title: Ca_05_RRBS

description: single cell RRBS


title: Het (Q50) 6 months Female Cortex miRNA rep3

status: Public on Mar 01 2016

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omnisoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omnisoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl miRBase.R21
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: Cortex

tag: genotype

value: Het (Q50) Knock-In

tag: age

value: 6 months

tag: Sex

value: Female

tag: housing condition

value: housed with Wild Type and Het (Q50) mice


title: yjm789_gly_S14

city: Morgantown

first: Xiaoqing

last: Rong-Mullins

state: West Virginia

address: 53 Campus Dr

institute: West Virginia University

data_processing:
Base-calling was performed via Illumina CASAVA version 1.7.
Tophat v2.0.12 (Kim et al. 2013; Trapnell et al. 2009) was used to map the RNA-Seq reads to the S288c genome and to generate .bam files for mapped reads. The reads were first mapped to ribosomal RNA and transfer RNA genes; 1.05-1.94 million read pairs per sample were not matched to those RNA genes, and 91.2-95.5% of those unmatched reads were then matched to the whole gene pool of S288c. The reads matched to rRNA and tRNA were excluded because these RNAs tend to be extracted at high and/or variable abundances across replicates, thus may bias the calculation of FPKM (fragments per kb gene per million mapped fragments).
The following approach was used to quantify gene expression from the mapped reads in .bam files. The R-package Rsubread v1.18.0 (Liao et al. 2013) was used to generate count tables based on the annotations of S288c genome release R64-1-1. Then DESeq2 v1.8.1 (Anders and Huber, 2010) was used to quantify differential expression.
Genome_build: sacCer3
Supplementary_files_format_and_content: Table S1 as a single .xlsx file with multiple worksheets: Read counts and differential expression data from RNA-Seq. In each comparison for differential expression in the format of 'condition_A...condition_B', condition_A is the denominator and condition_B is the numerator when calculating fold change. • Rsubread_count_table: count table generated by Rsubread package, input for differential expression analysis by DESeq2 package. • Rsubread_FPKM: FPKM data calculated based on 'Rsubread_count_table'. • DESeq: differential expression data generated by DESeq2 package.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Each of the three untagged isogenic strains with different alleles YRR1_S96, YRR1_YJM789, YRR1_S96-I775E, respectively, were grown as two replicated cultures in liquid YPD or YPglycerol medium to mid-log phase. Each YPD culture was diluted to early-log phase and divided into two subcultures. One subculture was incubated in liquid YPD medium with 0.25 µg/ml 4NQO and the other subculture without 4NQO. Both subcultures for each replicate were further grown for 2.5 h.

extract_protocol:
Total RNA was extracted from each sample and multiplexed unstranded paired-end cDNA libraries were prepared using Illumina TruSeq RNA Sample Prep Kit v2.
RNA libraries were prepared for sequencing on Illumina MiSeq using standard Illumina protocols

value: S96 YRR1_delta

tag: yrr1_ allele transformed

tag: growth medium

value: YPD, YPD + 4NQO, YPglycerol


title: Ca_04_RNA

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

country: China

institute: Peking University

description: single cell RNA seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Adapter sequence and low-quality sequences were trimmed.
For RNA seq data, TopHat (version 2.0.10) were used for sequence alignment to human hg19 genome. Gene expression level (FPKM) were calculated using Cufflinks (version 2.1.1).
For RRBS data, Bismark were used for sequence alignment to human (hg19) genome, and metlevel of each CpG site were calculated manually.
For gDNA seq data, bwa were used for sequence alignment to the human (hg19) genome, and the depth for each 10M window were calculated by summing the sequencing depth of all the positions in each window.
Genome_build: hg19

organism: Homo sapiens

source_name: human adult cancer cell

growth_protocol: The hepG2 cell line were cultured in RPMI 1640 with 10% FBS, and digested with trypsin before single cell picking.

extract_protocol:
The RNA and DNA of each single cell were separated and extracted by Trio-seq.
For RNA seq and genome DNA seq data, we constructed the sequencing libraries using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L). RRBS libraries were constructed using RRBS protocol as described in 2013 (Guo et al. 2013)

tag: gender

value: Male

value: liver cancer

tag: passage


title: Het (Q20) 6 months Male Cortex miRNA rep3

value: Het (Q20) Knock-In

value: housed with Wild Type and Het (Q20) mice


title: yjm789_gly_S13


title: Het (Q20) 6 months Male Cortex miRNA rep2


title: Ca_04_RRBS

description: single cell RRBS

library_source: genomic

molecule: genomic DNA


title: Ca_03_RNA

description: single cell RNA seq


title: Het (Q50) 10 months Female Cortex miRNA rep4

value: 10 months


title: Het (Q20) 6 months Male Cortex miRNA rep4


title: Het (Q20) 10 months Male Cortex miRNA rep4


title: Ca_02_RNA

description: single cell RNA seq


title: Het (Q20) 10 months Male Cortex miRNA rep3


title: s96ie_ypd_S6

value: YPD


title: Ca_03_RRBS

description: single cell RRBS


title: s96ie_nqo_S11

value: YPD + 4NQO


title: s96ie_ypd_S5


title: s96ie_nqo_S12


title: Het (Q20) 10 months Male Cortex miRNA rep2


title: Het (Q20) 10 months Male Cortex miRNA rep1


title: Ca_01_RNA

description: single cell RNA seq


title: Ca_02_RRBS

description: single cell RRBS


title: yjm789_nqo_S7


title: s96ie_gly_S18


title: Ca_01_RRBS

description: single cell RRBS


title: Het (Q20) 6 months Female Cortex miRNA rep4


title: Het (Q20) 6 months Female Cortex miRNA rep3


title: s96_ypd_S4


title: s96_ypd_S3


title: Het (Q20) 6 months Male Cortex miRNA rep1


title: Het (Q20) 6 months Female Cortex miRNA rep1


title: s96_nqo_S9


title: Het (Q20) 6 months Female Cortex miRNA rep2


title: s96_nqo_S10


title: s96_gly_S16


title: Het (Q20) 10 months Female Cortex miRNA rep4


title: Het (Q20) 10 months Female Cortex miRNA rep3


title: s96_gly_S15


title: Het (Q140) 6 months Male Cortex miRNA rep4

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q140) 6 months Male Cortex miRNA rep2


title: Het (Q140) 6 months Male Cortex miRNA rep3


title: Het (Q140) 6 months Male Cortex miRNA rep1


title: Het (Q140) 10 months Male Cortex miRNA rep4


title: Het (Q20) 10 months Female Cortex miRNA rep1


title: Het (Q140) 10 months Male Cortex miRNA rep2


title: ChIPseq_WT_NHS_SRF

city: Ithaca

first: Dig

middle: Bijay

last: Mahat

state: NY

address: 526 campus Rd

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
ChIP-seq: adapters were removed and the reads were trimmed to 36bp. The trimmed reads were mapped to the mouse genome mm10.
ChIP-seq:  Using MACS2, peaks were called against IgG and Input. p-value threshold of 1e-04 was used.
Genome_build: mm10
Supplementary_files_format_and_content: xls file of SRF peaks for ChIP-seq

source_name: MEFs

extract_protocol:
For ChIP-seq, isolated nuclei were sonicated to shear chromatin and IPed with SRF antibody and non-specific IgG. Input DNA was also sequenced for each condition.
ChIP-seq libraries were prepared the standard way using Illumnia TRU-seq adpapters.

tag: strain background

tag: genotype/variation

value: wild type

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)

tag: time point

value: before heat shock

tag: chip antibody

value: SRF (D71A9) from Cell Signaling (#5147)


title: ChIPseq_WT_60HS_SRF

value: after 60 min heat shock


title: Het (Q140) 10 months Male Cortex miRNA rep1

value: Cortex


title: CTCF_ChIP_preB_p3_2

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: ChIP

data_processing:
Fastq files were aligned to the mouse genome (mm9) using bwa aln.
Peak calling was performed using MACS2 (callpeak), with --extsize 180 and -g mm.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak

growth_protocol:
ESCs and iPSCs were cultured on Mitomycin-C treated MEFs in KO-DMEM (Invitrogen) supplemented with 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen), 1,000 U/ml LIF (Millipore) and 15% fetal bovine serum (FBS, Invitrogen) (ESC medium). Naïve ESCs were cultured in serum-free N2B27 medium on gelatin-coated dishes. N2B27 medium (500ml) was generated by inclusion of the following: 240ml DMEM/F12 (Invitrogen), 240ml Neurobasal (Invitrogen), 5ml N2 supplement (Invitrogen), 10ml B27 supplement (Invitrogen), 1,000 U/ml LIF (Millipore), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Invitrogen), and the small molecules PD0325901 (Stemgent, 1μM) and CHIR (Stemgent, 3μM). CD19 + pre-B cells and Mac1 + macrophages were isolated from bone marrow with monoclonal antibodies to CD19 and Mac-1 (BD Pharmingen) respectively, using MACS sorting (Miltenyi Biotech). B cells were grown in RPMI medium with 10% FBS and 10ng/ml IL-7 (Peprotech); macrophages in DMEM with 10% FBS and 10ng/ml each of CSF1 and IL-3 (Peprotech). MEFs were established from day 13.5 mouseembryos and cultured in DMEM containing 10% FBS. NSC were isolated and cultured aspreviously described (Di Stefano et al., 2009). All media were supplemented with L-glutamineand penicillin/streptomycin (GIBCO).
Reprogramming experiments with B cells were performed as previously described (Di Stefano et al., 2014); with MEFs, macrophages and NSCs were conducted by plating 100.000 cells/well on gelatinized plates seeded with irradiated MEFs, using ESC medium supplemented with 2 μg/ml of doxycycline. For the isolation of iPSC lines, doxycycline was washed out after 15 days of reprogramming and colonies with ESC-like morphology were picked at 20 days before further passaging. iPSC lines were expanded for an additional 9 days (3 passages) to obtain P3 iPS cell lines or for 20 passages to obtain P20 iPS cell lines.

extract_protocol: ChIP experiments were performed as described previously (van Oevelen et al., 2008) using an antibody against H3K27ac (ab4729, Abcam) and CTCF (Millipore, 07-729). DNA libraries were prepared using Illumina's reagents and instructions.

value: preB derived p3 iPS


title: Het (Q140) 6 months Female Cortex miRNA rep4

value: 6 months

value: Female


title: Het (Q140) 10 months Male Cortex miRNA rep3

value: Male


title: CTCF_ChIP_preB_p3_1

description: ChIP


title: ChIPseq_WT_12HS_SRF

value: after 12 min heat shock


title: CTCF_ChIP_preB_p20_2

description: ChIP

value: preB derived p20 iPS


title: Het (Q140) 6 months Female Cortex miRNA rep2


title: Het (Q140) 6 months Female Cortex miRNA rep3


title: Het (Q140) 10 months Female Cortex miRNA rep4

value: 10 months


title: Het (Q140) 6 months Female Cortex miRNA rep1


title: CTCF_ChIP_NSC_p3_2

description: ChIP

value: NSC derived p3 iPS


title: CTCF_ChIP_preB_p20_1

description: ChIP


title: Het (Q140) 10 months Female Cortex miRNA rep2


title: Het (Q20) 10 months Female Cortex miRNA rep2

value: Het (Q20) Knock-In

value: housed with Wild Type and Het (Q20) mice


title: CTCF_ChIP_NSC_p20_2

description: ChIP

value: NSC derived p20 iPS


title: s96ie_gly_S17

value: S96 YRR1_delta

value: YPD, YPD + 4NQO, YPglycerol


title: Het (Q140) 10 months Female Cortex miRNA rep3

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: CTCF_ChIP_MEF_p3_2

description: ChIP

value: MEF derived p3 iPS


title: Het (Q140) 10 months Female Cortex miRNA rep1

value: Cortex


title: CTCF_ChIP_NSC_p20_1

description: ChIP


title: WT 6 months Male Cerebellum miRNA rep4 (Q50)

source_name: Cerebellum

value: Cerebellum

value: Wild Type

value: housed with Wild Type and Het (Q50) mice


title: CTCF_ChIP_MEF_p20_2

description: ChIP

value: MEF derived p20 iPS


title: CTCF_ChIP_MEF_p20_1

description: ChIP


title: WT 6 months Male Cerebellum miRNA rep3 (Q50)

value: 6 months

value: Male


title: WT 6 months Male Cerebellum miRNA rep1 (Q50)


title: WT 6 months Male Cerebellum miRNA rep2 (Q50)


title: CTCF_ChIP_macrophage_p3_2

description: ChIP

value: macrophage derived p3 iPS


title: CTCF_ChIP_macrophage_p3_1

description: ChIP


title: WT 10 months Male Cerebellum miRNA rep1 (Q50)

value: 10 months


title: CTCF_ChIP_macrophage_p20_1

description: ChIP

value: macrophage derived p20 iPS


title: CTCF_ChIP_macrophage_p20_2

description: ChIP


title: WT 6 months Male Cerebellum miRNA rep4 (Q20)

value: housed with Wild Type and Het (Q20) mice


title: CTCF_ChIP_NSC_p3_1

description: ChIP

value: NSC derived p3 iPS


title: WT 6 months Male Cerebellum miRNA rep3 (Q20)


title: WT 6 months Male Cerebellum miRNA rep1 (Q20)


title: WT 10 months Male Cerebellum miRNA rep4 (Q20)


title: CTCF_ChIP_MEF_p3_1

description: ChIP


title: WT 6 months Male Cerebellum miRNA rep2 (Q20)


title: RIP-seq, rabbit control IgG

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: RIP sample by using control IgG

data_processing:
Reads were  processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with options -m 200 -u).
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, expression data of the four samples were summarized into single processed file by Cuffdiff and are in RNA-seq.genes.fpkm_tracking.txt. For RIP-seq, calculated FPKM values of immunoprecipitated RNA of the four samples were summarized into single processed file by Cuffdiff and are in RIP-seq.genes.fpkm_tracking.txt.

growth_protocol: A549 cells were maintained in Dulbecco's modified Eagle's medium (DMEM #11965; Thermo Scientific) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 µg/ml streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
For RNA-seq, total RNAs were extracted as described previously (Arase et al., 2014, Cancer Sci). RIP samples were obtained from A549 cells following the manufacturer's protocol (Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore)).
For RNA-seq, Libraries were prepared using  Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-seq kit v2 (Thermo Scientific). For RIP-seq, Ion Total RNA-seq kit v2 (Thermo Scientific) was used. Sequencing was performed using Ion PI Chip Kit v2, PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 (Thermo Scientific).

treatment_protocol: For RNA-seq, shRNAs were introduced into cells using lentiviral vectors. Cells were stimulated with 2.5 ng/ml TGF-beta or left untreated for 24 h before harvest. For RIP-seq, A549 cells were cultured in 10-cm dish before lysis.

tag: cell line

tag: shRNA

tag: rip

value: rabbit IgG, (provided by RIP kit)

tag: tgf-beta treatment

value: no

tag: histology

value: lung adenocarcinoma


title: RIP-seq, anti-snRNP70

description: RIP sample by using anti-snRNP70

value: anti-snRNP70 (provided by RIP-kit)


title: RIP-seq, anti-RBM47, biological replicate 1

description: RIP sample by using anti-RBM47, biological replicate 1

value: anti-RBM47 (Sigma-Aldrich, HPA006347), lot no not available


title: WT 10 months Male Cerebellum miRNA rep4 (Q50)

tag: strain

tag: tissue

tag: genotype

tag: age


title: RNA-seq, shRBM47, TGF-beta treated

description: RBM47 shRNA is stably expressed, TGF-beta treated

molecule: polyA RNA

value: yes


title: WT 10 months Male Cerebellum miRNA rep2 (Q50)

value: Cerebellum

tag: Sex

tag: housing condition


title: RNA-seq, shControl, TGF-beta treated

description: control shRNA is stably expressed, TGF-beta treated

value: Negative control


title: RNA-seq, shRBM47, without TGF-beta

description: RBM47 shRNA is stably expressed, without TGF-beta stimulation


title: WT 10 months Male Cerebellum miRNA rep3 (Q20)

value: Wild Type


title: WT 10 months Male Cerebellum miRNA rep3 (Q50)

value: housed with Wild Type and Het (Q50) mice


title: WT 10 months Male Cerebellum miRNA rep2 (Q20)


title: RNA-seq, shControl, without TGF-beta

description: control shRNA is stably expressed, without TGF-beta stimulation


title: WT 10 months Male Cerebellum miRNA rep1 (Q20)


title: RIP-seq, anti-RBM47, biological replicate 2

description: RIP sample by using anti-RBM47, biological replicate 2


title: WT 6 months Female Cerebellum miRNA rep1 (Q50)

value: 6 months

value: Female


title: WT 10 months Female Cerebellum miRNA rep4 (Q50)


title: WT 6 months Female Cerebellum miRNA rep4 (Q50)


title: WT 10 months Female Cerebellum miRNA rep2 (Q50)


title: WT 10 months Female Cerebellum miRNA rep1 (Q50)


title: WT 10 months Female Cerebellum miRNA rep3 (Q50)


title: WT 6 months Female Cerebellum miRNA rep4 (Q20)


title: WT 6 months Female Cerebellum miRNA rep3 (Q20)


title: WT 6 months Female Cerebellum miRNA rep1 (Q20)


title: WT 6 months Female Cerebellum miRNA rep2 (Q20)


title: WT 10 months Female Cerebellum miRNA rep4 (Q20)


title: WT 10 months Female Cerebellum miRNA rep3 (Q20)


title: WT 10 months Female Cerebellum miRNA rep2 (Q20)


title: Het (Q92) 6 months Male Cerebellum miRNA rep3

value: Het (Q92) Knock-In

value: Male

value: housed with Het (Q92) mice


title: Het (Q92) 6 months Male Cerebellum miRNA rep1


title: Het (Q92) 6 months Male Cerebellum miRNA rep4


title: Het (Q92) 6 months Male Cerebellum miRNA rep2


title: WT 6 months Female Cerebellum miRNA rep3 (Q50)


title: WT 6 months Female Cerebellum miRNA rep2 (Q50)


title: WT 10 months Female Cerebellum miRNA rep1 (Q20)

value: 10 months

value: housed with Wild Type and Het (Q20) mice


title: Het (Q92) 10 months Male Cerebellum miRNA rep3


title: Het (Q92) 6 months Female Cerebellum miRNA rep2


title: Het (Q92) 10 months Female Cerebellum miRNA rep4


title: Het (Q92) 6 months Female Cerebellum miRNA rep1


title: Het (Q92) 10 months Male Cerebellum miRNA rep1


title: Het (Q92) 10 months Female Cerebellum miRNA rep2


title: Het (Q92) 10 months Male Cerebellum miRNA rep2


title: Het (Q92) 6 months Female Cerebellum miRNA rep4


title: Het (Q92) 10 months Female Cerebellum miRNA rep3


title: Het (Q92) 10 months Female Cerebellum miRNA rep1


title: Het (Q50) 6 months Male Cerebellum miRNA rep4

value: Het (Q50) Knock-In


title: Het (Q92) 6 months Female Cerebellum miRNA rep3


title: Het (Q50) 10 months Male Cerebellum miRNA rep4


title: Het (Q50) 6 months Male Cerebellum miRNA rep2


title: Het (Q50) 6 months Male Cerebellum miRNA rep3


title: Het (Q50) 6 months Male Cerebellum miRNA rep1


title: Het (Q50) 10 months Male Cerebellum miRNA rep1


title: Het (Q50) 6 months Female Cerebellum miRNA rep4


title: Het (Q50) 10 months Male Cerebellum miRNA rep2


title: Het (Q92) 10 months Male Cerebellum miRNA rep4


title: Het (Q50) 6 months Female Cerebellum miRNA rep3


title: Het (Q50) 10 months Female Cerebellum miRNA rep2


title: Het (Q50) 10 months Female Cerebellum miRNA rep1


title: Het (Q20) 6 months Male Cerebellum miRNA rep3

value: Het (Q20) Knock-In


title: Het (Q20) 10 months Male Cerebellum miRNA rep3


title: Het (Q20) 6 months Female Cerebellum miRNA rep4


title: Het (Q50) 10 months Female Cerebellum miRNA rep4


title: Het (Q50) 6 months Male Cortex miRNA rep3

value: Cortex


title: Het (Q50) 6 months Female Cerebellum miRNA rep1


title: Het (Q50) 6 months Female Cerebellum miRNA rep2


title: Het (Q20) 6 months Male Cerebellum miRNA rep4


title: Het (Q50) 10 months Female Cerebellum miRNA rep3


title: Het (Q20) 10 months Male Cerebellum miRNA rep1


title: Het (Q20) 6 months Female Cerebellum miRNA rep3


title: Het (Q20) 10 months Female Cerebellum miRNA rep2


title: Het (Q20) 10 months Male Cerebellum miRNA rep4


title: Het (Q20) 6 months Male Cerebellum miRNA rep1


title: Het (Q20) 6 months Male Cerebellum miRNA rep2


title: Het (Q20) 6 months Female Cerebellum miRNA rep1


title: Het (Q20) 6 months Female Cerebellum miRNA rep2


title: Het (Q20) 10 months Female Cerebellum miRNA rep3


title: Het (Q20) 10 months Female Cerebellum miRNA rep4


title: Het (Q20) 10 months Female Cerebellum miRNA rep1


title: Het (Q50) 10 months Male Cerebellum miRNA rep3


title: Het (Q140) 6 months Male Cerebellum miRNA rep4

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q20) 10 months Male Cerebellum miRNA rep2


title: Het (Q140) 6 months Male Cerebellum miRNA rep3


title: Het (Q140) 6 months Male Cerebellum miRNA rep2


title: Het (Q140) 6 months Male Cerebellum miRNA rep1


title: Het (Q140) 10 months Male Cerebellum miRNA rep4


title: Het (Q140) 10 months Male Cerebellum miRNA rep3


title: Het (Q140) 10 months Male Cerebellum miRNA rep1


title: Het (Q140) 6 months Female Cerebellum miRNA rep4


title: Het (Q140) 6 months Female Cerebellum miRNA rep3


title: Het (Q140) 10 months Male Cerebellum miRNA rep2


title: Het (Q140) 6 months Female Cerebellum miRNA rep1


title: Het (Q140) 6 months Female Cerebellum miRNA rep2


title: Het (Q140) 10 months Female Cerebellum miRNA rep1


title: Het (Q140) 10 months Female Cerebellum miRNA rep4


title: Het (Q140) 10 months Female Cerebellum miRNA rep2


title: Het (Q140) 10 months Female Cerebellum miRNA rep3


title: Input_shMed23_OnDox_ChIPSeq

city: Cold Spring Harbor

first: Anand

middle: S

last: Bhagwat

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
ChIP-Seq
shMed23_OnDox_Brd4_ChIP_peaks.txt

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4.2 software was used.
After calling the peaks, peaks whose FDR(%) greater than 1.0 and fold enrichment over input lower than 10 were filtered, based on MACS peak calling results.
Datasets from Dox-induced shRNA treatment were normalized to read depth (total mapped tag counts) of corresponding control (no dox) treatment of cells.
Genome_build: mm9
Supplementary_files_format_and_content: peak information was generated by MACS software

source_name: MLL-AF9/NrasG12D murine cell line

growth_protocol: Cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing. These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.
These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.

value: Acute myeloid leukemia

tag: antibody


title: shMed8.934_RNASeq

description: RNA-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence to map with mouse genome (mm9) using Tophat with default parameters.
Cufflinks software was used to compare gene expression profiles by calculting Fragments Per Kilobase of exon per Megabase of library size (FPKM) for each sample.
For biological replicates of experiments, two individual shRNAs were used to prepare total RNA.
To define the expressed genes in further analysis of PolyA+ RNA-Seq, only the genes with FPKM≥5 and status=OK from Cuffdiff analysis were considered.
Processed data file contains a list of filtered genes with averaged FPKM from two biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for samples

extract_protocol:
Total RNAs were extracted using Trizol reagent.
These libraries were made following the instructions of illumina Truseq RNA sample prep kit v2.

treatment_protocol: To profile the basal transcription level, we performed PolyA+ (illumina TruSeq) in the murine AML RN2 cell line. To define the genes affected by Mediator subunit knockdown, RN2 cells which express dox-inducible shRNAs were cultured with Doxycyclin for 48 hour before harvest.


title: Input_shMed23_OffDox_ChIPSeq

description:
ChIP-Seq
shMed23_OffDox_Brd4_ChIP_peaks.txt


title: Input_shMed12_OnDox_ChIPSeq

description:
ChIP-Seq
shMed12_OnDox_Brd4_ChIP_peaks.txt


title: Brd4_shMed23_OnDox_ChIPSeq

value: Brd4 (A301-985A; Bethyl)


title: shMed8.933_RNASeq

description: RNA-Seq


title: Brd4_shMed23_OffDox_ChIPSeq


title: shRen_RNASeq_4

description: RNA-Seq


title: Brd4_shMed12_OnDox_ChIPSeq


title: D4 Mouse Infected CD45- cells IAV Primary Infection (Fig 2 I-M)

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
The reads were mapped to the mouse or human transcriptome as well as the influenza genome using Bowtie
Read numbers were normalized across samples.

source_name: Whole Lung

growth_protocol: Cells were grown under standard laboratory conditions.

extract_protocol:
Cells were sorted by a facs aira into wells of a 96 well plate containing RNA protection buffer.
TruSeq Nano DNA sample Preparation Kit (Illumina) was used as per the manufacturer’s instructions.

treatment_protocol: Mice or cells were infected for the indicated times.

tag: sequencing

value: Double Lane

tag: sample type


title: Input_shMed12_OffDox_ChIPSeq

description:
ChIP-Seq
shMed12_OffDox_Brd4_ChIP_peaks.txt

tag: cell type


title: D4 Mouse Infected CD45- cells IBV Primary Infection (Fig 2 I-M)


title: D25 Mouse tdTomato+ CD45- cells IBV Secondary Infection (Fig 2 I-M)


title: Day 50 Mouse CD45- tdTomato+ cells (Fig 1 J-M)

value: Single Lane

value: Day 50 Mouse CD45- tdTomato+ cells


title: Naïve Mouse tdTomato- CD45- cells (Fig 2 I-M)

value: Naïve Mouse tdTomato- CD45- cells


title: shRen_RNASeq_3

description: RNA-Seq


title: Day 5 Mouse CD45- tdTomato+ cells (Fig 1 J-M)

value: Day 5 Mouse CD45- tdTomato+ cells


title: D25 Mouse tdTomato+ CD45- cells No Secondary Infection (Fig 2 I-M)


title: Day 21 Mouse CD45- tdTomato+ cells (Fig 1 J-M)

value: Day 21 Mouse CD45- tdTomato+ cells


title: Naïve Mouse tdTomato- CD45- cells (Fig 1 J-M)


title: Brd4_shMed12_OffDox_ChIPSeq


title: H3K27Ac_ALL_mouse

city: Cambridge

first: Jennifer

middle: Lynn

last: Wilson

state: Massachusetts

address: 77 Massachusetts Ave, 16-244

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Basecalls were performed using standard Illumina software.
Trimmed reads were aligned to the mouses genome (mm9)
MACS was used for peak calling with the following parameters (--mfold=10,30 --format=SAM --pvalue=1e-5)
Supplementary_files_format_and_content: Bed files with MACS peaks and chromosome locations

source_name: cultured mouse pre-B-cell ALL

growth_protocol: Bcr-Abl-driven mouse acute B-cell lymphoblastic leukemia cells (Williams et al. 2006) were cultured in RPMI supplemented with 10% FBS, 4 mM L-glutamine, and 5 µM β-mercaptoethanol, and were split 1:5 daily.

extract_protocol:
8.5x106 pre-B-cells were cross-linked with 11% formaldehyde. After cross-linking cells were lysed and sonicated using a BioRuptor.
Libraries were prepared using the Illumina library prep kit according to manufacturer's instructions.

value: Acute Lymphoblastic Leukemia


title: GFP_ChIP

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing reads were aligned to genome using Bowtie-1.0.0 with default parameters.
Only the uniquely mapped reads were retained,and removing duplicated reads.
Peaks were called using MACS-1.4.2 with the following setting:p-value(1e-4),enrichment fold (10).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated by MACS-1.4.2 which show the tags enrichment evey 10-bp window on the genome, and bed files provide the binding regions of Smad2 or Smad3 on the genome.

source_name: neuroepithelia cells

growth_protocol: For mouse ESC neural differentiation, half million cells were suspended in DMEM-F12/neurobasal medium (1:1 DMEM-F12/neurobasal medium, 1X N2 neural supplement, 1X lipid concentrate, 1mM L-glutamine, 0.1mM β-mercaptoethanol and 60 μg/ml N-acetyl cysteine). After 4-6 days of culture in suspension, neuroepithelial aggregates were collected for ChIP-seq

extract_protocol:
Chromatin were sheared to fragements by using sonication,then protein-DNA complexes were isolated with antibody GFP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: ES-derived neural neuroepithelia cells

tag: passages


title: GFP_Smad2_input


title: GFP_Smad3_ChIP


title: GFP_Smad2_ChIP


title: GFP_Smad3_input


title: shMed12.401_RNASeq

description: RNA-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence to map with mouse genome (mm9) using Tophat with default parameters.
Cufflinks software was used to compare gene expression profiles by calculting Fragments Per Kilobase of exon per Megabase of library size (FPKM) for each sample.
For biological replicates of experiments, two individual shRNAs were used to prepare total RNA.
To define the expressed genes in further analysis of PolyA+ RNA-Seq, only the genes with FPKM≥5 and status=OK from Cuffdiff analysis were considered.
Processed data file contains a list of filtered genes with averaged FPKM from two biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with fold change FPKM values for shMediator samples relative to control shRen hairpin samples.


title: shRen_RNASeq_1

description: RNA-Seq


title: shMed12.5755_RNASeq

description: RNA-Seq


title: shMed23.678_RNASeq

description: RNA-Seq


title: Med1_RN2_ChIPSeq

description: ChIP-Seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4.2 software was used.
After calling the peaks, peaks whose FDR(%) greater than 1.0 and fold enrichment over input lower than 10 were filtered, based on MACS peak calling results.
Datasets from JQ1 treatment were normalized to read depth (total mapped tag counts) of corresponding DMSO treatment.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were converted from wiggle files generated by MACS software

tag: treatment

value: Med1 (A300-793A; Bethyl)


title: Med1_DMSO_ChIPSeq_Rep1

description: ChIP-Seq

value: DMSO for 2 hours


title: Input_JQ1_ChIPSeq

description: ChIP-Seq

value: 500nM JQ1 for 2 hours


title: Input_DMSO_ChIPSeq

description: ChIP-Seq


title: Med1_JQ1_ChIPSeq_Rep1

description: ChIP-Seq


title: Med1_DMSO_ChIPSeq_Rep2

description: ChIP-Seq


title: H3K4me3_ALL_mouse


title: Med1_JQ1_ChIPSeq_Rep2

description: ChIP-Seq


title: Brd4_JQ1_ChIPSeq

description: ChIP-Seq


title: IgG_control_ALL_mouse


title: ChIPseq_HSF1KO_60minHS_MM

data_processing:
PRO-seq: adapters were removed and the reads were trimmed to 36bp. Reverse complement of reads were generated.
PRO-seq: reads were first mapped to ribosomal genome and anything that did not map to ribosomal genome were mapped to rest of the genome using mm10. The bedgraph files were normalized with the custom normalization approach as discribed in the paper and the bigWig files were generated from the normalized bedgraph files.
ChIP-seq: adapters were removed and the reads were trimmed to 36bp. The trimmed reads were mapped to the mouse genome mm10.
ChIP-seq:  Using MACS, peaks were called against IgG and Input. p-value threshold of 1e-04 was used. Overlapping peaks from two different antibodies (CS and MM) were combind using fisher's method of combining p-value. The resulting peaks were selected against any peaks called in HSF1-/- lines.
Genome_build: mm10
Supplementary_files_format_and_content: peak.txt file of HSF1 peaks for ChIP-seq and normalized bigWig for PRO-seq

extract_protocol:
Nuclei were isolated for PRO-seq and run-on reactions were performed with biotinylated nucleotides. For ChIP-seq, isolated nuclei were sonicated to shear chromatin and IPed with two different antibodies (CS and MM) and non-specific IgG. Input DNA was also sequenced for each condition.
PRO-seq libraries were performed according to the paper: Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. PMID: 23430654. ChIP-seq libraries were prepared the standard way using Illumnia TRU-seq adpapters.

tag: strain background

tag: genotype/variation

value: Mouse embryonic fibroblasts (MEFs)

tag: time point

value: after 60 min heat shock

tag: chip antibody

value: gift from Morimoto lab (MM)


title: ChIPseq_HSF1KO_60minHS_CS

value: Cell Signaling (CS) #4356


title: Brd4_DMSO_ChIPSeq

description: ChIP-Seq

value: Acute myeloid leukemia


title: ChIPseq_HSF1KO_12minHS_MM

value: after 12 min heat shock


title: ChIPseq_HSF1KO_12minHS_CS


title: GFP_input


title: ChIPseq_HSF1KO_NHS_MM

value: before heat shock


title: shMed23.4061_RNASeq

description: RNA-Seq


title: ChIPseq_HSF1KO_NHS_CS


title: shRen_RNASeq_2

description: RNA-Seq


title: ChIPseq_WT_60minHS_IgG

value: wild type

value: non-specific IgG


title: ChIPseq_WT_60minHS_input


title: ChIPseq_WT_60minHS_MM


title: ChIPseq_WT_12minHS_input


title: ChIPseq_WT_60minHS_CS


title: ChIPseq_WT_12minHS_IgG


title: ChIPseq_WT_12minHS_MM


title: ChIPseq_WT_12minHS_CS


title: PROseq_HSF1KO_12minHS

data_processing:
library strategy: PRO-seq
PRO-seq: adapters were removed and the reads were trimmed to 36bp. Reverse complement of reads were generated.
PRO-seq: reads were first mapped to ribosomal genome and anything that did not map to ribosomal genome were mapped to rest of the genome using mm10. The bedgraph files were normalized with the custom normalization approach as discribed in the paper and the bigWig files were generated from the normalized bedgraph files.
ChIP-seq: adapters were removed and the reads were trimmed to 36bp. The trimmed reads were mapped to the mouse genome mm10.
ChIP-seq:  Using MACS, peaks were called against IgG and Input. p-value threshold of 1e-04 was used. Overlapping peaks from two different antibodies (CS and MM) were combind using fisher's method of combining p-value. The resulting peaks were selected against any peaks called in HSF1-/- lines.
Genome_build: mm10
Supplementary_files_format_and_content: peak.txt file of HSF1 peaks for ChIP-seq and normalized bigWig for PRO-seq

tag: molecule subtype

value: nascent RNA


title: ChIPseq_WT_NHS_MM


title: PROseq_HSF1&2KO_NHS


title: PROseq_HSF1&2KO_12minHS


title: ChIPseq_WT_NHS_CS


title: PROseq_HSF1&2KO_60minHS


title: PROseq_HSF1KO_60minHS


title: ChIPseq_WT_NHS_input


title: PROseq_HSF1KO_150secHS

value: after 150 sec heat shock


title: PROseq_WT_60minHS


title: PROseq_HSF1KO_NHS


title: PROseq_WT_NHS


title: PROseq_WT_12minHS


title: Gene trap RNA-Seq coverage

city: Columbia

first: William

last: Reid

state: Missouri

address: Connaway Hall, Bouchelle Ave

department: Veterinary Pathobiology

institute: University of Missouri

description: mRNA

data_processing:
Trimmomatic v0.32 to clean adapter and low quality reads
Tophat2 to align data to the Anopheles stephensi genome (v AsteS1)
Cufflinks2 to estimate gene expression levels and to generate the gtf coverage file
Genome_build: Vectorbase Anopheles stephensi genome (v. AsteS1) https://www.vectorbase.org/organisms/anopheles-stephensi/sda-500/astes1
Supplementary_files_format_and_content: File 1: GTv3_Ansteph_expr.txt (Estimated gene expression for pooled dataset); File 2: GTv3_Ansteph.gtf (Cufflinks rebuilt gtf file to display additional UTR coverage for ab initio predicted genes in the AsteS1 genome release)

organism: Anopheles stephensi

source_name: Whole body

extract_protocol:
Total RNA was extracted using the Trizol reagent followed by DNAse I treatment and reprecipitation.
Illumina mRNA
RNA-Seq (PE 50)

tag: strain

value: SDA 500


title: miR34-3

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
Reads were mapped to the mouse genome using STAR [default settings]
Reads were quantitated using the Rsubread package for R using RefSeq annotation
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing abundance measurements of mRNA features from refseq (gfp* and mir* samples) or ensembl (ip* samples). Whitespace separated. Columns: [GeneID – length - #reads mapping to feature]

source_name: Freshly frozen hippocampal tissue

extract_protocol:
RNA was extracted from fresh hippocampal tissue using the RNeasy mini kit from Qiagen.
RNA libraries were prepared using Illumina kits.

treatment_protocol: AAV5 injections into the hippocampus of adult C57BL/6 mice producing either of the following under a synapsin promoter: GFP only (Samples beginning with ‘GFP34…’ and GFP9), GFP-miR34sp (Samples beginning with ‘miR34…’) or GFP-miR9sp (Samples beginning with miR-9).

value: hippocampal neurons


title: 9sp-23


title: 9sp-17


title: GFP34-4


title: GFP-2


title: miR34-13


title: PROseq_WT_150secHS


title: miR34-18


title: 9sp-9


title: GFP34-10


title: GFP-8


title: ChIPseq_WT_NHS_IgG


title: GFP-16


title: PROseq_HSF1&2KO_150secHS


title: GFP34-8


title: Rib_Chondrocyte_Jun_ChIPseq

status: Public on Feb 29 2016

city: Los Angeles

first: Xinjun

last: He

state: CA

address: 1425 San Pablo St

department: BROAD CIRM Center

institute: University of Southern California

description: Enzyme digested rib chondrocytes

data_processing:
ChIP libraries were sequenced on Illumina Hiseq 2000
the first 25nt of sequence reads were aligned with Eland software (Illumina), allowing not more than 2 mismatches per reads to mouse genome version mm9/Build 37
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008; Jiang et al., 2010) with a P-value cutoff of 10e-5, by comparing with the input control without antibody immunoprecipitation. Peaks were incorporated into further analysis displaying an FDR<0.01.
Genome_build: mouse mm9
Supplementary_files_format_and_content: bed

source_name: p1 mouse rib chondrocytes

growth_protocol: Neonatal ICR wild-type mice postnatal day 1 rib cartilage

extract_protocol:
postnatal day 1 (p1) rib chondrocytes isolated from wild-type ICR mice were immediately cross-linked with 1% formaldehyde for 10 minutes at room temperature, then 0.125 M Glycine was added to quench formaldehyde.  20,000,000 cells were used for a ChIP reaction. Chromatin was sonicated by 10 sessions of 30 pulses (1 sec on and 1 sec off) at 50% amplitude using the Branson sonifier 250D (Branson Ultrasonics Corporation, Danbury, CT) in order to obtain 100 – 600 bp of DNA fragments. One hundred microlitters of Dynabeads M-280 Sheep anti-Rabbit IgG was combined with 9 μg of antibodies for Jun.
ChIPseq libraries were constructed with input control samples (input DNA) using ChIP-seq DNA Sample Prep Kit (IP-102-1001; Illumina Inc., San Diego, CA), according to manufacturer’s instruction. Adaptor-modified DNA fragments were enriched by 18 cycles of PCR.

treatment_protocol: Wild type, not treated

value: chondrocytes

tag: tissue

value: rib

tag: developmental stage

value: ICR mice

value: Jun(Abcam Cat#ab31419)


title: cKO_1

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (genes.fpkm tracking)

source_name: Chd7 cKO_spinal cord

extract_protocol:
Spinal cords were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

value: mixed

tag: age

value: Postnatal day 8

tag: geneotype/variation

value: Chd7f/f; Olig1-cre

value: spinal cord


title: cKO_2


title: RhlR_mutant_sample1

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

description: PA14 RhlR mutant ID 37943

data_processing:
RNA-seq reads were mapped to the PA14 genome using the Stampy aligner with default settings.
Differential expression was estimated using the R library edgeR excluding rRNA/tRNA genes and making use of the biological replicates for each condition
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: The processed files in CSV format include Genes, log2FC, uncorrected P-value and corrected P-value (Padj). The P-values are presented in the Phred-scale (-10*log10(actual P-value))

organism: Pseudomonas aeruginosa

source_name: RhlR_mutant_planktonic culture

growth_protocol: The Harvard Medical School PA14 transposon mutants [PMID:16477005] were grown in LB medium at 37°C and 180 r.p.m. until OD600=2.0.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.

value: RhlR transposon mutant

tag: culture type

value: planktonic culture


title: fes1DS rep 2

city: Stockholm

first: Claes

last: Andréasson

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: Stockholm University

data_processing:
The quality control and data processing were performed by National Genomics Infrastructure NGI, Science for Life Laboratory, Sweden
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite, The quality scale is Sanger / phred33 / Illumina 1.8+.
The sequencing reads were mapped to the sacCer2 genome with ensemble annotation saccharomyces cerevisiae EF2.62 using Tophat v 2.0.4.
The duplicate reads were removed using picard-tools/1.29
Gene counts and FPKM values were estimated using HTSeq v 0.6.1 and Cufflinks v 2.1.1 respectively.
Genome_build: sacCer2, EF2.62
Supplementary_files_format_and_content: a tab-delimited text file include raw counts for all samples
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

source_name: Yeast log phase cells

growth_protocol: Cells were grown in YPD at 25°C.

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit for Yeast (Ambion). The libraries were prepared using Illumina TruSeq Stranded mRNA (polyA-selection)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype


title: fes1DS rep 3


title: fes1D rep 2


title: fes1DL rep 2


title: fes1DL rep 3


title: fes1D rep 3


title: wild type rep 2

description: WT

value: WT


title: fes1D rep 1


title: wild type rep 1

description: WT


title: fes1DS rep 1


title: ALL-SORT BioRep4.TechRep2

city: Raleigh, NC

first: Robert

last: Franks

address: Campus Box 7614

department: Plant & Microbial Biology Department

institute: NC State University

description: processed data file: TableCounts_CTRs.txt

data_processing:
Quality control and preprocessing of metagenomic data was performed using FastQC software. Adapters and low quality sequences were filtered out with Ea-Utils software. Reads with phred-like quality score > 30 and read length > 50-bp were kept and aligned against the TAIR10 Arabidopsis reference genome.
Splice junction mapper TopHat2 (version 2.0.10)  was used to align filtered RNA-seq reads to the Arabidopsis thaliana TAIR10 genome (Ensembl annotation) downloaded from the iGenome database. Default parameters for TopHat2 were used except for strand specificity (--library-type=fr-firststrand) to match to the first strand of cDNA synthesized (anti-sense to the RNA) and maximal intron length (--I 2000)
The ‘HTSeq: Analyzing high-throughput sequencing data with Python’ software was used with default parameters except for the ‘stranded=reverse’ mode to generate tables-counts for downstream differential expression analysis (for edgeR and DESeq2 [33].
Gene expression and differential gene expression analysis was carried out using ‘R’ packages edgeR and DESeq2  and the Linux-based Cufflinks program (v2.2.1) (- G option)
Genome_build: TAIR10
Supplementary_files_format_and_content: counting the overlap of reads with annotation features; produced with HtSeq for YFPs (YFP-positive/YFP-negative) and CTRs (All-sorted/non-sorted) samples

organism: Arabidopsis thaliana

source_name: Cells from inflorescence_ALL-SORT

extract_protocol:
YFP-positive, YFP-negative and all-sorted were isolated via fluorescence-activated cell sorting (FACS) and protoplasts collected in Trizol; no-sorted sample derived form inflorescences frozen in liquid nitrogen. The RNA integrity number (RIN) for the 15 samples was higher than 7.3.
Strand-specific cDNA libraries were constructed from approximately 100 ng of total RNA using a NEB Ultra Directional Library Prep Kit for Illumina (New England Biolabs). The average size of the cDNA fragments was ~ 250 bp.
The 15 bar-coded libraries were pooled and single-end sequencing was performed in a HiSeq 2500 Illumina (Illumina, Inc.) with ‘HiSeq SR Cluster Kit v4’ for the flow-cell and ‘HiSeq SBS v4’ for sequencing reagents.  cDNA libraries were sequenced in 125-cycle plus 7-cycle for multiplexed samples.

tag: genotype background

value: ap1; cal; pAP1::AP1:GR background

tag: transgenic plants used in the experiment

value: pSHP2-GAL4; pUAS-3xYpet crossed to pAP1-AP1::GR; ap1; cal

tag: tissue/cell type

value: Cells from inflorescence


title: ALL-SORT BioRep2.TechRep2


title: Rib_Chondrocyte_Input_Control_ChIPseq

description: Enzyme digested rib chondrocytes

tag: cell type

value: none (input)


title: NO-SORT BioRep4.TechRep2

source_name: whole inflorescence_NO-SORT

value: whole inflorescence


title: ALL-SORT BioRep4.TechRep1


title: ALL-SORT BioRep1.TechRep2


title: Ctrl_2

source_name: control_spinal cord

value: Chd7f/+; Olig1-cre


title: NO-SORT BioRep4.TechRep1


title: fes1DL rep 1


title: wild type rep 3

description: WT


title: NO-SORT BioRep3.TechRep2


title: ALL-SORT BioRep1.TechRep1


title: NO-SORT BioRep2.TechRep1


title: NO-SORT BioRep2.TechRep2


title: ALL-SORT BioRep3.TechRep1


title: NO-SORT BioRep1.TechRep2


title: Ctrl_1


title: YFP-POS BioRep1.TechRep2

description: processed data file: TableCounts_YFPs.txt

source_name: YFP-POS_Medial domain, Arabidopsis gynoecium

value: Medial domain, Arabidopsis gynoecium


title: YFP-POS BioRep2.TechRep2


title: NO-SORT BioRep3.TechRep1


title: ALL-SORT BioRep3.TechRep2


title: YFP-POS BioRep1.TechRep1


title: YFP-POS BioRep3.TechRep1


title: YFP-NEG BioRep4.TechRep2

source_name: Cells from inflorescence_YFP-NEG


title: YFP-NEG BioRep2.TechRep2


title: YFP-NEG BioRep2.TechRep1


title: ALL-SORT BioRep2.TechRep1


title: YFP-NEG BioRep1.TechRep2


title: Rib_Chondrocyte_Col10a1mCherry_Sorted-4_RNA-seq

description: Enzyme digested rib chondrocytes

data_processing:
RNA-seq libraries were sequenced on Illumina Nextseq 500
75nt of single end sequence reads were aligned with tophat2 software to mouse genome version mm9/Build 37
Aligned sequence reads were imported into Partek Genomics Suite software (Partek Inc. St. Louis, Missouri) for mRNA quantification
Genome_build: mouse mm9
Supplementary_files_format_and_content: excel file contains raw read count and RPKM values.

source_name: Enzyme digested rib chondrocytes_P3

growth_protocol: Col10a1mCherry transgenic mice was raised in standard mouse husbandary at USC mouse facility

extract_protocol:
Rib cages were isolated from Col10a1mCherry mice by manual dissecting. Dissected rib cages were washed in Dulbecco's Phosphate-Buffer Saline (DPBS) briefly and then disgested in 2 mg/mL Collagenase D (Cat# 11088866001, Roche) in DMEM for 30 minutes in a rotating shaker at 37°C to digest off surface soft tissues. The rib cages were then extensively washed in DPBS for 3 times by votex to remove the digested soft tissues. At this stage, the ribs were free of other tissues and were further digested in 2 mg/mL Collagenase D in DMEM for 3 hours with three changes of fresh Collagenase D solution. Collected cells were pooled together and filtered in 40 uM fiter and centrifuged by 500g to collect for FACS sorting. Total RNA was isolated with RNeasy Micro Kit (RNeasy Micro Kit, Cat#74004; Qiagen, Basel, Switzerland) follwoing FACS sorting.
RNA-seq libraries were constructed with RNA-seq Sample Prep Kit (Cat#RS-122-2101, Illumina, San Diego, CA), according to manufacturer’s instruction. RNA-seq barcoded pooled.

value: chondrocytes

value: rib

value: Postnatal day 3

tag: mouse strain

value: Swiss Webster


title: NO-SORT BioRep1.TechRep1


title: YFP-POS BioRep3.TechRep2


title: Rib_Chondrocyte_Col10a1mCherry_Sorted-2_RNA-seq

description: Enzyme digested rib chondrocytes

source_name: Enzyme digested rib chondrocytes_P1

value: Postnatal day 1


title: YFP-NEG BioRep4.TechRep1


title: Rib_Chondrocyte_Col10a1mCherry_Sorted-3_RNA-seq

description: Enzyme digested rib chondrocytes

source_name: Enzyme digested rib chondrocytes_E18.5

value: Prenatal E18.5


title: YFP-NEG BioRep3.TechRep1


title: Rib_Chondrocyte_Col10a1mCherry_Sorted-1_RNA-seq

description: Enzyme digested rib chondrocytes


title: YFP-POS BioRep2.TechRep1


title: YFP-NEG BioRep3.TechRep2


title: BS-seq-P1-N

first: Jing

last: Zhang

address: 1130 St Nicholas Ave ICRC, room403

institute: Columbia University Medical Center

description: BS-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end TAB-seq reads were  mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
Paired-end BS-seq reads were  mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
For patient 1, in BSseq or TABseq, the CG sites covered by at least 5 reads were considered.  5mC level or 5hmC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of TGs. CG sites were considered as hydromethylated, if the following three criterias were met (1.BH corrected binormial P value less than or equal to 0.05; 2. CpG sites identified both methylated and hydroxymethylated; 3. 5mC level larger than or equal to 5hmC level).  For CpG sites identified both methylated and hydroxymethylated, the methylation levels of CpG sites were corrected by subtracting the 5hmC level.
For patient 2, in BSseq or TABseq,  the CG sites covered by at least 1 reads were listed.  5mC level or 5hmC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of TGs.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include 5mC and 5hmC level for each sample (real 5hmC level for each CG site covered by at least 5 reads, real 5mC level for each CG site covered by at least 5 reads)

source_name: kidney

extract_protocol:
genomic DNA(Qiagen, Cat#: 51306) were extracted according to manufacturer’s instructions.
The DNA was directed to bisulfite conversion using the EZ DNA methylation-Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using Illumina HiSeq 2000.

tag: gender

value: male

tag: individual

value: matched normal


title: BS-seq-P1-T

description: BS-seq

value: tumor


title: BS-seq-P2-T

description: BS-seq

value: female


title: TAB-seq-P2-T

data_processing:
library strategy: TAB-seq
Illumina Casava1.7 software used for basecalling.
Paired-end TAB-seq reads were  mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
Paired-end BS-seq reads were  mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
For patient 1, in BSseq or TABseq, the CG sites covered by at least 5 reads were considered.  5mC level or 5hmC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of TGs. CG sites were considered as hydromethylated, if the following three criterias were met (1.BH corrected binormial P value less than or equal to 0.05; 2. CpG sites identified both methylated and hydroxymethylated; 3. 5mC level larger than or equal to 5hmC level).  For CpG sites identified both methylated and hydroxymethylated, the methylation levels of CpG sites were corrected by subtracting the 5hmC level.
For patient 2, in BSseq or TABseq,  the CG sites covered by at least 1 reads were listed.  5mC level or 5hmC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of TGs.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include 5mC and 5hmC level for each sample (real 5hmC level for each CG site covered by at least 5 reads, real 5mC level for each CG site covered by at least 5 reads)

extract_protocol:
genomic DNA(Qiagen, Cat#: 51306) were extracted according to manufacturer’s instructions.
Genomic DNA with spike-in controls was glucoslyated and oxidized using the kit from Wisegene (Cat#: K001). Then, the DNA was further directed to bisulfite conversion using the EZ DNA methylation-Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using Illumina HiSeq 2000.


title: BS-seq-P2-N

description: BS-seq


title: YFP-NEG BioRep1.TechRep1

value: ap1; cal; pAP1::AP1:GR background


title: TAB-seq-P1-N


title: TAB-seq-P2-N


title: TAB-seq-P1-T


title: RNAseq-P2-T

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired reads were treated as single end and mapped to hg19 whole genome using bwa with default parameters, followed by extracting uniquly mapped reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from one transcript of a gene (not including microRNA) were used. The number of reads falling in the exons of this gene were counted, followed by being log-transformed, and scaled between 0 and 1. Given a patient, the transformed RPKMs of ccRCC sample were scaled according to the average value of transformed RPKMs of normal tissue.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values for each Sample

extract_protocol:
Tissues of ccRCC and matched normal were removed and frozened in RNA Later and stored in -80°. And RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNAseq-P2-N


title: RNAseq-P1-N


title: RNAseq-P1-T


title: Fiber 20 dpa

city: Anyang

first: Lei

last: Ma

state: Henan

address: NO.38 Yellow River Road

institute: Institute of Cotton Research, Chinese Academy of Agricultural Sciences

description: high-throughput profiling of transcriptome

data_processing:
The genome sequences were downloaded from the Cotton Genome Project (CGP) (Li, Fan et al. 2014). Using the spliced reads aligner Tophat-2.0.11 (Trapnell, Pachter et al. 2009), we mapped 125 nt reads from twenty-one RNA-Seq libraries to cotton genome with following parameters: ‘min-anchor-length = 8’ and other parameters with default option. After running TopHat, transcriptome assembly was performed to obtain high-quality transcript sequences by cufflinks v2.2.1 (Trapnell, Roberts et al. 2012) using the resulting alignment files from twenty-one samples.
Genome_build: G. hirsutum
Supplementary_files_format_and_content: bigwig files

organism: Gossypium hirsutum

source_name: Fiber 20 dpa

extract_protocol:
Total RNAs of these twenty-one individual samples were extracted from collected materials using Trizol according to the manufacturer’s recommendations and were then treated with RNase-free DNase I to remove DNA contamination
Total RNAs were extracted from seedling using TRIzol Reagent. Polyadenylated RNAs were isolated using Dynabeads® mRNA Purification Kit (Invitrogen). The RNA-Seq libraries were sequenced on Illumina HiSeq 2500 platform with 2x125 base paired-end reads..

value: Fiber 20 dpa


title: Ovule 20 dpa

source_name: Ovule 20dpa

value: Ovule 20 dpa


title: Ovule 10 dpa

source_name: Ovule 10dpa

value: Ovule 10 dpa


title: Bracts

source_name: Bracts

value: Bracts


title: Fiber 10 dpa

source_name: Fiber 10 dpa

value: Fiber 10 dpa


title: Ovule 40 dpa

source_name: Ovule 40dpa

value: Ovule 40 dpa


title: Ovule 30 dpa

source_name: Ovule 30dpa

value: Ovule 30 dpa


title: Ovule 0 dpa

source_name: Ovule 0dpa

value: Ovule 0 dpa


title: A & G

source_name: A & G

value: A & G


title: Corollas

source_name: Corollas

value: Corollas


title: Stem Y2

source_name: Stem

value: Stem


title: New leaves

source_name: New leaves

value: New leaves


title: Old leaf

source_name: Old leaf

value: Old leaf


title: Stem Y1


title: New leaf

source_name: New leaf

value: New leaf


title: Cotyledon Y2

source_name: Cotyledon

value: Cotyledon


title: Cotyledon Y1


title: RBPjk null_sample2

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

data_processing:
First, sequences were aligned to the reference mm10 genome with TopHat (Trapnell et al., 2009), which efficiently aligns reads spanning known or novel splice junctions.
Each sample was then independently processed with Cufflinks (Trapnell et al., 2010) in order to generate an initial transcriptome.
To accurately quantify expression of all known or novel transcripts Cuffmerge tool was used to merge the individual transcriptomes into a single reference, and at the same time annotate known genes and extend partial transcripts (Roberts et al., 2011a).
This common transcriptome was then used for a second pass with Cufflinks, which quantifies each transcript and gene (known or novel) in each sample (Roberts et al., 2011b) and annotates based on the UCSC known Genes table (Hsu et al., 2006). Long non-coding RNAs annotation was based on (Cabili et al., 2011).
Genome_build: mm10

source_name: Hair Follicle

extract_protocol:
Skin samples were embedded in OCT immediately after collecting and snap-frozen in liquid nitrogen before storing at -80°C
Sectioned at 20μm thickness, tissue slices were placed on poly-lysine (Sigma-P8920; 1:10 dilution) treated PEN membrane glass slides (Arcturus, LCM0522), dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure
Laser capture was performed with Arcturus Veritas and Arcturus CapSure HS LCM Caps (Arcturus Engineering, Inc., Mountain View, CA) within 45 minutes to avoid degradation. 4 membrane with ~25-30 hair follicles each were pooled and stored in QIAzol (Qiagen) at -80°C. RNA extracted as described in methods was QCed for sequencing using an Agilent 2100 Bioanalyzer requiring integrity numbers >8 to pass.
Libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1ng of cDNA was tagmented with the Amplicon Tagment Mix at 55°C for 10min. NT Buffer was added to neutralize the samples.
Libraries were PCR amplified (Nextera PCR Master Mix) in the following program: one cycle of 72°C for 3min, one cycle of 98°C for 30s, 12 cycles of 95°C for 10s, 55°C for 30s, and 72°C for 1min, and one cycle of 72°C for 5min and (N7XX, and N5XX). The purified cDNA was captured on an Illumina flow cell for cluster generation and sequenced (75bp paired-end, 20 million reads, Illumina HiSeq2500) following the manufacturer's protocol.

value: Mixed background

value: Postnatal day (P) 3

value: RBPjk deficient hair follicle


title: RBPjk null_sample3


title: RBPjk null_sample1


title: Root

source_name: Root

value: Root


title: Old leaves

source_name: Old leaves

value: Old leaves


title: Psen 1&2 null_sample3

value: Psen 1&2 deficient hair follicle


title: Psen 1&2 null_sample2


title: Boll-shell 10 dpa

value: Boll-shell 10 dpa


title: Notch 1&2 null_sample3

value: Notch 1&2 deficient hair follicle


title: Notch 1&2 null_sample2


title: Notch 1&2 null_sample1


title: Psen 1&2 null_sample1


title: Wildtype from Preselin Line

value: Wild-type


title: Mixture of wildtypes from N, PS, and RBPj lines


title: Wildtype from RBPjk line


title: Calyxs

source_name: Calyxs

value: Calyxs


title: Wildtype from Notch line


title: H9 uninfected

city: Newark

first: Aditi

last: Gupta

state: NEW JERSEY

address: 185 South Orange Ave, MSB-A920G

department: Medicine

institute: Rutgers University

description: RNA from uninfected H9 T-cell line

data_processing:
Quality control analysis: trimming adaptors using Trimmomatic, and pruning reads using Fastx toolkit
Cleaned up reads were aligned to reference human transcriptome using Tophat2
Tophat2 output was supplied to Cuffdiff for identifying gene-expression for all the genes in two samples.
Genome_build: Homo_sapiens.GRCh37.75.gtf
Supplementary_files_format_and_content: Tab delimited file that is given by Cuffdiff. Each row has a gene, its expression in infected and uninfected Tcells, and the log2(fold change in gene expression), among other information such as chromosomal location of the gene.

source_name: T-cell RNA

growth_protocol: H9 T-cells were growing in RPMI+FBS medium

extract_protocol:
Qiagen's RNEasy mini kit was used to extract cellular RNA from infected and uninfected T cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: H9 T-cells were infected with clonal HIV-1 obtained by transfecting the 293T cells with pNL43.

value: 1 week

tag: cell line


title: Chd7_d3

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the rn5 genome assembly using Bowtie2 with the default configuration
Peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) (http://liulab.dfci.harvard.edu/MACS) with a p value cut off of 1x e9.
Genome_build: rn5
Supplementary_files_format_and_content: bed files were generated using Macs14

organism: Rattus norvegicus

source_name: Oligodendrocyte

growth_protocol: primary rat oligodendrocyte progenitors were induced to differentiate for three days in the presence of T3

extract_protocol:
Lysates were clarified from sonicated nuclei and proteine-DNA complexes were isolated with antibody.
OLs (~20 million cells) were cross-linked in 1% formaldehyde at room temperature for 10 min and then quenched with 125 mM glycine for 5 min. Cells were rinsed, resuspended in lysis buffer (50 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.25% Triton X-100 and 0.5% NP-40 and protease inhibitor cocktail) and incubated on ice for 10 min. Lysates were centrifuged and pellets were resuspended in nuclei washing buffer  (200 mM NaCl, 1 mM EDTA, 1 mM EGTA, 10 mM Tris pH 8.0, and protease inhibitor cocktail) with gentle rocking at 4°C. Nuclei were pelleted and resuspended in 1 ml of sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Nuclear suspensions were sonicated with a Covaris S220 sonicator (total time 8 min). Antibody (chromatin: antibody = 4:1) was added to chromatin and incubated at 4°C overnight. Chromatin-protein complex was immunoprecipitated with protein A/G plus agarose beads and washed sequentially, twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 150 mM NaCl), twice with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 500 mM NaCl) and twice with LiCl buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris [pH 8.0]) and once with 1xTE buffer. Immunoprecipitates were then eluted in elution buffer at 65°C for 1 h. Eluted chromatin was subjected to reverse-crosslink and chromatin fragment purification with QIAGEN PCR purification columns. ChIP-Seq libraries were prepared using NEBNext ChIP-Seq Library Prep Kit according to manufacturer’s instructions.

tag: strain background

value: Sprague Dawley

value: differentiating oligodendrocytes

tag: chip antibody


title: Sox10_d3

value: Sox10 (Abcam ab27655)


title: H9 infected

description: RNA from H9 T-cell line infected with NL4-3 strain of HIV-1

value: 1 week post-infection


title: WT-2

city: SALT LAKE CITY

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah School of Medicine

data_processing:
base-calling by Illumina HiSeq 50 Cycle Single Read Sequencing v3
RNA-seq reads were aligned to the dm3 genome build with Ensembl transcript splice alignments using novoalign
Converted splice coordinates to genome coordinates with SamTranscriptomeParser
Generated ReadCoverage USeq file
Ran DefinedRegionDifferentialSeq using Ensembl transcripts and default settings
Genome_build: dm3
Supplementary_files_format_and_content: xlsx file containing analyzed output from DESeq including counts of reads overlapping gene of interest, Variance corrected per gene in log space from DESeq, and FPKM

organism: Drosophila melanogaster

source_name: Whole fly lysate

extract_protocol:
Flies were flash frozen in liquid nitrogen and RNA isolated using Trizol reagent. RNA was then further purified using the Qiagen RNeasy clean-up procedure.
Libraries were prepared using Illumina TruSeq RNA Sample Prep v2 with oligo dT selection

tag: genetic background

value: 2 week old adults

value: wild type


title: WT-4


title: WT-3


title: Sir2 mutant-2


title: Sir2 mutant-1


title: Sir2 mutant-3


title: Sir2 mutant-4


title: WT_GV_1

status: Public on Feb 28 2016

city: beijing

first: yujiao

last: dang

address: Yihe road

institute: BIOPIC

description: Bulk RNA seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the mouse refference genome (mm9) using Tophat software
gene expression level was calculated Cufflink.
Genome_build: mm9
Supplementary_files_format_and_content: txt files reflect FPKM of each gene in Refseq.

growth_protocol: Mice were maintained under SPF conditions in a controlled environment of 20-22oC, with a 12/12 h light/dark cycle, 50-70% humidity, and food and water provided ad libitum. Animal care and experimental procedures were conducted in accordance with the Animal Research Committee guidelines of Zhejiang University.

extract_protocol:
60 oocytes/embryos were picked into the RLT lysis buffer, and RNA was prepared follow the protocol of QIAGEN's RNAeasy kit.
Cells were picked into the lysis buffer to extracted mRNAs; then the purifed mRNAs were used to construct the cDNA library with the NEB RNA library construct kit. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.

treatment_protocol: Oocytes/embryos were collected from 21-23-day-old female WT and YAP-/- mice after injection of PMSG/hCG and mated for embryos.

value: ICR

tag: maternal mouse info

value: WT female mice

tag: oocyte genotype/variation

value: GV stage

tag: tissue

value: oocyte


title: WT-1

tag: age


title: YAPko_4cell

description: Bulk RNA seq

value: YAP-/- female mice

tag: embryo genotype

value: YAP-/-; Yap1-deleted

tag: developmental stage

value: 4-cell stage

value: embryo


title: CSLKO1-28

first: Urban

last: Lendahl

state: State...

address: SE-171 77 Stockholm

department: CMB

institute: Karolinska Insitute

description:
smart seq 2 single cell RNA
Processed data file: single_cell_all_rpkm.txt

data_processing:
Reads were aligned using STAR to genomes mm10 and hg19
For xenograft bulk sequencing, reads were separated for different species using S^3 (https://github.com/danielramskold/S3_species-specific_sequencing) with default settings (-Ms 1 -Mu 1 -D 2)
Unique reads were selected using mapping quality threshold 255
Gene expression values were calculated using rpkmforgenes.py (http://sandberg.cmb.ki.se/rnaseq) with options -rmnameoverlap -bothendsceil and using RefSeq annotation from 1 July 2014
Genome_build: mm10; hg19
Supplementary_files_format_and_content: RPKM expression values (tab-delimited text format)

source_name: Single Cell from Xenograft Tumor

growth_protocol:
[cell samples only] MDA-MB-231 were purchased from American Type Culture Collection (ATCC) and maintained in Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Life Techonologies).
[xenograft samples only] 1.5 x 106 MDA-MB-231 control or CSL-deficient cells in culture media were orthotopically injected into the left and right 4th inguinal mammary fat pads of 4-6 weeks old female immunodeficient NOD/SCID mice. Tumor growth and size was measured twice per week using caliper. Tumor volume was calculated according to the formula L × W2.  Mice were sacrificed at the 3rd and 5th week after transplantation.

extract_protocol:
Tumors with surrounding stromal tissues from xenografts were minced and nonenzymaticallydigested using cell dissociation enzyme-free PBS-based (Gibco) for 30 minutes at 37o C withoccasional pipetting. The dissociated cells were then filtered through a 40 mm nylon mesh strainer. Single cellsuspension was obtained by re-suspension in CO2 -independent medium (Gibco) for single cell picking. Singlecells of xenografts were manually picked under the microscope as previously described (Picelli et al., 2013).Briefly, a single cell was picked using mouth pipette under 20X magnification in 0.5 ml solution. The pickedsingle cell was released into RNase-free PCR strip tube containing hypotonic Smart-seq RNA lysis bufferconsisting of 2.3 ml of 19:1 ratio of 0.4% TritonX-100 and RNase inhibitor (Clontech), 1 ml of 10 mM dNTP(Fermentas), 1 ml of 10 mM oligo-dT primer, and ERCC spike-in (Ambion) at 72o C for 3 min.
Total RNA from tumors and cells was purified using the RNeasy Mini  Kit(QIAGEN), according to the manufacturer’s instructions. RNA concentration and RNA integrity number (RIN)were calculated by using the Agilent RNA 6000 Nano  Kit (Agilent Technologies). Two biological replicates for each RNA sample were processed to cDNA library preparations using the Illumina TruSeq™ RNA sample preparation  kit (Low-Throughput protocol) according to the manufacturer’s protocol. Quantification and qualitycontrol of the cDNA libraries were done using the Agilent DNA 1000 Kit (Agilent Technologies). The libraries were sequenced on an Illumina HiSeq 2000 system.

treatment_protocol: [cell samples only] To block Notch signaling cells were treated with 10 μ M DAPT overnight. To activate Notch signaling cells were mechanical dissociated and seeded on 12 well plate precoated with control Fc or Jagged1-Fc (Jag) fragment for 7h.

tag: data subset

value: Single Cell

tag: genotype/variation

value: CSL -/-

tag: tumor status

value: CSL KO Xenograft Tumor 1st

tag: treatment (notch activation or inhibition)


title: CSLKO1-82


title: YAPko_GV1

description: Bulk RNA seq


title: CSLKO1-94


title: WT2-96

value: CSL +/+

value: CSL +/+ Xenograft Tumor 2nd


title: WT2-95


title: WT2-91


title: WT2-92


title: WT2-94


title: WT2-90


title: WT2-9


title: WT_GV_2

description: Bulk RNA seq


title: WT2-87


title: YAPko_GV2

description: Bulk RNA seq


title: CSLKO1-31


title: WT2-86


title: WT2-84


title: WT2-89


title: WT2-80


title: WT2-82


title: WT2-85


title: WT2-83


title: WT2-8


title: WT2-78


title: WT2-76


title: WT2-75


title: WT2-77


title: WT2-74


title: WT2-73


title: WT2-72


title: WT2-71


title: WT2-7


title: WT2-79


title: WT2-70


title: WT2-69


title: WT2-67


title: WT2-65


title: WT2-66


title: WT2-81


title: WT2-63


title: WT2-60


title: WT2-61


title: WT_4cell

description: Bulk RNA seq

tag: embryo genotyp/variatione


title: WT2-58


title: WT2-6


title: WT2-57


title: WT2-56


title: CSLKO2-48

description: Processed data file: single_cell_all_rpkm.txt

value: CSL KO Xenograft Tumor 2nd


title: WT2-62


title: WT2-55


title: WT2-68


title: WT2-50


title: WT2-54


title: WT2-51


title: WT2-53


title: WT2-52


title: WT2-48


title: WT2-47


title: WT2-5


title: WT2-49


title: WT2-46


title: WT2-45


title: WT2-59


title: WT2-44


title: WT2-41


title: WT2-39


title: WT2-42


title: WT2-4


title: WT2-38


title: WT2-40


title: WT2-43


title: WT2-37


title: WT2-36


title: WT2-33


title: WT2-34


title: WT2-93


title: WT2-32


title: WT2-31


title: WT2-30


title: WT2-29


title: WT2-3


title: WT2-28


title: WT2-25


title: WT2-24


title: WT2-27


title: WT2-22


title: WT2-23


title: WT2-12


title: WT2-16


title: WT2-18


title: WT2-13


title: WT2-21


title: WT2-1


title: WT2-10


title: WT2-11


title: WT2-20


title: WT2-15


title: WT1-96

value: CSL +/+ Xenograft Tumor 1st


title: WT2-19


title: WT1-95


title: WT1-94


title: WT1-93


title: WT2-2


title: WT2-14


title: WT1-90


title: WT2-35


title: WT1-92


title: WT1-91


title: WT2-26


title: WT1-9


title: WT1-89


title: WT1-87


title: WT1-88


title: WT1-84


title: WT1-82


title: WT1-8


title: WT1-81


title: WT2-17


title: WT1-77


title: WT1-78


title: WT1-80


title: WT1-79


title: WT1-71


title: WT1-7


title: WT1-70


title: WT1-72


title: WT1-76


title: WT1-73


title: WT1-75


title: WT1-69


title: WT1-74


title: WT1-66


title: WT1-67


title: WT1-64


title: WT1-65


title: WT1-68


title: WT1-83


title: WT1-86


title: WT1-85


title: WT1-58


title: WT1-60


title: WT1-6


title: WT1-55


title: WT1-62


title: WT1-61


title: WT1-54


title: WT1-53


title: WT1-59


title: WT1-52


title: WT1-48


title: WT1-51


title: WT1-56


title: WT1-5


title: WT1-47


title: WT1-50


title: WT1-44


title: WT1-46


title: WT2-88


title: WT1-43


title: WT1-42


title: WT1-45


title: WT1-63


title: WT1-40


title: WT1-39


title: WT1-4


title: WT1-41


title: WT1-38


title: WT1-57


title: WT1-37


title: WT1-3


title: WT1-33


title: WT1-31


title: WT1-35


title: WT1-36


title: WT1-49


title: WT1-32


title: WT1-34


title: WT1-24


title: WT1-28


title: WT1-20


title: WT1-27


title: WT1-21


title: WT1-22


title: WT1-2


title: WT1-18


title: WT1-17


title: WT1-19


title: WT1-23


title: WT1-15


title: WT1-14


title: WT1-16


title: WT1-13


title: WT1-12


title: WT1-30


title: WT1-11


title: WT1-26


title: WT1-29


title: CSLKO2-96


title: WT1-25


title: CSLKO2-93


title: CSLKO2-91


title: CSLKO2-94


title: CSLKO2-89


title: CSLKO2-88


title: CSLKO2-9


title: WT1-10


title: CSLKO2-95


title: CSLKO2-92


title: CSLKO2-90


title: CSLKO2-85


title: WT1-1


title: CSLKO2-83


title: CSLKO2-84


title: CSLKO2-82


title: CSLKO2-80


title: CSLKO2-8


title: CSLKO2-79


title: CSLKO2-78


title: CSLKO2-77


title: CSLKO2-75


title: CSLKO2-73


title: CSLKO2-72


title: CSLKO2-71


title: CSLKO2-87


title: CSLKO2-70


title: CSLKO2-86


title: CSLKO2-69


title: CSLKO2-81


title: CSLKO2-67


title: CSLKO2-66


title: CSLKO2-68


title: CSLKO2-61


title: CSLKO2-6


title: CSLKO2-63


title: CSLKO2-65


title: CSLKO2-58


title: CSLKO2-55


title: CSLKO2-56


title: CSLKO2-53


title: CSLKO2-54


title: CSLKO2-57


title: CSLKO2-52


title: CSLKO2-50


title: CSLKO2-5


title: CSLKO2-49


title: CSLKO2-51


title: CSLKO2-47


title: CSLKO2-46


title: CSLKO2-45


title: CSLKO2-43


title: CSLKO2-44


title: CSLKO2-64


title: CSLKO2-62


title: CSLKO2-40


title: CSLKO2-60


title: CSLKO2-35


title: CSLKO2-4


title: CSLKO2-41


title: CSLKO2-36


title: CSLKO2-59


title: CSLKO2-42


title: CSLKO2-34


title: CSLKO2-30


title: CSLKO2-32


title: CSLKO2-38


title: CSLKO2-29


title: CSLKO2-3


title: CSLKO2-31


title: CSLKO2-27


title: CSLKO2-28


title: CSLKO2-26


title: CSLKO2-24


title: CSLKO2-22


title: CSLKO2-25


title: CSLKO2-23


title: CSLKO2-37


title: CSLKO2-21


title: CSLKO2-39


title: CSLKO2-16


title: CSLKO2-33


title: CSLKO2-17


title: CSLKO2-2


title: CSLKO2-19


title: CSLKO2-20


title: CSLKO2-18


title: CSLKO2-14


title: CSLKO2-15


title: CSLKO2-10


title: CSLKO2-11


title: CSLKO2-12


title: CSLKO2-1


title: CSLKO1-95


title: CSLKO1-96


title: CSLKO1-91


title: CSLKO1-90


title: CSLKO1-92


title: CSLKO1-93


title: CSLKO1-89


title: CSLKO1-87


title: CSLKO1-86


title: CSLKO1-84


title: CSLKO1-88


title: CSLKO1-9


title: CSLKO1-85


title: CSLKO1-81


title: CSLKO1-80


title: CSLKO1-8


title: CSLKO1-83


title: CSLKO2-13


title: CSLKO1-79


title: CSLKO1-75


title: CSLKO1-77


title: CSLKO1-78


title: CSLKO1-74


title: CSLKO1-76


title: CSLKO1-72


title: CSLKO1-69


title: CSLKO1-71


title: CSLKO1-68


title: CSLKO1-70


title: CSLKO1-67


title: CSLKO1-66


title: CSLKO1-65


title: CSLKO1-63


title: CSLKO1-61


title: CSLKO1-60


title: CSLKO1-62


title: CSLKO1-6


title: CSLKO1-59


title: CSLKO1-57


title: CSLKO1-56


title: CSLKO1-58


title: CSLKO1-54


title: CSLKO1-52


title: CSLKO1-50


title: CSLKO1-73


title: CSLKO1-49


title: CSLKO1-5


title: CSLKO1-46


title: CSLKO1-48


title: CSLKO1-45


title: CSLKO1-40


title: CSLKO1-42


title: CSLKO1-43


title: CSLKO1-64


title: CSLKO1-38


title: CSLKO1-34


title: CSLKO1-36


title: CSLKO1-35


title: CSLKO1-39


title: CSLKO1-33


title: CSLKO1-32


title: CSLKO1-29


title: CSLKO1-51


title: CSLKO1-3


title: CSLKO1-30


title: CSLKO1-25


title: CSLKO1-26


title: CSLKO1-44


title: CSLKO1-27


title: CSLKO1-22


title: CSLKO1-21


title: CSLKO1-23


title: CSLKO1-41


title: CSLKO1-24


title: CSLKO1-55


title: CSLKO1-4


title: CSLKO1-20


title: CSLKO1-19


title: CSLKO1-17


title: CSLKO1-37


title: CSLKO1-18


title: CSLKO1-16


title: Xl_ear_s_1_sequence

city: Las Cruces

first: Daniel

last: Ramire-Gordillo

state: New Mexico

address: PO Box 30001, MSC 3AF

department: Biology

institute: New Mexico State University

description: RNA isolated from 16-20 inner ears (8-10 animals).

data_processing:
36-cycle single-end reads were processed using Illumina software v1.0.
Illumina reads were aligned to the X. tropicalis genome using the algorithm for genomic mapping and alignment program (GMAP) and Alpheus® Sequence Variant Detection System v3.1.
Genome_build: xenTro3
Supplementary_files_format_and_content: Excel file includes OMIM genes name, sequence aligment scores, scaffold # and coordinates, # of reads, GCRMA value etc.

organism: Xenopus laevis

source_name: inner ear

extract_protocol:
X. laevis stages 56-58 inner ear RNA was isolated with the Qiagen® RNeasy® Mini Kit according to established procedures Trujillo_Provencio et al 2010.  RNA quality was assessed using the Agilent 2100 Bioanalyzer.  Experimental samples had a minimum RNA integrity number (RIN) of 9.0.
Short-insert paired end (SIPE) libraries were generated from total RNA according to Illumina’s mRNA-Seq Sample Prep Protocol v2.0. The cDNA libraries were cluster amplified on Illumina flowcells.

tag: phenotype

value: Wild type

value: inner ear

value: stages 56-58


title: Input (PU.1) - TPP Macrophages

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Basecalls performed using CASAVA software version 1.8
ChIP-seq reads were aligned to the NCBI Build GRCh36/UCSC Build hg18 genome assembly using Bowtie v0.12.8 with following options: -t -q -e 70 -l 28 -n 2 --best  --maxbts 125 -S
After ChIP-seq quality control using HOMER v4.3, reads of biological replicates were pooled, and peaks were called using HOMER 4.3 with findPeaks.pl script with pooled Input samples used as background control files using default options and following additional settings: -style factor
Annotation of peak positions and counting of normalized tag counts in called regions was performed with HOMER v4.3 annotatePeaks.pl script.
Genome_build: hg18
Supplementary_files_format_and_content: Annotated HOMER called peak positions in tab-delimited text format

source_name: primary human macrophages

growth_protocol: MACS beads isolated CD14 primary human monocytes were cultured for 72 h with granulocyte/macrophage colony stimulating factor (GM-CSF; 500U/ml) in RPMI1640 medium containing 10 % fetal calf serum (FCS) and 1% Penicillin/Streptomycin to generate unstimulated baseline macrophages

extract_protocol:
Chromatin from 0.5x10E6 macrophages was cross-linked for ChIP reactions with 1 % formaldehyde. Nuclei were lysed and chromatin was sheared with the Covaris S220 ultrasound system. For ChIP antibody reactions a PU.1 polyclonal rabbit antibody was used (SantaCruz, sc-352). Washing and DNA purifications as well as size selections were performed with AMPure XP SPRI beads (Beckman Coulter).
Published library construction protocol was adapted (Blecher-Gonen et al., Nature Protocols, 2013) and performed with 0.5 ng ChIP DNA. Barcodes from the NEXTflex adapter oligonucleotides kit (Bioo Scientific) were ligated to the ChIP-seq DNA fragments. Final DNA purification with additional size selection was performed with SPRI beads. ChIP-seq libraries were sequenced on the HiScanSQ/Hiseq 1000 sequencer (Illumina)

treatment_protocol: Fractions of baseline macrophages were further stimulated for 72h in culture medium with the addition of three stimulatory cocktails containing IFN-γ (200U/ml), IL-4 (500U/ml) or a combination of TNF-α (800U/ml), PGE2 (1µg/ml) and Pam3CSK4 (1µg/ml) to differentiate macrophages into subtypes

tag: cell type

value: peripheral blood derived macrophage

tag: treatment

value: GM-CSF for 72h and additional 72h with GM-CSF + TNF-a + PGE2 + Pam3CSK4

value: PU.1 polyclonal rabbit antibody (SantaCruz, sc-352)


title: CSLKO1-14


title: Input (PU.1) - IL4 Macrophages

value: GM-CSF for 72h and additional 72h with GM-CSF + IL4


title: CSLKO1-47


title: CSLKO1-15


title: CSLKO1-13


title: CSLKO1-12


title: CSLKO1-10


title: ChIP-Seq of PU1 in TPP Macrophages


title: Input (PU.1) - baseline Macrophage

value: GM-CSF (72h)


title: ChIP-Seq of PU1 in IL4 Macrophages


title: KO_JAG_DAPT_2

description:
smart seq 2 single cell RNA
Processed data file: bulk_rpkm.txt

source_name: MDA_MB_231 Cells

value: Cell Population

value: Jag1-Fc + DAPT


title: ChIP-Seq of PU1 in IFN-y Macrophages

value: GM-CSF for 72h and additional 72h with GM-CSF + IFN-y


title: ChIP-Seq of PU1 in baseline Macrophages


title: CSLKO1-1

value: Single Cell

value: CSL -/-


title: KO_JAG_DAPT_1

description: Processed data file: bulk_rpkm.txt


title: KO_JAG_2

description: Processed data file: bulk_rpkm.txt


title: Input - IL4 Macrophages

data_processing:
Basecalls performed using CASAVA software version 1.8
ChIP-seq reads were aligned to the NCBI Build GRCh36/UCSC Build hg18 genome assembly using Bowtie v0.12.8 with following options: -t -q -e 70 -l 28 -n 2 --best  --maxbts 125 -S
After ChIP-seq quality control using HOMER v4.3, reads of biological replicates were pooled, and peaks were called using HOMER 4.3 with findPeaks.pl script with pooled Input samples used as background control files using default options and following additional settings: -style histone -size 1000 -minDist 2500 -nfr
Annotation of peak positions and counting of normalized tag counts in called regions was performed with HOMER v4.3 annotatePeaks.pl script.
Genome_build: hg18
Supplementary_files_format_and_content: Annotated HOMER called peak positions in tab-delimited text format

extract_protocol:
Chromatin from 0.5x10E6 macrophages was cross-linked for ChIP reactions with 1 % formaldehyde. Nuclei were lysed and chromatin was sheared with the Covaris S220 ultrasound system. For ChIP antibody reactions polyclonal rabbit antibodies were used (H3K4me1 (Abcam), H3K27Ac (Abcam), H3K27me3 (Millipore)). Washing and DNA purifications as well as size selections were performed with AMPure XP SPRI beads (Beckman Coulter).
Published library construction protocol was adapted (Blecher-Gonen et al., Nature Protocols, 2013) and performed with 0.5 ng ChIP DNA. Barcodes from the NEXTflex adapter oligonucleotides kit (Bioo Scientific) were ligated to the ChIP-seq DNA fragments. Final DNA purification with additional size selection was performed with SPRI beads. ChIP-seq libraries were sequenced on the HiScanSQ/Hiseq 1000 sequencer (Illumina)

value: rabbit polyclonal anti-H3K4me1 antibody (Abcam cat.# 8895)


title: Input - TPP Macrophages


title: KO_JAG_1

description: Processed data file: bulk_rpkm.txt


title: KO_Fc_DAPT_1

description: Processed data file: bulk_rpkm.txt

value: Fc + DAPT


title: Input - baseline Macrophages


title: KO_Fc_2

description: Processed data file: bulk_rpkm.txt

value: Fc


title: Input - IFN-y Macrophages


title: M-TPP-3

description:
M-TPP-1
Normalized-RNA-seq-tag-counts-annotated.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against the hg19 reference genome (RefSeq database release 64).
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10. Sequencing datasets for M-IFNy and M-IL4 are available on Gene expression omnibus (GEO) platform with reference number GSE36952 labeled as M1 and M2 macrophages.
Genome_build: hg 19
Supplementary_files_format_and_content: Normalized RNA-seq tag counts annotated to the hg19 reference genome for three independent biological replicates

source_name: TPP stimulated primary human macrophages

extract_protocol:
Cultured macrophages were lysed in TRIZOL (Invitrogen) and total RNA was extracted according to the manufacturers’ protocol
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: Fractions of baseline macrophages were further stimulated for 72h in culture medium with the addition of a combination of TNF-α (800U/ml), PGE2 (1µg/ml) and Pam3CSK4 (1µg/ml) (=TPP) to differentiate macrophages into subtypes

tag: donor

value: human monocyte derived macrophages

tag: stimulated with

value: TNF-α, PGE2 and Pam3CSK4 (TPP) for 72 hrs


title: ChIP-Seq of H3K27me3 in TPP Macrophages

tag: chip antibody

value: rabbit polyclonal anti-H3K27me3 antibody (Millipore cat.# 17-622)


title: KO_Fc_DAPT_2

description: Processed data file: bulk_rpkm.txt


title: M-TPP-2


title: KO_Fc_1

description: Processed data file: bulk_rpkm.txt


title: Input (PU.1) - IFN-y Macrophages


title: WT_JAG_DAPT_2

description: Processed data file: bulk_rpkm.txt

value: CSL +/+


title: M-TPP-1


title: WT_JAG_DAPT_1

description: Processed data file: bulk_rpkm.txt


title: M-baseline-3

description:
Mb-1
Normalized-RNA-seq-tag-counts-annotated.txt

source_name: unstimulated primary human macrophages

value: none (unstimulated)


title: ChIP-Seq of H3K27me3 in IL4 Macrophages

value: peripheral blood derived macrophage


title: WT_JAG_2

description: Processed data file: bulk_rpkm.txt


title: WT_Fc_DAPT2

description: Processed data file: bulk_rpkm.txt


title: M-baseline-2


title: ChIP-Seq of H3K27me3 in IFN-y Macrophages


title: M-baseline-1


title: WT_Fc_2

description: Processed data file: bulk_rpkm.txt


title: ChIP-Seq of H3K27me3 in baseline Macrophages


title: WT_Fc_1

description: Processed data file: bulk_rpkm.txt


title: ChIP-Seq of H3K27Ac in IL4 Macrophages

value: rabbit polyclonal anti-H3K27Ac antibody (Abcam cat.# 4729)


title: ChIP-Seq of H3K27Ac in TPP Macrophages

value: GM-CSF for 72h and additional 72h with GM-CSF + TNF-a + PGE2 + Pam3CSK4


title: Primary_CSLKO

description: Processed data file: bulk_rpkm.txt

source_name: Primary Culture from Xenograft Tumor


title: Primary_WT

description: Processed data file: bulk_rpkm.txt


title: ChIP-Seq of H3K27Ac in IFN-y Macrophages


title: MDA_WT

description: Processed data file: bulk_rpkm.txt


title: KO_Tumor_11_5

description: Processed data file: bulk_rpkm.txt

source_name: Xenograft Tumor

value: Xenograft

value: Early graft


title: WT_Tumor_R_11_20

description: Processed data file: bulk_rpkm.txt

value: Late graft


title: MDA_CSLKO

description: Processed data file: bulk_rpkm.txt

value: Cell Population


title: KO_Tumor_11_19

description: Processed data file: bulk_rpkm.txt


title: KO_Tumor_11_19_L

description: Processed data file: bulk_rpkm.txt


title: KO_Tumor_L_11_5

description: Processed data file: bulk_rpkm.txt


title: ChIP-Seq of H3K27Ac in baseline Macrophages

value: GM-CSF (72h)


title: WT_Tumor_R_19_11

description: Processed data file: bulk_rpkm.txt


title: ChIP-Seq of H3K4me1 in IL4 Macrophages

value: GM-CSF for 72h and additional 72h with GM-CSF + IL4


title: ChIP-Seq of H3K4me1 in TPP Macrophages

value: rabbit polyclonal anti-H3K4me1 antibody (Abcam cat.# 8895)


title: WT_Tumor_11_5

description: Processed data file: bulk_rpkm.txt


title: ChIP-Seq of H3K4me1 in baseline Macrophages


title: WT_Fc_DAPT_1

description: Processed data file: bulk_rpkm.txt

value: Fc + DAPT


title: WT_JAG_1

description: Processed data file: bulk_rpkm.txt


title: ImmB_WT_rep1_ATAC

status: Public on Feb 27 2016

city: New York

first: Jane

last: Skok

address: 550 First Ave, Smillow 307

institute: NYU

data_processing:
Library strategy: ATAC-Seq
RNA-Seq: reads were mapped using Tophat2 to the mm10 genome. Counts per gene was obtained using htseq-count and normalization was done using DESeq2.
ATAC-Seq:Reads were mapped to the mm10 genome using Bowtie2. Peaks were called using PeakDeck
Genome_build: mm10

source_name: Immature B cells

growth_protocol:
Mice from C57BL/6 were used to isolate lymphocytes from either the thymus or spleen
CD19+, IgD-, B220+, IgM+ cells are sorted from the bone marrow of 5-6w old mice

extract_protocol:
ATAC-Seq libraries were amplified with KAPA HiFi polymerase.
ATAC-Seq; Paired-end 50 cycles

tag: strain/background

value: Wild-type

value: Immature B cells


title: DN_WT_rep2_ATAC

source_name: Double negative T cells

growth_protocol:
Mice from C57BL/6 were used to isolate lymphocytes from either the thymus or spleen
Thy1.2+, TCRb-/lo, CD4-CD8-, CD25+CD44-/+ (DN2/3) cells are sorted from the thymi of 5-6w old mice

value: Double negative T cells


title: ImmB_WT_rep2_ATAC


title: E12.5 input

city: san francisco

first: olga

last: golonzhka

address: 1550 4th street

department: psychiatry

institute: UCSF

data_processing:
Samples were sequenced on Illumina HiSeq 2000 platform (50bp single-end reads). Base calls were performed using RTA 1.13.48 software.
All reads were mapped to the mouse genome (mm9) using the Burrows-Wheeler Alignment (BWA).
Peaks were filtered to remove regions where the majority of supporting reads originated in repeat sequence and annotated to genomic features.
Peaks were called using MACS1.4 with default settings.
We used the union of peaks called against input control and negative blocking peptide control.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: bigWig files

source_name: E12.5 cortex, input

extract_protocol:
WT cortices (one litter of E12.5) were dissected, triturated in 1% formaldehyde in PBS and fixed for total of 10min at room temperature. Fixed cells were pelleted and washed with cold PBS. Pellets were lysed in 500ul of lysis buffer (1% SDS, 10mM EDTA and 50mM Tris, pH 8.1) on ice for 10min and lysates were sonicated using Bioruptor (Diagenode) on High Settings for 15 cycles (7.5 min of total sonication time). Resulting average chromatin size was 200-500 bp as verified by the Bioanalyzer. Cleared Chromatin was diluted 10 times with Dilution buffer (0.01% SDS, 1.1% Triton X- 100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) and was incubated overnight at 4C with 3ug of appropriate antibody. Mixture of protein A and G magnetic beads (Life Technologies) was preblocked overnight with BSA and tRNA and was added to the chromatin next day for 3 hours. Immune complexes were washed once with Low Salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP-40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris, pH 8.1) and TE buffer. Complexes were eluted in 1% SDS, 10mM Sodium bicarbonate buffer at 65C for 10min. Crosslinks were reversed at 65C overnight, proteins were digested using proteinase K and DNA was purified using Zymo Chip DNA Clean and Concentrator kit (Zymo research). Immunoprecipitation was performed using the following antibody: Pbx1/2/3/ (sc-888, Santa Cruz). As a negative control in PBX ChIP experiments, the PBX antibody was incubated with PBX blocking peptide (sc-888P, Santa Cruz) at 1:400 molar ratio, and added to the chromatin lysates.
ChIP-Seq libraries were prepared using NEBNext library Prep kit (New England Biolabs) and Illumina standard adaptors. 50bp single end.

value: mixed

value: wild type

value: cerebral cortex


title: ImmB_WT_rep1_RNA

data_processing:
RNA-Seq: reads were mapped using Tophat2 to the mm10 genome. Counts per gene was obtained using htseq-count and normalization was done using DESeq2.
ATAC-Seq:Reads were mapped to the mm10 genome using Bowtie2. Peaks were called using PeakDeck
Genome_build: mm10

extract_protocol:
RNA-Seq libraries were prepared using Ribo-Zero kit.
RNA-Seq; Paired-end 50 cycles


title: ImmB_WT_rep2_RNA


title: E12.5 plus

description: Immunoprecipitated genomic DNA. Antibody recognizes three Pbx isoforms: Pbx1, Pbx2 and Pbx3.

source_name: E12.5 cortex, Pbx1/2/3 ChIP

value: Pbx1/2/3 (Santa Cruz, sc-888)


title: E12.5 minus

description: Immunoprecipitated genomic DNA (with antibody preblocked with blocking peptide).

source_name: E12.5 cortex, negative control

value: Pbx1/2/3 (Santa Cruz, sc-888) mixed with the PBX blocking peptide (Santa Cruz, sc-888P) at 1:400 molar ratio


title: DN_WT_rep2_RNA


title: ChIP-Seq of H3K4me1 in IFN-y Macrophages

value: peripheral blood derived macrophage

value: GM-CSF for 72h and additional 72h with GM-CSF + IFN-y


title: WT_Tumor_11_5_L

description: Processed data file: bulk_rpkm.txt

value: Xenograft

value: CSL +/+

value: Early graft


title: DN_WT_rep1_RNA