title: rpb1-1 T0 RNA-seq

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009).
The coverage of each base pair was computed across the genome and rendered in the Integrative Genomics Viewer. For the RNA-seq, the coverage was cacluated for the Watson and Crick strands, respectively.
spt16 peaks detection indentified by MACS (Feng et al. 2012), we used P-value < 1 × 10-5. The dynamic nucleosome were called by DANPOS (Chen et al. 2013).
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Wild type (WT) ,spt16(G132D) , rpb1-1 and spt16(G132D) rpb1-1 mutant cells were arrested in G1 phase using α-factor at 25 °C. These cells were either kept at 25 °C or shifted to the non-permissive temperature (37 °C) for 45 min.

extract_protocol:
For MNase-seq, Cells were cross-linked by 0.1% Para formaldehyde for 15 min and then treated with 0.125 M glycine. The pellets were subjected to MNase digestion as previously reported (Kaplan et al. 2008). The DNA with the size of mononucleosomes was used to construct libraries. For RNA-seq, Total RNAs were extracted as previously described with phenol/freeze method (Schmitt et al. 1990). RNA qualities were checked with the Fragment Analyzer (AATI).
The DNA from Mmase and ChIP was used to construct libraries according to manufacture’s guide (Illumina). The library was sequenced using the Illumina 1G Genome Analyzer and Highseq-2000. For RNA-seq, The extracted RNAs were further processed to RNA fragmentation and construct library for Illumina sequencing with the TruSeq Stranded mRNA Sample Prep Kit - Illumina.

tag: genotype/variation

tag: media

value: YPD

tag: cell cycle stage

value: G1 phase

value: no


title: rpb1-1 T45 RNA-seq

status: Public on May 05 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: chip antibody


title: NP1131_3C_0912B

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description:
NP1131_3C_0912
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ACTGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Neuron

growth_protocol: Flies were raised at 25C.  Parents consisted of 5 females of the UAS-eGFP;UAS-eGFP;+ and 4 males of corresponding GAL4 line.  Parents were placed in a new vial every 4 days for 2 weeks to minimize overcrowding and keep the larval density relatively constant.  All flies were kept in a 12:12 Light Dark cycle.

extract_protocol:
Neurons were identified through anatomical location and GFP expression and then harvested into a patch pipet on an electrophysiology rig from alive flies.  Cells were harvested into .5ul Nuclease Free water to cause the cells to lyse.
cDNA was made and amplified using the Clontech SMARTer Ultra low RNA kit (version 2 HV). 15 rounds of amplification was perfromed on the samples.   This was then sheared to 200bp and put into an IXI Chip-seq protocol  (automated system) and barcoded following another 12 rounds of amplification. 12 samples were run in a lane and each sample was run across two lanes.

treatment_protocol: Animals undergoing memory formation were subjected to 8 spaced trainings of an odor (either 3-Octanol or 4-Methylcyclohexanol) with a 12 cycle 5 second 60V shock for 1 minute.

tag: cell class

value: Gamma Kenyon Cells (NP1131-GAL4)

tag: number cells

tag: training

value: Control

tag: quality

value: more than >4 million mapped reads-across 2 lanes


title: sample 54_RNA_GT_NCRILC3_rpt2

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

data_processing:
alignment, ATAC-seq: ATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
peak-calling, ATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used for peak calling with MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Peaks called from replicates of the same cell type were merged using the mergePeaks module in HOMER. Only peaks called in both replicates were used to generate a bed file for a cell type.
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0.
bw file, RNA-seq: Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
alignment, ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
peaks, ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958 for histone mark K27Ac. Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0E-05 fortransscription factors p300 and Tbet.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq (p300, Tbet); bedgraph for histone modification ChIP-seq (K27Ac). bed file for common ATAC-seq peaks of replicates (linked as supplementary files on Series record).

organism: Mus musculus

source_name: Group 3 innate lymphoid cells

growth_protocol:
cell isolation protocol: Cells from bone marrow, liver, and spleen were obtained by mechanical disruption. Cells from lung were isolated after incubating lungfragments with 0.5 mg/ml Liberase TL for 1h followed by purification with 40% Percoll (GE Healthcare) (Meylan et al., 2013). Cells from siLP were isolated after incubating fine-cut intestine in HBSS solution with 0.5 mg/ml DNase I (Roche) and 0.25 mg/ml  Liberase TL (Roche) followed by filtering with 100 μm cell strainer and purification with 40% Percoll (Sciumé et al., 2012). NK cells were isolated from spleen and liver; ILC1s were isolated from liver; Treg, IL17GFP+Th17, ILC2s, CD4+ILC3 and NCR+ILC3 were isolated from siLP; HSC, CLP, NKp, immature NK, and ILC2p were isolated from bone marrow; Nippo-infected ILC2 and Th2 cells were isolated from lung. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Nippostrongylus brasiliensis infection protocol: Mice of at least 8 weeks of age were infected with 500 infective third-stage N. brasiliensis by subcutaneous injection. Cells from lungs were isolated after 10 days of infection.

extract_protocol:
RNA-seq was performed as described previously with slight modification (Hirahara et al., Immunity 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol following manufacture’s protocol (Life Technologies).
RNA-seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ATAC-seq was performed according to published protocol (Buenrostro et al., 2013) with minor modification. 50,000 cells were pelleted and washed with 50ul 1xPBS, followed by treatment with 50ul lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% of IGEPAL CA-630). After pelleting the nuclei by centrifuging at 500x g for 10min, the pellets were re-suspended in 40ul transposition reaction with 2ul Tn5  transposase (Illumina Cat# FC-121-1030) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37ºC with shaking at 300rpm for 30min. The fragmentalized DNAs were then purified using Qiagen MinElute Kit and amplified with 10-11 cycles of PCR based on the amplification curve. Once the libraries are purified using Qiagen PCR Cleanup Kit, they were further sequenced for 50 cycles (paired-end reads) on HiSeq2500.
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on GAII, HiSeq 2000 or 2500 following the manufacturer's protocols.

tag: strain

tag: tissue

value: Small intestine lamina propria

tag: surface marker

tag: culture condition

value: ex vivo

tag: cell type

value: Group 3 innate lymphoid cells


title: sample 46_ATAC_Sp_NK_IL2_IL12_rpt2

library_source: genomic

molecule: genomic DNA

source_name: Natural killer cells

value: Spleen

value: in vitro culture for 6 hours w/ IL2 +IL12

value: Natural killer cells


title: NP1131_16T_0916B

description:
NP1131_16T_0916
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GTGGCC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Trained


title: Spt16(G132D) T45 RNA-seq


title: sample 42_ATAC_Sp_Naïve_CD4_rpt2

source_name: Naïve CD4 T cells

value: Naive CD4 T cells


title: NP1131_16T_0912B

description:
NP1131_16T_0912
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CGTACG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: Spt16(G132D)rpb1-1 T45 RNA-seq


title: Spt16(G132D)rpb1-1 T0 RNA-seq


title: Spt16(G132D) T0 RNA-seq


title: NP1131_3C_0924B

description:
NP1131_3C_0924
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GGTAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: NP1131_3C_0916

description:
NP1131_3C_0916
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: AGTCAA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 14_ATAC_BM_MPP_rpt2

description:
150109_150122_combined_s10
BM_MPP_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

source_name: Multipotent progenitor cells

value: Bone marrow

value: Multipotent progenitor cells


title: sample 61_RNA_GT_NCRILC3_IL23_rpt1

value: in vitro culture for 4 hours w/ IL23


title: WT T0 RNA-seq

value: wild type

value: YPD


title: NP1131_14T_09

description:
NP1131_14T_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATGAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 41_ATAC_Sp_Naïve_CD4_rpt1


title: 3wtALID4 sRNA-Seq

city: Göttingen

first: Orr

last: Shomroni

address: Grisebachstraße 5

country: Germany

institute: DZNE

description: WT rep3 day 4

data_processing:
Mapping, prediction of novel miRNAs, quality control, and differential expression (DE) analysis were carried out using Oasis1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Excel sheets containing sheets with (1) RPM normalised read counts for small RNA in each sample, and (2) base mean, log 2 fold change and adjusted p-value generated by DESeq2 for each small RNA in each day

source_name: Trachea

growth_protocol: Primary cultures of mouse tracheal epithelial cells (MTECs) were established on Transwell membranes  and  differentiated into multiciliated cells using air-liquid interface (ALI) conditions as previously described (You et al, Am J Physiol Lung Cell Mol Physiol, 2002, PMID 12388377)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina)

value: primary mouse tracheal epithelial cultures (MTECs)

tag: treatment

value: air-liquid interface (ALI)

tag: day

value: post ALI day 4

tag: genotype


title: NP1131_13T_0924

description:
NP1131_13T_0924
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Gamma Kenyon Cells (NP1131-GAL4)

value: more than >4 million mapped reads-across 2 lanes


title: sample 13_ATAC_BM_MPP_rpt1

description:
150109_150122_combined_s09
BM_MPP_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

value: ex vivo


title: WT T45 RNA-seq

value: G1 phase

value: no


title: ZK2 RNA-seq

city: WuHan

first: jin

middle: zhi

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

country: China

institute: Huazhong Agricultural University

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis.
Filter steps:
Remove reads with adaptors;
Remove reads in which unknown bases are more than 10%;
Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
de novo assembly
Supplementary_files_format_and_content: RPKM represent the expression of genes

organism: Citrus trifoliata

source_name: citrus-wildtype

growth_protocol: The terminal bud and the five following buds (the major node position for flower formation) from spring flushes of the MT and the WT 2-year-old trees were also collected at flower initiation (after self-pruning).

extract_protocol:
Approximate 2 to 3 g of powdered material was subjected to each RNA extraction, including 10 mL buffer extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol precipitation, 5 mL 75% ethanol cleaning and RNA purification as described by Camacho-Villasana YM et al.
mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification

treatment_protocol: No treatment

tag: development stage

value: After self-pruning

tag: cultivar

value: normal trifoliate orange


title: NP1131_13T_0916B

description:
NP1131_13T_0916
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GTAGAC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Trained


title: ZAO1 RNA-seq

department: College of Horticulture and Forestry Science

source_name: citrus-mutant

value: The terminal bud and the five following buds (the major node position for flower formation) from spring flushes

value: precocious trifoliate orange


title: NP1131_4C_09

description:
NP1131_4C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: AGTTCC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Control


title: sample 9_ATAC_BM_iNK_rpt1

description:
150109_150122_combined_s13
BM_iNK_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

source_name: Immature NK cells

value: Bone marrow

value: Immature NK cells


title: NP1131_7C_09

description:
NP1131_7C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GAGTGG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: NP1131_2C_09

description:
NP1131_2C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATGTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 4_ATAC_BM_CLP_rpt2

description:
150109_150122_combined_s12
BM_CLP_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

source_name: Common lymphoid progenitor cells

value: Common lymphoid progenitor cells


title: sample 5_ATAC_BM_HSC_rpt1

description:
150109_150122_combined_s07
BM_HSC_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

source_name: Hematopoietic stem cells

value: Hematopoietic stem cells


title: sample 6_ATAC_BM_HSC_rpt2

description:
150109_150122_combined_s08
BM_HSC_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: NP1131_3C_0912

description:
NP1131_3C_0912
Samples run across two lanes and pooled


title: sample 3_ATAC_BM_CLP_rpt1

description:
150109_150122_combined_s11
BM_CLP_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: NP1131_13T_0916


title: NP1131_16T_0912

description:
NP1131_16T_0912
Samples run across two lanes and pooled


title: DAL_1C_11B

description:
DAL_1C_11
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GCGCTA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: DAL_4C_11B

description:
DAL_4C_11
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CTCAGA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: DAL_1T_12

value: more than >4 million mapped reads-single lane


title: NP1131_9T_09

description:
NP1131_9T_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: DAL_7C_11

description:
DAL_7C_11
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CTAGCT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: DAL_1C_11


title: DAL_1C_12


title: DAL_4C_11


title: DAL_10T_09

data_processing:
Multiplexing barcode: TCGGCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: DAL_16T_09


title: DAL_6C_09

data_processing:
Multiplexing barcode: TACAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: WT rep 1

status: Public on May 04 2016

city: Honolulu

first: Keith

middle: S

last: Fong

state: HI

address: 651 Ilalo Street; BSB 110

department: Anatomy, Biochemistry and Physiology

institute: University of Hawai'i John A. Burns School of Medicine

data_processing:
Ion Torrent Suite used to obtain FASTQ data
Single-end reads trimmed and filtered using PRINSEQ (Schmieder and Edwards 2011).  Low quality sequences trimmed from ends until a bp of Phred quality score of at least 20 (at least 99% accurate) not found, and filtered out sequences having < 20 nt
UCSC mm10 reference genome indexed by Bowtie2 v2.2.5. Processed reads then aligned with ref genome using Tophat v2.0.14 (Kim et al., 2013).
Resulting .BAM files were then analyzed with Cufflinks v2.1.1 (Trapnell et al., 2010) to quantify transcript abundance as Reads Per Kilobase of exon model per Million mapped reads (RPKM)
SAMtools v0.1.18 (Li et al., 2009) used for sorting and BAM conversion.  Htseq-count script (HTSeq package) used to count reads mapped to mouse gene models
Differential gene expression from count data identified using the non-parametric NOISeq-sim program (Tarazona et al., 2011) with default parameters. A trimmed mean of M-values normalization and estimated probablity of differential expression PNOI > 0.95 as a threshold.
Genome_build: mm10
Supplementary_files_format_and_content: counts, tab-delimited text files

source_name: embryo

extract_protocol:
Rostrums dissected, homogenized in QIAzol Lysis Reagent from QIAgen Rnasy Plus Universal Kit.  Samples purified for RNA.  Remaining embryonic tissue used for genotyping.
30 ng from 3 biological replicates with RIN of at least 9 pooled for library construction.  Standard protocols for sequencing with Ion Torrent were used

value: 3H1 Balb

value: rostrum

tag: Stage

value: E9 (18-22 somites)


title: NP1131_16T_0916

description:
NP1131_16T_0916
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GTGGCC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Gamma Kenyon Cells (NP1131-GAL4)

value: more than >4 million mapped reads-across 2 lanes


title: S. aureus USA300 (JE2) WT with TEX treatment, unfragmented transcripts

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
Fastq quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping  (READemption 0.1.9)
Size filtering: discarding reads shorter than 12 nt (READemption 0.1.9)
Read mapping (READemption 0.1.9 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.1.9)
Genome_build: NC_007790.1, NC_007791.1, NC_007792.1, NC_007793.1
Supplementary_files_format_and_content: wiggle

organism: Staphylococcus aureus

source_name: S. aureus bacteria

growth_protocol: S. aureus strains were grown aerobically in trypticase soz broth (TSB) at 37 °C and 200 rpm shaking in culture volumes that did not exceed 1/8 volume of the erlenmeyer beaker. Bacteria were inoculated from an overnight culture to an OD of 0.1 at 600 nm and were harvested at an OD of 0.6 and flash frozen in liquid nitrogen

extract_protocol:
Bacterial pellets were resuspended in a buffer containing 10 mM Tris pH7.6, 100 mM EDTA, 10% glucose and lysed with a FastPrep machine (MP Biochemicals; spee 6, 45 s, 4 °C) using Lysing Matrix B and by adding 0.5 ml acid phenol.  After centrifugation (10 min, 14,000 rpm, 4 °C) the aqueous phase was collected. 1 ml TRIzol was added, mixed and incubated at RT for 5 min. The solution was extracted twice by addition of 100 µL (in the second step 200 µL) chloroform and incubation at room temperatur for several minutes, followed by centrifugation. RNA was precipitated from the aqueous solution by addition of 500 µL 2-propanol and a 15 min incubation at room temperature.    RNA was pelleted by centrifugation for 15 min at 14,000 rpm, 4 °C. Pellets were washed with 75% ethanol, air dried and resuspended in DEPC-treated water.
The cDNA libraries were constructed as previously described (Dugar et al. 2013) by vertis Biotechnology AG, Germany.

treatment_protocol: For Terminator 5’ exonuclease treatment and enrichment of transcription initiation sites RNA samples were poly(A)-tailed using poly(A) polymerase and 5'-triphosphates were removed by treatment with tobacco acid pyrophosphatase. RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA was generated using an oligo(dT)-primer and M-MLV reverse transcriptase. Using a high fidelity DNA polymerase cDNA was amplified by PCR.

tag: growth phase

value: exponential

tag: genotype/variation

value: WT

tag: protocol


title: DAL_7C_11B

tag: cell class

tag: number cells


title: S. aureus USA300 (JE2) WT, fragmented transcripts

value: fragmented transcripts


title: tuft rep1


title: NP1131_3C_0924

description:
NP1131_3C_0924
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GGTAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

tag: training

tag: quality


title: S. aureus USA300 (JE2) WT without TEX treatment, unfragmented transcripts

description: Sa_WT_without_TEX_treatment_unfragmented

tag: strain


title: C002_P1-3

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
The raw sequencing reads were filtered for adapter and low quality sequences using cutadapt (Martin, 2011) and custom scripts. Low quality reads were defined as sequencing reads with more than 5% unknown bases (‘N’) and reads with more than 50% of the bases having a base quality value of ≤ 10. Reads with length < 40bp were further discarded. Finally, sequencing reads were filtered for rRNA sequence and remaining high quality reads were used for downstream analysis.
The high-quality reads were aligned against human genome assembly (NCBI Build 37.1/hg19) using TopHat v2.0.8b (Kim et al, 2013). Expression estimation and tests for differential expression were processed by Cufflinks v2.1.1 (Trapnell et al, 2013). All data was expressed as Fragments Per Kilobase of exon per Million fragments mapped (FPKM) values and fold changes in transcript levels relative to the Bel-7402 shCtl group.
Genome_build: hg19

organism: Homo sapiens

source_name: Hepatocellular Carcinoma Cell Line

growth_protocol: Bel-7402 cells were cultured in DMEM-HG supplemented with 10%FBS and 1%PS

extract_protocol:
Total RNA were extracted using TRIzol Reagent, and the quality of total RNA was checked by Agilent 2100 bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: shRNAs targeting FRA1 (shFRA1-2) and non-target control (shCtl) were delivered into Bel-7402 cells by lenti-viruses. The stably transduced cells were selected by puromycin.

tag: cell line

value: Hepatocellular Carcinoma

tag: shRNA transduced

value: vector control


title: 41_P1-3

tag: cell type

value: FRA1 knockdown


title: DAL_12T_09

data_processing:
Multiplexing barcode: TCGAAG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Trained


title: DAL_1T_08


title: p53-CPT

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Chromatin IP against p53.

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1.
Peak-calling by HOMER v4.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bedGraph files, HOMER peak output files.

source_name: HCT116 colon cancer cells, p53-WT, camptothecin, p53 ChIP

growth_protocol: Cells were generated by AAV-mediated homologous recombination.

extract_protocol:
Chromatin was sheared by sonication using Bioruptor to an average fragment size of 500 bp, immunoprecipitated using the indicated antibody, purified and sequenced using Illumina HiScanSQ following protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: ATF3-wildtype (ATF3-WT), -knockout (ATF3-KO), p53-knockout (p53-KO) cells were treated with DMSO (Ctrl) or 1.5 uM of camptothecin (CPT) for 4 h, and then crosslinked by 1 mM of di(N-succinimidyl) glutarate (DSG) for 45 min and 1% of formaldehyde for 10 min.

value: colon cancer cell line

tag: treatment

value: camptothecin

tag: chip antibody


title: TGMouse3_TestisRNA

city: Durham

first: Graham

middle: David

last: Johnson

state: NC

address: 101 Science Drive

department: GCB

institute: Duke University

description:
tgTestis3
Processed data file: TG_Testis_TPM_Values.txt

data_processing:
Illumina Casava v 1.8.2 software used for basecalling and demultiplexing sequencing reads.
RNA sequencing libraries were aligned to the custom mm10 genome with TopHat (version 2.0.9), using the following parameters: tophat2 -r 30 --mate-std-dev 50 --no-coverage-search. RNA abundance is presented as transcripts per million (TPM; Wagner et al. 2012) values.
Genome_build: custom transgenic mm10 (inserted human protamine domain at nucleotide position chr19:39397384-3939738510)
Supplementary_files_format_and_content: M00138.bed: Genomic coordinates for M00138 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00422.bed: Genomic coordinates for M00422 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00724.bed: Genomic coordinates for M00724 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00791.bed: Genomic coordinates for M00791 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01200.bed: Genomic coordinates for M01200 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01259.bed: Genomic coordinates for M01259 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01504.bed: Genomic coordinates for M01504 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0138.2.bed: Genomic coordinates for MA0138.2 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0139.1.bed: Genomic coordinates for MA0139.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0149.1.bed: Genomic coordinates for MA0149.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: PBM0051.bed: Genomic coordinates for PBM0051 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MergedHomeoBoxFactors.bed: Genomic coordinates for homeobox motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: TG_Testis_TPM_Values.txt: TPM values for RefSeq genes in transgenic mouse testes.

source_name: mouse testis, transgenic

extract_protocol:
Decapsulated testes were homogenized and total RNA extracted using the Qiagen RNeasy system.
Pre-amplified cDNA libraries were generated from 5 ng of total testis RNA using the Seq-plex system (Sigma) and used to construct sequencing libraries (DNA Ultra-Low, NEB). RNA-seq libraries were subjected to paired-end sequencing on the Illumina HiSeq 2500 platform.

tag: strain/background

value: single copy of the human protamine gene cluster

tag: tissue

value: testis


title: TGMouse4_TestisRNA

description:
tgTestis4
Processed data file: TG_Testis_TPM_Values.txt


title: tuft rep 2


title: ATF3-KO

description: Chromatin IP against ATF3.

source_name: HCT116 colon cancer cells, ATF3-KO, ATF3 ChIP

value: DMSO


title: ATF3-CPT

description: Chromatin IP against ATF3.

source_name: HCT116 colon cancer cells, ATF3-WT, camptothecin, ATF3 ChIP


title: TGMouse2_TestisRNA

description:
tgTestis2
Processed data file: TG_Testis_TPM_Values.txt


title: TGMouse1_TestisRNA

description:
tgTestis1
Processed data file: TG_Testis_TPM_Values.txt


title: wt_DNA_mnase.bam

description:
Control for MNase-seq.
Processed data file: M00138.bed, M00422.bed, M00724.bed, M00791.bed, M01200.bed, M01259.bed, M01504.bed, MA0138.2.bed, MA0139.1.bed, MA0149.1.bed, PBM0051.bed, MergedHomeoBoxFactors.bed

data_processing:
Illumina Casava v 1.8.2 software used for basecalling and demultiplexing sequencing reads.
Mouse DNA sequencing libraries were aligned to the mouse genome assembly mm10 with Bowtie (version 2.0.2), using the following parameters: bowtie2 -X 1000 --very-sensitive. Transgenic samples were additionally aligned to a custom version of the mm10 build containing the inserted human protamine domain at nucleotide position chr19:39397384-3939738510.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: M00138.bed: Genomic coordinates for M00138 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00422.bed: Genomic coordinates for M00422 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00724.bed: Genomic coordinates for M00724 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00791.bed: Genomic coordinates for M00791 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01200.bed: Genomic coordinates for M01200 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01259.bed: Genomic coordinates for M01259 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01504.bed: Genomic coordinates for M01504 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0138.2.bed: Genomic coordinates for MA0138.2 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0139.1.bed: Genomic coordinates for MA0139.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0149.1.bed: Genomic coordinates for MA0149.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: PBM0051.bed: Genomic coordinates for PBM0051 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MergedHomeoBoxFactors.bed: Genomic coordinates for homeobox motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: TG_Testis_TPM_Values.txt: TPM values for RefSeq genes in transgenic mouse testes.

source_name: mouse sperm, wild type

extract_protocol:
Genomic DNA was isolated from sperm by proteinase K digestion and recovered by phenol-chloroform extraction and subsequently precipitated with ethanol. Purified DNA was digested with micrococcal nuclease.
DNAs were used to construct multiplexed DNA sequencing libraries with the NEBNext ChIP-Seq kit (New England BioLabs). All libraries were subjected to 50 cycles of paired-end sequencing on the Illumina HiSeq 2500 platform.

value: wild type

value: sperm


title: wt_DNA_sheared.bam

extract_protocol:
Genomic DNA was isolated from sperm by proteinase K digestion and recovered by phenol-chloroform extraction and subsequently precipitated with ethanol. Purified DNA was sheared using the Covaris system.
DNAs were used to construct multiplexed DNA sequencing libraries with the NEBNext ChIP-Seq kit (New England BioLabs). All libraries were subjected to 50 cycles of paired-end sequencing on the Illumina HiSeq 2500 platform.


title: S. aureus USA300 (JE2) Delta NE 1304 , fragmented transcripts

value: Delta NE 1304


title: wt_mono_dff.bam

description:
Chromatin
Processed data file: M00138.bed, M00422.bed, M00724.bed, M00791.bed, M01200.bed, M01259.bed, M01504.bed, MA0138.2.bed, MA0139.1.bed, MA0149.1.bed, PBM0051.bed, MergedHomeoBoxFactors.bed

data_processing:
Library strategy: DFF-Seq
Illumina Casava v 1.8.2 software used for basecalling and demultiplexing sequencing reads.
Mouse DNA sequencing libraries were aligned to the mouse genome assembly mm10 with Bowtie (version 2.0.2), using the following parameters: bowtie2 -X 1000 --very-sensitive. Transgenic samples were additionally aligned to a custom version of the mm10 build containing the inserted human protamine domain at nucleotide position chr19:39397384-3939738510.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: M00138.bed: Genomic coordinates for M00138 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00422.bed: Genomic coordinates for M00422 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00724.bed: Genomic coordinates for M00724 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00791.bed: Genomic coordinates for M00791 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01200.bed: Genomic coordinates for M01200 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01259.bed: Genomic coordinates for M01259 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01504.bed: Genomic coordinates for M01504 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0138.2.bed: Genomic coordinates for MA0138.2 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0139.1.bed: Genomic coordinates for MA0139.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0149.1.bed: Genomic coordinates for MA0149.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: PBM0051.bed: Genomic coordinates for PBM0051 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MergedHomeoBoxFactors.bed: Genomic coordinates for homeobox motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: TG_Testis_TPM_Values.txt: TPM values for RefSeq genes in transgenic mouse testes.

extract_protocol:
Mature spermatozoa were isolated from cauda epididymides and vas deferens harvested from individual 6-month-old mice on ice into PBS. Following filtration through an 80-micron mesh, the cells were washed twice and resuspended in 1 mL of a PBS solution containing 0.5% Triton X-100. The absence of somatic cells was confirmed by light microscopy. The cells were incubated for 10 minutes on ice with occasional mixing. Subsequently, ice-cold PBS was added to 10 mL and the cells were washed twice prior to counting with a hemocytomoter. Tritonized sperm suspensions were adjusted to 5x10^6 cells/mL in 5 mM CaCl2, 10 mM dithiothreitol, buffered with 50 mM Tris-HCl, pH 7.9. The suspension was placed 37°C for 30 minutes. Subsequently, the sample was diluted with prewarmed reaction buffer to a final concentration of 5x10^6 cells/mL in 5 mM CaCl2, 10 mM dithiothreitol, 2 Kunitz unit/mL MNase (New England BioLabs), buffered with 50 mM Tris-HCl, pH 7.9. The sample was digested for 5 minutes and the reactions were stopped with the addition of 0.5 M EDTA pH 8.0 to a final concentration of 20 mM. The cell suspension was then rotated at 4°C for 30 minutes prior to centrifugation at 20,000 rcf for 10 minutes. Soluble nucleosome-bound DNAs were recovered from the supernatant by proteinase K digestion and subsequent phenol-chloroform extraction and ethanol precipitation. Purified DNAs were resolved by gel electrophoresis. Bands corresponding to the length of DNA associated with a mononucleosome (~150 bp) were excised and column purified. Sperm digested with DNA Fragmentation Factor (DFF) were similarly collected and permeabilized. Following washing, sperm were resuspended to 5x10^6 cells/mL in 1x NEB1 [10 mM Bis-Tris-Propane-HCl; 10 mM MgCl2; 1 mM dithiothreitol; pH 7.0] (New England BioLabs), supplemented with 10 mM dithiothreitol. Following incubation at 37 °C for 30 minutes, the sperm suspension was diluted to 2.5x10^6 cells/mL with prewarmed 1x NEB1. The sample was digested for 16 hours at 37 °C following the addition of 10 units Tobacco Etch Virus (TEV) protease and 24 of µl DFF enzyme.
DNAs were used to construct multiplexed DNA sequencing libraries with the NEBNext ChIP-Seq kit (New England BioLabs). All libraries were subjected to 50 cycles of paired-end sequencing on the Illumina HiSeq 2500 platform.


title: wt_mono_mnase.bam


title: tg_DNA_mnase.bam

data_processing:
Illumina Casava v 1.8.2 software used for basecalling and demultiplexing sequencing reads.
Mouse DNA sequencing libraries were aligned to the mouse genome assembly mm10 with Bowtie (version 2.0.2), using the following parameters: bowtie2 -X 1000 --very-sensitive. Transgenic samples were additionally aligned to a custom version of the mm10 build containing the inserted human protamine domain at nucleotide position chr19:39397384-3939738510.
Genome_build: custom transgenic mm10 (inserted human protamine domain at nucleotide position chr19:39397384-3939738510)
Supplementary_files_format_and_content: M00138.bed: Genomic coordinates for M00138 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00422.bed: Genomic coordinates for M00422 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00724.bed: Genomic coordinates for M00724 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00791.bed: Genomic coordinates for M00791 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01200.bed: Genomic coordinates for M01200 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01259.bed: Genomic coordinates for M01259 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01504.bed: Genomic coordinates for M01504 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0138.2.bed: Genomic coordinates for MA0138.2 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0139.1.bed: Genomic coordinates for MA0139.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0149.1.bed: Genomic coordinates for MA0149.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: PBM0051.bed: Genomic coordinates for PBM0051 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MergedHomeoBoxFactors.bed: Genomic coordinates for homeobox motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: TG_Testis_TPM_Values.txt: TPM values for RefSeq genes in transgenic mouse testes.

source_name: mouse sperm, transgenic

extract_protocol:
Genomic DNA was isolated from transgenic sperm by proteinase K digestion and recovered by phenol-chloroform extraction and subsequently precipitated with ethanol. Purified DNA was digested with micrococcal nuclease.
DNAs were used to construct multiplexed DNA sequencing libraries with the NEBNext ChIP-Seq kit (New England BioLabs). All libraries were subjected to 50 cycles of paired-end sequencing on the Illumina HiSeq 2500 platform.


title: Tet2ko_m2

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

description:
genes.fpkm_tracking_wt_R__ko_R
gene_exp.diff_wt_R__ko_R

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 250bp
Differentially expressed genes were called using Cuffdiff 2.0.2 (PMID: 20436464)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression compared to the untreated (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

source_name: Primary bone marrow-derived mast cells (BMMCs)

growth_protocol: Primary murine mast cells were differentiated from bone marrow of C57BL/6 mice as previously described (PMID: 20827536) and cultured in the presence of IL-3 as survival factor. Briefly, bone marrow cells were isolated from femurs and tibias of 6-12 weeks old C57BL/6 mice and differentiated in IMDM complete medium until they were homogeneously mast cells (>95% Kit+ FcεRIα+ at surface staining) (IMDM complete medium: Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% (v/v) heat-inactivated fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.1 mM nonessential amino acids, and 50 mM beta-mercaptoethanol, recombinant murine IL-3). Since Tet2-/- cultures display reduced differentiation capabilities, Kit+ FcεRIα+ cells were separated by sorting after 4 weeks of differentiation.The resulting bone marrow-derived mast cells (BMMCs) were obtained from two independent animals for each genotype, either Tet2+/+ or Tet2-/-.

extract_protocol: Total RNA was extracted immediately after sorting and subjected to library preparation under Standard Illumina Protocol.

value: BMMC

tag: time

value: 4th week of differentiation

value: Untreated


title: Tet2wt_m2


title: GLIB_5hmC.Tet2.KO

description:
library strategy: 5-hmC CapSeq
Biotin-glucosyl tagging and enrichment of 5hmC (5 hmc cap-seq)

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the UCSC mm9 reference genome using Bowtie2 with "--very-sensitive" parameter (PMID: 22388286). Subsequently, only uniquely mapping reads were considered in the analysis.
Peaks were called using using MACS2 with added parameters " -g mm -B --SPMR --nomodel --extsize 200 -p 1.00e-04"
Genome_build: mm9 (NCBI Build 37), transcripts from Mus musculus UCSC iGenome
Supplementary_files_format_and_content: narrowPeak: chrom, start, end, name, score, strand, fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start.

extract_protocol: Chemical labeling-based 5hmC enrichment was performed according to Hydroxymethyl Collector™ kit from Active Motif (cat#55013, Active Motif-Carlsbad, CA) to selectively label 5hmC bases with glucose and biotin moieties to form biotin-N3-5-gmC as previously described by Song et al (Song CX, et al. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature biotechnology 29(1):68-72). Briefly 4 ug of genomic DNA was sonicated with COVARIS S2 to target size 200-400 bp (250 bp protocol for 150 seconds), purified with 1X AMPure XP beads (Agencourt A63880) and then subjected to biotin-based enrichment of 5-hydroxymethylcytosine following the recommended procedure. Captured 5hmc DNA enriched fragments were then processed for Illumina sequencing as previously described (Garber et al. 2012) with slight modifications (Ostuni et al. 2013).

tag: enrichment method

value: hmC-pulldown according to Hydroxymethyl Collector kit


title: Caki2 with empty vector, Replicate_B

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S University St

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Reads were aligned to hg19 using STAR with the following parameters: readFilesCommand zcat outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical
BAM files from STAR were sorted by coordinate.
Gene expression levels were computed using htseq-count using default parameters
Differential expression was performed with DESeq2 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimted text file showing normalized read counts (DESeq normalization method)

source_name: Caki2 cell line, Vector Control

growth_protocol: Caki-2 cells (Caki2-Ø as well as Caki2-PBRM1) were cultured in McCoy’s 5A (Corning Mediatech, Inc., Manassas, VA) supplemented with 10% fetal bovine serum (Omega Scientific,Inc, Tarzana, CA), 1% antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin; Corning Mediatech, Inc., Manassas, VA), 1% nonessential aminoacids (Corning Mediatech, Inc., Manassas, VA) and 1% L-glutamine (Corning Mediatech, Inc., Manassas, VA) at 37°C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Doxycycline is added to the culture media at 2µg/ml.

value: Caki2-empty vector

tag: construct

value: empty doxycycline-inducible lentiviral vector

value: No PBRM1 expression


title: tg_mono_mnase.bam

tag: genotype/variation


title: Caki2 with empty vector, Replicate_A


title: H3K4me1.WT

description: Chromatin IP against H3K4me1

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the UCSC mm9 reference genome using Bowtie2 with "--very-sensitive" parameter (PMID: 22388286). Subsequently, only uniquely mapping reads were considered in the analysis.
Peaks were called using using MACS2 with added parameters " -g mm -B --SPMR --nomodel --extsize 146 -p 1.00e-04"
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: narrowPeak: chrom, start, end, name, score, strand, fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start.

growth_protocol: Wild type BMMCs grown in IL-3 as survival and differentiation factor. No other modification or stimulation

extract_protocol: Library preparation for Illumina sequencing (HiSeq 2000) was carried out using a described protocol (Garber et al., 2012) with slight modifications (Ostuni et al., 2013). The purified DNA libraries were quantified both with a 2100 Bioanalyzer (Agilent Technologies) and Qubit (LifeTechnologies) and diluted to a working concentration of 10 nM.

tag: growth protocol

tag: antibody

value: H3K4me1:Abcam ab8895

value: No treatment


title: Tet2wt_m1


title: GLIB_5hmC.Tet2.WT


title: Tet2ko_m3


title: Caki2 expressing PBRM1, Replicate_B

source_name: Caki2 cell line, Lentiviral mediated stable expression of PBRM1

value: doxycycline-inducible lentiviral vector bearing PBRM1

value: stable expression of PBRM1


title: Caki2 expressing PBRM1, Replicate_C


title: Caki2 with empty vector, Replicate_C


title: 3wtALID0 sRNA-Seq

description: WT rep3 day 0

data_processing:
Mapping, prediction of novel miRNAs, quality control, and differential expression (DE) analysis were carried out using Oasis1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Excel sheets containing sheets with (1) RPM normalised read counts for small RNA in each sample, and (2) base mean, log 2 fold change and adjusted p-value generated by DESeq2 for each small RNA in each day

source_name: Trachea

value: primary mouse tracheal epithelial cultures (MTECs)

value: air-liquid interface (ALI)

tag: day

value: post ALI day 0

tag: genotype


title: human_mono.bam

description:
Proven fertile donor.
Chromatin

data_processing:
Illumina Casava v 1.8.2 software used for basecalling and demultiplexing sequencing reads.
Human DNA sequencing libraries were aligned to the human genome assembly hg19 with Bowtie (version 2.0.2), using the following parameters: bowtie2 -X 1000 --very-sensitive.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: M00138.bed: Genomic coordinates for M00138 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00422.bed: Genomic coordinates for M00422 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00724.bed: Genomic coordinates for M00724 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M00791.bed: Genomic coordinates for M00791 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01200.bed: Genomic coordinates for M01200 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01259.bed: Genomic coordinates for M01259 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: M01504.bed: Genomic coordinates for M01504 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0138.2.bed: Genomic coordinates for MA0138.2 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0139.1.bed: Genomic coordinates for MA0139.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MA0149.1.bed: Genomic coordinates for MA0149.1 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: PBM0051.bed: Genomic coordinates for PBM0051 motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: MergedHomeoBoxFactors.bed: Genomic coordinates for homeobox motifs predicted to be bound in mouse sperm.
Supplementary_files_format_and_content: TG_Testis_TPM_Values.txt: TPM values for RefSeq genes in transgenic mouse testes.

source_name: human sperm

extract_protocol:
Following liquefaction, sperm were washed twice and frozen as dry pellets in liquid nitrogen. Sperm were thawed on ice and washed twice with PBS. Following filtration through an 80-micron mesh, the cells were washed twice and resuspended in 1 mL of a PBS solution containing 0.5% Triton X-100. The absence of somatic cells was confirmed by light microscopy. The cells were incubated for 10 minutes on ice with occasional mixing. Subsequently, ice-cold PBS was added to 10 mL and the cells were washed twice prior to counting with a hemocytomoter. Tritonized sperm suspensions were adjusted to 5x10^6 cells/mL in 5 mM CaCl2, 10 mM dithiothreitol, buffered with 50 mM Tris-HCl, pH 7.9. The suspension was placed 37°C for 30 minutes. Subsequently, the sample was diluted with prewarmed reaction buffer to a final concentration of 5x10^6 cells/mL in 5 mM CaCl2, 10 mM dithiothreitol, 2 Kunitz unit/mL MNase (New England BioLabs), buffered with 50 mM Tris-HCl, pH 7.9. The sample was digested for 5 minutes and the reactions were stopped with the addition of 0.5 M EDTA pH 8.0 to a final concentration of 20 mM. The cell suspension was then rotated at 4°C for 30 minutes prior to centrifugation at 20,000 rcf for 10 minutes. Soluble nucleosome-bound DNAs were recovered from the supernatant by proteinase K digestion and subsequent phenol-chloroform extraction and ethanol precipitation. Purified DNAs were resolved by gel electrophoresis. Bands corresponding to the length of DNA associated with a mononucleosome (~150 bp) were excised and column purified.
DNAs were used to construct multiplexed DNA sequencing libraries with the NEBNext ChIP-Seq kit (New England BioLabs). All libraries were subjected to 50 cycles of paired-end sequencing on the Illumina HiSeq 2500 platform.


title: 369 BN-P4

city: Kansas City

first: Pramod

last: Dhakal

state: Kansas

address: 3901 Rainbow Boulevard

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

description: barcode: AGTCAA

data_processing:
Base calling by Real-time analysis software (Illumina)
Base call files converted to qseq files by BCL converter (Illumina) and coverted to fastq format for downstream analysis
Reads were mapped to Rat reference genome (Ensembl Rnor_5.0.78) using CLC Bio genmonics workbench 8.0 9 (CLC, Aarhus, Denmark)
Genome_build: Ensembl Rnor_5.0.78
Supplementary_files_format_and_content: Excel (.xls) file containing reads per kilobase per million (RPKM) values

organism: Rattus norvegicus

source_name: Uterus

extract_protocol:
RNA extracted by Trizol based protocol
PolyA containing RNA were used to prepare library using TruSeq RNA Sample Preparation Kit (Illumina) acording to manufacturer's guidelines.

treatment_protocol: Progesterone @ 40µg/gm body weight (treatment) and Sesame oil (control) for 9 hours subcutaneously.

value: uterus

value: Brown Norway (BN)

tag: age

value: 10 weeks

tag: sampling interval post treatment

value: 9 hour


title: 359 BN-P4

description: barcode: GTGGCC

tag: strain


title: 377 BN-Oil

description: barcode: AGTTCC

value: Oil


title: 375 BN-P4

description: barcode: AGTCAA