title: Het (Q80) 10 months Female  Cerebellum miRNA rep4

source_name: Het (Q80) 10 months_Female_Cerebellum miRNA


title: Het (Q80) 10 months Female  Cerebellum miRNA rep3

status: Public on Nov 03 2015

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 2.0
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 R.75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

molecule: total RNA

organism: Mus musculus

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 background

tag: genotype/variation

value: Het (Q80) Knock-In

tag: age

value: 10 months

tag: Sex

value: Female

tag: tissue

value: Brain - Cerebellum

tag: housing condition

value: housed with Het (Q80) mice

tag: molecule subtype

value: miRNA


title: Het (Q80) 10 months Female  Cerebellum miRNA rep1


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

source_name: Het (Q20) 6 months_Male_Cerebellum miRNA

value: Het (Q20) Knock-In

value: 6 months

value: Male

value: housed with Het (Q20) and WT mice


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


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


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

source_name: Het (Q20) 6 months_Female_Cerebellum miRNA


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


title: Het (Q20) 2 months Male  Cerebellum miRNA rep4

source_name: Het (Q20) 2 months_Male_Cerebellum miRNA

value: 2 months


title: Het (Q20) 2 months Male  Cerebellum miRNA rep2


title: Het (Q80) 6 months Male  Cerebellum miRNA rep2

source_name: Het (Q80) 6 months_Male_Cerebellum miRNA


title: Het (Q20) 2 months Male  Cerebellum miRNA rep3


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


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


title: Het (Q20) 2 months Female  Cerebellum miRNA rep4

source_name: Het (Q20) 2 months_Female_Cerebellum miRNA


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


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

source_name: Het (Q20) 10 months_Male_Cerebellum miRNA


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


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


title: Het (Q20) 2 months Female  Cerebellum miRNA rep3


title: Het (Q20) 2 months Female  Cerebellum miRNA rep2


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

source_name: Het (Q20) 10 months_Female_Cerebellum miRNA


title: Het (Q20) 2 months Male  Cerebellum miRNA rep1


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


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


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


title: Het (Q20) 10 months Female  Cerebellum miRNA rep5


title: Het (Q80) 10 months Female  Cerebellum miRNA rep2


title: Het (Q175) 6 months Male  Cerebellum miRNA rep4

source_name: Het (Q175) 6 months_Male_Cerebellum miRNA

value: Het (Q175) Knock-In

value: housed with Het (Q175) mice


title: Het (Q175) 6 months Male  Cerebellum miRNA rep3


title: Het (Q175) 6 months Male  Cerebellum miRNA rep1


title: Het (Q175) 6 months Male  Cerebellum miRNA rep2


title: Het (Q175) 6 months Female  Cerebellum miRNA rep3

source_name: Het (Q175) 6 months_Female_Cerebellum miRNA


title: Het (Q175) 6 months Female  Cerebellum miRNA rep2


title: Het (Q20) 2 months Female  Cerebellum miRNA rep1


title: Het (Q175) 2 months Male  Cerebellum miRNA rep3

source_name: Het (Q175) 2 months_Male_Cerebellum miRNA


title: Het (Q175) 2 months Male  Cerebellum miRNA rep1


title: Het (Q175) 2 months Female  Cerebellum miRNA rep1

source_name: Het (Q175) 2 months_Female_Cerebellum miRNA


title: Het (Q175) 2 months Female  Cerebellum miRNA rep2


title: Het (Q175) 2 months Female  Cerebellum miRNA rep4


title: Het (Q175) 2 months Male  Cerebellum miRNA rep2


title: Het (Q175) 2 months Female  Cerebellum miRNA rep3


title: Het (Q175) 10 months Female  Cerebellum miRNA rep4

source_name: Het (Q175) 10 months_Female_Cerebellum miRNA


title: Het (Q175) 10 months Female  Cerebellum miRNA rep3


title: Het (Q175) 2 months Male  Cerebellum miRNA rep4


title: Het (Q175) 10 months Male  Cerebellum miRNA rep1

source_name: Het (Q175) 10 months_Male_Cerebellum miRNA


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

source_name: Het (Q140) 6 months_Male_Cerebellum miRNA

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q175) 10 months Male  Cerebellum miRNA rep4


title: Het (Q175) 10 months Female  Cerebellum miRNA rep2


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


title: Het (Q175) 10 months Male  Cerebellum miRNA rep3


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


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

source_name: Het (Q140) 6 months_Female_Cerebellum miRNA


title: Het (Q175) 10 months Male  Cerebellum miRNA rep2


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


title: Het (Q175) 10 months Female  Cerebellum miRNA rep1


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


title: Het (Q175) 6 months Female  Cerebellum miRNA rep1


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


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


title: Het (Q140) 2 months Male  Cerebellum miRNA rep4

source_name: Het (Q140) 2 months_Male_Cerebellum miRNA


title: Het (Q140) 2 months Male  Cerebellum miRNA rep3


title: Het (Q140) 2 months Male  Cerebellum miRNA rep2


title: Het (Q140) 2 months Female  Cerebellum miRNA rep4

source_name: Het (Q140) 2 months_Female_Cerebellum miRNA


title: Het (Q140) 2 months Female  Cerebellum miRNA rep2


title: Het (Q140) 2 months Female  Cerebellum miRNA rep3


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

source_name: Het (Q140) 10 months_Male_Cerebellum miRNA


title: Het (Q140) 2 months Female  Cerebellum miRNA rep1


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


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

source_name: Het (Q140) 10 months_Female_Cerebellum miRNA


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


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


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


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


title: Het (Q111) 6 months Male  Cerebellum miRNA rep3

source_name: Het (Q111) 6 months_Male_Cerebellum miRNA

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: Het (Q111) 6 months Male  Cerebellum miRNA rep2


title: Het (Q111) 6 months Female  Cerebellum miRNA rep2

source_name: Het (Q111) 6 months_Female_Cerebellum miRNA


title: Het (Q111) 6 months Female  Cerebellum miRNA rep3


title: Het (Q111) 6 months Female  Cerebellum miRNA rep4


title: Het (Q111) 6 months Male  Cerebellum miRNA rep1


title: Het (Q111) 6 months Male  Cerebellum miRNA rep4


title: Het (Q111) 2 months Male  Cerebellum miRNA rep4

source_name: Het (Q111) 2 months_Male_Cerebellum miRNA


title: Het (Q111) 2 months Male  Cerebellum miRNA rep1


title: Het (Q111) 2 months Male  Cerebellum miRNA rep2


title: Het (Q111) 2 months Female  Cerebellum miRNA rep3

source_name: Het (Q111) 2 months_Female_Cerebellum miRNA


title: Het (Q111) 2 months Female  Cerebellum miRNA rep4


title: Het (Q111) 2 months Female  Cerebellum miRNA rep2


title: Het (Q111) 2 months Male  Cerebellum miRNA rep3


title: Het (Q140) 2 months Male  Cerebellum miRNA rep1


title: Het (Q111) 6 months Female  Cerebellum miRNA rep1


title: Het (Q175) 6 months Female  Cerebellum miRNA rep4


title: Het (Q111) 10 months Male  Cerebellum miRNA rep3

source_name: Het (Q111) 10 months_Male_Cerebellum miRNA


title: Het (Q111) 2 months Female  Cerebellum miRNA rep1


title: Het (Q111) 10 months Male  Cerebellum miRNA rep2


title: Het (Q111) 10 months Male  Cerebellum miRNA rep1


title: WT 2 month Female  Hippocampus mRNA rep1

source_name: WT 2 month_Female_Hippocampus

value: Wild Type

value: Brain - Hippocampus


title: WT 10 month Male  Hippocampus mRNA rep2

source_name: WT 10 month_Male_Hippocampus

value: 10 months


title: WT 10 month Female  Hippocampus mRNA rep3

source_name: WT 10 month_Female_Hippocampus

value: Female


title: WT 10 month Female  Hippocampus mRNA rep2


title: WT 2 month Male  Hippocampus mRNA rep1

source_name: WT 2 month_Male_Hippocampus


title: WT 10 month Female  Hippocampus mRNA rep1


title: WT 6 month Male  Hippocampus mRNA rep2

source_name: WT 6 month_Male_Hippocampus


title: WT 2 month Male  Hippocampus mRNA rep3


title: WT 10 month Male  Hippocampus mRNA rep1


title: WT 10 month Male  Hippocampus mRNA rep4


title: WT 6 month Male  Hippocampus mRNA rep3


title: WT 6 month Female  Hippocampus mRNA rep3

source_name: WT 6 month_Female_Hippocampus


title: WT 2 month Female  Hippocampus mRNA rep3


title: Het (Q111) 10 months Female  Cerebellum miRNA rep3

source_name: Het (Q111) 10 months_Female_Cerebellum miRNA

value: Brain - Cerebellum


title: WT 6 month Male  Hippocampus mRNA rep1


title: WT 6 month Male  Hippocampus mRNA rep4


title: Het (Q111) 10 months Female  Cerebellum miRNA rep1

value: miRNA


title: WT 2 month Male  Hippocampus mRNA rep2


title: WT 2 month Male  Hippocampus mRNA rep4


title: WT 6 month Female  Hippocampus mRNA rep4


title: WT 2 month Female  Hippocampus mRNA rep2


title: WT 10 month Male  Hippocampus mRNA rep3


title: Het (Q111) 10 months Female  Cerebellum miRNA rep2


title: Het (Q111) 10 months Female  Cerebellum miRNA rep4


title: WT 6 month Female  Hippocampus mRNA rep1


title: Het (Q92) 6 month Male  Hippocampus mRNA rep4

source_name: Het (Q92) 6 month_Male_Hippocampus

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: WT 2 month Female  Hippocampus mRNA rep4


title: WT 10 month Female  Hippocampus mRNA rep4


title: Het (Q92) 6 month Male  Hippocampus mRNA rep2

value: 6 months

value: Male


title: Het (Q92) 6 month Male  Hippocampus mRNA rep3


title: Het (Q92) 6 month Male  Hippocampus mRNA rep1


title: Het (Q92) 6 month Female  Hippocampus mRNA rep4

source_name: Het (Q92) 6 month_Female_Hippocampus


title: Het (Q92) 2 month Male  Hippocampus mRNA rep4

source_name: Het (Q92) 2 month_Male_Hippocampus

value: 2 months


title: Het (Q92) 2 month Male  Hippocampus mRNA rep3


title: Het (Q92) 6 month Female  Hippocampus mRNA rep3


title: Het (Q92) 6 month Female  Hippocampus mRNA rep1


title: Het (Q92) 10 month Male  Hippocampus mRNA rep3

source_name: Het (Q92) 10 month_Male_Hippocampus


title: Het (Q80) 6 month Female  Hippocampus mRNA rep4

source_name: Het (Q80) 6 month_Female_Hippocampus

value: Het (Q80) Knock-In

value: housed with Het (Q80) mice


title: Het (Q80) 6 month Male  Hippocampus mRNA rep2

source_name: Het (Q80) 6 month_Male_Hippocampus


title: Het (Q92) 10 month Male  Hippocampus mRNA rep1


title: Het (Q92) 10 month Female  Hippocampus mRNA rep4

source_name: Het (Q92) 10 month_Female_Hippocampus


title: Het (Q92) 2 month Male  Hippocampus mRNA rep1


title: Het (Q92) 2 month Female  Hippocampus mRNA rep3

source_name: Het (Q92) 2 month_Female_Hippocampus


title: Het (Q92) 10 month Male  Hippocampus mRNA rep2


title: Het (Q92) 2 month Female  Hippocampus mRNA rep1


title: Het (Q80) 6 month Male  Hippocampus mRNA rep1


title: Het (Q80) 6 month Male  Hippocampus mRNA rep4


title: Het (Q92) 10 month Male  Hippocampus mRNA rep4


title: Het (Q92) 10 month Female  Hippocampus mRNA rep1


title: Het (Q92) 2 month Male  Hippocampus mRNA rep2


title: Het (Q92) 2 month Female  Hippocampus mRNA rep4


title: Het (Q80) 2 months Male  Cerebellum miRNA rep3

source_name: Het (Q80) 2 months_Male_Cerebellum miRNA


title: Het (Q92) 10 month Female  Hippocampus mRNA rep3


title: Het (Q80) 6 month Male  Hippocampus mRNA rep3


title: WT 6 month Female  Hippocampus mRNA rep2

value: housed with Het (Q20) and WT mice


title: Het (Q92) 10 month Female  Hippocampus mRNA rep2


title: Het (Q92) 6 month Female  Hippocampus mRNA rep2


title: Het (Q92) 2 month Female  Hippocampus mRNA rep2


title: Het (Q80) 6 month Female  Hippocampus mRNA rep3


title: Het (Q80) 2 month Male  Hippocampus mRNA rep5

source_name: Het (Q80) 2 month_Male_Hippocampus


title: Het (Q80) 2 month Male  Hippocampus mRNA rep4


title: Het (Q80) 6 month Female  Hippocampus mRNA rep2


title: Het (Q80) 6 month Female  Hippocampus mRNA rep1


title: Het (Q20) 2 month Female  Hippocampus mRNA rep1

source_name: Het (Q20) 2 month_Female_Hippocampus

value: Het (Q20) Knock-In


title: Het (Q80) 10 month Male  Hippocampus mRNA rep3

source_name: Het (Q80) 10 month_Male_Hippocampus


title: Het (Q20) 6 month Female  Hippocampus mRNA rep3

source_name: Het (Q20) 6 month_Female_Hippocampus


title: Het (Q20) 2 month Male  Hippocampus mRNA rep2

source_name: Het (Q20) 2 month_Male_Hippocampus


title: Het (Q80) 2 month Male  Hippocampus mRNA rep3


title: Het (Q80) 2 month Male  Hippocampus mRNA rep1


title: Het (Q20) 6 month Female  Hippocampus mRNA rep2


title: Het (Q20) 6 month Male  Hippocampus mRNA rep2

source_name: Het (Q20) 6 month_Male_Hippocampus


title: Het (Q80) 10 month Female  Hippocampus mRNA rep4

source_name: Het (Q80) 10 month_Female_Hippocampus


title: Het (Q80) 10 month Male  Hippocampus mRNA rep4


title: Het (Q80) 10 month Female  Hippocampus mRNA rep2


title: Het (Q20) 2 month Male  Hippocampus mRNA rep3


title: Het (Q20) 2 month Male  Hippocampus mRNA rep4


title: Het (Q20) 2 month Female  Hippocampus mRNA rep4


title: Het (Q80) 2 month Female  Hippocampus mRNA rep1

source_name: Het (Q80) 2 month_Female_Hippocampus


title: Het (Q80) 10 month Female  Hippocampus mRNA rep3


title: Het (Q80) 2 month Male  Hippocampus mRNA rep2


title: Het (Q80) 10 month Male  Hippocampus mRNA rep1


title: Het (Q20) 2 month Female  Hippocampus mRNA rep3


title: Het (Q80) 10 month Male  Hippocampus mRNA rep2


title: Het (Q20) 6 month Male  Hippocampus mRNA rep4


title: Het (Q80) 10 month Female  Hippocampus mRNA rep1


title: Het (Q20) 6 month Male  Hippocampus mRNA rep1


title: Het (Q80) 2 month Female  Hippocampus mRNA rep2


title: Het (Q20) 2 month Male  Hippocampus mRNA rep1


title: Het (Q20) 6 month Male  Hippocampus mRNA rep3


title: Het (Q80) 2 month Female  Hippocampus mRNA rep3


title: Het (Q20) 6 month Female  Hippocampus mRNA rep4


title: Het (Q20) 6 month Female  Hippocampus mRNA rep1


title: Het (Q20) 2 month Female  Hippocampus mRNA rep2


title: Het (Q20) 10 month Male  Hippocampus mRNA rep3

source_name: Het (Q20) 10 month_Male_Hippocampus


title: Het (Q20) 10 month Male  Hippocampus mRNA rep2


title: Het (Q20) 10 month Female  Hippocampus mRNA rep5

source_name: Het (Q20) 10 month_Female_Hippocampus


title: Het (Q20) 10 month Male  Hippocampus mRNA rep1


title: Het (Q20) 10 month Female  Hippocampus mRNA rep3


title: Het (Q175) 10 month Female  Hippocampus mRNA rep4

source_name: Het (Q175) 10 month_Female_Hippocampus

value: Het (Q175) Knock-In

value: housed with Het (Q175) mice


title: Het (Q175) 10 month Male  Hippocampus mRNA rep4

source_name: Het (Q175) 10 month_Male_Hippocampus


title: Het (Q175) 10 month Male  Hippocampus mRNA rep2


title: Het (Q175) 6 month Male  Hippocampus mRNA rep3

source_name: Het (Q175) 6 month_Male_Hippocampus


title: Het (Q175) 6 month Female  Hippocampus mRNA rep3

source_name: Het (Q175) 6 month_Female_Hippocampus


title: Het (Q175) 6 month Female  Hippocampus mRNA rep1


title: Het (Q175) 2 month Female  Hippocampus mRNA rep3

source_name: Het (Q175) 2 month_Female_Hippocampus


title: Het (Q175) 2 month Male  Hippocampus mRNA rep1

source_name: Het (Q175) 2 month_Male_Hippocampus


title: Het (Q20) 10 month Female  Hippocampus mRNA rep2


title: Het (Q175) 10 month Male  Hippocampus mRNA rep1


title: Het (Q175) 10 month Female  Hippocampus mRNA rep3


title: Het (Q175) 2 month Male  Hippocampus mRNA rep2


title: Het (Q175) 2 month Male  Hippocampus mRNA rep4


title: Het (Q175) 2 month Male  Hippocampus mRNA rep3


title: Het (Q175) 6 month Female  Hippocampus mRNA rep4


title: Het (Q175) 2 month Female  Hippocampus mRNA rep4


title: Het (Q175) 2 month Female  Hippocampus mRNA rep1


title: Het (Q175) 10 month Male  Hippocampus mRNA rep3


title: Het (Q175) 6 month Male  Hippocampus mRNA rep2


title: Het (Q20) 10 month Female  Hippocampus mRNA rep1


title: Het (Q175) 6 month Male  Hippocampus mRNA rep1


title: Het (Q20) 10 month Female  Hippocampus mRNA rep4


title: Het (Q175) 6 month Male  Hippocampus mRNA rep4


title: Het (Q175) 6 month Female  Hippocampus mRNA rep2


title: Het (Q175) 2 month Female  Hippocampus mRNA rep2


title: Het (Q140) 10 month Male  Hippocampus mRNA rep4

source_name: Het (Q140) 10 month_Male_Hippocampus

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q140) 2 month Female  Hippocampus mRNA rep1

source_name: Het (Q140) 2 month_Female_Hippocampus

value: Brain - Hippocampus


title: Het (Q140) 2 month Female  Hippocampus mRNA rep3

value: Female


title: Het (Q140) 6 month Female  Hippocampus mRNA rep2

source_name: Het (Q140) 6 month_Female_Hippocampus


title: Het (Q175) 10 month Female  Hippocampus mRNA rep1

value: 10 months


title: Het (Q140) 10 month Male  Hippocampus mRNA rep1


title: Het (Q140) 6 month Female  Hippocampus mRNA rep1


title: Het (Q175) 10 month Female  Hippocampus mRNA rep2


title: Het (Q140) 6 month Female  Hippocampus mRNA rep4


title: Het (Q140) 6 month Male  Hippocampus mRNA rep3

source_name: Het (Q140) 6 month_Male_Hippocampus


title: Het (Q140) 2 month Male  Hippocampus mRNA rep4

source_name: Het (Q140) 2 month_Male_Hippocampus


title: Het (Q140) 6 month Male  Hippocampus mRNA rep4


title: Het (Q140) 6 month Male  Hippocampus mRNA rep1


title: Het (Q140) 6 month Male  Hippocampus mRNA rep2


title: Het (Q140) 2 month Female  Hippocampus mRNA rep2


title: Het (Q140) 10 month Female  Hippocampus mRNA rep3

source_name: Het (Q140) 10 month_Female_Hippocampus


title: Het (Q140) 2 month Female  Hippocampus mRNA rep4


title: Het (Q140) 10 month Male  Hippocampus mRNA rep3


title: Het (Q140) 2 month Male  Hippocampus mRNA rep3


title: Het (Q140) 2 month Male  Hippocampus mRNA rep1


title: Het (Q140) 10 month Female  Hippocampus mRNA rep4


title: Het (Q111) 6 month Male  Hippocampus mRNA rep3

source_name: Het (Q111) 6 month_Male_Hippocampus

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: Het (Q140) 10 month Male  Hippocampus mRNA rep2


title: Het (Q140) 6 month Female  Hippocampus mRNA rep3


title: Het (Q140) 10 month Female  Hippocampus mRNA rep1


title: Het (Q140) 10 month Female  Hippocampus mRNA rep2


title: Het (Q111) 6 month Male  Hippocampus mRNA rep1


title: Het (Q111) 6 month Male  Hippocampus mRNA rep2


title: Het (Q111) 6 month Male  Hippocampus mRNA rep4


title: Het (Q140) 2 month Male  Hippocampus mRNA rep2


title: Het (Q111) 6 month Female  Hippocampus mRNA rep4

source_name: Het (Q111) 6 month_Female_Hippocampus


title: Het (Q111) 2 month Male  Hippocampus mRNA rep3

source_name: Het (Q111) 2 month_Male_Hippocampus


title: Het (Q111) 2 month Male  Hippocampus mRNA rep4


title: Het (Q111) 6 month Female  Hippocampus mRNA rep1


title: Het (Q111) 6 month Female  Hippocampus mRNA rep3


title: Het (Q111) 10 month Female  Hippocampus mRNA rep4

source_name: Het (Q111) 10 month_Female_Hippocampus


title: Het (Q111) 10 month Female  Hippocampus mRNA rep3


title: Het (Q111) 2 month Male  Hippocampus mRNA rep2


title: Het (Q111) 10 month Female  Hippocampus mRNA rep1


title: Het (Q111) 2 month Female  Hippocampus mRNA rep1

source_name: Het (Q111) 2 month_Female_Hippocampus


title: Het (Q111) 10 month Male  Hippocampus mRNA rep4

source_name: Het (Q111) 10 month_Male_Hippocampus


title: WT 6 month Male  Cerebellum mRNA rep1

source_name: WT 6 month_male_cerebellum

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 1.25 ug of total RNA were used to collect polyA-enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Wild Type

value: Brain - Cerebellum


title: Het (Q111) 2 month Female  Hippocampus mRNA rep3


title: WT 6 month Female  Cerebellum mRNA rep4

source_name: WT 6 month_female_cerebellum

value: 6 months


title: Het (Q111) 2 month Female  Hippocampus mRNA rep4

value: 2 months


title: WT 6 month Female  Cerebellum mRNA rep3


title: Het (Q111) 6 month Female  Hippocampus mRNA rep2


title: WT 6 month Male  Cerebellum mRNA rep3

value: Male


title: Het (Q111) 2 month Female  Hippocampus mRNA rep2


title: WT 6 month Male  Cerebellum mRNA rep4


title: Het (Q111) 10 month Male  Hippocampus mRNA rep1


title: WT 6 month Male  Cerebellum mRNA rep2


title: WT 6 month Female  Cerebellum mRNA rep2


title: Het (Q111) 2 month Male  Hippocampus mRNA rep1


title: WT 2 month Male  Cerebellum mRNA rep4

source_name: WT 2 month_male_cerebellum


title: WT 2 month Male  Cerebellum mRNA rep3


title: WT 6 month Female  Cerebellum mRNA rep1


title: Het (Q111) 10 month Male  Hippocampus mRNA rep3


title: Het (Q111) 10 month Male  Hippocampus mRNA rep2


title: Het (Q111) 10 month Female  Hippocampus mRNA rep2


title: WT 2 month Male  Cerebellum mRNA rep2


title: WT 2 month Male  Cerebellum mRNA rep1


title: WT 2 month Female  Cerebellum mRNA rep3

source_name: WT 2 month_female_cerebellum


title: WT 10 month Male  Cerebellum mRNA rep3

source_name: WT 10 month_male_cerebellum


title: WT 2 month Female  Cerebellum mRNA rep1


title: WT 10 month Female  Cerebellum mRNA rep2

source_name: WT 10 month_female_cerebellum


title: WT 10 month Female  Cerebellum mRNA rep1


title: WT 10 month Male  Cerebellum mRNA rep1


title: Het (Q92) 6 month Female  Cerebellum mRNA rep2

source_name: Het (Q92) 6 month_female_cerebellum

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: Het (Q92) 6 month Male  Cerebellum mRNA rep2

source_name: Het (Q92) 6 month_male_cerebellum


title: Het (Q92) 6 month Male  Cerebellum mRNA rep1


title: Het (Q92) 6 month Male  Cerebellum mRNA rep4


title: Het (Q92) 6 month Male  Cerebellum mRNA rep3


title: WT 10 month Male  Cerebellum mRNA rep2

value: housed with Het (Q20) and WT mice


title: WT 2 month Female  Cerebellum mRNA rep2


title: WT 10 month Male  Cerebellum mRNA rep4


title: Het (Q92) 2 month Male  Cerebellum mRNA rep2

source_name: Het (Q92) 2 month_male_cerebellum


title: Het (Q92) 6 month Female  Cerebellum mRNA rep1


title: WT 10 month Female  Cerebellum mRNA rep4


title: Het (Q92) 2 month Female  Cerebellum mRNA rep4

source_name: Het (Q92) 2 month_female_cerebellum


title: Het (Q92) 2 month Male  Cerebellum mRNA rep3


title: Het (Q92) 2 month Male  Cerebellum mRNA rep4


title: Het (Q92) 2 month Male  Cerebellum mRNA rep1


title: WT 2 month Female  Cerebellum mRNA rep4


title: Het (Q92) 2 month Female  Cerebellum mRNA rep2


title: Het (Q92) 10 month Male  Cerebellum mRNA rep3

source_name: Het (Q92) 10 month_male_cerebellum


title: Het (Q92) 10 month Male  Cerebellum mRNA rep4


title: Het (Q92) 2 month Female  Cerebellum mRNA rep3


title: Het (Q92) 2 month Female  Cerebellum mRNA rep1


title: WT 10 month Female  Cerebellum mRNA rep3


title: Het (Q92) 6 month Female  Cerebellum mRNA rep3


title: Het (Q92) 10 month Male  Cerebellum mRNA rep2


title: Het (Q92) 6 month Female  Cerebellum mRNA rep4


title: Het (Q92) 10 month Female  Cerebellum mRNA rep1

source_name: Het (Q92) 10 month_female_cerebellum


title: Het (Q92) 10 month Female  Cerebellum mRNA rep4


title: Het (Q92) 10 month Female  Cerebellum mRNA rep2


title: Het (Q80) 6 month Male  Cerebellum mRNA rep3

source_name: Het (Q80) 6 month_male_cerebellum

value: Het (Q80) Knock-In

value: housed with Het (Q80) mice


title: Het (Q92) 10 month Female  Cerebellum mRNA rep3


title: Het (Q80) 6 month Male  Cerebellum mRNA rep2


title: Het (Q80) 6 month Male  Cerebellum mRNA rep1


title: Het (Q80) 6 month Male  Cerebellum mRNA rep4


title: Het (Q80) 6 month Female  Cerebellum mRNA rep3

source_name: Het (Q80) 6 month_female_cerebellum


title: Het (Q80) 6 month Female  Cerebellum mRNA rep4


title: Het (Q80) 2 month Male  Cerebellum mRNA rep5

source_name: Het (Q80) 2 month_male_cerebellum


title: Het (Q80) 6 month Female  Cerebellum mRNA rep2


title: Het (Q80) 2 month Male  Cerebellum mRNA rep1


title: Het (Q80) 2 month Female  Cerebellum mRNA rep2

source_name: Het (Q80) 2 month_female_cerebellum


title: Het (Q80) 6 month Female  Cerebellum mRNA rep1


title: Het (Q80) 10 month Male  Cerebellum mRNA rep2

source_name: Het (Q80) 10 month_male_cerebellum


title: Het (Q80) 2 month Female  Cerebellum mRNA rep1


title: Het (Q80) 10 month Male  Cerebellum mRNA rep4


title: Het (Q80) 10 month Female  Cerebellum mRNA rep4

source_name: Het (Q80) 10 month_female_cerebellum


title: Het (Q92) 10 month Male  Cerebellum mRNA rep1


title: Het (Q80) 10 month Male  Cerebellum mRNA rep1


title: Het (Q80) 2 month Male  Cerebellum mRNA rep3


title: Het (Q80) 2 month Male  Cerebellum mRNA rep2


title: Het (Q80) 2 month Female  Cerebellum mRNA rep3


title: Het (Q80) 10 month Male  Cerebellum mRNA rep3


title: Het (Q80) 10 month Female  Cerebellum mRNA rep2


title: Het (Q20) 6 month Male  Cerebellum mRNA rep2

source_name: Het (Q20) 6 month_male_cerebellum

value: Het (Q20) Knock-In


title: Het (Q20) 6 month Male  Cerebellum mRNA rep3


title: Het (Q20) 6 month Female  Cerebellum mRNA rep4

source_name: Het (Q20) 6 month_female_cerebellum


title: Het (Q20) 6 month Male  Cerebellum mRNA rep1


title: Het (Q20) 6 month Female  Cerebellum mRNA rep3


title: Het (Q20) 6 month Male  Cerebellum mRNA rep4


title: Het (Q80) 2 month Male  Cerebellum mRNA rep4


title: Het (Q80) 10 month Female  Cerebellum mRNA rep3


title: Het (Q20) 6 month Female  Cerebellum mRNA rep1


title: Het (Q20) 2 month Male  Cerebellum mRNA rep3

source_name: Het (Q20) 2 month_male_cerebellum


title: Het (Q20) 2 month Male  Cerebellum mRNA rep4


title: Het (Q20) 2 month Male  Cerebellum mRNA rep2


title: Het (Q20) 6 month Female  Cerebellum mRNA rep2


title: Het (Q20) 2 month Female  Cerebellum mRNA rep3

source_name: Het (Q20) 2 month_female_cerebellum


title: Het (Q20) 2 month Female  Cerebellum mRNA rep4


title: rad21_mut_smc3_rep2

city: Stanford

first: Howard

last: Chang

state: CA

address: 269 Campus Dr. Stanford, CA

institute: Stanford University

library_source: genomic

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using Bowtie2, duplicate fragments were then removed using Picard. Peaks were called using MACS2.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab separated format, which includes the following columns: chromosome, start, stop, name, score, strand, signalValue, pValue, qValue, peak

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells from obtained from New York Blood Center and grown in HPGM Medium supplemented with cytokines

extract_protocol:
~100,000,000 cells were were crosslinked in 1% formaldehyde for 10 minutes at room temperature. Typically, 5 million cells were used for each ChIP experiment and chromatin was sheared on a Bioruptor (Diagenode) to an average of 200-400bp.  The following antibodies were used for ChIP studies: SMC3 (clone: ab9263, Abcam), GATA2 (Clone: sc-9008, Santa Cruz Biotechnology) and RUNX1 (Clone: sc-365644, Santa Cruz Biotechnology)
After specific recovery of chromatin bound proteins via immunoprecipitation, samples were reverse crosslinked at 65°C overnight and DNA was purified for subsequent library preparation. ChIP-seq libraries were prepared according to the NEBNext protocol and sequenced using Illumina NextSeq.

treatment_protocol: TF-1 RAD21 Q592* and TF-1 RAD21 WT were induced with DOX for 6 days.

tag: cell line

tag: cell type

value: Erythroleukemia Cell Line

tag: transduction


title: rad21_mut_smc3_rep1


title: Het (Q80) 10 month Female  Cerebellum mRNA rep1


title: Het (Q20) 10 month Male  Cerebellum mRNA rep3

source_name: Het (Q20) 10 month_male_cerebellum


title: Het (Q20) 2 month Female  Cerebellum mRNA rep1


title: Het (Q20) 2 month Male  Cerebellum mRNA rep1


title: Het (Q20) 2 month Female  Cerebellum mRNA rep2


title: rad21_wt_runx1_rep2

source_name: TF-1-RAD21 WT (RUNX1 #2)

value: TF-1-RAD21 WT (RUNX1 #2)


title: rad21_mut_runx1_rep1


title: rad21_wt_smc3_rep1

source_name: TF-1-RAD21 WT (SMC3 #1)

value: TF-1-RAD21 WT (SMC3 #1)


title: rad21_wt_runx1_rep1

source_name: TF-1-RAD21 WT (RUNX1 #1)

value: TF-1-RAD21 WT (RUNX1 #1)


title: Het (Q20) 10 month Male  Cerebellum mRNA rep2

value: 10 months


title: Het (Q20) 10 month Male  Cerebellum mRNA rep1


title: rad21_mut_gata2_rep1


title: Het (Q20) 10 month Female  Cerebellum mRNA rep4

source_name: Het (Q20) 10 month_female_cerebellum

value: Female


title: Het (Q20) 10 month Female  Cerebellum mRNA rep5


title: rad21_wt_gata2_rep2

source_name: TF-1-RAD21 WT (GATA2 #2)

value: TF-1-RAD21 WT (GATA2 #2)


title: rad21_mut_gata2_rep2


title: rad21_wt_gata2_rep1

source_name: TF-1-RAD21 WT (GATA2 #1)

value: TF-1-RAD21 WT (GATA2 #1)


title: Het (Q20) 10 month Female  Cerebellum mRNA rep2

value: Brain - Cerebellum


title: rad21_mut_input_rep1


title: rad21_wt_input_rep2

source_name: TF-1-RAD21 WT (Input #2)

value: TF-1-RAD21 WT (Input #2)


title: rad21_mut_input_rep2


title: Het (Q175) 6 month Male  Cerebellum mRNA rep4

source_name: Het (Q175) 6 month_male_cerebellum

value: Het (Q175) Knock-In

value: 6 months

value: Male

value: housed with Het (Q175) mice


title: rad21_wt_smc3_rep2

source_name: TF-1-RAD21 WT (SMC3 #2)

value: TF-1-RAD21 WT (SMC3 #2)


title: Het (Q175) 6 month Male  Cerebellum mRNA rep3


title: Het (Q175) 6 month Male  Cerebellum mRNA rep2


title: Het (Q175) 6 month Male  Cerebellum mRNA rep1


title: CB553_SMC1A_MUT_Rep2

data_processing:
Library strategy: ATAC-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.99 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand

source_name: human CD34+ HSPC

extract_protocol:
Around 10-50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: Cells were transduced with lentivirus and GFP+ sorted after 72 hours and subjected to ATAC-Seq

value: human CD34+ HSPC

value: CB553-SMC1A Mutant #2


title: Het (Q20) 10 month Female  Cerebellum mRNA rep3

value: Het (Q20) Knock-In

value: housed with Het (Q20) and WT mice


title: CB553_SMC1A_WT_Rep2

value: CB553-SMC1A WT #2


title: Het (Q175) 6 month Female  Cerebellum mRNA rep4

source_name: Het (Q175) 6 month_female_cerebellum


title: CB553_EV_Rep2

value: CB553-Empty Vector


title: CB552_SMC1A_MUT_Rep1

value: CB552-SMC1A Mutant   #1


title: CB552_SMC1A_WT_Rep1

value: CB552-SMC1A WT  #1


title: CB552_EV_Rep1

value: CB552-Empty Vector


title: Het (Q175) 6 month Female  Cerebellum mRNA rep2

value: Female


title: Het (Q175) 6 month Female  Cerebellum mRNA rep3

value: Brain - Cerebellum


title: Het (Q175) 6 month Female  Cerebellum mRNA rep1


title: CB551_RAD21_MUT_Rep2

value: CB551-RAD21 Mutant  #2


title: Het (Q175) 2 month Male  Cerebellum mRNA rep4

source_name: Het (Q175) 2 month_male_cerebellum

value: Het (Q175) Knock-In

value: 2 months


title: CB551_EV_Rep2

value: CB551-Empty Vector


title: Het (Q20) 10 month Female  Cerebellum mRNA rep1

value: 10 months


title: Het (Q175) 2 month Male  Cerebellum mRNA rep1

value: Male

value: housed with Het (Q175) mice


title: Het (Q175) 2 month Female  Cerebellum mRNA rep4

source_name: Het (Q175) 2 month_female_cerebellum


title: CB550_RAD21_MUT_Rep1

value: human CD34+ HSPC

value: CB550-RAD21 Mutant  #1


title: rad21_wt_input_rep1

source_name: TF-1-RAD21 WT (Input #1)

value: Erythroleukemia Cell Line

value: TF-1-RAD21 WT (Input #1)


title: CB550_RAD21_WT_Rep1


title: Het (Q175) 10 month Male  Cerebellum mRNA rep4

source_name: Het (Q175) 10 month_male_cerebellum


title: Het (Q175) 2 month Female  Cerebellum mRNA rep2


title: Het (Q175) 2 month Female  Cerebellum mRNA rep3


title: CB551_RAD21_WT_Rep2


title: Het (Q175) 10 month Female  Cerebellum mRNA rep4

source_name: Het (Q175) 10 month_female_cerebellum


title: Het (Q175) 10 month Male  Cerebellum mRNA rep1


title: Het (Q175) 10 month Female  Cerebellum mRNA rep2


title: Het (Q175) 10 month Male  Cerebellum mRNA rep3


title: CB550_EV_Rep1

value: CB550-Empty Vector


title: Het (Q175) 2 month Female  Cerebellum mRNA rep1


title: Het (Q175) 10 month Female  Cerebellum mRNA rep1


title: Het (Q175) 10 month Female  Cerebellum mRNA rep3


title: Het (Q140) 6 month Male  Cerebellum mRNA rep4

source_name: Het (Q140) 6 month_male_cerebellum

value: Het (Q140) Knock-In

value: 6 months

value: housed with Het (Q140) mice


title: Het (Q140) 6 month Male  Cerebellum mRNA rep1


title: Het (Q140) 6 month Female  Cerebellum mRNA rep4

source_name: Het (Q140) 6 month_female_cerebellum

value: Female


title: Het (Q140) 6 month Male  Cerebellum mRNA rep3

value: Brain - Cerebellum


title: WT_DN3_H3K4me3

city: Illkirch

first: Attila

last: Oravecz

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling was performed with the Illumina pipeline, and reads were aligned to the mm9 mouse genome with Bowtie
FASTQ files were generated by CASAVA
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated by extending the reads to 200 bp length, and the read densities in 25 bp bins were normalized to the library size. BedGraph tracks were generated after the quantile-normalization of read densities in  200 bp bins.

source_name: thymus

growth_protocol: ILC87 cells were grown in RPMI medium w/25mM HEPES and 10% heat-inactivated FCS in standard humidified incubator at 5% CO2

extract_protocol: The ChIP protocol was adapted from the Millipore ChIP Assay Kit (17-295). Cells were cross-linked with 1% formaldehyde at 37°C for 10min in PBS/0.5% BSA and lysed in 1% Triton X-100, 50 mM MgCl2, 100 mM Tris-HCl ([pH 7.1), 11% sucrose, 1x PIC  buffer. Pelleted nuclei were then lysed in 1% SDS lysis buffer and sonicated to 200-500 bp fragments using a Bioruptor 200 (Diagenode). Chromatin samples were incubated with the appropriate antibodies. DNA was purified using the iPure Kit (Diagenode). Libraries were prepared according to standard Illumina protocols, and were validated with the Agilent Bioanalyzer.

treatment_protocol: ILC87 cells were treated with 100 nM 4-hydroxytamoxifen (4OHT, Sigma) or vehicle (EtOH)

tag: strain

tag: genotype

value: wild-type

value: 4-5 weeks

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes

tag: chip antibody

value: anti-H3K4me3 (ab8580, Abcam)


title: Het (Q140) 6 month Male  Cerebellum mRNA rep2


title: Het (Q140) 6 month Female  Cerebellum mRNA rep2


title: ILC87-Ik1-ER_4OHT_1d_input

description: processed data file: ILC87-Ik1-ER_EtOH+4OHT_1d_input.wig.gz

value: ILC87 cell line derived from a thymic T cell tumor

value: Ikf/f Lck-Cre+

value: 1d 4-hydroxytamoxifen-treated ILC87 cells expressing Ikaros-ER fusion protein


title: ILC87-Ik1-ER_EtOH_3d_H3K27me3

value: 3d EtOH-treated ILC87 cells expressing Ikaros-ER fusion protein

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: ILC87-Ik1-ER_4OHT_3d_H3K27me3

value: 3d 4-hydroxytamoxifen-treated ILC87 cells expressing Ikaros-ER fusion protein


title: Het (Q175) 10 month Male  Cerebellum mRNA rep2

value: Het (Q175) Knock-In

value: 10 months

value: Male

value: housed with Het (Q175) mice


title: Het (Q140) 2 month Male  Cerebellum mRNA rep4

source_name: Het (Q140) 2 month_male_cerebellum

value: Het (Q140) Knock-In

value: 2 months

value: housed with Het (Q140) mice


title: Het (Q175) 2 month Male  Cerebellum mRNA rep2

value: Brain - Cerebellum


title: Het (Q140) 6 month Female  Cerebellum mRNA rep1

value: 6 months

value: Female


title: ILC87-Ik1-ER_EtOH_1d_Ikaros

value: 1d EtOH-treated ILC87 cells expressing Ikaros-ER fusion protein

value: Ikaros

tag: chip antibody reference


title: ILC87-Ik1-ER_EtOH_1d_input

value: ILC87 cell line derived from a thymic T cell tumor

value: Ikf/f Lck-Cre+


title: Het (Q140) 2 month Male  Cerebellum mRNA rep3


title: WT_DN3_Ikaros

value: wild-type

value: 4-5 weeks

value: thymus

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes


title: Het (Q175) 2 month Male  Cerebellum mRNA rep3

value: Het (Q175) Knock-In


title: ILC87-Ik1-ER_4OHT_1d_Ikaros

value: 1d 4-hydroxytamoxifen-treated ILC87 cells expressing Ikaros-ER fusion protein


title: Het (Q140) 2 month Male  Cerebellum mRNA rep1

value: Male


title: WT_DN4_Ikaros

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25-, CD44- thymocytes


title: Het (Q140) 10 month Male  Cerebellum mRNA rep3

source_name: Het (Q140) 10 month_male_cerebellum

value: Het (Q140) Knock-In

value: 10 months


title: WT_LSK_H3K27me3_exp1

value: bone marrow

value: FACS-sorted B220-, CD11b-, Gr1-, Ter119-, Sca1+, c-Kit+ bone marrow

value: Millipore


title: WT_DP_Ikaros

value: FACS-sorted CD4+, CD8+, CD3low thymocytes


title: Het (Q140) 2 month Female  Cerebellum mRNA rep2

source_name: Het (Q140) 2 month_female_cerebellum

value: 2 months

value: Female

value: Brain - Cerebellum

value: housed with Het (Q140) mice


title: Het (Q140) 2 month Female  Cerebellum mRNA rep3


title: IkL/L_LSK_H3K27me3_exp2

value: IkL/L mutant

value: 3-4 weeks


title: Het (Q140) 2 month Female  Cerebellum mRNA rep1


title: IkL/L_LSK_H3K27me3_exp1


title: Het (Q140) 6 month Female  Cerebellum mRNA rep3

value: 6 months


title: IkL/L_DN4_H3K27me3

value: thymus


title: Het (Q140) 10 month Male  Cerebellum mRNA rep4


title: Het (Q140) 10 month Male  Cerebellum mRNA rep1


title: IkL/L_DN2_H3K27me3

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44+ thymocytes


title: Het (Q140) 10 month Female  Cerebellum mRNA rep1

source_name: Het (Q140) 10 month_female_cerebellum


title: Het (Q140) 10 month Male  Cerebellum mRNA rep2

value: Male


title: Het (Q140) 10 month Female  Cerebellum mRNA rep3


title: IkL/L_DN3_H3K27me3

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes


title: IkL/L_DN1_H3K27me3

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25-, CD44+ thymocytes


title: Het (Q111) 6 month Male  Cerebellum mRNA rep3

source_name: Het (Q111) 6 month_male_cerebellum

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: Het (Q140) 2 month Male  Cerebellum mRNA rep2

value: Het (Q140) Knock-In


title: Het (Q111) 6 month Male  Cerebellum mRNA rep2


title: Het (Q111) 6 month Male  Cerebellum mRNA rep4


title: Het (Q111) 6 month Male  Cerebellum mRNA rep1


title: IkL/L_DP_H3K27me3

value: Millipore


title: Het (Q111) 6 month Female  Cerebellum mRNA rep4

source_name: Het (Q111) 6 month_female_cerebellum


title: WT_DP_input_exp1

description: processed data file: WT_DP_input_exp1+2.wig.gz

value: wild-type

value: 4-5 weeks

value: FACS-sorted CD4+, CD8+, CD3low thymocytes


title: Het (Q111) 6 month Female  Cerebellum mRNA rep1

value: Female

value: Brain - Cerebellum


title: WT_DP_H3K27me3_exp1

description: processed data file: WT_DP_H3K27m3_exp1+2.bedGraph.gz


title: Het (Q111) 6 month Female  Cerebellum mRNA rep2


title: Het (Q111) 6 month Female  Cerebellum mRNA rep3


title: WT_DP_H3K27me3_exp2


title: Het (Q111) 2 month Male  Cerebellum mRNA rep4

source_name: Het (Q111) 2 month_male_cerebellum

value: 2 months


title: WT_LSK_H3K27me3_exp2

value: bone marrow

value: FACS-sorted B220-, CD11b-, Gr1-, Ter119-, Sca1+, c-Kit+ bone marrow


title: WT_DP_input_exp2

value: thymus


title: WT_DN4_input_exp1

description: processed data file: WT_DN4_input_exp1+2.wig.gz

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25-, CD44- thymocytes


title: Het (Q111) 2 month Male  Cerebellum mRNA rep3

value: Male


title: Het (Q111) 2 month Male  Cerebellum mRNA rep2


title: WT_DN4_H3K27me3_exp2

description: processed data file: WT_DN4_H3K27m3_exp1+2.wig.gz


title: WT_DN4_H3K27me3_exp1


title: WT_DN4_input_exp2


title: Het (Q111) 2 month Male  Cerebellum mRNA rep1


title: WT_DN2_H3K27me3

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44+ thymocytes


title: WT_DN3_H3K27me3_exp1

description: processed data file: WT_DN3_H3K27m3_exp1+2.wig.gz

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes


title: Het (Q111) 2 month Female  Cerebellum mRNA rep3

source_name: Het (Q111) 2 month_female_cerebellum

value: Het (Q111) Knock-In


title: WT_DN3_H3K27me3_exp2


title: Het (Q111) 2 month Female  Cerebellum mRNA rep1

value: housed with Het (Q111) mice


title: Het (Q111) 10 month Male  Cerebellum mRNA rep2

source_name: Het (Q111) 10 month_male_cerebellum

value: 10 months


title: WT_DN3_input_exp1

description: processed data file: WT_DN3_input_exp1+2.wig.gz


title: Het (Q111) 10 month Male  Cerebellum mRNA rep1


title: WT_DN1_H3K27me3

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25-, CD44+ thymocytes

value: Millipore


title: WT_DN3_input_exp2

value: wild-type

value: 4-5 weeks


title: WT_DPe_Ikaros

value: thymocytes enriched for CD4+CD8+ double positive cells by positive selection using anti-CD8-bio and MACS beads

value: Ikaros


title: IkL/L_DPe_input_exp1

value: IkL/L mutant

value: 3-4 weeks


title: IkL/L_DPe_H3K27me3_exp2


title: IkL/L_DPe_H3K4me3

value: Abcam


title: IkL/L_DPe_input_exp2

value: thymus


title: Het (Q111) 10 month Female  Cerebellum mRNA rep4

source_name: Het (Q111) 10 month_female_cerebellum

value: Female

value: Brain - Cerebellum


title: Het (Q111) 10 month Female  Cerebellum mRNA rep3


title: WT_DPe_input_exp2


title: Het (Q111) 2 month Female  Cerebellum mRNA rep4

value: 2 months


title: IkL/L_DPe_H3K27me3_exp1


title: Het (Q111) 10 month Female  Cerebellum mRNA rep2


title: Het (Q140) 2 month Female  Cerebellum mRNA rep4

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: WT_DN3_Mi2beta

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes

value: anti-CHD4 (70469, Abcam)


title: WT_DPe_input_exp1


title: WT_DPe_H3K27me3_exp1


title: WT_DN3_input_exp3


title: Het (Q111) 2 month Female  Cerebellum mRNA rep2

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: WT_DPe_H3K4me3

value: wild-type


title: WT_DPe_H3K27me3_exp2

value: 4-5 weeks

value: Millipore


title: Het (Q111) 10 month Male  Cerebellum mRNA rep3

value: 10 months

value: Male


title: ILC87-Ik1-ER_EtOH_1d_input_exp2

source_name: ILC87 cell line derived from a thymic T cell tumor

value: Ikf/f Lck-Cre+

value: 1d EtOH-treated ILC87 cells expressing Ikaros-ER fusion protein


title: WT_DN3_Mta2

value: anti-Mta2 (ab8106, Abcam)


title: hrde1 +sensor

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using the fastX toolkit fastx_collapser module
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed to give only unique sequence, along with read count for each, the using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: Fasta header: id_number of reads

organism: Caenorhabditis elegans

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions and followed by an overnight precipitation at -20C using isopropanol and glycogen as a carrier.
Before library preparation, 1-5ug of total RNA was treated with 1ul of RNA polyphosphatase (Epicentre) for 30 minutes at 37C.  RNA was then extracted using Phenol/chloroform and precipitated overnight at -20C using Ethanol and Sodium Acetate.  Following this we followed the Illumina Truseq small RNA protocol according to the manufacturer's instructions

tag: developmental stage

value: adult

tag: transgenes

value: GFP piRNA sensor

value: whole animal


title: ILC87-Ik1-ER_EtOH_3d_Suz12

value: 3d EtOH-treated ILC87 cells expressing Ikaros-ER fusion protein

value: anti-Suz12 (3737, Cell Signaling)


title: Het (Q140) 10 month Female  Cerebellum mRNA rep2

tag: strain background

tag: genotype/variation

value: Het (Q140) Knock-In

value: Female

value: Brain - Cerebellum

value: housed with Het (Q140) mice


title: ILC87-Ik1-ER_4OHT_3d_Suz12

tag: age

value: 3d 4-hydroxytamoxifen-treated ILC87 cells expressing Ikaros-ER fusion protein


title: ZT22-B tech rep2

city: Oxford

first: William

last: Pembroke

address: South Parks Road

institute: Functional Genomics Unit, Oxford University

data_processing:
To retain only high quality reads an in-house script was used to i) trim ends of reads with a Phred base quality score below 3, ii) remove specified over-represented adapter or contaminating sequences, iii) remove reads with a length below 50bp , and iv) remove any reads with an average Phred quality score below 30. Reads were multimapped against the Genomic Mapping and Alignment Program for mRNA and EST sequences (GMAP; version 2012-07-20 ; (Wu and Watanabe, 2005)) processed mm10/GRCm38.70 reference genome using Genomic Short Nucleotide Alignment Program (GSNAP; (Wu and Nacu, 2010)) with the option to consider novel splice sites.
Count tables were generated using HTseq (version 0.5.4p1 ) and normalised using DESeq2 .
Genome_build: mm10
Supplementary_files_format_and_content: Count tables contain number of reads mapped to that gene for each biological replicate.

molecule: polyA RNA

source_name: Suprachiasmatic nucleus

growth_protocol: Male C3H/HeH mice at 10-12 weeks of age were group housed in light-tight chambers equipped with LED lighting at 150 lux at the cage floor. After 7 days of acclimatisation, mice were singly housed for 7 days prior to tissue harvesting.

extract_protocol:
Brains were removed at one of six zeitgeiber times (ZT) and immediately frozen on dry ice in OCT mounting media (VWR, Lutterworth, UK). Eighteen frozen coronal sections at 15mM were cut spanning the entire rostral to caudal region of the SCN and mounted onto polyethylene napthalate (PEN) slides (Carl Zeiss Ltd. Cambridge, UK). Laser-capture microdissection was carried out from dehydrated, Nissl-stained sections using the PALM system (Carl Zeiss Ltd. Cambridge, UK) as previously described (Dulneva et al., 2015).
Tissue from five animals was pooled to generate one biological replicate sample and total RNA was purified using the RNeasy micro kit (Qiagen, Manchester, UK). RNA quality was determined using an RNA Picochip (Agilent, Stockport, UK), with RIN values over 8 for all samples and average yield of approximately 10ng per replicate.  Approximately 1ng of RNA was amplified using the SMARTer protocol (Takata Clontech Bio Europe SAS, France) and the resulting libraries were 100bp paired-end sequenced on the HiSeq (Illumina, Fulbourne, UK; Wellcome Trust Centre for Human Genetics Sequencing Core).

value: 10-12 weeks

tag: zeitgeber time

tag: tissue

value: Suprachiasmatic nucleus


title: ZT22-A tech rep3


title: ZT22-A tech rep2


title: ZT22-C tech rep1


title: ZT22-B tech rep3


title: ZT22-C tech rep3


title: Het (Q111) 10 month Female  Cerebellum mRNA rep1

value: Het (Q111) Knock-In

value: 10 months

tag: Sex

tag: housing condition

value: housed with Het (Q111) mice


title: ZT22-B tech rep1


title: ZT18-C tech rep2


title: ZT18-C tech rep3


title: ZT18-B tech rep3


title: ZT22-A tech rep1


title: ZT18-C tech rep1


title: ZT18-B tech rep1


title: ZT18-B tech rep2


title: ZT18-A tech rep1


title: ZT18-A tech rep3


title: ZT22-C tech rep2


title: ZT18-A tech rep2


title: ZT14-C tech rep3


title: ZT14-C tech rep1


title: ZT14-C tech rep2


title: ZT14-B tech rep1


title: ZT14-B tech rep2


title: ZT14-A tech rep1


title: ZT10-C tech rep3


title: ZT14-A tech rep3


title: ZT10-C tech rep2


title: ZT10-C tech rep1


title: ZT10-B tech rep1


title: ZT10-B tech rep2


title: ZT10-A tech rep3


title: ZT10-B tech rep3


title: ZT10-A tech rep2


title: ZT10-A tech rep1


title: ZT6-C tech rep3


title: ZT6-C tech rep2


title: ZT14-B tech rep3


title: ZT6-C tech rep1


title: ZT6-B tech rep2


title: ZT6-B tech rep1


title: ZT6-A tech rep2


title: ZT2-C tech rep3


title: ZT14-A tech rep2


title: ZT2-B tech rep1


title: ZT2-B tech rep3


title: ZT2-A tech rep3


title: ZT2-A tech rep1


title: ZT2-C tech rep2


title: ZT2-C tech rep1


title: ZT2-B tech rep2


title: IkL/L_DN3_Suz12

value: IkL/L mutant

value: 3-4 weeks

value: thymus

tag: cell type

value: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes

value: Cell Signaling


title: WT_DN3_Suz12

value: wild-type

value: 4-5 weeks


title: ZT2-A tech rep2


title: ZT6-B tech rep3


title: ZT6-A tech rep3


title: WT sperm nucleosome

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing:
Low-complexity reads were filtered out on the basis of dinucleotide entropy.
Reads are aligned by using Bowtie.
Wig files were generated in the same way as described in Stadler et al., Nature 2011 (PubMed ID: 22170606).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Wig files show the average coverage per base in 100 bp windows in the genome.

source_name: Sperm, WT

extract_protocol:
Mouse spermatozoa were collected by swim-up procedure. Mono-nucleosomal chromatin samples were prepared by MNase treatment. ChIP experiments with an antibody against H3K4me2 were performed on native chromatin.
ChIP-seq and MNase-seq libraries were produced using the Illumina ChIP-seq DNA Sample Prep Kit (Cat# IP-102-1001).

tag: strain/background

value: wildtype

value: sperm


title: WT sperm H3K4me2, replicate 2

source_name: Sperm, WT, H3K4me2 ChIP

value: anti-H3K4me2 (Millipore 07-030)


title: Hira-KO3_RNA-Seq [Zp3-Cre]

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

description:
KO3
Whole cell

data_processing:
mRNA-seq reads were aligned to the mouse genome (mm9, NCBI build 37) with Bowtie v0.12.8/TopHat v2.0.2 (http://tophat.cbcb.umd.edu), which allows mapping across splice sites by reads segmentation.
Annotations from Ensembl Gene version 67 were used as gene models with TopHat.
Spike-in reads were aligned to ERCC spike-in sequences using bowtie2 with the following settings:  -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.
For differential expression analysis, read counts per annotated gene were computed using HTSeq and expression level of each gene was quantified with FPKM using R script. Differential expression analysis was performed using edgeR (version 3.1.10).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: HiraKO_FPKM.txt: Tab-delimited text file includes FPKM counts for each sample.

source_name: MII oocyte, Hira-KO

extract_protocol:
cDNA synthesis and amplification were performed directly on single Hiraf/f and Hiraf/f Zp3-Cre MII oocytes with the SMARTer Ultra Low Input RNA kit (Clontech). 0.5 uL of ERCC RNA spike-in mix 1 (Life Technologies), diluted 1:105, was added to each reaction prior to cDNA synthesis.
The amplified cDNA was fragmented by Covaris S2 sonicator (Covaris) and converted to sequencing libraries following the NEBNext DNA Library Prep (NEB) using the NEBNext Multiplex Oligos for Illumina (NEB). Bar-coded libraries were pooled and sequenced on two lanes of the Illumina HiSeq 2500 instrument.

value: Hiraf/f, Zp3-Cre

value: oocyte

value: MII


title: Hira-KO4_RNA-Seq [Zp3-Cre]

description:
KO4
Whole cell


title: nonTG sperm H3K4me2

source_name: Sperm, non-transgenic, H3K4me2 ChIP

value: non-transgenic offspring of C57BL/6; EF-1alpha (promoter)-KDM1A (transgene) sire (sire from 2nd generation of transgenic line 1)


title: TG sperm H3K4me2

source_name: Sperm, KDM1A transgenic, H3K4me2 ChIP

value: EF-1alpha (promoter)-KDM1A (transgene); 3rd generation after establishment of transgenic line 1


title: Hira-KO2_RNA-Seq [Zp3-Cre]

description:
KO2
Whole cell


title: Hira-WT4_RNA-Seq [Zp3-Cre]

description:
WT4
Whole cell

source_name: MII oocyte, Hira-WT

value: Hiraf/f


title: ZT6-A tech rep1

tag: strain

value: 10-12 weeks

value: Suprachiasmatic nucleus


title: Hira-WT2_RNA-Seq [Zp3-Cre]

description:
WT2
Whole cell


title: Hira-KO1_RNA-Seq [Zp3-Cre]

description:
KO1
Whole cell


title: Hira-WT1_RNA-Seq [Zp3-Cre]

description:
WT1
Whole cell


title: Hira-KO6_RNA-Seq [Gdf9-Cre+]

data_processing:
mRNA-seq reads were aligned to the mouse genome (mm9, NCBI build 37) with Bowtie v0.12.8/Tophat v2.0.2 (http://tophat.cbcb.umd.edu), which allows mapping across splice sites by reads segmentation. Annotations from Ensembl Gene version 67 were used as gene model with Tophat. Spike-in reads were aligned to ERCC spike-in sequences using bowtie2 with the following settings:  -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. For differential expression analysis, read counts per annotated gene were computed using HTSeq and expression level of each gene was quantified with FPKM using R script. Differential expression analysis was performed using edgeR (version 3.1.10)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

extract_protocol: cDNA synthesis and amplification was performed directly on single Hiraf/f and Hiraf/f Gdf9-Cre+ MII oocytes with the SMARTer Ultra Low Input RNA kit (Clontech). 0.5 uL of ERCC RNA spike-in mix 1 (Life Technologies), diluted 1:105, was added to each reaction prior to cDNA synthesis. The amplified cDNA was fragmented by Covaris S2 sonicator (Covaris) and converted to sequencing libraries following the NEBNext DNA Library Prep (NEB) using the NEBNext Multiplex Oligos for Illumina (NEB). Bar-coded libraries were pooled and sequenced on two lanes of the Illumina HiSeq 2500 instrument.

value: Hiraf/f, Gdf9-Cre+


title: Hira-KO3_RNA-Seq [Gdf9-Cre+]


title: Hira-KO5_RNA-Seq [Gdf9-Cre+]


title: Hira-WT5_RNA-Seq [Gdf9-Cre+]


title: Hira-WT2_RNA-Seq [Gdf9-Cre+]


title: Hira-WT1_RNA-Seq [Gdf9-Cre+]


title: Hira-WT4_RNA-Seq [Gdf9-Cre+]


title: Hira-KO1_RNA-Seq [Gdf9-Cre+]


title: TG sperm nucleosome

source_name: Sperm, KDM1A transgenic


title: WT sperm H3K4me2, replicate 1


title: nonTG sperm nucleosome

source_name: Sperm, non-transgenic


title: input_ChIP-seq

city: Hershey

first: chunhua

last: song

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

data_processing:
ChIP-seq reads were aligned to the HG19 genome assembly with pipeline CASAVA 1.7 using ELANDv2 or CASAVA-1.8.2 using ELANDv2e.  For H3K4me3 and H3K27me3 ChIP-seq data, the bed files are made from a BAM file created from the CASAVA pipeline, which contains uniquely mapping reads as described above. The FASTQ under this pipeline is Phred33 or Phred64.
BED files (applied for SISSRS) were converted directly from the original ELAND export files; they were filtered to exclude tags that do not align uniquely to the hg19 genome, tags that do not pass filter, tags that contain Ns, and tags that contain more than 2 mismatches.
ALN files (used for CisGenome) were also converted directly from the ELAND export files using the program tool built-in CisGenome.
Cisgenome 2.0 was used for peak calling of Ikaros, HDAC1, H3K4me3 and H3K27me3. Parameters lpcut = 3 and c = 2 were selected for Ikaros, lpcut = 3 and w = 5 for HDAC1, and w = 5 for H3K4me3 and H3K27me3 datasets, respectively. Other parameters remain in default to run the program. Peaks with FDR ≤ 0.05 and Log2FC ≥ 1 were selected for further analysis.
SISSRS 1.4 was applied to find peaks of histone modification markers H3K9ac, H3K9me3 and H3K36me3 with parameter P-value ≤ 0.05 and other parameters remain in default. The output peaks with FC ≥ 2 were kept for further data analysis.
Genome_build: hg19
Supplementary_files_format_and_content: The final processed files are all in COD format. Each file contains peaks for a sample.

source_name: Nalm6 ALL leukemia cells

growth_protocol: 10% FBS RPMI1640 + A/P + b-ME in 5% CO2, 37°C, change media every 2-3 days, cell density in  2x10^5 to 1x10^6

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 200-400bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The resulted library was validated by using Agilent Technologies 2100 Bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II and HiSeq 2000 following the manufacturer's protocols.

value: pre-B ALL leukemia cells

tag: culture condition

value: 10% FBS RPMI1640 in 5% CO2, 37°C

tag: ChIP

value: none,input


title: H3K36me3_ChIP-seq

tag: antibody vendor/catalog

value: Abcam, ab9050


title: H3K9me3_ChIP-seq

value: Abcam, ab8898


title: H3K9ac_ChIP-seq

value: Abcam, ab4441


title: H3K27me3_ChIP-seq

value: Millipore, 07-449


title: 03-M2 Animal M2 uninfected

city: Umeå

first: Christer

last: Larsson

address: Bldng. 6K

country: Sweden

institute: Umeå universitet

data_processing:
Reads were aligned to the Oryctolagus cuniculus genome using the Bioscope 1.3 Whole Transcriptome Analysis Pipeline using default settings (Applied Biosystems, Carlsbad, CA). The number of reads mapped to each transcript was calculated using HTSeq-count v0.5.3. The overlap resolution mode was set to “intersection-nonempty” and feature type was set to “exon”. (http://www.huber.embl.de/users/anders/HTSeq/doc/install.html#download)
Differential expression between the sample groups was determined using DESeq v1.4.1 (http://genomebiology.com/2010/11/10/R106), using a test based on the negative binomial distribution, modeling both biological and technical variation. p-values are adjusted for multiple comparisons using the Benjamini-Hochberg method. Transcripts with adjusted p-values less than 0.05 were considered significant.
Genome_build: Orycun2.0
Genome_build: GCA_000003625.1
Supplementary_files_format_and_content: Abundance measurements matrix table of counts and fpkm for each sample. Barcoded quadruplicates merged.

organism: Oryctolagus cuniculus

source_name: Lung, uninfected animal

extract_protocol:
Rabbits were euthanized following anesthesia by a lethal i.v. injection of 3ml Euthasol (Virbac, Fort Worth, TX). In order to maintain the in vivo transcription profile, tissues for RNAseq analysis were transferred to RNAlater (Ambion, Life technologies, Grand Island, NY, USA) within 10 minutes of euthanasia.  After 24h in RNAlater, tissue samples were frozen at -80°C. RNA was then extracted by bead beating with 3mm beads in Trizol according to the manufacturer’s instructions and spin purified on columns (Qiagen, Valencia, CA, USA). Finally, the RNA was treated with AMBION TURBO DNA-free DNase (Life Technologies, Grand Island, NY). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and mRNA was enriched using the RIBOMinus kit according to the manufacturer's instructions (Life Technologies, Grand Island, NY). Successful removal of rRNA was verified by a second Bioanalyzer assay.
mRNA libraries were prepared for sequencing and barcoded using standard ABI SOLiD protocols

value: New Zealand White

tag: barcoded replicate

value: lung tissue from uninfected rabbit.


title: 01-M2 Animal M2 uninfected


title: 04-M2 Animal M2 uninfected


title: 03-I1 Animal I1 uninfected


title: 04-I1 Animal I1 uninfected


title: 04-N1 Animal N1 uninfected


title: 02-M2 Animal M2 uninfected


title: Ikaros_ChIP-seq

value: Affinity-purified anti-Ikaros antibody

value: Ikaros


title: 01-I1 Animal I1 uninfected


title: 03-N1 Animal N1 uninfected


title: 02-N1 Animal N1 uninfected


title: hpo-gfp_WT

city: Eugene

first: Eric

last: Selker

state: OR

address: 1585 E 13th Ave

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
The raw data (fastq) files were mapped to the Ncrassa12 genome using Bowtie2, generating .sam files
Samtools was next used to convert sam files to bam files, remove duplicates, sort the bam files, and create index files for the bam files to view later.
The bam files, along with their indices, were then converted into tdf files using IGVtools.  The Ncrassa12 genome was used as a reference genome and window size was set to 200 bp.
Genome_build: Ncrassa version 12
Supplementary_files_format_and_content: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp.  The tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV.

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC

extract_protocol:
Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP or 30 min in 1% formaldehyde for GFP ChIP.  Tissue was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power.  DNA was purified using the QIAquick PCR purification kit  and eluted in 25 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 18 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking

value: mycelia

tag: chip antibody

value: anti-GFP (Abcam, 6556)

tag: genotype

value: hpo tagged with gfp at C terminus


title: hpo-gfp_R8A

value: hpo tagged with gfp at C terminus in background histone H3 substitution R8A


title: 04_AN Animal A Normal

source_name: Lungtissue wo. pathology

value: tissue from left lung with no pathology


title: 03_AN Animal A Normal


title: hpo-gfp_dim-5

value: hpo tagged with gfp at C terminus in background deletion of dim-5


title: 01-N1 Animal N1 uninfected


title: H3K9me3_S10A

value: anti-H3K9me3 (Active Motif, 39161)

value: histone H3 substitution S10A


title: hpo-gfp_S10A

value: hpo tagged with gfp at C terminus in background histone H3 substitution S10A


title: 02_AN Animal A Normal


title: H3K9me3_set-7

value: deletion of set-7


title: H3k9me3_hpo

value: deletion of hpo


title: H3K9me3_R8A

value: histone H3 substitution R8A


title: H3K9me3_eed

value: deletion of eed


title: 02-I1 Animal I1 uninfected

value: New Zealand White


title: H3K9me3_dim-8

value: deletion of dim-8


title: 03_CN Animal C Normal


title: 04_CN Animal C Normal


title: 02_CN Animal C Normal


title: H3K27me2_H3K27me3_S10A

value: anti-H3K27me2/3 (Active Motif, 39535)


title: H3K27me2_H3K27me3_wt

value: wild-type


title: 04_FN Animal F Normal


title: 03_FN Animal F Normal


title: H3K9me3_wt

value: mycelia


title: H3K27me2_H3K27me3_hpo


title: H3K27me2_H3K27me3_R8A


title: 01_CN Animal C Normal


title: 02_FN Animal F Normal


title: H3K27me2_H3K27me3_dim-9

value: deletion of dim-9


title: 04_AC Animal A Cavity

source_name: Lungtissue adj to cavity

value: lung tissue adjacent to cavity


title: 01_AN Animal A Normal


title: 02_AC Animal A Cavity


title: 01_AC Animal A Cavity


title: H3K27me2_H3K27me3_dim-5

value: deletion of dim-5


title: H3K27me2_H3K27me3_dim-8_biological_replicate


title: H3K27me2_H3K27me3_dim-7

value: deletion of dim-7


title: H3K27me2_H3K27me3_dim-5_biological_replicate


title: 01_FN Animal F Normal

value: tissue from left lung with no pathology


title: 04_CC Animal C Cavity


title: 02_CC Animal C Cavity


title: 03_CC Animal C Cavity


title: H3K27me2_H3K27me3_dim-2_N1851

value: deletion of dim-2


title: H3K27me2_H3K27me3_dim-2_N1850


title: H3K27me2_H3K27me3_cul4

value: deletion of cul4


title: 01_CC Animal C Cavity


title: 04_FC Animal F Cavity


title: 02_FC Animal F Cavity


title: 01_FC Animal F Cavity


title: HepG2-p53-miRNA-seq rep 1

city: Chengdu

first: Ding

last: ruofan

address: southwest jiaotong university JiuLi campus

country: China

institute: southwest jiaotong university

data_processing:
reads were cleaned with cutadapter and sickle
known and novel miRNA were detected by mirdeep2
detected miRNA were normalized with TPM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Reads and counts for each Sample

source_name: Hepatocellular carcinoma cells

growth_protocol: HepG2 were  cultured with DMEM with 10% FBS,100 IU/ml penicillin and 100 µg/ml streptomycin solution.Cell cultures were maintained at 37°C and at 5% CO2.

extract_protocol:
Total RNA was extracted from the cultured cells using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions.Length of 18–30 nt small RNAs were isolated from total RNA using 15% denaturing polyacrylamide gel electrophoresis.
Small RNAs were ligated to a 5'adaptor and a 3'adaptor by T4-RNA ligase and reverse-transcribed to cDNA. Samples were treated with Dox for 0h and 24h twice, four libraries were obtained marked as HepG2 0h-1, HepG2 24h-1, HepG2 0h-2, HepG2 24h-2. Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System were applied to test the quality, purity and concentrations of the samples. Finally, cDNA libraries were sequenced using Illumina HiSeq 2000 platform (Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

treatment_protocol: HepG2 cells were treated with doxorubicin (1µg/ml) for 24 hours to induce the expression of p53.

value: Hepatocellular carcinoma cells

tag: treatment

value: 1µg/ml doxorubicin for 24 hours


title: HepG2-p53-miRNA-seq rep 2


title: H3K27me2_H3K27me3_dim-8


title: H3K4me3_ChIP-seq

value: pre-B ALL leukemia cells

value: 10% FBS RPMI1640 in 5% CO2, 37°C

value: Abcam, ab8580


title: HDAC1_ChIP-seq

value: Abcam, ab7028


title: 03_AC Animal A Cavity

value: New Zealand White


title: HepG2-nop53-miRNA-seq rep 2

value: untreated


title: THP1_JMJD1C _ChIP seq

status: Public on Nov 02 2015

city: New York

first: Mo

last: Chen

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie 2 version 2.1.0  with default parameters
To limit PCR amplification bias, in-house scripts were applied to remove redundant reads at the same genomic location.
Peak calling was done with FindPeaks module in Homer package (Heinz et al., 2010) using IP and input samples. Peak regions were selected with a false discovery rate cutoff of 0.1%.
To generate the visualization files for the IGV genome browser (Robinson et al., 2011), mapped reads were converted to density plots (tdf files) by using IGV tools count command.
Genome_build: hg19
Supplementary_files_format_and_content: density plots (tdf files) by IGV tools count command

source_name: THP-1 cells

growth_protocol: All cells were cultured in RMPI-1640 medium (Life Technologies) with 10% fetal bovine serum (Life Technologies)

extract_protocol:
Lysates were clarified from crosslinked and sonicated cells and JMJD1C-DNA or LYL1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: cell line

value: monocyte

tag: disease

value: acute myeloblastic leukemia

value: anti-JMJD1C serum


title: NB4_LYL1_ChIP seq

source_name: NB4 cells

value: Acute Promyelocytic Leukemia


title: HepG2-nop53-miRNA-seq rep 1


title: THP1_LYL1_ChIP seq


title: NB4_input DNA


title: HL60_LYL1_ChIP seq

source_name: HL60 cells

value: myeloblast


title: Kasumi_LYL1_ChIP seq

source_name: Kasumi-1 Cells


title: UNC0255_RNA-seq

city: Cambridge

first: John

last: Krill-Burger

address: 415 Main Street

department: Cancer Program

institute: Broad Institute

description: Biological replicate 2

data_processing:
RNA-seq reads were mapped against human genome build hg19, downloaded from the UCSC genome browser, using TopHat version 2.0.13. Coding transcripts from GENCODE Release 12 (http://www.gencodegenes.org/) were provided in GTF format using the following options: “tophat -p 8 -G gencode.v12.annotation.gtf --no-novel-juncs Homo_sapiens_assembly19.”
Unambiguously mapped reads were counted at a gene-level using the HTSeq package version 0.6.1p1 in union mode with the following options: “htseq-count -s no -a 10 <alignment_file> gencode.v12.annotation.gtf.”
Filtering was applied to remove genes in which greater than half the samples had less than one count per million using the cpm() function in edgeR.
Counts were normalized using TMM normalization in edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: TMM normalized counts with samples as columns and gene-level features as rows.

source_name: Erythroblasts

growth_protocol: Primary human CD34+ hematopoietic stem and progenitor cells were differentiated in vitro towards the erythroid lineage using a 3-phase culture method, as described by Giarranata MC et al., Blood 2011

extract_protocol:
Total RNA was extracted using the PrepEase RNA Spin Kit (USB Corporation) according to the manufacturer’s protocol.
The cDNA library was prepared from 50-100 ng of total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: RNA-Seq analysis was performed in primary adult human erythroid cells at day 11 of erythroid differentiation and after 7 days of treatment with 0.25 μM UNC0638 or the vehicle control

value: Erythroblasts


title: HL60_input DNA


title: UNC0256_RNA-seq

description: Biological replicate 3


title: HL60_JMJD1C _ChIP seq


title: NB4_JMJD1C _ChIP seq


title: DMSO5_RNA-seq

description: Biological replicate 2

value: vehicle control


title: UNC0251_RNA-seq

description: Biological replicate 1


title: DMSO6_RNA-seq

description: Biological replicate 3


title: 03_FC Animal F Cavity

value: lung tissue adjacent to cavity


title: DMSO1_RNA-seq

description: Biological replicate 1


title: mRNA fibroblasts infected for 24hr

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to 200bp sequences that spanned splice junctions
Wig files were then generated by summing the numbers of reads obtained from each position in the human genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: hg19+NC_006273.2
Supplementary_files_format_and_content: Wiggle files, contains aligned reads following the described pre-processing steps

source_name: mRNA fibroblasts infected for 24hr

extract_protocol:
Cells were lysed with 0.5% Triton, and the lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. RNA was then isolated from cells using the acid:phenol extraction method.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

value: Primary fibroblasts


title: mRNA fibroblasts infected for 5hr

source_name: mRNA fibroblasts infected for 5hr


title: mRNA fibroblasts infected for 72hr

source_name: mRNA fibroblasts infected for 72hr


title: footprints fibroblasts infected for 24hr


title: mRNA uninfected fibroblasts

source_name: mRNA uninfected fibroblasts


title: footprints fibroblasts infected for 5hr

source_name: footprints fibroblasts infected for 5hr


title: mRNA fibroblasts infected with irradiated virus


title: footprints fibroblasts infected with irradiated virus


title: footprints uninfected fibroblasts treated with type 1 interferon


title: footprints uninfected fibroblasts

source_name: footprints uninfected fibroblasts


title: footprints fibroblasts infected for 12hr


title: KO10

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.70
Supplementary_files_format_and_content: Raw counts measurements

source_name: Decapsulated testis

extract_protocol:
Testes were decapsulated and flash frozen in liquid nitrogen.  Total RNA was extracted using Qiagen RNEasy Midi Kit columns and reagents; Cat 75142
Libraries were prepared according to Illumina's instructions using the Truseq RNA-seq protocol.

value: C57BL/6|129/Sv|FVB/N Mixed BKG

value: Testis

tag: age

value: post  natal day 21


title: JMJD1C shRNA95 treated cells rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b with parameters --library-type fr-unstranded   --no-novel-juncs
FPKM and significant regulated genes were checked by cuffdiff v2.1.1 with parameters  --multi-read-correct  --min-reps-for-js-test  2  --emit-count-tables
To generate the visualization files for the IGV genome browser (Robinson et al., 2011), mapped reads were converted to density plots (tdf files) by using IGV tools count command.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample and statistic for signficance by p-value and q-value; comparing control and shRNA treated RNA abundance_two replicates

source_name: Kasumi-1_JMJD1C shRNA95 treated cells

growth_protocol: Kasumi-1 cells were cultured in RMPI-1640 medium (Life Technologies) with 10% fetal bovine serum (Life Technologies)

extract_protocol:
RNA was extracted with RNeasy plus kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Kasumi-1 cells were infected with either control shRNA or JMJD1C shRNA viruses for 4 days and cells were collected for RNA extraction.  PLKO-shRNA expressing viruses were generated by transfecting 293T cells with viral packaging vectors.

tag: treated with

value: JMJD1C shRNA95


title: KO9

tag: tissue


title: JMJD1C shRNA63 treated cells rep2

source_name: Kasumi-1_JMJD1C shRNA63 treated cells

value: JMJD1C shRNA63


title: Kasumi_input DNA

extract_protocol:
Lysates were clarified from crosslinked and sonicated cells and JMJD1C-DNA complexes were isolated with antibody. The antibody was home-made and hasn't been published yet. The antigen used for this antibody generation is the N-terminus of JMJD1C protein.
Libraries were prepared according to Illumina's instructions


title: Control shRNA treated cells rep2

source_name: Kasumi-1_Control shRNA treated

value: Control shRNA


title: KO11


title: JMJD1C shRNA95 treated cells rep2


title: JMJD1C shRNA63 treated cells rep1


title: Kasumi_JMJD1C _ChIP seq


title: mRNA fibroblasts infected for 12hr

source_name: mRNA fibroblasts infected for 12hr


title: KO8


title: Control shRNA treated cells rep1


title: KO6


title: WT5

value: wild type


title: KO7


title: WT4


title: mRNA uninfected fibroblasts treated with type 1 interferon


title: footprints fibroblasts infected for 72hr


title: WT2


title: WT3


title: 209KO

value: post  natal day 29-30


title: WT1


title: 183KO


title: 182KO


title: 207WT


title: 141KO


title: 197WT


title: 194WT


title: 174WT


title: 173WT


title: input_WT_exp1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using bowtie 0.12.7 with -m 1
Fragment length was estimated using phantompeakqualtools 2.0
Peaks were called using macs2 2.0.10.20130520 with -p 0.01 –to-large –nomodel and shiftsize set to half the estimated fragment length using inputs as control
Reproducible peaks were obtained by IDR procedure with -p 0.01
Genome_build: GRCm38.70

extract_protocol:
Chromatine was isolated, fragmented by sonication and immunoprecipitated with anti Rfx2 antibody
Libraries were prepared according to Illumina's instructions using the Truseq ChIP-seq protocol.

value: none, input


title: input_WT_exp2


title: RFX2_WT_exp1

value: RFX2 antibody from Santa Cruz Biotechnology – Catalog # sc-10657 – Lot # L0413


title: RFX2_WT_exp2


title: WEX [CC55]

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

data_processing:
Sequence read quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were aligned to the rat transcriptome (reference sequence NCBI version Rnor_5.0) using TopHat version 2.0.12 by providing the GTF file and parameters -r 200 -G
Differential gene expression was determined using Cufflinks version 2.2.1. Cuffdiff command was used with parameters -u (multi read correction algorithm) and -b (bias detection and correction algorithm).
Genome_build: Rattus norvegicus NCBI version Rnor_5.0
Supplementary_files_format_and_content: Differential gene expression

organism: Rattus norvegicus

source_name: WEX_femoral diaphysis

growth_protocol: 24 healthy weanling (21 day old) male rats were obtained from four Sprague-Dawley dams. The animals were housed in a temperature (19.9oC-21.8C) and light-dark cycle (12:12, lights on at 6 AM) controlled facility with adlibitum access to food and water.

extract_protocol:
Following cull, a sterile saw was used to separate the mid diaphysis from the rest of the femur. total RNA was extracted using TRIzol® and cleaned up using Rneasy Mini Kit. 1.5 ug of total RNA was sent for sequencing to BGI.
Illumina TruSeq Transcriptome library prep kit.

treatment_protocol: There were three exercise groups. Control (CON); Bipedal stance (BPS); Wheel exercise (WEX). The CON animals were in standard cages. The BPS animals were in special cages whose feed height could eb adjusted and the WEX animals had access to a running wheel. Each group sonsisted of 8 animals. The animals were allowed to exercise for 15 days.

value: Sprague-Dawley

value: 36 days

tag: Sex

value: male

tag: exercise group

value: wheel exercise (WEX) for 15 days

value: Femoral mid-diaphysis


title: WEX [CC44]


title: NeuroD1_R2_ChIPSeq

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: ChIP-seq in ES

data_processing: Quality control of the ChIP-sequencing output was undertaken using FASTQC. NeuroD1 ChIP-seq was generated in ES cells following 24 hours NeuroD1 induction in two biological replicates. Bowtie v0.12.9 (Langmead, 2010) with default parameters was used to align the reads to the mouse mm9 genome with annotations from UCSC (Karolchik et al, 2014). Each read was aligned to maximally one position in the genome. SAMTOOLS v0.1.19 was used to convert the SAM file into BAM format and to sort and index the BAM file. The peaks were called using MACS2 v2.0.10.20120913 (Zhang et al, 2008) using default parameters. Peaks reproducible across two biological replicates with margin of 100 base pairs were retained. WIG files were generated using the QuasR (Gaidatzis et al, 2014) package and visualized using the UCSC genome browser. The raw read counts that aligned to each genomic feature (promoters, peaks and enhancers) were calculated using QuasR. Enrichment at these sites were calculated.

source_name: Embryonic stem cells

growth_protocol: Murine ESCs were cultured at 37°C, 7% CO2 and 88% relative air humidity in 8 ml ES medium (DMEM supplemented with 10% fetal calf serum, 1X MEM NEAA, 2mM L-glutamine and LIF on feeders (inactivated MEFs). For further experiments, feeders were removed by splitting mESCs every 2 days on tissue-culture dishes coated with 0.2% gelatin with daily media change. Experiments were performed at feeder-free five state.

extract_protocol: Cells were cross-linked in medium containing 1% formaldehyde for 10 min at room temperature, neutralized with 0.125M glycine, scraped off and rinsed twice with cold 10 ml 1X PBS. Cells were pelleted by centrifugation for 7 min at 4°C at 600g. Pellets were resuspended in 10 mL of Buffer L1 (50mM Hepes KOH, pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP-40, 0.25% Triton-X 100) and incubated at 4°C for 10 min. This was followed by centrifugation for 5 min at 4°C at 1300g. The pellet was again resuspended in 10 ml of Buffer L2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0) and incubated at room temperature for 10 min, followed by centrifugation for 5 min at 4°C at 1300g. The pellet was then resuspended in 900 µl Buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate, 0.17mM N-Lauroyl sarcosine) containing protease inhibitors and incubated at 4°C for overnight following sonication using Bioruptor plus (Diagenode). After clearing cellular debris by spinning at 14,000 g for 10 min at 4°C DNA 60 µg of chromatin were incubated at 4 °C overnight with respective antibodies after 1h of preclearing. The mixture was then incubated with 40 µl protein A-Sepharose beads preblocked with tRNA and BSA for 3 h at 4°C. Beads were washed twice with 1 ml buffer L3 and once with 1 ml DOC buffer (10 mM Tris (pH 8.0), 0.25 M LiCl, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA), and bound chromatin was eluted in 1% SDS/0.1 M NaHCO3. This followed treatment with RNase A (0.2mg/ml) for 30 min at 37°C and then with Proteinase K (50 µg/ml) for 2.5 h at 55°C. The crosslinking was reversed at 65°C overnight with gentle shaking. DNA was purified by phenol-chloroform extraction followed by ethanol precipitation and recovered in 40 µl TE buffer.

treatment_protocol: Ectopic NeuroD1 expression was induced with Docyxyclin (500 ng/ml final. conc.) for 24 hours

tag: cell type

value: dox-inducible transgenic A2lox mouse embryonic stem cells

tag: genetic background


title: A2lox_Neurod1_minusdox_R1_RNASeq

description: For RNA-seq, PolyA library type was used.

data_processing: The RNA-sequencing output was in FASTQ format. NeuroD1 RNA-seq datasets derived from ES cells after NeuroD1 induction for 48 hours (+Dox) or under non-induced condition (-Dox) in two biological replicates each. After a quality check using FASTQC v2.6.14 (Andrews), the output was aligned to the mouse genome (mm9) with UCSC’s annotations using TopHat v2.0.8 (Trapnell et al, 2009). Only uniquely mapped reads were retained for further analysis. SAMTOOLS v0.1.19 (Li et al, 2009) was used to convert the BAM output to SAM format and to sort the BAM file. The read counts per gene were calculated using the HTSeq program, v0.5.4p1 (Anders et al, 2015). The DESeq package (Oshlack et al, 2010) was used to generate normalized read counts and for differential gene expression analysis. DESeq called differentially expressed genes with FDR cutoff of 0.05 and abs(FC) > 1.5 were considered as significant differentially expressed genes.

extract_protocol: Total RNA of cultured cells was prepared using TRIzol reagent (Invitrogen)

treatment_protocol: No induction was performed.

value: -Doxycycline


title: ES_Input_genomicDNA

description: ChIP-seq in ES (input)

data_processing: Quality control of the ChIP-sequencing output was undertaken using FASTQC. Bowtie v0.12.9 (Langmead, 2010) with default parameters was used to align the reads to the mouse mm9 genome with annotations from UCSC (Karolchik et al, 2014). Each read was aligned to maximally one position in the genome. SAMTOOLS v0.1.19 was used to convert the SAM file into BAM format and to sort and index the BAM file. WIG files were generated using the QuasR (Gaidatzis et al, 2014) package and visualized using the UCSC genome browser. The raw read counts that aligned to each genomic feature (promoters, peaks and enhancers) were calculated using QuasR.


title: A2lox_Neurod1_plusdox_R2_RNASeq

description: For RNA-seq, PolyA library type was used

treatment_protocol: Ectopic NeuroD1 expression was induced with Docyxyclin (500 ng/ml final. conc.) for 48 hours


title: A2lox_Neurod1_minusdox_R2_RNASeq


title: A2lox_Neurod1_plusdox_R1_RNASeq


title: BPS [BB55]

source_name: BPS_femoral diaphysis

tag: strain


title: BPS [BB33]

value: bipedal stance (BPS) for 15 days


title: WEX [CC11]


title: WEX [CC22]


title: WEX [CC33]


title: BPS [BB22]


title: BPS [BB11]


title: phototrophy 24h sample2

city: Shanghai

first: Jianhua

last: Fan

address: 130 Meilong Road

institute: East China University of Science & Technology

data_processing:
Default parameters were used to pass reads using Illumina quality-control pipeline. All the filtered reads were trimmed to 50 bp. The processed sequence files (total of 187, 503, 403 reads) were then mapped to the assembled genome by TopHat 1.3.3 with a tolerance of up to 2 mismatches and 3 indels.
The Cufflinks was used to assemble the read into transcripts and a set of transcripts was generated for each condition.
Genome_build: de novo assembly
Supplementary_files_format_and_content: FASTA
Supplementary_files_format_and_content: gff3

organism: Auxenochlorella pyrenoidosa

growth_protocol: Chlorella cells were cultivated heterotrophically to achieve high cell density, heterotrophic growth with glucose and urea as organic carbon source and nitrogen source.

extract_protocol: the total RNA was isolated using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions. The RNA samples were cleaned up using RNeasy columns (Qiagen, http://www.qiagen.com) following the manufacturer’s instruction.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: After glucose consumption was complete, the broth was then diluted to ~2 g/L dry biomass and transferred to light environment for photoautotrophy.

value: whole cells


title: phototrophy 8h sample2


title: phototrophy 8h sample3


title: phototrophy 24h sample1


title: CON [AA33]

source_name: control_femoral diaphysis

value: control (CON) for 15 days


title: phototrophy 8h sample1


title: phototrophy 24h sample3


title: CON [AA44]


title: NeuroD1_R1_ChIPSeq

description: ChIP-seq in ES


title: CON [AA22]


title: CON [AA11]


title: H3K4me3 ChIP in control

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

institute: University of Stirling

data_processing:
Sequencing reads were quality checked by FastQC (version 0.10.0) and NGS-QC generator (version 1.5.1).
Sequence reads were then aligned to the human genome (hg19) for MDA-MB-231L cells with Bowtie (version 1.0.0) using the following parameters: seed length (l) = 70 bp, maximum mismatch (n) = 2, suppression (m) = 20, and reported alignments (k) = 1.
MACS2 (version 2.1.0) was used to generate Bedgraph files that show fold change enrichment of ChIP over input. Bedgraph files were then converted into BigWig files by BedClip program and uploaded onto UCSC genome browser for visualization and plotting.
SICER-df was used to reveal significantly changed peaks between the untreated and SID treated MDA-MB-231 cells using the following parameters: window size = 50bp, gap size = 400bp, island calling = FDR<1x10-15 for H3K4me3
Genome_build: hg19
Supplementary_files_format_and_content: BED files include all the differential peaks calculated by SICER-df
Supplementary_files_format_and_content: BigWig files include the RPKM fold enrichment of each sample over input.

source_name: MDA-MB-231 cells

extract_protocol:
Chromatin from MDA-MB-231 cells was digested with micrococcal nuclease (MNase) and used for ChIP with indicated antibodies, essentially as described (Gaspar-Maia et al., 2013). Sequencing libraries were generated and barcoded for multiplexing as previously described (Gaspar-Maia et al., 2013) and resulting libraries were submitted for 100-bp, single-end Illumina sequencing on a HiSeq 2500 instrument.
Total of 10ng MNase-ChIPed mononucleosome DNA was gel extracted for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2500 illumina platform.

value: anti-H3K4me3 (Abcam ab1012)


title: H3K4me3 ChIP in SID 1uM treated cells


title: H3K4me3 ChIP in SID 2.5uM treated cells


title: Input control


title: BPS [BB44]


title: HUVEC_VEGF_1

city: Shenyang

first: Fang

last: Liu

state: Liaoning

address: Nanqi west road no.5

department: Department of Neurology

institute: center hospital affiliated to Shenyang medical college

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality sequences were filtered by NGSQC Toolkit, then mapped to hg19 by tophat2 with parameters -p 4 --no-mixed.
FPKM (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) were calculated using Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HUVEC (Human umbilical vein vascular endothelial cells) treated with VEGF, replicate 1

growth_protocol: HUVECs were obtained from Cell Bank at the Chinese Academy of Sciences and incubated in medium 1640 (Life technologies, Gaithersburg, MD, USA) plus fetal bovine serum (FBS; Gibco, UK; 10% (v/v)), penicillin (Gibco, UK; 100 U/ml), streptomycin (Gibco, UK; 100 µg/ml), and endothelial cell growth supplements (ECGS; R&D Systems, Minneapolis, MN, USA), at 37°C in 5% CO2 humidified incubator (Thermo Labsystems, Vantaa, Finland).

extract_protocol:
RNA were extracted by using Trizol agent (Invitrogen, Carlsbad, CA). RNA integrity was validated by using 2% agarose gel electrophoresis with Agilent 2100 Bioanalyzer, and RNA purity were verified based on absorbance (Abs) at 260 and 280 nm (Abs260/Abs280 > 1.8).
cDNA library was constructed according to the standard protocol of NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Invitrogen, Carlsbad, CA), and then, cDNAs were amplified by using polymerase chain reaction for 12 cycles. The amplified cDNA library was sequenced by utilizing Illumina HiSeq™ 2500 sequencer (Illumina, San Diego, CA, USA).

treatment_protocol: The 3th generation of HUVECs were inoculated on 60 mm plate (2×105 cells/plate) and incubated for 1 day. For the VEGF group (2 samples), vascular endothelial growth factor 165 (VEGF165; PeproTech, Rocky Hill, NJ, USA) dissolved in medium 1640 was then added (final concentration based on pre-experiment: 16 ng/mL). In contrast, for the control group (2 samples), only medium 1640 was added with the same volume.


title: HUVEC_Control_2

source_name: HUVEC (Human umbilical vein vascular endothelial cells), replicate 2


title: HUVEC_VEGF_2

source_name: HUVEC (Human umbilical vein vascular endothelial cells) treated with VEGF, replicate 2


title: HUVEC_Contrlol_1

source_name: HUVEC (Human umbilical vein vascular endothelial cells), replicate 1


title: HiSeq_H3_lo_CB_DMSO2

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description: ChIP-seq

data_processing:
Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.

source_name: Cord blood

extract_protocol:
Mint-ChIP: Cells were lysed and native chromatin was digested using Mnase. Subsequently, nucleosomes were indexed by adapter ligation and pooled for immunoprecipiation of H3K9ac (Active Motif, 39917), H3K9me2 (Abcam, ab1220) and total H3 (Abcam, ab1791).
Mint-ChIP: Immunoprecipitated DNA was amplified by in vitro transcription, followed by reverse transcription. Resulting fragments, tagged on both ends, were amplified by PCR using primers compatible with Illumina sequencing.

value: Cord blood

tag: immunprecipitation

value: Total H3

tag: mnase for chromatin digestion

value: Low

value: DMSO


title: HiSeq_H3_hi_BM_DMSO3

description: ChIP-seq

source_name: Bone marrow

value: Bone marrow

value: High


title: HiSeq_H3_hi_CB_DMSO1

description: ChIP-seq


title: HiSeq_H3_lo_BM_UNC3

description: ChIP-seq


title: HiSeq_H3_lo_BM_DMSO2

description: ChIP-seq


title: HiSeq_H3_lo_BM_UNC2

description: ChIP-seq


title: HiSeq_H3_lo_BM_UNC1

description: ChIP-seq


title: HiSeq_H3_hi_CB_DMSO3

description: ChIP-seq


title: HiSeq_H3_lo_BM_DMSO1

description: ChIP-seq


title: HiSeq_H3_hi_BM_UNC1

description: ChIP-seq


title: HiSeq_H3_hi_CB_DMSO2

description: ChIP-seq