica Applicata (IGA) in Udine (http://www.appliedgenomics.org/) according to Illumina TruSeq RNA Sample Preparation Kits v2

treatment_protocol: BT168FO cell cultures were treated with 250 ng/ml Doxycycline for different time periods (0-48 hours) before isolating RNA

value: BT168 glioblastoma stem cells (De Bacco et al., Cancer Res. 2012) with Dox inducible FLAG-Omomyc

value: Dox treated

tag: time


title: G1-RAP1-wt1

source_name: G1 RAP1 wt1


title: d5_24h


title: RAP1-ko2

description:
genomic DNA
G0_WTvsKO_InputCleaned.147.bed

source_name: RAP1 ko2


title: ZH11-1


title: DpnII_HiC

description: HiC Library digested with DpnII


title: Ahr+/+ B cells replicate 3


title: RAP1-ko1

source_name: RAP1 ko1


title: RAP1-wt2

source_name: RAP1 wt2


title: RAP1-wt1

source_name: RAP1 wt1


title: d4_16h


title: Hi-C_NT_53_Rep3_re-analyzed

description: HiC Library digested with DpnII


title: ZIPIC_ChIPseq

description: ChIP-seq (Chromatin immunoprecipitation) for ZIPIC

data_processing:
Reads were aligned to the dm6 reference genome using bowtie version 1.0.0, using default settings with the addition of the (-m 1) parameter. PCR duplicates were removed using samtools version 0.1.18 .
Wiggle files were generated with MACS (version 1.4.2) and peaks were called with a p value of 1e-10. Data from biological replicates was combined.
Genome_build: dm6
Supplementary_files_format_and_content: wiggle files

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. Nuclear lysates were sonicated to generate 200-500 bp fragments. Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods.
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

tag: chip-antibody

value: ZIPIC


title: Hi-C_NT_89_Rep4_re-analyzed

description: HiC Library digested with DpnII


title: d3_8h


title: G3_WT2

description: Isolation of poly A+ RNA from total RNA

source_name: G3 WT2


title: G3-Rap1-wt2

source_name: G3 Rap1 wt2


title: Pita_ChIPseq

description: ChIP-seq (Chromatin immunoprecipitation) for Pia

value: Pita


title: G3_WT1

description: Isolation of poly A+ RNA from total RNA

source_name: G3 WT1


title: G3_KO2

description: Isolation of poly A+ RNA from total RNA

source_name: G3 KO2


title: G1-RAP1-wt2

source_name: G1 RAP1 wt2


title: Ibf2_ChIPseq

description: ChIP-seq (Chromatin immunoprecipitation) for Ibf2


title: d2_4h


title: G3_KO1

description: Isolation of poly A+ RNA from total RNA

source_name: G3 KO1


title: Ibf1_ChIPseq

description: ChIP-seq (Chromatin immunoprecipitation) for Ibf1


title: d1_0h (no Dox treatment)

value: Untreated with Dox


title: G1_WT2

description: Isolation of poly A+ RNA from total RNA

source_name: G1 WT2


title: G1_WT1

description: Isolation of poly A+ RNA from total RNA

source_name: G1 WT1


title: G1_KO1

description: Isolation of poly A+ RNA from total RNA

source_name: G1 KO1


title: c4_16h


title: H3K27me3_Rep2_ChIPseq

description:
ChIP-seq (Chromatin immunoprecipitation) for H3K27me3
Processed data for H3K27me3 were combined. Wig file is available on GSM2133764.

value: H3K27me3 (Millipore #07-449)


title: Nup98_ChIPseq

description: ChIP-seq (Chromatin immunoprecipitation) for Nup98


title: c3_8h


title: G0_WT2

description: Isolation of poly A+ RNA from total RNA

source_name: G0 WT2


title: G0_WT1

description: Isolation of poly A+ RNA from total RNA

source_name: G0 WT1


title: H3K27me3_Rep1_ChIPseq


title: G0_KO2

description: Isolation of poly A+ RNA from total RNA

source_name: G0 KO2


title: c1_0h (no Dox treatment)

source_name: BT168FO (Glioblastoma stem cells)


title: c2_4h


title: mtTGFB2_n2

city: Nashville

first: Daniel

last: DeLaughter

state: TN

address: Preston Research Building Room 460

department: Cell and Developmental Biology

institute: Vanderbilt University Medical School

data_processing:
HiSeq 2000 reads are aligned by TOPHAT2 (http://tophat.cbcb.umd.edu/) to produce bam files.
Gene expression profiles were generated using a Bayesian p-value
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include expression values (normalized reads to total per million and total reads)

source_name: Immortalized epicardial cells

growth_protocol: Cells were grown at 33°C in DMEM containing 10% fetal bovine serum, 100 U/ml penicillin/streptomycin, Insulin– Transferrin–Selenium (ITS: 1 μg/ml insulin, 5.5 × 10−4 μg/ml transferrin, 0.677 μg/ml selenium), and 10 U/ml interferon γ (INFγ).

extract_protocol:
Standard phenol-chloroform extraction of RNA was performed.  RNA integrity was checked with Agilent 2100 Bioanalyzer
RNAseq libraries were generated without normalizations or RNA/cDNA fragmentation

treatment_protocol: For experiments, the T-antigen was inactivated by culturing at 37°C in the absence of ITS or INFγ. Cells were seeded at 200,000 cells per well of a 6-well tissue culture plate and allowed to adhere overnight at 37˚C. The following day the medium was replaced with media containing either VEH, 250 pM TGFβ1, 250 pM TGFβ2, or 5 nM BMP2 and incubated at 37˚C for 72 hours.

value: Immortalized epicardial cells

tag: stage isolated

value: C57BL/6 SV129 mixed background


title: mtBMP2_n2


title: mtVEH_n2


title: wtVEH_n2


title: G0_KO1

description: Isolation of poly A+ RNA from total RNA

source_name: G0 KO1


title: Histone3_ChIPseq

description: ChIP-seq (Chromatin immunoprecipitation) for H3

value: H3 (Abcam ab1791)


title: wtBMP2_n2


title: GAF_ChIPseq

description: ChIP-seq (Chromatin immunoprecipitation) for GAF

value: GAF


title: 5_24h


title: 6_48h


title: wtTGFB2_n2


title: 4_0h (no Dox treatment)


title: nf-ycQ rep2

city: Guangzhou

first: Yang

last: Tang

state: Guangdong Province

address: No.723 Xingke Road, Tianhe District

department: South China Botanical Garden

institute: Chinese Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
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.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: TAIR10 (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas)
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings of Arabidopsis thaliana were grown  on  half-strength Murashige-Skoog (1/2 MS) medium containing 0.3% sucrose and 0.8% agar.

extract_protocol:
Seedlings were removed, flash frozen on dry ice, and RNA was harvested using the E.Z.N.A. Total RNA Kit I (Omega).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings of Arabidopsis thaliana were grown under red light (20 μmol•m-2•s-1)for 2 days.

value: seedling

tag: ecotype

value: Columbia background

value: 2 days under red light

tag: genotype/variation

value: T-DNA knockout mutant of nf-ycQ


title: nf-ycQ rep3

tag: tissue


title: mtVEH_n1

tag: strain


title: mtBMP2_n1

tag: genotype


title: BT IP-RNA POL II, + Dox

description:
IP genomic DNA
Sample_a5-140228

data_processing:
Read alignment: Bowtie 0.12.7; bowtie -v 2 -S -y -m 1 --best --strata -p 6
Peak calling: MACS 1.4.2; macs14  --format='SAM'  --gsize='2700000000' --tsize='50' --bw='300' --pvalue='1e-05' --mfold='10,30'  -w
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: bigwig files were generated from the bam mapping files using bedtools genomecov -scale X, where X = 1000000/(mapped reads), resulting height normalized as Read Per Million (RPM)

growth_protocol: Human glioblastoma cells U-87 MG (ATCC® HTB-14™) cells harboring a Dox inducible FLAG-Omomyc (U87FO) were grown on tissue culture plates - avoiding confluency - in DMEM supplemented with 10% foetal bovine serum. Glioblastoma stem cells BT168 (De Bacco et al., Cancer Res. 2012) carrying a Dox inducible FLAG-Omomyc (BT168FO) were grown as neurospheres in serum free neural stem cell medium supplemented with EGF and bFGF.

extract_protocol:
U87FO cells were processed according to Myers Lab ChIP-seq Protocol v041610.2. BT168FO cells were processed through the MAGnify Chromatin Immunoprecipitation System (Thermo Fisher).
Libraries were prepared at the Istituto di Genomica Applicata (IGA) in Udine (http://www.appliedgenomics.org/) according to Illumina TruSeq DNA Sample Preparation Guide

treatment_protocol: Cell cultures were treated or not with 250 ng/ml Doxycycline for 24 h before formaldehyde cross-linking and processing for ChIP-seq.

tag: treatment

value: Pol II (N-20) rabbit polyclonal antibody (sc-899X, Santa Cruz lot# L0312)


title: Col rep3

value: wild-type


title: G3-Rap1-KO2

source_name: G3 Rap1 KO2

value: embryonic fibroblast


title: Col rep2


title: nf-ycQ rep1


title: wtTGFB1_n2


title: BT IP-MYC, + Dox

description:
IP genomic DNA
Sample_a3-140228
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.

value: BT168 glioblastoma stem cells (De Bacco et al., Cancer Res. 2012) with Dox inducible FLAG-Omomyc

value: c-Myc N-262 rabbit polyclonal antibody (sc-764X, Santa Cruz Biotech)


title: BT IP-MYC, - Dox

description:
IP genomic DNA
Sample_a2-140228
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.


title: Col rep1


title: wtBMP2_n1


title: mtTGFB2_n1


title: U87 IP-RNA POL II, + Dox

description:
IP genomic DNA
Sample_u10-130719

source_name: U87FO (Glioblastoma cell line)

value: U-87 MG (ATCC HTB-14) cells with Dox inducible FLAG-Omomyc

value: Dox treated

value: Pol II (N-20) rabbit polyclonal antibody (sc-899X, Santa Cruz; lot# L0312)


title: BT IP-RNA POL II, - Dox

description:
IP genomic DNA
Sample_a4-140228

value: Untreated with Dox


title: U87 IP-RNA POL II, - Dox

description:
IP genomic DNA
Sample_u9-130719


title: U87 IP-RNA POL II phospho Ser2, + DOX

description:
IP genomic DNA
Sample_15-130618
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.

value: RNA pol II CTD phospho Ser2 rat monoclonal antibody (Clone 3E10; Active Motif, 61083)


title: Control

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

data_processing:
The original image data was transferred into sequence data by base calling(using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
To obtain clean reads, it is necessary to remove the dirty raw reads prior to data analysis. This process encompasses the following procedures: (1) remove reads with adaptors; (2) remove reads in which unknown bases are greater than 10%; (3) remove low-quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read)
A comparison of “clean reads” by SOAPaligner/soap2(parameters:-m 0 -x 1000 -s 28 -l 32 -v 2 -r 2) was carried out using the reference databases from large-scale transcriptome profiling
Genome_build: The reference library is from the article "Transcriptome Sequencing and Characterization for the Sea Cucumber Apostichopus japonicus (Selenka, 1867)". The FASTA file with assembled sequences can be downloaded in supporting information from the website: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033311.
Supplementary_files_format_and_content: text file with RPKM values.

organism: Apostichopus japonicus

source_name: Apostihopus japonicus intestine

extract_protocol:
Total RNA from body wall was extracted and DNase-treated using RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Germany), following the manufacturer’ s instructions.
The quality and concentration of RNA were measured by NanoDrop 1000 (Thermo) after which the mRNA in total RNA was enriched by using the oligo(dT) magnetic beads. After the addition of fragmentation buffer, the mRNA was interrupted and formed short fragments (~200 bp). The first strand cDNA was then synthesized by the random hexamer-primer, using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified using the QiaQuick PCR extraction kit, and washed with EB buffer so as to facilitate end repair and the addition of a single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. The required fragments were purified by means of agarose gel electrophoresis and enriched by PCR amplification.

value: body wall

tag: light exposure level

value: Control


title: Light

value: Light


title: wtVEH_n1

value: Immortalized epicardial cells

value: C57BL/6 SV129 mixed background


title: mtTGFB1_n1


title: mtTGFB1_n2


title: WT_Sil_n2

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

country: Switzerland

institute: ETHZ

data_processing:
Basecalls performed using CASAVA 1.8.
RNAseq reads were aligned to the TAIR10 genome assembly using Tophat2.
Genome_build: TAIR10
Supplementary_files_format_and_content: Cufflink output
Supplementary_files_format_and_content: merged.gtf is linked as a supplementary file on the Series record (because extra transcripts annotated by Cufflinks as CUFF are not detailed in the cufflinks files.)

source_name: WT

growth_protocol: Arabidopsis thaliana  plants grown on soil under long day light conditions

extract_protocol:
Total RNA was isolated with Quiagen RNAeasy mini kit
Libraries construction was contracted out to Functionnal Genomic Center Zurich , barcoded libraries were prepared such that four samples could be run per lane.
Libraries were prepared according to Illumina's instructions accompanying the stranded sequencing Kit TruSeq™ SBS v3 and RNA enrichment was performed with RNA-Ribosomal Depletion (Ribo Zero).

value: WT

tag: tissues

value: Siliques 1-5DAP


title: Het_1

city: Zürich

first: Hind

last: Hashwah

address: Winterthurerstrasse 190

department: Institute of Molecular Cancer Research

institute: University of Zürich

data_processing:
RNA-seq reads were quality-checked with fastqc, which computes various quality metrics for the raw reads.
RNA-seq reads were mapped to the GRCh38 reference human genome using STAR and reads were counted according to Ensembl gene annotation using the featureCounts function in the Rsubread Bioconductor package.
Statistical analysis of differential expression was conducted with the DESeq2 package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts per sample

source_name: DLBCL cell line

growth_protocol: U2932 cells were maintained at 37°C, 5% CO2 in a humidified atmosphere in RPMI supplemented with 20% heat-inactivated FBS and antibiotics.

extract_protocol:
Cells were collected by spinning for 5 minutes at 350 rcf, frozen in liquid nitrogen, then RNA was isolated using the NucleoSping RNA Kit (Macherey-Nagel).
Library preparation was performed using the TruSeq RNA Sample Prep Kit v4 (Illumina) and 1 µg of total RNA.

tag: crebbp status

value: CREBBP+/-


title: Het_4


title: WT_5

value: CREBBP+/+


title: WT_4


title: wtTGFB2_n1

tag: cell type


title: WT_Sil_n1


title: WT_3


title: BT INPUT, - Dox

description:
Input genomic DNA
Sample_1-121005

tag: chip antibody


title: U87 INPUT +

description:
Input genomic DNA
Sample_u6-130719


title: Dark

value: Dark


title: Het_5


title: U87 IP-MYC, + DOX

description:
IP genomic DNA
Sample_13-130618
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.


title: U87 INPUT

description:
Input genomic DNA
Sample_11-130618


title: U87 IP-FLAG, - Dox

description:
IP genomic DNA
2-120808
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.

value: FLAG® M2 mouse monoclonal antibody (Sigma-Adlrich, F1804)


title: Het_3


title: h6_8h

value: BT168 glioblastoma stem cells (De Bacco et al., Cancer Res. 2012) with Dox inducible FLAG-Omomyc


title: Het_2


title: BT INPUT

description:
Input genomic DNA
Sample_a1-140228


title: MNase_HCT116_WT

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

data_processing:
Reads were trimmed of adapters and low quality sequences using BBDuk
MNase-seq reads were aligned to the hg19 genome assembly using BWA
Mapped reads were filtered for duplicates, multi-mappers, and unmapped reads using samtools and picard
Nucleosome positions were called using DANPOS2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file generated by converting normalized MACS2 bedgraphs using bedtools

source_name: Human Colonic Carcinoma Cell

growth_protocol: HCT116 cells were cultured in DMEM (HyClone with 10% fetal bovine serum, 100 U/mL penicillin and 100 ug/mL streptomycin (invitrogen)

extract_protocol:
Chromatin was cross-linked with 0.5% formaldehyde for 10 min at room temperature in PBS on the plate. The reaction was stopped by the addition of glycine to a final concentration of 125 mM and cells were harvested by scraping. Cells were washed twice with PBS and re-suspended in 1 mL lysis buffer (PBS, 0.5% Triton X-100, protease inhibitor (Roche)) at 1x106 cells/ml. Incubated on ice for 5 min then washed twice with 1 mL MNase buffer (20mM Tris-HCl pH 7.5, 15 mM KCl, 60 mM NaCl, 1 mM CaCl2). Cells then resuspended in 500 uL MNase buffer and MNase (NEB) added to a final concentration of 120 U/1x106 cells. Incubated at 37 C for 10 min the added 50 ul stop buffer (20 mM EDTA, 20 mM EGTA). Briefly sonicated 4 cycles (20 sec ON/40 sec OFF). Crosslinks were removed and proteins digested in Proteinase K buffer (500 mM NaCl, 2 mM EDTA, 20 mM Tris HCl pH 6.8, 0.5mg/ml proteinase K) for 2 hrs at 65 C. DNA was purified by adding 1 volume phenol chloroform isoamyl to proteinase K treated samples. Upper aqueous phase transferred to new tube and 1 volume of chloroform added. Upper aqueous phase transferred to new tube and DNA was ethanol precipitated. Purified DNA was ran on agarose gel to confirm MNase digestion and the mononucleosome band was gel extracted (~150 bp band) with the Zymo Gel DNA Recovery Kit.
500 ng of DNA was used to prepare sequencing libraries according to the KAPA Hyper Prep Kit instructions using adaptors and illumina barcode primers purchased from NEB. Libraries were amplified for 7 cycles and fragment size was confirmed on a Agilent 2100 bioanalyzer.

tag: tissue type

value: Human Colonic Carcinoma Cell

value: Wild Type


title: U87 IP-MYC, - DOX

description:
IP genomic DNA
Sample_12-130618
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.

value: U-87 MG (ATCC HTB-14) cells with Dox inducible FLAG-Omomyc

value: c-Myc N-262 rabbit polyclonal antibody (sc-764X, Santa Cruz Biotech)


title: BT INPUT, + Dox

description:
Input genomic DNA
Sample_3-121005

value: Dox treated


title: wtTGFB1_n1


title: BT IP-FLAG, - Dox

description:
IP genomic DNA
Sample_2-121005
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.

value: Untreated with Dox


title: h3_4h


title: h1_0h (no Dox treatment)


title: OoD7-DNA

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Lsd1 mko/mko oocyte 8 RNA seq

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality reads were discarded
Mapped to mm10 whole genome using  Tophat2 (2.0.6), Method: Global alignment - No mismatch in seed alignment (of size 22), 3 mismatches in read length, Keep uniques best hits
reads count estimation with HTSeq-0.5.3p9
differential expression with R (R-3.2.0), DESeq2 (1.4.5)
Genome_build: mm10

source_name: Oocyte

extract_protocol:
two-cell stage embryos were recovered and flash frozen;reverse transcription was carried out directly on the whole  embryos lysate, and total cDNA were then prepared according to Tang et al Nature Protocol  2010 to be used to  construct sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed B6;129

tag: developmental stage

value: mouse oocytes

value: Lsd1/Kdm1a mko/mko


title: OoD4-DNA

description: Lsd1 mko/mko oocyte 6 RNA seq


title: U87 IP-RNA POL II phospho Ser2, - DOX

description:
IP genomic DNA
Sample_14-130618
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.

tag: cell line

value: RNA pol II CTD phospho Ser2 rat monoclonal antibody (Clone 3E10; Active Motif, 61083)


title: U87 IP-FLAG, + Dox

description:
IP genomic DNA
4-120808
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.


title: WT_2


title: WT_1


title: U87 INPUT, + Dox

description:
Input genomic DNA
3-120808


title: OoD3-DNA

description: Lsd1 mko/mko oocyte 4 RNA seq


title: f3_24h

tag: time


title: OoC3

description: f/f oocyte 2 RNA seq

value: Lsd1/Kdm1a flox/flox


title: OoD1

description: Lsd1 mko/mko oocyte 2 RNA seq


title: e5_48h


title: OoC3-DNA

description: f/f oocyte 1 RNA seq


title: h7_8h


title: U87 INPUT, - Dox

description:
Input genomic DNA
1-120808


title: BT IP-FLAG, + Dox

description:
IP genomic DNA
Sample_4-121005
ChIP antibody lot# identifier unavailable.   However, all the IPs were performed with antibodies from the same lot#.


title: h9_16h


title: OoD4

description: Lsd1 mko/mko oocyte 7 RNA seq


title: g3_24h


title: g5_48h


title: Oo_21_R1

description: wt/wt oocyte 4 RNA seq

value: Lsd1/Kdm1a wt/wt


title: e1_0h (no Dox treatment)


title: Oo_20_R1

description: wt/wt oocyte 3 RNA seq


title: g1_0h (no Dox treatment)


title: Zucchini and Nibbler depleted ovaries_polyA selected RNAs

city: Vienna

first: Jakob

last: Schnabl

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
the first and last 6 bases were trimmed and the reads are split into three reads (37, 38, 38nt).
reads were mapped with bowtie v0.12.9 to transposon sequences allowing up to three mismatches.
Genome_build: Drosophila melanogaster dm3, release 5.55
Supplementary_files_format_and_content: RNAseq_TE_RPKM_table.txt: tab separated file of the counts per 1 milion genome mapped reads per kb (RPKM) of 122 TE for all genotypes

source_name: Zucchini and Nibbler depleted ovaries

extract_protocol:
total RNA was isolated with Trizol; polyA RNA selection
libraries are made using NEBNext Ultra directional RNA library prep kit for Illumina (NEB) using polyA selected RNAs

tag: age

value: 4-6 days old

value: adult

tag: gender

value: female

tag: knock-out or depletion

value: Zucchini and Nibbler depletion

tag: rna fraction

value: polyA selected RNA

value: ovary

tag: growth protocol

value: Flies were kept at strandard conditions at 25º C.


title: Nibbler -/- ovaries_polyA selected RNAs

source_name: Nibbler -/- ovaries

value: nibbler knock-out

tag: tissue


title: f1_0h (no Dox treatment)

value: BT168 glioblastoma stem cells (De Bacco et al., Cancer Res. 2012) with Dox inducible FLAG-Omomyc


title: f5_48h

value: Dox treated


title: h4_4h


title: OoD7

description: Lsd1 mko/mko oocyte 9 RNA seq

tag: strain

tag: genotype


title: OoD2

description: Lsd1 mko/mko oocyte 3 RNA seq


title: w1118 ovaries_polyA selected RNAs

source_name: w1118 ovaries

value: wild type


title: Zuc_Nbr_depletion_oxidized

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings
the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini)
reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3, release 5)
BigWig files were generated with Homertools v4.6
Genome_build: Drosophila melanogaster dm3, release 5.55
Supplementary_files_format_and_content: *depletion.txt: miRNA normalized read counts mapping to the plus and minus strand of the indicated sensor construct (1bp resolution)
Supplementary_files_format_and_content: genome_mapping_read_counts.txt: table indicating read counts for all genome mapping small RNA sequences in the indicated libraries (0MM, Uextra excluded)

source_name: small RNAs (18-40nt) from Zucchini and Nibbler depleted ovaries with 2S rRNA depletion and oxidation

extract_protocol:
total RNA was isolated with Trizol
small RNAs were PAGE selected and 3' and 5' linkers was ligated. 1st strand cDNA synthesis was performed using SuperScript II (Invitrogen) and the library was amplified using the Kapa HiFi Library Amp real time Kit (Peqlab) with Illumina TruSeq compatible primers.

tag: Sex

tag: transgenic construct

value: total small RNAs


title: e6_24h

tag: treatment


title: Zuc_Nbr_depletion_rep3

source_name: small RNAs (18-40nt) from Zucchini and Nibbler depleted ovaries with 2S rRNA depletion


title: Zuc_depletion_rep3

source_name: small RNAs (18-40nt) from Zucchini and depleted ovaries with 2S rRNA depletion

value: Zucchini depletion


title: Oo_4_R1

description: wt/wt oocyte 5 RNA seq

value: mouse oocytes


title: e3_24h

source_name: BT168FO (Glioblastoma stem cells)


title: Zuc_Nbr_depletion_rep2


title: OoD3

description: Lsd1 mko/mko oocyte 5 RNA seq

value: mixed B6;129

value: Lsd1/Kdm1a mko/mko


title: control depletion ovaries_polyA selected RNAs

source_name: control depletion ovaries

value: control depletion


title: Zucchini depleted ovaries_polyA selected RNAs

source_name: Zucchini depleted ovaries

value: 4-6 days old


title: Zuc_depletion_rep4

value: adult


title: Biogenisis_repoter_2_two_sites+Zuc_Papi_depletion

source_name: small RNAs (18-40nt) from flies containing  piRNA biogenesis repoter_2 with two target sites with Zucchini and Papi depletion and 2S rRNA depletion

value: female

value: Zucchini and Papi depletion


title: Biogenisis_repoter_2_two_sites+Zuc_Nbr_depletion

source_name: small RNAs (18-40nt) from flies containing  piRNA biogenesis repoter_2 with two target sites with Zucchini and Nibbler depletion and 2S rRNA depletion

value: Zucchini and Nibbler depletion


title: Oo_18_R1

description: wt/wt oocyte 1 RNA seq

value: Lsd1/Kdm1a wt/wt


title: Biogenisis_repoter_2_two_sites+Zuc_depletion

source_name: small RNAs (18-40nt) from flies containing  piRNA biogenesis repoter_2 with two target sites with Zucchini depletion and 2S rRNA depletion

value: ovary

value: Flies were kept at strandard conditions at 25º C.


title: CuH-sRNA

city: Norwich

first: Hannah

last: Gaimster

address: Norwich Research Park

institute: UEA

data_processing:
Alignment of reads to reference genome (NC_018750.1) using bowtie2 (bowtie2-2.2.3) options [bowtie2 -x reference_genome -S output.sam -U read_file]
Aligned sam file was split into strand specific files using the below script and adding a suitable sam header:  use strict;  my $file=$ARGV[0];    open (INFIL, "<$file");  open (POS, ">$file.pos.sam");  open (NEG, ">$file.neg.sam");    while (<INFIL>){  chomp;  my @ar = split (/\t/, $_);  if ($ar[0] =~ m/^@/ or $ar[1] == 163){  print NEG "$_\n";  }  if ($ar[0] =~ m/^@/ or $ar[1] == 99){  print POS "$_\n";  }  }
conversion to .bam format and sorting using samtools (version 1.2).  Commands: samtools view -bS [input.sam] > [output.bam].  samtools [input.bam] [output.sortedbam]
Conversion of sorted bam file to a bedgraph format using bedtools.  Command: genomeCoverageBed -ibam sorted.bam -g reference_genome.fna -bga file.bedgraph
production of a wig file suitable for visualisation in IGB using personal unpublished script file contains header (track   type=wiggle_0   name=WT_16h       graphType=points        visibility=full color=168,130,88  fixedStep       chrom=Sven      start=1 step=1  span=1) with each subsequent line corresponding to the number of times a single base was sequenced with each base represented by a seperate line.
Additional visual inspection was carried out using the wig files and IGB to validate target peaks.
Genome_build: CP000489, CP000490, CP000491
Supplementary_files_format_and_content: wig files were generated using the below perl (v5.8.8) script: =for comment  ---------------------------------------------------------------------------------------------  this is an example of a bedfile format output from the tools "genomeCoverageBed" in bedtools-  ---------------------------------------------------------------------------------------------        -some weird reference       base     base                               postion  position  frequency                                from     to  i|408675720|ref|NC_018750.1|   0       1       7  gi|408675720|ref|NC_018750.1|   1       2       11  gi|408675720|ref|NC_018750.1|   2       3       12  gi|408675720|ref|NC_018750.1|   3       5       13  gi|408675720|ref|NC_018750.1|   5       7       14  gi|408675720|ref|NC_018750.1|   7       13      15  gi|408675720|ref|NC_018750.1|   13      14      16  gi|408675720|ref|NC_018750.1|   14      15      18  =cut        use strict;  use warnings;  my $file = <STDIN>;  my @array;  my $from;  my $to;  my $cc=1;  open (BED, "$file");    while (<BED>){  chomp $_;  @array = split (/\t/, $_);    $from = $array[1];  $to = $array[2];  my $freq= $array[3];  my $count = 0;  my $dif = $to-$from;  while ($dif-$count>0){  $count++;  my $tt = $from + $count;  print "$freq\n";    }    }  close (BED);  exit;  )
Supplementary_files_format_and_content: 24.1_cuL-sRNA_491.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuL for cp000491
Supplementary_files_format_and_content: 24.2_cuL-sRNA_491.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuL for cp000491
Supplementary_files_format_and_content: 23.1_cuL-sRNA_489 wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuL for cp000489
Supplementary_files_format_and_content: 23.2_cuL-sRNA_489.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuL for cp000489
Supplementary_files_format_and_content: 22.1_cuL-sRNA_490.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuL for cp000490
Supplementary_files_format_and_content: 22.2_cuL-sRNA_490.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuL for cp000490
Supplementary_files_format_and_content: 15.1_cuH-sRNA_491.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuHfor cp000491
Supplementary_files_format_and_content: 15.2_cuH-sRNA_491.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuH for cp000491
Supplementary_files_format_and_content: 13.1_cuH-sRNA_489.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuHfor cp000489
Supplementary_files_format_and_content: 13.2_cuH-sRNA_489.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuH for cp000489
Supplementary_files_format_and_content: 14.1_cuH-sRNA_490.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuHfor cp000490
Supplementary_files_format_and_content: 14.2_cuH-sRNA_490.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuH for cp000490
Supplementary_files_format_and_content: 6.1_cuH-o2-sRNA_491.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuH o2 for cp000491
Supplementary_files_format_and_content: 6.2_cuH-o2-sRNA_491.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuH o2 for cp000491
Supplementary_files_format_and_content: 5.1_cuH-o2-sRNA_490.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuH o2 for cp000490
Supplementary_files_format_and_content: 5.2_cuH-o2-sRNA_490.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuH o2 for cp000490
Supplementary_files_format_and_content: 4.1_cuH-o2-sRNA_489.wig: wig - a file containg the frequency each base was sequenced for the positive strand for CuH o2 for cp000489
Supplementary_files_format_and_content: 4.2_cuH-o2-sRNA_489.wig: wig - a file containg the frequency each base was sequenced for the negative strand for CuH o2 for cp000489

organism: Paracoccus denitrificans

growth_protocol: P. denitrificans was grown in a defined minimal medium which contained 29 mmol/L Na2HPO4,11 mmol/L KH2PO4,10mmol/L NH4Cl, 0.4 mmol/L MgSO4,and supplemented with 30 mmol/L sodium succinate, 20 mmol/L NaNO3,and 2 mL/L Vishniac and Santer trace elements solution [130 mmol/L EDTA,7.64 mmol/L ZnSO4, 25 mmol/L MnCl2, 18.5 mmol/L FeSO4,0.89 mmol/L (NH4)6Mo7O24, 6.4 mmol/L CuSO4,6.72mmol/LCoCl2, 37.4 mmol/L CaCl] [8].    For high N2O emitting culture conditions, CuSO4 was omitted from the trace elements solution as in Sullivan et al., 2013. Anaerobic batch cultures (200 mL) inoculated with 1% (v/v) of stationary phase cells that had been pre-grown in minimal media. Vessels used were 250 mL Duran bottles with screw-cap lids and gas-tight silicone septa. Cultures were sparged with N2 for 10 minutes to impose an anaerobic environment and incubated statically at 30 oC. Aerobic conditions were created by using 50 ml of media in a 250 ml flask and shaking at 200 rpm at 30 oC

extract_protocol:
For RNA extraction, 30 mL of mid exponential phase cells (OD600 ≈ 0.4) was added to 12 mL of ice-cold 95% ethanol/5% phenol (pH= 4.3) (v/v) solution, and incubated on ice for 30 min to stabilize RNA and prevent degradation. RNA was isolated, using the Trizol method according to the protocol described in [9]. Trace DNA contamination was removed using Turbo DNA-free DNase (Ambion) and this was confirmed by PCR amplification of RNA samples using MyFi DNA polymerase (Bioline) according to the manufacturer’s instructions. RNA was quantified spectrophotometrically using a Nanodrop 2000 (Thermo Scientific), and integrity of RNA samples was analyzed using an Experion Automated Electrophoresis platform (Bio-Rad) using RNA StdSens chips (Bio-Rad) according to the manufacturer’s instructions.
Library preparation and sequencing were performed by Vertis Biotechnology AG, Germany. Briefly, the total RNA samples were split into two, one was enriched for the small RNA fractions <200 nt (s) specifically using the RNeasy MinElute Cleanup Kit (Qiagen). Ribosomal RNA molecules were depleted from both samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). The rRNA depleted RNA fractions were first treated with Tobacco Acid Pyrophosphatase (TAP, Epicentre). Afterwards, oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’adapter as primer. The resulting cDNAs were amplified by PCR using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

tag: genotype/variation

value: WT

value: CuH ANEROBIC

value: LOW N2O ANAEROBIC

tag: growth time point (hours from innuculation)


title: CuL-sRNA

value: CuL ANEROBIC

value: HIGH N2O ANEROBIC


title: Zuc_Nbr_depletion_rep1

value: total small RNAs


title: Biogenisis_repoter_1_two_sites+Zuc_Papi_depletion

source_name: small RNAs (18-40nt) from flies containing  piRNA biogenesis repoter_1 with two target sites with Zucchini and Papi depletion and 2S rRNA depletion


title: Zuc_depletion_rep1

value: Zucchini depletion


title: Zuc_depletion_rep2


title: Biogenisis_repoter_1_two_sites+Zuc_depletion

source_name: small RNAs (18-40nt) from flies containing  piRNA biogenesis repoter_1 with two target sites with Zucchini depletion and 2S rRNA depletion


title: Zuc_Nbr_depletion_AubIP

source_name: Aub bound small RNAs (18-50nt) from Zucchini and Nibbler depleted ovaries

value: Aub bound small RNAs


title: Papi_KO_Ago3IP

source_name: Ago3 bound small RNAs (18-40nt) from Papi -/- ovaries

value: papi knock-out

value: Ago3 bound small RNAs


title: Biogenisis_repoter_2_three_sites+Zuc_Nbr_depletion

source_name: small RNAs (18-40nt) from flies containing  piRNA biogenesis repoter_2 with three target sites with Zucchini and Nibbler depletion and 2S rRNA depletion

value: 4-6 days old

value: adult


title: Zuc_depletion_AubIP

source_name: Aub bound small RNAs (18-50nt) from Zucchini depleted ovaries

value: female


title: Papi_KO_AubIP

source_name: Aub bound small RNAs (18-40nt) from Papi -/- ovaries


title: Nibbler_KO_PiwiIP

source_name: Piwi bound small RNAs (18-40nt) from Nibbler -/- ovaries

value: nibbler knock-out

value: Piwi bound small RNAs


title: CuH-O2-sRNA

source_name: WT

value: CuH AEROBIC

value: LOW N2O AEROBIC


title: Nibbler_KO_AubIP

source_name: Aub bound small RNAs (18-40nt) from Nibbler -/- ovaries

value: ovary

value: Flies were kept at strandard conditions at 25º C.


title: Biogenisis_repoter_1_two_sites+Zuc_Nbr_depletion

source_name: small RNAs (18-40nt) from flies containing  piRNA biogenesis repoter_1 with two target sites with Zucchini and Nibbler depletion and 2S rRNA depletion

value: Zucchini and Nibbler depletion


title: Papi_KO_PiwiIP

source_name: Piwi bound small RNAs (18-40nt) from Papi -/- ovaries


title: w1118_AubIP

source_name: Aub bound small RNAs (18-40nt) from w1118 ovaries

value: wild type


title: Zuc_Nbr_depletion_Ago3IP

source_name: Ago3 bound small RNAs (18-50nt) from Zucchini and Nibbler depleted ovaries


title: Nibbler_KO_Ago3IP

source_name: Ago3 bound small RNAs (18-40nt) from Nibbler -/- ovaries


title: w1118_Ago3IP

source_name: Ago3 bound small RNAs (18-40nt) from w1118 ovaries


title: Nibbler_KO_total

source_name: small RNAs (18-40nt) from Nibbler knock-out ovaries with 2S rRNA depletion


title: w1118_PiwiIP

source_name: Piwi bound small RNAs (18-40nt) from w1118 ovaries


title: H3K4me3 PLAC-seq 1.3 million of cells rep2

status: Public on Nov 15 2016

city: La Jolla

first: Rongxin

last: Fang

state: CA

institute: Ludwig Institute for Cancer Research

description:
chip antibody: H3K4me3
PLAC-seq library

data_processing:
Library strategy: PLAC-Seq
Basecalls performed using CASAVA version 1.4
PLAC-seq data is mapped using PLACseq pipeline (https://github.com/r3fang/PLACseq)
Read pairs are splited into short-range (<1kb) and long-range (>10kb) based on insert distance.
Singificant PLAC-seq enriched interactions relative to in-situ Hi-C as an input control are identified using PLACseq pipeline (https://github.com/r3fang/PLACseq)
Genome_build: mm9
Supplementary_files_format_and_content: long.txt: tab-delimited text files include mapped mon-clonal cis long-range interaction read pairs with following columns: read_name, chrom, pos1, pos2
Supplementary_files_format_and_content: short.txt: tab-delimited text files include mapped mon-clonal cis short-range PLACE-seq read pairs with following columns: read_name, chrom, pos1, pos2
Supplementary_files_format_and_content: PLACE.interactions.bed: tab-delimited bed files include singificant PLAC-Enriched interactions with following columns: chrom1, start1, end1, chrom2, start2, end2, read count, background_p, fold change, p-value and q-value

source_name: embryonic stem cells

extract_protocol:
The fragmented DNA was purified by either Ampure beads or Phenol/Chloroform/Isoamyl Alcohol (25:24:1) extraction followed by ethanol precipitation
Libraries were prepared following Illumina protocols with end-repair, adding A and adapter ligation steps.

value: F1 Mus musculus castaneus x S129/SvJae

tag: cell type

value: mouse ESC line


title: Pol II PLAC-seq 5 million of cells rep2

description:
chip antibody: Pol II
PLAC-seq library


title: H3K27Ac PLAC-seq 0.5 million of cells rep2

description:
chip antibody: H3K27ac
PLAC-seq library


title: w1118_total

source_name: small RNAs (18-40nt) from w1118 ovaries with 2S rRNA depletion

tag: developmental stage

value: total small RNAs


title: w1118_total_no_2S_rRNA_depletion

source_name: small RNAs (18-29nt) from w1118 ovaries without 2S rRNA depletion


title: in situ Hi-C

description:
chip antibody: none
in situ Hi-C library

data_processing:
Library strategy: PLAC-Seq
Basecalls performed using CASAVA version 1.4
PLAC-seq data is mapped using PLACseq pipeline (https://github.com/r3fang/PLACseq)
Read pairs are splited into short-range (<1kb) and long-range (>10kb) based on insert distance.
Singificant PLAC-seq enriched interactions relative to in-situ Hi-C as an input control are identified using PLACseq pipeline (https://github.com/r3fang/PLACseq)
Genome_build: mm9
Supplementary_files_format_and_content: long.txt: tab-delimited text files include mapped mon-clonal cis long-range interaction read pairs with following columns: read_name, chrom, pos1, pos2
Supplementary_files_format_and_content: short.txt: tab-delimited text files include mapped mon-clonal cis short-range PLACE-seq read pairs with following columns: read_name, chrom, pos1, pos2
Supplementary_files_format_and_content: PLACE.interactions.bed: tab-delimited bed files include singificant PLAC-Enriched interactions with following columns: chrom1, start1, end1, chrom2, start2, end2, read count, background_p, fold change, p-value and q-value
PLAC-Seq data can be visualized at 3D Genome Browser (3dgenome.org)


title: Pol II PLAC-seq 5 million of cells rep1

description:
chip antibody: Pol II
PLAC-seq library


title: Actin_24hrs_rep1

first: Naren

last: Srinivasan

address: 1 Midland Road

department: Immunobiology Laboratory

data_processing:
Sequenced reads were mapped to Flybase gene set (Dmel version 6.01) from BDGP6 assembly [http://flybase.org/], using RSEM (version 1.2.11). RSEM uses the bowtie2 alignment tool.
TMM (treated mean of M-values) normalisation and differential expression analysis using the negative binomial model was carried out with the R-Bioconductor package “EdgeR” (www.bioconductor.org version 3. 1.0)
Genome_build: dmel6
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent Flybase genes and columns represent individual samples. Three bioloigical replicates per group.

extract_protocol:
Following collection, flies were stored at -20 ˚C until further use. Flies were mashed using a hand-held tissue homogenizer (Kontes) and a small pestle (Sigma) before clarification by Qiashredder columns (Qiagen). Subsequently RNA was extracted using a column-based method with DNAS digestions (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A 1mg/ml purified rabbit muscle G-actin (Cytoskeleton Inc.) solution was prepared as per manufacturer’s instruction and 36.8nl was administered into Wiso flies by intrathoracic injection (Nanoject II apparatus; Drummond Scientific). Injection of the same volume of G-actin buffer (5 mM Tris HCl [pH 8.0] + 0.2 mM CaCl2) was used as a control.Subsequently flies were euthanized at 3, 6 of 24 hours post injection.

value: 3-6 days old

value: Wiso

value: whole body


title: Actin_24hrs_rep3


title: Actin_buffer_24hrs_rep3


title: H3K4me3 PLAC-seq 1.3 million of cells rep1

description:
chip antibody: H3K4me3
PLAC-seq library


title: Actin_buffer_24hrs_rep2


title: Actin_6hrs_rep2


title: Actin_6hrs_rep1


title: Actin_buffer_6hrs_rep3


title: Actin_buffer_6hrs_rep2


title: Actin_3hrs_rep3


title: H3K27Ac PLAC-seq 0.5 million of cells rep1

description:
chip antibody: H3K27ac
PLAC-seq library


title: H3K27Ac PLAC-seq 2.5 million of cells rep1

description:
chip antibody: H3K27ac
PLAC-seq library


title: H3K27Ac PLAC-seq 2.5 million of cells rep2

description:
chip antibody: H3K27ac
PLAC-seq library


title: Actin_3hrs_rep2


title: Actin_buffer_3hrs_rep3


title: Actin_24hrs_rep2


title: Actin_buffer_24hrs_rep1


title: Actin_buffer_3hrs_rep1


title: Actin_6hrs_rep3


title: Actin_buffer_3hrs_rep2


title: Lane4_38870_0169

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

description:
ExpectCounts_all_samples.txt.gz
TPM_all_samples.txt.gz

data_processing:
FASTQ files were generated by CASAVA (v1.8.2).
Reads were mapped to the human transcriptome (RefGene v1.1.17) using Bowtie 0.12.8 (Langmead et al. 2009) allowing up to 2-mismatches and a maximum of 20 multiple hits.
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
Genome_build: hg19
Supplementary_files_format_and_content: .txt files report gene expression values

source_name: Human embryonic stem cell line H1

growth_protocol: Human embryonic stem cell line H1 was cultured on Matrigel coated plates in E8 medium

extract_protocol:
Cells were lysed directly on plate with RLT lysis buffer (Qiagen) and total RNA was purified with RNeasy Mini Kit (Qiagen)
LM-Seq: mRNA is isolated from purified 100 ng total RNA using oligo-dT beads (NEB). Isolated mRNA is fragmented in reverse transcription buffer with heat and then reverse-transcribed with SmartScribe reverse transcriptase (Clontech) using a random hexamer oligo. Illumina TruSeq: cDNA libraries were prepared and indexed with Illumina’s TruSeq RNA Sample Prep Kit v2
Indexed cDNA libraries are pooled and sequenced on an Illumina HiSeq2500

treatment_protocol: E8 medium

tag: cell line

value: H1 stem cell line

value: LM-Seq

tag: multiplex

value: 6 samples per lane


title: Lane4_38869_0168


title: Lane4_38871_0170


title: Lane4_38873_0172


title: Lane3_38875_0166

value: 24 samples per lane


title: Lane3_38876_0167


title: Actin_buffer_6hrs_rep1

tag: age

value: female


title: Lane3_38873_0164


title: Lane4_38874_0173


title: Lane3_38871_0162


title: Lane4_38872_0171


title: Lane3_38870_0161


title: Lane3_38863_0154


title: Lane3_38865_0156


title: Lane3_38864_0155


title: Lane3_38872_0163


title: Lane3_38874_0165


title: Lane3_38869_0160


title: Lane3_38859_0150


title: Lane3_38868_0159


title: Lane3_38866_0157


title: Actin_3hrs_rep1


title: Lane3_38862_0153


title: Lane3_38861_0152


title: Lane3_38854_0145


title: Lane3_38853_0144


title: Lane3_38867_0158


title: Lane2_38869_0136

value: 48 samples per lane


title: Lane3_38860_0151


title: Lane2_38873_0140


title: Lane2_38871_0138


title: Lane3_38856_0147


title: Lane3_38855_0146


title: Lane2_38868_0135


title: Lane2_38866_0133


title: Lane2_38872_0139


title: Lane2_38874_0141


title: Lane2_38870_0137


title: Lane2_38864_0131


title: Lane2_38867_0134


title: Lane2_38863_0130


title: Lane2_38876_0143


title: Lane2_38862_0129


title: Lane3_38858_0149


title: Lane2_38855_0122


title: Lane3_38857_0148


title: Lane2_38860_0127


title: Lane2_38859_0126


title: Lane2_38852_0119


title: Lane2_38848_0115


title: Lane2_38851_0118


title: Lane2_38850_0117


title: Lane2_38857_0124


title: Lane2_38847_0114


title: Lane2_38844_0111


title: Lane2_38856_0123


title: Lane2_38875_0142


title: Lane2_38841_0108


title: Lane2_38845_0112


title: Lane2_38842_0109


title: Lane2_38854_0121


title: Lane2_38861_0128


title: Lane2_38849_0116


title: Lane2_38846_0113


title: Lane2_38865_0132


title: Lane2_38840_0107


title: Lane2_38858_0125


title: Lane2_38838_0105


title: Lane2_38837_0104


title: Lane2_38853_0120


title: Lane2_38836_0103


title: Lane2_38833_0100


title: Lane2_38835_0102


title: Lane2_38832_0099


title: Lane2_38834_0101


title: Lane2_38831_0098


title: Lane1_38876_0094

value: 95 samples per lane


title: Lane2_38843_0110


title: Lane1_38877_0095


title: Lane2_38829_0096


title: Lane2_38830_0097


title: Lane2_38839_0106


title: Lane1_38869_0087


title: Lane1_38874_0092


title: Lane1_38872_0090


title: Lane1_38871_0089


title: Lane1_38867_0085


title: Lane1_38863_0081


title: Lane1_38866_0084


title: Lane1_38864_0082


title: Lane1_38865_0083


title: Lane1_38875_0093


title: Lane1_38861_0079


title: Lane1_38870_0088


title: Lane1_38859_0077


title: Lane1_38858_0076


title: Lane1_38856_0074


title: Lane1_38860_0078


title: Lane1_38857_0075


title: Lane1_38854_0072


title: Lane1_38853_0071


title: Lane1_38855_0073


title: Lane1_38873_0091


title: Lane1_38852_0070


title: Lane1_38868_0086


title: Lane1_38851_0069


title: Lane1_38846_0064


title: Lane1_38849_0067


title: Lane1_38848_0066


title: Lane1_38847_0065


title: Lane1_38850_0068


title: Lane1_38845_0063


title: Lane1_38862_0080


title: Lane1_38843_0061


title: Lane1_38844_0062


title: Lane1_38841_0059


title: Lane1_38842_0060


title: Lane1_38839_0057


title: Lane1_38836_0054


title: Lane1_38837_0055


title: Lane1_38840_0058


title: Lane1_38835_0053


title: Lane1_38833_0051


title: Lane1_38834_0052


title: Lane1_38828_0046


title: Lane1_38827_0045


title: Lane1_38829_0047


title: Lane1_38826_0044


title: Lane1_38831_0049


title: Lane1_38832_0050


title: Lane1_38830_0048


title: Lane1_38823_0041


title: Lane1_38825_0043


title: Lane1_38820_0038


title: Lane1_38818_0036


title: Lane1_38819_0037


title: Lane1_38817_0035


title: Lane1_38821_0039


title: Lane1_38838_0056


title: Lane1_38815_0033


title: Lane1_38811_0029


title: Lane1_38808_0027


title: Lane1_38816_0034


title: Lane1_38813_0031


title: Lane1_38806_0025


title: Lane1_38814_0032


title: Lane1_38807_0026


title: Lane1_38804_0023


title: Lane1_38803_0022


title: Lane1_38810_0028


title: Lane1_38805_0024


title: Lane1_38824_0042


title: Lane1_38822_0040


title: Lane1_38798_0017


title: Lane1_38801_0020


title: Lane1_38802_0021


title: Lane1_38796_0015


title: Lane1_38800_0019


title: Lane1_38799_0018


title: Lane1_38795_0014


title: Lane1_38797_0016


title: Lane1_38790_0009


title: Lane1_38792_0011


title: Lane1_38794_0013


title: Lane1_38812_0030


title: Lane1_38793_0012


title: Lane1_38787_0006


title: Lane1_38789_0008


title: Lane1_38788_0007


title: Lane1_38783_0002


title: Lane1_38785_0004


title: Lane1_38784_0003


title: Lane1_38782_0001


title: Lane1_38786_0005


title: H1p43_rep2

value: TruSeq

value: 12 samples per lane


title: H1p16_rep3


title: H1p43_rep1


title: H1p16_rep2


title: Blood pre-cDC_S341

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description: Blood pre-cDC_S341

data_processing:
Raw sequencing data were processed as previously described (Shalek et al., 2014). Briefly, short sequencing reads were aligned to the UCSC hg19 transcriptome and were also used as input in RSEM v 1.2.1 to quantify gene expression levels (transcripts per million; TPM) for all UCSC hg19 genes in all samples.
We filtered out cells from our dataset where we detected less than 1,000 unique genes per cell. All genes that were not detected in at least 1% of all our single cells were discarded, leaving 20,869 genes for all further analyses. Data were log transformed (log TPM+1) for all downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: matrix of gene expression estimates across good quality samples

source_name: Blood pre-cDCs

extract_protocol: cDNA from each sample was prepared using the SMART-Seq 2 protocol (Picelli et al., 2013).

value: Blood pre-cDC

value: blood pre-conventional dendritic cells (cDCs)


title: H1p16_rep1


title: Blood pre-cDC_S338

description: Blood pre-cDC_S338


title: Lane1_38791_0010


title: Blood pre-cDC_S340

description: Blood pre-cDC_S340


title: Blood pre-cDC_S335

description: Blood pre-cDC_S335


title: Blood pre-cDC_S339

description: Blood pre-cDC_S339


title: Blood pre-cDC_S337

description: Blood pre-cDC_S337


title: Blood pre-cDC_S336

description: Blood pre-cDC_S336


title: Blood pre-cDC_S334

description: Blood pre-cDC_S334


title: Blood pre-cDC_S332

description: Blood pre-cDC_S332


title: Blood pre-cDC_S331

description: Blood pre-cDC_S331


title: Blood pre-cDC_S330

description: Blood pre-cDC_S330


title: Blood pre-cDC_S329

description: Blood pre-cDC_S329


title: Blood pre-cDC_S328

description: Blood pre-cDC_S328


title: Blood pre-cDC_S333

description: Blood pre-cDC_S333


title: H1p43_rep3


title: Blood pre-cDC_S326

description: Blood pre-cDC_S326


title: Blood pre-cDC_S325

description: Blood pre-cDC_S325


title: Blood pre-cDC_S324

description: Blood pre-cDC_S324


title: Blood pre-cDC_S323

description: Blood pre-cDC_S323


title: Blood pre-cDC_S322

description: Blood pre-cDC_S322


title: Blood pre-cDC_S320

description: Blood pre-cDC_S320


title: Blood pre-cDC_S319

description: Blood pre-cDC_S319


title: Blood pre-cDC_S317

description: Blood pre-cDC_S317


title: Blood pre-cDC_S315

description: Blood pre-cDC_S315


title: Blood pre-cDC_S316

description: Blood pre-cDC_S316


title: Blood pre-cDC_S314

description: Blood pre-cDC_S314


title: Blood pre-cDC_S313

description: Blood pre-cDC_S313


title: Blood pre-cDC_S305

description: Blood pre-cDC_S305


title: Blood pre-cDC_S308

description: Blood pre-cDC_S308


title: Blood pre-cDC_S306

description: Blood pre-cDC_S306


title: Blood pre-cDC_S311

description: Blood pre-cDC_S311


title: Blood pre-cDC_S309

description: Blood pre-cDC_S309


title: Blood pre-cDC_S303

description: Blood pre-cDC_S303


title: Blood pre-cDC_S304

description: Blood pre-cDC_S304


title: Blood pre-cDC_S310

description: Blood pre-cDC_S310


title: Blood pre-cDC_S327

description: Blood pre-cDC_S327


title: Blood pre-cDC_S299

description: Blood pre-cDC_S299


title: Blood pre-cDC_S301

description: Blood pre-cDC_S301


title: Blood pre-cDC_S321

description: Blood pre-cDC_S321


title: Blood pre-cDC_S300

description: Blood pre-cDC_S300


title: Blood pre-cDC_S296

description: Blood pre-cDC_S296


title: Blood pre-cDC_S298

description: Blood pre-cDC_S298


title: Blood pre-cDC_S295

description: Blood pre-cDC_S295


title: Blood pre-cDC_S297

description: Blood pre-cDC_S297


title: Blood pre-cDC_S302

description: Blood pre-cDC_S302


title: Blood pre-cDC_S318

description: Blood pre-cDC_S318


title: Blood pre-cDC_S293

description: Blood pre-cDC_S293


title: Blood pre-cDC_S294

description: Blood pre-cDC_S294


title: Blood pre-cDC_S292

description: Blood pre-cDC_S292


title: Blood pre-cDC_S291

description: Blood pre-cDC_S291


title: Blood pre-cDC_S290

description: Blood pre-cDC_S290


title: Blood pre-cDC_S288

description: Blood pre-cDC_S288


title: Blood pre-cDC_S289

description: Blood pre-cDC_S289


title: Blood pre-cDC_S287

description: Blood pre-cDC_S287


title: Blood pre-cDC_S312

description: Blood pre-cDC_S312


title: Blood pre-cDC_S307

description: Blood pre-cDC_S307


title: Blood pre-cDC_S286

description: Blood pre-cDC_S286


title: Blood pre-cDC_S285

description: Blood pre-cDC_S285


title: Blood pre-cDC_S278

description: Blood pre-cDC_S278


title: Blood pre-cDC_S279

description: Blood pre-cDC_S279


title: Blood pre-cDC_S284

description: Blood pre-cDC_S284


title: Blood pre-cDC_S282

description: Blood pre-cDC_S282


title: Blood pre-cDC_S280

description: Blood pre-cDC_S280


title: Blood pre-cDC_S277

description: Blood pre-cDC_S277


title: Blood pre-cDC_S276

description: Blood pre-cDC_S276


title: Blood pre-cDC_S269

description: Blood pre-cDC_S269


title: Blood pre-cDC_S273

description: Blood pre-cDC_S273


title: Blood pre-cDC_S271

description: Blood pre-cDC_S271


title: Blood pre-cDC_S270

description: Blood pre-cDC_S270


title: Blood pre-cDC_S275

description: Blood pre-cDC_S275


title: Blood pre-cDC_S272

description: Blood pre-cDC_S272


title: Blood pre-cDC_S274

description: Blood pre-cDC_S274


title: Blood pre-cDC_S268

description: Blood pre-cDC_S268


title: Blood pre-cDC_S267

description: Blood pre-cDC_S267


title: Blood pre-cDC_S264

description: Blood pre-cDC_S264


title: Blood pre-cDC_S261

description: Blood pre-cDC_S261


title: Blood pre-cDC_S266

description: Blood pre-cDC_S266


title: Blood pre-cDC_S258

description: Blood pre-cDC_S258


title: Blood pre-cDC_S263

description: Blood pre-cDC_S263


title: Blood pre-cDC_S260

description: Blood pre-cDC_S260


title: Blood pre-cDC_S256

description: Blood pre-cDC_S256


title: Blood pre-cDC_S283

description: Blood pre-cDC_S283


title: Blood pre-cDC_S259

description: Blood pre-cDC_S259


title: Blood pre-cDC_S281

description: Blood pre-cDC_S281


title: Blood pre-cDC_S252

description: Blood pre-cDC_S252


title: Blood pre-cDC_S255

description: Blood pre-cDC_S255


title: Blood pre-cDC_S253

description: Blood pre-cDC_S253


title: Blood pre-cDC_S251

description: Blood pre-cDC_S251


title: Blood pre-cDC_S250

description: Blood pre-cDC_S250


title: Blood pre-cDC_S249

description: Blood pre-cDC_S249


title: Blood pre-cDC_S247

description: Blood pre-cDC_S247


title: Blood pre-cDC_S244

description: Blood pre-cDC_S244


title: Blood pre-cDC_S242

description: Blood pre-cDC_S242


title: Blood pre-cDC_S265

description: Blood pre-cDC_S265


title: Blood pre-cDC_S245

description: Blood pre-cDC_S245


title: Blood pre-cDC_S248

description: Blood pre-cDC_S248


title: Blood pre-cDC_S262

description: Blood pre-cDC_S262


title: Blood pre-cDC_S241

description: Blood pre-cDC_S241


title: Blood pre-cDC_S235

description: Blood pre-cDC_S235


title: Blood pre-cDC_S234

description: Blood pre-cDC_S234


title: Blood pre-cDC_S243

description: Blood pre-cDC_S243


title: Blood pre-cDC_S240

description: Blood pre-cDC_S240


title: Blood pre-cDC_S233

description: Blood pre-cDC_S233


title: Blood pre-cDC_S246

description: Blood pre-cDC_S246


title: Blood pre-cDC_S238

description: Blood pre-cDC_S238


title: Blood pre-cDC_S239

description: Blood pre-cDC_S239


title: Blood pre-cDC_S237

description: Blood pre-cDC_S237


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source_name: Cord Blood pre-cDCs

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value: cord blood pre-conventional dendritic cells (cDCs)


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