title: HET (Q20) 2 month Male cortex mRNA rep3

description:
299982_Q20B0017_06_L6.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Male cortex mRNA rep2

status: Public on Feb 15 2016

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

description:
299974_Q20B0017_04_L4.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

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:
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: Text file containing abundance measurements in FPKM
Supplementary_files_format_and_content: Text file containing abundance measurements in counts

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 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.

tag: strain

tag: tissue

value: cortex

tag: genotype

value: Het (Q20) Knock-In

tag: age

value: 2 month

tag: Sex

value: Male

tag: housing condition

value: housed with Het (Q20) mice


title: HET (Q20) 2 month Male cortex mRNA rep1

description:
300018_Q20B0017_02_L5.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Female cortex mRNA rep3

description:
299985_Q20B0021_08_L7.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: X4p53_Chr16_sgRNA_2_APH_ExpD

city: San Francisco

first: Bjoern

last: Schwer

state: CA

institute: University of California, San Francisco

description:
HTGTS
X4p53_Chr16_sgRNA_2_APH_comb.tlx

library_source: genomic

data_processing:
HTGTS Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
HTGTS reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30 nt and bait sequences shorter than 50 nt.  Junctions in regions with repetitive sequence and telomeric sequences were filtered out.
GRO-Seq data sets were aligned using Bowtie software to mouse genome build mm9/NCBI37. We used Homer software to de novo identify transcripts from both strands of the genome in the context of the GRO-Seq data.
Genome_build: mm9
Supplementary_files_format_and_content: HTGTS: tab delimited text files (translocation junctions) contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (note).
Supplementary_files_format_and_content: GRO-seq: bigWig

molecule: genomic DNA

source_name: Neural stem/progenitor cells

growth_protocol: NSPCs were isolated and cultured as described in Wei et al.

extract_protocol:
HTGTS: DNA was extracted overnight at 55 degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH 8.0, 0.2 mg/mL proteinase K, prior to DNA fragmentation
GRO-seq: BrU-labeled nascent transcripts were extracted with TriPure reagent and affinity-purified with anti-BrU antibody-conjugated agarose beads.  Affinity-purified nascent RNA transcripts were fragmented with NaOH, RNA was decapped with Tobacco Acid Pyrophosphatase and end-repaired with T4 polynucleotide kinase.
HTGTS: LAM-PCR-mediated HTGTS (Frock et al., 2015; see manuscript for details)
GRO-seq: Illumina adapters were ligated to RNA with T4 RNA ligase and cDNA was generated with reverse transcriptase.  Libraries were PCR-amplified with Illumina primers and sequenced (Illumina Hiseq2000 or HiSeq2500 platform).

treatment_protocol: See details in Wei et al.; treatment of samples is indicated in "characteristics: treatment" column

tag: bait dsb

tag: treatment

value: APH


title: X4p53_Chr16_sgRNA_2_DMSO_ExpA

description:
HTGTS
X4p53_Chr16_sgRNA_2_DMSO_comb.tlx

value: DMSO


title: X4p53_Chr16_sgRNA_2_APH_ExpC

description:
HTGTS
X4p53_Chr16_sgRNA_2_APH_comb.tlx


title: X4p53_Chr16_sgRNA_2_DMSO_ExpC

description:
HTGTS
X4p53_Chr16_sgRNA_2_DMSO_comb.tlx


title: HET (Q20) 2 month Female cortex mRNA rep2

description:
300016_Q20B0021_04_L5.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Female cortex mRNA rep4

description:
300000_Q20B0021_02_L2.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr16_sgRNA_2_APH_ExpB

description:
HTGTS
X4p53_Chr16_sgRNA_2_APH_comb.tlx


title: X4p53_Chr16_sgRNA_2_DMSO_ExpB

description:
HTGTS
X4p53_Chr16_sgRNA_2_DMSO_comb.tlx


title: HET (Q20) 6 month Female cortex mRNA rep3

description:
28373_1_654L_cortex_Q20_HET_F_L6.LB25
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: X4p53_Chr16_sgRNA_2_APH_ExpA

description:
HTGTS
X4p53_Chr16_sgRNA_2_APH_comb.tlx


title: X4p53_Chr16_sgRNA_1_ExpC

description:
HTGTS
X4p53_Chr16_sgRNA_1_comb.tlx

value: untreated


title: X4p53_Chr16_sgRNA_1_ExpB

description:
HTGTS
X4p53_Chr16_sgRNA_1_comb.tlx


title: HET (Q175) 10 month Male cortex mRNA rep4

description:
300140_Q175B0582_06_L6.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q175) Knock-In

value: 10 month

value: housed with Het (Q175) mice


title: X4p53_Chr16_sgRNA_1_ExpA

description:
HTGTS
X4p53_Chr16_sgRNA_1_comb.tlx


title: HET (Q20) 2 month Female cortex mRNA rep1

description:
300006_Q20B0021_10_L3.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Male cortex mRNA rep1

description:
300163_Q175B0582_02_L2.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr15_Myc_sgRNA_DMSO_ExpC

description:
HTGTS
X4p53_Chr15_Myc_sgRNA_DMSO_comb.tlx


title: ATMKO.NSC486.Rep1

description: GRO-seq

molecule: total RNA

value: ATM-/- GR-I-SceI 25xI-SceI-c-Myc

value: TA


title: X4p53_Chr15_Myc_sgRNA_DMSO_ExpB


title: HET (Q175) 10 month Female cortex mRNA rep4

description:
300141_Q175B0586_04_L1
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Female cortex mRNA rep3

description:
300152_Q175B0586_08_L8.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr15_Myc_sgRNA_DMSO_ExpA


title: HET (Q175) 10 month Female cortex mRNA rep2

description:
300181_Q175B0586_06_L6.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Female cortex mRNA rep1

description:
300184_Q175B0586_02_L6.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr15_Myc_SgRNA_APH_ExpC

description:
HTGTS
X4p53_Chr15_Myc_sgRNA_APH_comb.tlx


title: X4p53_Chr15_Myc_SgRNA_APH_ExpB


title: HET (Q175) 10 month Male cortex mRNA rep3

description:
300183_Q175B0582_10_L6.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Male cortex mRNA rep4

description:
20999_1_456L_cortex_Q175_HET_M_L5.LB4
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Male cortex mRNA rep2

description:
300172_Q175B0582_08_L4.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr15_Myc_SgRNA_APH_ExpA


title: X4p53_Chr15_Myc_sgRNA_ExpB

description:
HTGTS
X4p53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q175) 6 month Male cortex mRNA rep3

description:
20973_1_454L_cortex_Q175_HET_M_L4.LB3
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr15_Myc_sgRNA_ExpA

description:
HTGTS
X4p53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q175) 6 month Male cortex mRNA rep1

description:
20921_1_450L_cortex_Q175_HET_M_L2.
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr15_Myc_sgRNA_ExpD

description:
HTGTS
X4p53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q175) 6 month Female cortex mRNA rep3

description:
21077_1_462L_cortex_Q175_HET_F_L7.LB7
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr15_Myc_sgRNA_ExpC

description:
HTGTS
X4p53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q175) 6 month Male cortex mRNA rep2

description:
20947_1_452L_cortex_Q175_HET_M_L8.LB2
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_DMSO_ExpE

description:
HTGTS
WT_Chr15_Myc_sgRNA_DMSO_comb.tlx

value: wild type


title: HET (Q175) 6 month Female cortex mRNA rep2

description:
21051_1_460L_cortex_Q175_HET_F_L3.LB6
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Female cortex mRNA rep1

description:
21025_1_458L_cortex_Q175_HET_F_L6.LB6
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Male cortex mRNA rep4

description:
300013_Q175B0591_10_L4.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_DMSO_ExpC

description:
HTGTS
WT_Chr15_Myc_sgRNA_DMSO_comb.tlx


title: WT_Chr15_Myc_sgRNA_DMSO_ExpA

description:
HTGTS
WT_Chr15_Myc_sgRNA_DMSO_comb.tlx


title: WT_Chr15_Myc_sgRNA_APH_ExpE

description:
HTGTS
WT_Chr15_Myc_sgRNA_APH_comb.tlx


title: WT_Chr15_Myc_sgRNA_APH_ExpC

description:
HTGTS
WT_Chr15_Myc_sgRNA_APH_comb.tlx


title: HET (Q175) 2 month Male cortex mRNA rep1

description:
300015_Q175B0591_02_L5.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Male cortex mRNA rep2

description:
299975_Q175B0591_08_L28
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Female cortex mRNA rep4

description:
300025_Q175B0595_10_L7.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_APH_ExpD

description:
HTGTS
WT_Chr15_Myc_sgRNA_APH_comb.tlx


title: WT_Chr15_Myc_sgRNA_DMSO_ExpB

description:
HTGTS
WT_Chr15_Myc_sgRNA_DMSO_comb.tlx


title: HET (Q175) 2 month Female cortex mRNA rep1

description:
300007_Q175B0595_04_L3.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_APH_ExpB

description:
HTGTS
WT_Chr15_Myc_sgRNA_APH_comb.tlx


title: HET (Q175) 2 month Female cortex mRNA rep2

description:
300009_Q175B0595_02_L3.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Female cortex mRNA rep4

description:
21103_1_464L_cortex_Q175_HET_F_L3.LB8
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 10 month Male cortex mRNA rep4

description:
300178_Q140B0001_02_L5.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: HET (Q140) 10 month Male cortex mRNA rep2

description:
300175_Q140B0001_04_L5.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex


title: HET (Q140) 10 month Male cortex mRNA rep3

description:
300188_Q140B0001_06_L7.D712
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_ExpB

description:
HTGTS
WT_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q140) 10 month Male cortex mRNA rep1

description:
300165_Q140B0001_08_L3.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_ExpA_2

description:
HTGTS
WT_Chr15_Myc_sgRNA_comb.tlx


title: WT_Chr15_Myc_sgRNA_ExpC

description:
HTGTS
WT_Chr15_Myc_sgRNA_comb.tlx


title: WT_Chr15_Myc_sgRNA_DMSO_ExpD

description:
HTGTS
WT_Chr15_Myc_sgRNA_DMSO_comb.tlx


title: HET (Q140) 10 month Female cortex mRNA rep4

description:
300171_Q140B0005_02_L4.D707
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_APH_ExpA

description:
HTGTS
WT_Chr15_Myc_sgRNA_APH_comb.tlx


title: HET (Q140) 10 month Female cortex mRNA rep3

description:
300174_Q140B0005_04_L4.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 10 month Female cortex mRNA rep1

description:
300162_Q140B0005_06_L2.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr15_Myc_sgRNA_ExpA_1

description:
HTGTS
WT_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q140) 6 month Male cortex mRNA rep4

description:
33108_1_774L_cortex_Q140_HET_M_L5.LB12
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 6 month Male cortex mRNA rep3

description:
33082_1_772L_cortex_Q140_HET_M_L4.LB11
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Male cortex mRNA rep3

description:
300008_Q175B0591_04_L3.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 2 month


title: HET (Q175) 2 month Female cortex mRNA rep3

description:
300010_Q175B0595_08_L8
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 6 month Male cortex mRNA rep2

description:
33056_1_770L_cortex_Q140_HET_M_L7.LB10
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Male


title: HET (Q140) 6 month Female cortex mRNA rep2

description:
33160_1_778L_cortex_Q140_HET_F_L5.LB14
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr15_Myc_sgRNA_ExpD_2

description:
HTGTS
P53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q140) 6 month Female cortex mRNA rep3

description:
33186_1_780L_cortex_Q140_HET_F_L2.LB15
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 6 month Male cortex mRNA rep1

description:
33030_1_768L_cortex_Q140_HET_M_L4.LB9
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 6 month Female cortex mRNA rep4

description:
33212_1_782L_cortex_Q140_HET_F_L4.LB16
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr15_Myc_sgRNA_ExpD_1

description:
HTGTS
P53_Chr15_Myc_sgRNA_comb.tlx


title: p53_Chr15_Myc_sgRNA_ExpC_2

description:
HTGTS
P53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q140) 10 month Female cortex mRNA rep2

description:
300185_Q140B0005_07_L7.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 2 month Male cortex mRNA rep2

description:
300002_Q140B0017_04_L2.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 2 month Male cortex mRNA rep3

description:
300017_Q140B0017_10_L5.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 6 month Female cortex mRNA rep1

description:
33134_1_776L_cortex_Q140_HET_F_L3.LB13
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr15_Myc_sgRNA_ExpB_2

description:
HTGTS
P53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q140) 2 month Male cortex mRNA rep1

description:
300003_Q140B0017_02_L2.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr15_Myc_sgRNA_ExpB_1

description:
HTGTS
P53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q140) 2 month Female cortex mRNA rep3

description:
299992_Q140B0021_02_L8.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 2 month Male cortex mRNA rep4

description:
300022_Q140B0017_08_L6.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr15_Myc_sgRNA_ExpC_1

description:
HTGTS
P53_Chr15_Myc_sgRNA_comb.tlx


title: p53_Chr15_Myc_sgRNA_ExpA

description:
HTGTS
P53_Chr15_Myc_sgRNA_comb.tlx


title: HET (Q140) 2 month Female cortex mRNA rep4

description:
299989_Q140B0021_10_L27
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 2 month Female cortex mRNA rep2

description:
299996_Q140B0021_04_L1.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 10 month Male cortex mRNA rep4

description:
300139_Q111B0009_02_L5.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q111) Knock-In

value: housed with Het (Q111) mice


title: HET (Q111) 10 month Male cortex mRNA rep3

description:
300161_Q111B0009_06_L2.D709
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 10 month Male cortex mRNA rep2

description:
300169_Q111B0009_08_L3.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4P53_Chr12_sgRNA_2_ExpB

description:
HTGTS
X4p53_Chr12_sgRNA_2_comb.tlx


title: X4P53_Chr12_sgRNA_2_ExpA

description:
HTGTS
X4p53_Chr12_sgRNA_2_comb.tlx


title: HET (Q111) 10 month Female cortex mRNA rep4

description:
300160_Q111B0013_04_L2.D708
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: HET (Q111) 10 month Female cortex mRNA rep2

description:
300167_Q111B0013_08_L3.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr12_sgRNA_1_DMSO_ExpC

description:
HTGTS
X4p53_Chr12_sgRNA_1_DMSO_comb.tlx

value: DMSO


title: HET (Q111) 10 month Female cortex mRNA rep3

description:
300182_Q111B0013_02_L6.D706
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 10 month Male cortex mRNA rep1

description:
300151_Q111B0009_07_L8.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 10 month Female cortex mRNA rep1

description:
300153_Q111B0013_10_L8.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr12_sgRNA_1_DMSO_ExpB

description:
HTGTS
X4p53_Chr12_sgRNA_1_DMSO_comb.tlx


title: HET (Q111) 6 month Male cortex mRNA rep2

description:
23379_1_516L_cortex_Q111_HET_M_L1.LB10
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: X4p53_Chr12_sgRNA_1_DMSO_ExpA

description:
HTGTS
X4p53_Chr12_sgRNA_1_DMSO_comb.tlx


title: X4p53_Chr12_sgRNA_1_APH_ExpC

description:
HTGTS
X4p53_Chr12_sgRNA_1_APH_combined.tlx

value: APH


title: HET (Q111) 6 month Male cortex mRNA rep1

description:
23353_1_514L_cortex_Q111_HET_M_L1.LB9
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 2 month Female cortex mRNA rep1

description:
299999_Q140B0021_06_L1.D701
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 6 month Female cortex mRNA rep4

description:
23535_1_528L_cortex_Q111_HET_F_L3.
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4P53_Chr12_sgRNA_2_ExpC

description:
HTGTS
X4p53_Chr12_sgRNA_2_comb.tlx

value: untreated


title: X4p53_Chr12_sgRNA_1_APH_ExpB


title: HET (Q111) 2 month Male cortex mRNA rep4

description:
300014_Q111B0017_04_L4.D705
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 6 month Female cortex mRNA rep2

description:
23483_1_524L_cortex_Q111_HET_F_L2.LB14
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 2 month Male cortex mRNA rep3

description:
299978_Q111B0017_08_L5.D704
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 2 month Male cortex mRNA rep2

description:
299977_Q111B0017_06_L5.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr12_sgRNA_1_APH_ExpA


title: X4p53_Chr12_sgRNA_1_ExpD

description:
HTGTS
X4p53_Chr12_sgRNA_1_comb.tlx


title: X4p53_Chr12_sgRNA_1_ExpC

description:
HTGTS
X4p53_Chr12_sgRNA_1_comb.tlx


title: HET (Q111) 2 month Male cortex mRNA rep1

description:
300011_Q111B0017_10_L4.D702
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 2 month Female cortex mRNA rep4

description:
300019_Q111B0021_10_L5.D710
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 6 month Male cortex mRNA rep4

description:
23431_1_520L_cortex_Q111_HET_M_L5.LB12
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 10 month Male cortex microRNA rep4

description:
323139_Q20B0009_03_L8.LB11.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

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.

value: Wild Type

value: 10 month

value: housed with HET (Q20) mice


title: HET (Q111) 2 month Female cortex mRNA rep2

description:
299973_Q111B0021_06_L4.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr12_sgRNA_1_ExpB

description:
HTGTS
X4p53_Chr12_sgRNA_1_comb.tlx


title: WT 10 month Male cortex microRNA rep3

description:
323132_Q20B0009_01_L8.LB4.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_DMSO_ExpD

description:
HTGTS
WT_Chr12_sgRNA_1_DMSO_comb.tlx


title: HET (Q111) 6 month Male cortex mRNA rep3

description:
23405_1_518L_cortex_Q111_HET_M_L6.LB11
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 10 month Male cortex microRNA rep1

description:
323092_Q20B0009_09_L6.LB36.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 10 month Male cortex microRNA rep2

description:
323099_Q20B0009_05_L6.LB7.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 2 month Female cortex mRNA rep1

description:
300012_Q111B0021_02_L4.D703
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: X4p53_Chr12_sgRNA_1_ExpA

description:
HTGTS
X4p53_Chr12_sgRNA_1_comb.tlx


title: HET (Q111) 6 month Female cortex mRNA rep3

description:
23509_1_526L_cortex_Q111_HET_F_L2.LB15
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 6 month Female cortex mRNA rep1

description:
23457_1_522L_cortex_Q111_HET_F_L2.LB13
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 10 month Female cortex microRNA rep3

description:
323135_Q20B0013_03_L8.LB7.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 10 month Female cortex microRNA rep2

description:
323109_Q20B0013_09_L7.LB17.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_DMSO_ExpC

description:
HTGTS
WT_Chr12_sgRNA_1_DMSO_comb.tlx


title: WT 10 month Female cortex microRNA rep4

description:
323136_Q20B0013_05_L8.LB8.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_DMSO_ExpB

description:
HTGTS
WT_Chr12_sgRNA_1_DMSO_comb.tlx


title: WT 10 month Female cortex microRNA rep1

description:
323104_Q20B0013_01_L6.LB12.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 6 month Male cortex microRNA rep4

description:
323202_Q20B0001_07_L3.LB3.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 6 month Male cortex microRNA rep3

description:
323200_Q20B0001_01_L3.LB1.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 6 month Male cortex microRNA rep2

description:
323198_Q20B0001_05_L3.LB35.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 6 month Male cortex microRNA rep1

description:
323195_Q20B0001_03_L3.LB32.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_APH_ExpD

description:
HTGTS
WT_Chr12_sgRNA_1_APH_comb.tlx


title: HET (Q111) 2 month Female cortex mRNA rep3

description:
299997_Q111B0021_08_L1.D711
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_DMSO_ExpA

description:
HTGTS
WT_Chr12_sgRNA_1_DMSO_comb.tlx


title: WT 6 month Female cortex microRNA rep2

description:
323197_Q20B0005_03_L3.LB34.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_APH_ExpB

description:
HTGTS
WT_Chr12_sgRNA_1_APH_comb.tlx


title: WT 2 month Male cortex microRNA rep4

description:
322966_Q20B0017_09_L7.LB17.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_APH_ExpA

description:
HTGTS
WT_Chr12_sgRNA_1_APH_comb.tlx


title: WT 6 month Female cortex microRNA rep1

description:
323196_Q20B0005_07_L3.LB33.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_ExpG

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx


title: WT 2 month Male cortex microRNA rep3

description:
322950_Q20B0017_05_L2.LB36.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 2 month Male cortex microRNA rep2

description:
322939_Q20B0017_07_L2.LB25.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 2 month Female cortex microRNA rep4

description:
322971_Q20B0021_05_L3.LB22.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 2 month Female cortex microRNA rep3

description:
322946_Q20B0021_09_L2.LB32.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 2 month Female cortex microRNA rep2

description:
322938_Q20B0021_07_L2.LB24.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 2 month Male cortex microRNA rep1

description:
322929_Q20B0017_03_L1.LB15.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_ExpF

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 10 month Male cortex microRNA rep4

description:
323134_Q92B0002_05_L8.LB6.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q92) Knock-In

value: housed with HET (Q92) mice


title: WT_Chr12_sgRNA_1_ExpD

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx

value: wild type


title: HET (Q92) 10 month Male cortex microRNA rep3

description:
323131_Q92B0001_08_L8.LB3.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 6 month Female cortex microRNA rep4

description:
323201_Q20B0005_09_L3.LB2.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_ExpE

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 10 month Male cortex microRNA rep2

description:
323101_Q92B0001_10_L6.LB9.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT 6 month Female cortex microRNA rep3

description:
323199_Q20B0005_05_L3.LB36.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 10 month Male cortex microRNA rep1

description:
323094_Q92B0001_06_L6.LB2.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 10 month Female cortex microRNA rep3

description:
323095_Q92B0006_01_L6.LB3.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_APH_ExpC

description:
HTGTS
WT_Chr12_sgRNA_1_APH_comb.tlx


title: WT_Chr12_sgRNA_1_ExpC

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx


title: WT 2 month Female cortex microRNA rep1

description:
322928_Q20B0021_01_L1.LB14.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 10 month Female cortex microRNA rep1

description:
323087_Q92B0006_03_L6.LB31.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_ExpB

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 6 month Male cortex microRNA rep2

description:
35501_1_835L_cortex_Q92_HET_M_L6.LB30.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 6 month Male cortex microRNA rep1

description:
35475_1_833L_cortex_Q92_HET_M_L6.LB29.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 6 month Female cortex microRNA rep4

description:
35657_1_847L_cortex_Q92_HET_F_L5.LB36.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 10 month Female cortex microRNA rep4

description:
323118_Q92B0005_05_L7.LB26.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 6 month Female cortex microRNA rep2

description:
35605_1_843L_cortex_Q92_HET_F_L5.LB34.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_ExpA_2

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 10 month Female cortex microRNA rep2

description:
323089_Q92B0006_05_L6.LB33.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr12_sgRNA_1_ExpB_2

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 6 month Male cortex microRNA rep4

description:
35553_1_839L_cortex_Q92_HET_M_L7.LB32.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: WT_Chr12_sgRNA_1_ExpA_1

description:
HTGTS
WT_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 6 month Male cortex microRNA rep3

description:
35527_1_837L_cortex_Q92_HET_M_L7.LB31.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr12_sgRNA_1_ExpB_1

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: p53_Chr12_sgRNA_1_ExpA

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 6 month Female cortex microRNA rep1

description:
35579_1_841L_cortex_Q92_HET_F_L5.LB33.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 6 month Female cortex microRNA rep3

description:
35631_1_845L_cortex_Q92_HET_F_L5.LB35.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 2 month Male cortex microRNA rep4

description:
322969_Q92B0017_04_L3.LB20.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr12_sgRNA_1_ExpD_1

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: p53_Chr12_sgRNA_1_ExpD_2

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 2 month Male cortex microRNA rep3

description:
322933_Q92B0017_06_L2.LB19.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr12_sgRNA_1_ExpC_1

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: p53_Chr12_sgRNA_1_ExpD_3

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 2 month Female cortex microRNA rep2

description:
322932_Q92B0021_06_L2.LB18.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 2 month Female cortex microRNA rep3

description:
322935_Q92B0021_04_L2.LB21.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q92) 2 month Male cortex microRNA rep1

description:
322924_Q92B0017_10_L1.LB10.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: p53_Chr12_sgRNA_1_ExpC_2

description:
HTGTS
P53_Chr12_sgRNA_1_comb.tlx


title: HET (Q92) 2 month Male cortex microRNA rep2

description:
322926_Q92B0017_08_L1.LB12.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: ATMKO_ISceI_ExpD

description:
HTGTS
ATMKO_ISceI_comb.tlx

value: ATM-/- GR-I-SceI 25xI-SceI-c-Myc

value: TA


title: HET (Q92) 2 month Female cortex microRNA rep4

description:
322940_Q92B0021_02_L2.LB26.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex

value: 2 month


title: ATMKO_ISceI_ExpC

description:
HTGTS
ATMKO_ISceI_comb.tlx


title: ATMKO_ISceI_ExpB

description:
HTGTS
ATMKO_ISceI_comb.tlx


title: HET (Q80) 10 month Male cortex microRNA rep4

description:
323138_Q80B0001_06_L7.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q80) Knock-In

value: Male

value: housed with HET (Q80) mice


title: ATMKO_ISceI_ExpA

description:
HTGTS
ATMKO_ISceI_comb.tlx


title: HET (Q92) 2 month Female cortex microRNA rep1

description:
322925_Q92B0021_10_L1.LB11.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: HET (Q80) 10 month Female cortex microRNA rep4

description:
323125_Q80B0005_02_L7.LB33.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 10 month Male cortex microRNA rep2

description:
323102_Q80B0001_03_L6.LB10.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 6 month Male cortex microRNA rep4

description:
30727_1_712L_cortex_Q80_HET_M_L2.LB16.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: HET (Q80) 6 month Male cortex microRNA rep2

description:
30675_1_708L_cortex_Q80_HET_M_L2.LB14.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 10 month Male cortex microRNA rep1

description:
323100_Q80B0001_04_L6.LB8.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 10 month Female cortex microRNA rep3

description:
323121_Q80B0005_10_L7.LB29.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 10 month Female cortex microRNA rep1

description:
323091_Q80B0005_08_L6.LB35.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 6 month Female cortex microRNA rep4

description:
30831_1_720L_cortex_Q80_HET_F_L1.LB20.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 6 month Female cortex microRNA rep2

description:
30779_1_716L_cortex_Q80_HET_F_L2.LB18.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Male cortex microRNA rep3

description:
322936_Q80B0017_06_L2.LB22.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Male cortex microRNA rep2

description:
322931_Q80B0017_10_L2.LB17.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Male cortex microRNA rep4

description:
322943_Q80B0017_04_L2.LB29.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Female cortex microRNA rep2

description:
322949_Q80B0021_08_L2.LB35.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Female cortex microRNA rep3

description:
322965_Q80B0021_04_L7.LB16.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Female cortex microRNA rep1

description:
322917_Q80B0021_06_L1.LB3.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 10 month Male cortex microRNA rep3

description:
323137_Q20B0009_07_L8.LB9.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q20) Knock-In


title: HET (Q20) 10 month Male cortex microRNA rep2

description:
323122_Q20B0009_08_L7.LB30.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 10 month Male cortex microRNA rep1

description:
323103_Q20B0009_04_L6.LB11.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 10 month Female cortex microRNA rep2

description:
323113_Q80B0005_04_L7.LB21.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 10 month Female cortex microRNA rep5

description:
323124_Q20B0009_02_L7.LB32.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 10 month Female cortex microRNA rep3

description:
323093_Q20B0013_08_L6.LB1.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 10 month Female cortex microRNA rep4

description:
323111_Q20B0013_02_L7.LB19.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 6 month Male cortex microRNA rep3

description:
30701_1_710L_cortex_Q80_HET_M_L2.LB15.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 10 month Female cortex microRNA rep2

description:
323090_Q20B0013_04_L6.LB34.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 10 month Female cortex microRNA rep1

description:
323088_Q20B0013_10_L6.LB32.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 6 month Male cortex microRNA rep1

description:
30649_1_706L_cortex_Q80_HET_M_L67.V67.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Control, rep4

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: Pool of 50 resected ventrical samples, 2 weeks after surgery

data_processing:
Base calling was with Illumina GAP Pipeline Software v1.70
Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX-Toolkit
Sequences were aligned to mouse mature microRNA sequences (from miRBase Version 17) and non-coding RNA sequences (Rfam Version 10) using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as (a/q) x p where a= alignment length, q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches (based on % query) were selected. If a sequence had more than one top match against different database sequences, it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase.
Genome_build: miRBase17
Supplementary_files_format_and_content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format

organism: Danio rerio

source_name: Heart, Control

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Libraries of small RNAs for sequencing were prepared using the DGE-Small RNA Sample Kit, Alternative v1.5 Protocol (Illumina; San Diego, California) according to the protocol supplied with the reagents (Protocol Rev. A, published February 2009) and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx (Illumina) using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents (Catalog FC-104-5020 and GD-300-1001)

value: heart


title: Heart, Control, rep3


title: HET (Q80) 6 month Female cortex microRNA rep3

description:
30805_1_718L_cortex_Q80_HET_F_L70.V70.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 10 month Male cortex microRNA rep3

description:
323115_Q80B0001_08_L7.LB23.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 6 month Male cortex microRNA rep3

description:
28269_1_646L_cortex_Q20_HET_M_L3.LB7.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Control, rep2


title: Heart, Control, rep1


title: HET (Q80) 6 month Female cortex microRNA rep1

description:
30753_1_714L_cortex_Q80_HET_F_L2.LB17.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Male cortex microRNA rep1

description:
322916_Q80B0021_10_L1.LB2.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q80) 2 month Male cortex microRNA rep5

description:
322968_Q80B0017_08_L3.LB19.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 6 month Male cortex microRNA rep1

description:
28217_1_642L_cortex_Q20_HET_M_L4.LB5.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 6 month Female cortex microRNA rep4

description:
28399_1_656L_cortex_Q20_HET_F_L4.LB12.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Resected, rep4

description: Pool of 50 control ventrical samples, 2 weeks after surgery

source_name: Heart, Resected


title: Heart, Resected, rep3


title: HET (Q20) 6 month Female cortex microRNA rep3

description:
28373_1_654L_cortex_Q20_HET_F_L4.LB11.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Resected, rep1


title: Heart, Resected, rep2


title: HET (Q20) 2 month Male cortex microRNA rep4

description:
322963_Q20B0017_02_L7.LB14.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Male cortex microRNA rep3

description:
322927_Q20B0017_06_L1.LB13.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 6 month Female cortex microRNA rep1

description:
28321_1_650L_cortex_Q20_HET_F_L4.LB9.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 6 month Female cortex microRNA rep2

description:
28347_1_652L_cortex_Q20_HET_F_L4.LB10.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 6 month Male cortex microRNA rep4

description:
28295_1_648L_cortex_Q20_HET_M_L3.LB8.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Male cortex microRNA rep2

description:
322921_Q20B0017_08_L1.LB7.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Female cortex microRNA rep4

description:
322961_Q20B0021_04_L3.LB11.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Male cortex microRNA rep1

description:
322919_Q20B0017_04_L1.LB5.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Female cortex microRNA rep3

description:
322951_Q20B0021_10_L2.LB1.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 6 month Male cortex microRNA rep2

description:
28243_1_644L_cortex_Q20_HET_M_L3.LB6.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Female cortex microRNA rep2

description:
322945_Q20B0021_02_L2.LB31.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q20) 2 month Female cortex microRNA rep1

description:
322930_Q20B0021_08_L1.LB16.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Male cortex microRNA rep1

description:
323085_Q175B0582_06_L6.LB29.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q175) Knock-In

value: housed with HET (Q175) mice


title: HET (Q175) 10 month Female cortex microRNA rep4

description:
323129_Q175B0586_02_L8.LB1.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 10 month


title: HET (Q175) 10 month Male cortex microRNA rep2

description:
323108_Q175B0582_02_L7.LB16.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Male cortex microRNA rep3

description:
323117_Q175B0582_08_L7.LB25.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Male cortex microRNA rep4

description:
20999_1_456L_cortex_Q175_HET_M_L2.LB28.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Male cortex microRNA rep4

description:
323128_Q175B0582_10_L7.LB36.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Female cortex microRNA rep3

description:
323126_Q175B0586_06_L7.LB34.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Female cortex microRNA rep2

description:
323097_Q175B0586_08_L6.LB5.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Male cortex microRNA rep2

description:
20947_1_452L_cortex_Q175_HET_M_L1.LB26.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Male cortex microRNA rep3

description:
20973_1_454L_cortex_Q175_HET_M_L1.LB27.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 10 month Female cortex microRNA rep1

description:
323086_Q175B0586_04_L6.LB30.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Female cortex microRNA rep2

description:
21051_1_460L_cortex_Q175_HET_F_L68.V68.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Male cortex microRNA rep1

description:
20921_1_450L_cortex_Q175_HET_M_L66.V66.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Female cortex microRNA rep3

description:
21077_1_462L_cortex_Q175_HET_F_L1.LB31.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Infarcted, rep3

description: 12 week old mice, border zone of infarct, 2 weeks after surgery

source_name: Heart, Infarcted

value: 12 week-old


title: HET (Q175) 6 month Female cortex microRNA rep4

description:
21103_1_464L_cortex_Q175_HET_F_L1.LB32.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 6 month Female cortex microRNA rep1

description:
21025_1_458L_cortex_Q175_HET_F_L71.V71.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Infarcted, rep2


title: HET (Q175) 2 month Male cortex microRNA rep4

description:
322960_Q175B0591_02_L3.LB10.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Sham, rep3

description: 12 week old mice, border zone of sham infarct, 2 weeks after surgery

source_name: Heart, Sham


title: HET (Q175) 2 month Male cortex microRNA rep3

description:
322958_Q175B0591_10_L4.LB8.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Male cortex microRNA rep2

description:
322953_Q175B0591_04_L2.LB3.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Sham, rep2


title: Heart, Infarcted, rep1


title: HET (Q175) 2 month Male cortex microRNA rep1

description:
322920_Q175B0591_08_L1.LB6.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Female cortex microRNA rep4

description:
322970_Q175B0595_10_L3.LB21.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Female cortex microRNA rep2

description:
322954_Q175B0595_02_L2.LB4.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 4hr-CA1-2

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

description: HUVECs were starved with serum-free Opti-MEM for 6 h and incubated with 0.2 μg/ml of Angiopoietin1 (COMP-Ang1)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer v.0.0.14), then mapped to hg19 whole genome using tophat2 v.2.0.9
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a cufflinks package(tuxedo protocol).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: HUVEC

growth_protocol: HUVECs were cultured in 60 mm dish until cells reach confluent state.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN mRNA-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: HUVECs were starved with serum-free Opti-MEM for 6 h and incubated with either 0.2 μg/ml of Ang1 (COMP-Ang1) or 2 μg/ml of human Ang2 (R&D systems) in the presence of ABTAA or ABA for 4 h.

tag: passage

value: Passage 5

value: Angiopoietin1 (COMP-Ang1)

tag: cell type

value: HUVEC


title: HET (Q175) 2 month Female cortex microRNA rep3

description:
322955_Q175B0595_08_L2.LB5.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q175) 2 month Female cortex microRNA rep1

description:
322952_Q175B0595_04_L2.LB2.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 4hr-ABA-2

description: HUVECs were starved with serum-free Opti-MEM for 6 h and incubated with 2 μg/ml of human Angiopoietin2 in the presence of Angiopoietin2 Blocking Antibody for for 4 h


title: 4hr-Con-2

description: HUVECs were starved with serum-free Opti-MEM for 6 h

value: control


title: 4hr-ABTAA-2

description: HUVECs were starved with serum-free Opti-MEM for 6 h and incubated with 2 μg/ml of human Angiopoietin2 in the presence of Angiopoietin2 Binding and Tie2 Activating Antibody


title: HET (Q140) 10 month Male cortex microRNA rep4

description:
323133_Q140B0001_06_L8.LB5.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex

value: Het (Q140) Knock-In

value: housed with HET (Q140) mice


title: 4hr-ABTAA-1

value: Angiopoietin2 in the presence of Angiopoietin2 Binding and Tie2 Activating Antibody


title: 4hr-ABA-1

value: Angiopoietin2 in the presence of Angiopoietin2 Blocking Antibody


title: HET (Q140) 10 month Male cortex microRNA rep3

description:
323123_Q140B0001_02_L7.LB31.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Male


title: HET (Q140) 10 month Male cortex microRNA rep2

description:
323120_Q140B0001_04_L7.LB28.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 10 month Female cortex microRNA rep4

description:
323130_Q140B0005_07_L8.LB2.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: 4hr-CA1-1

description: HUVECs were starved with serum-free Opti-MEM for 6 h and incubated with 0.2 μg/ml of Angiopoietin1 (COMP-Ang1) for 4 h


title: HET (Q140) 10 month Female cortex microRNA rep3

description:
323119_Q140B0005_04_L7.LB27.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 4hr-Con-1

description: HUVECs were starved with serum-free Opti-MEM


title: HET (Q140) 10 month Male cortex microRNA rep1

description:
323110_Q140B0001_08_L7.LB18.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 10 month Female cortex microRNA rep2

description:
323116_Q140B0005_02_L7.LB24.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 10 month Female cortex microRNA rep1

description:
323107_Q140B0005_06_L7.LB15.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: Heart, Sham, rep1

description: 12 week old mice, border zone of sham infarct, 2 weeks after surgery


title: HET (Q140) 6 month Male cortex microRNA rep4

description:
33108_1_774L_cortex_Q140_HET_M_L5.LB24.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: HET (Q140) 6 month Male cortex microRNA rep3

description:
33082_1_772L_cortex_Q140_HET_M_L31.V31.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 6 month Male cortex microRNA rep2

description:
33056_1_770L_cortex_Q140_HET_M_L69.V69.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 02-59_V

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
reads were mapped to hg19 Refseq annotation using Bowtie 2 version 2.2.2 as part of Tophat 2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: PBMCs

extract_protocol:
PBMCs were isolated from fresh whole blood using Ficoll (Ficoll-Paque Plus, GE Healthcre) and total RNA was extracted from 10e7 PBMCs using TRIzol reagent (Life Technologies).  Messenger RNA was isolated with Oligotex mRNA mini kit (Qiagen)
Scriptseq RNA-seq library preparation kit (Epicentre) was used to generate the RNA-seq libraries according to the manufacturer's protocol.

tag: individual

value: control 02-59

tag: disease state

value: Healthy controls

tag: time

value: PBMC


title: 02-56_V

value: control 02-56


title: 02-83_V

value: control 02-83


title: 02-61_V

value: control 02-61


title: 02-60_V

value: control 02-60


title: 02-58_V

value: control 02-58


title: 02-57_V

value: control 02-57

value: control


title: HET (Q140) 6 month Male cortex microRNA rep1

description:
33030_1_768L_cortex_Q140_HET_M_L1.LB21.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex

value: Het (Q140) Knock-In


title: 02-55_V

value: control 02-55


title: 02-41_V

value: control 02-41


title: HET (Q140) 6 month Female cortex microRNA rep2

description:
33160_1_778L_cortex_Q140_HET_F_L7.LB26.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: housed with HET (Q140) mice


title: 02-21_V

value: control 02-21


title: HET (Q140) 6 month Female cortex microRNA rep4

description:
33212_1_782L_cortex_Q140_HET_F_L8.LB28.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month

value: Female


title: HET (Q140) 6 month Female cortex microRNA rep1

description:
33134_1_776L_cortex_Q140_HET_F_L6.LB25.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 02-19_V

value: control 02-19

value: Healthy controls


title: HET (Q140) 2 month Male cortex microRNA rep4

description:
322967_Q140B0017_08_L3.LB18.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 2 month

value: Male


title: HET (Q140) 2 month Male cortex microRNA rep1

description:
322947_Q140B0017_04_L2.LB33.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 2 month Male cortex microRNA rep3

description:
322962_Q140B0017_10_L5.LB12.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q140) 2 month Male cortex microRNA rep2

description:
322948_Q140B0017_02_L2.LB34.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-54_V5

value: patient 01-54

value: Lyme disease

value: 6 months following treatment completion (V5)

value: PBMC


title: 02-18_V

value: control 02-18

value: control


title: 01-53_V5

value: patient 01-53


title: 01-52_V5

value: patient 01-52


title: HET (Q140) 2 month Female cortex microRNA rep4

description:
322944_Q140B0021_06_L2.LB30.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex

value: Het (Q140) Knock-In


title: 01-51_V5

value: patient 01-51


title: HET (Q140) 2 month Female cortex microRNA rep2

description:
322937_Q140B0021_02_L2.LB23.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: housed with HET (Q140) mice


title: 01-50_V5

value: patient 01-50


title: HET (Q140) 2 month Female cortex microRNA rep1

description:
322934_Q140B0021_10_L2.LB20.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: HET (Q140) 2 month Female cortex microRNA rep3

description:
322941_Q140B0021_04_L2.LB27.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-48_V5

value: patient 01-48


title: 01-46_V5

value: patient 01-46


title: 02-22_V

value: control 02-22

value: Healthy controls


title: HET (Q140) 6 month Female cortex microRNA rep3

description:
33186_1_780L_cortex_Q140_HET_F_L7.LB27.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: HET (Q111) 10 month Male cortex microRNA rep2

description:
323096_Q111B0009_07_L6.LB4.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q111) Knock-In

value: 10 month

value: Male

value: housed with HET (Q111) mice


title: HET (Q111) 10 month Male cortex microRNA rep3

description:
323106_Q111B0009_06_L7.LB14.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 10 month Male cortex microRNA rep4

description:
323114_Q111B0009_08_L7.LB22.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 10 month Female cortex microRNA rep4

description:
323127_Q111B0013_02_L7.LB35.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-44_V5

value: patient 01-44

value: Lyme disease

value: 6 months following treatment completion (V5)

value: PBMC


title: 01-45_V5

value: patient 01-45


title: HET (Q111) 10 month Male cortex microRNA rep1

description:
323084_Q111B0009_02_L6.LB28.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex


title: 01-47_V5

value: patient 01-47


title: HET (Q111) 10 month Female cortex microRNA rep3

description:
323112_Q111B0013_08_L7.LB20.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: HET (Q111) 10 month Female cortex microRNA rep2

description:
323105_Q111B0013_04_L7.LB13.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-40_V5

value: patient 01-40


title: HET (Q111) 10 month Female cortex microRNA rep1

description:
323098_Q111B0013_10_L6.LB6.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-39_V5

value: patient 01-39


title: 01-37_V5

value: patient 01-37


title: 01-36_V5

value: patient 01-36


title: HET (Q111) 6 month Male cortex microRNA rep4

description:
23431_1_520L_cortex_Q111_HET_M_L35.V35.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: HET (Q111) 6 month Male cortex microRNA rep3

description:
23405_1_518L_cortex_Q111_HET_M_L24.V24.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q111) Knock-In


title: 01-34_V5

value: patient 01-34


title: 01-33_V5

value: patient 01-33


title: 01-49_V5

value: patient 01-49


title: HET (Q111) 6 month Female cortex microRNA rep4

description:
23535_1_528L_cortex_Q111_HET_F_L4.LB4.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: housed with HET (Q111) mice


title: 01-32_V5

value: patient 01-32

value: Lyme disease


title: HET (Q111) 6 month Female cortex microRNA rep3

description:
23509_1_526L_cortex_Q111_HET_F_L3.LB3.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-42_V5

value: patient 01-42

value: 6 months following treatment completion (V5)

value: PBMC


title: 01-30_V5

value: patient 01-30


title: neusRNA-seq mock(DMSO)-labeled IMR90hTert cells, (SS) rep1

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

description:
NC_SS_rep1
small RNAs
neusRNA-seq

data_processing:
Sequenced tags were first cleared of adapters with Cutadapt
First alignment step : Tags were mapped on the Human  hg19 genome assembly using Bowtie, including only perfect matches..
Second alignment step : Tags were aligned on the human Pol III loci using BLAT with a tile size of 18 and a percent identity of 98
Third alignment step : The remaining tags were aligned in a third round with BLAT to sequences corresponding to spliced tRNAs
Tags weights : Each tag contribution to the gene score was weighted according to its length, its number of matches on the transcriptome and the number of times it was sequenced. The cutoff for tags with multiple matches was calculated as a function of the tag length.
Genes scores : To build scores, we first calculated for each gene the mean of three negative DMSO control replicates and then subtracted this value to the gene tag count of every EU-labeled sample.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: bedgraph

source_name: immortalized fetal lung fibroblasts

growth_protocol: IMR90hTert  cells were cultured at 37°C and 5% CO2 in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
A small RNAs enriched sample was used for biotinylation and beads purified with the click-iT Nascent RNA capture kit (Life technologies, C10365) according to manufacturer’s instructions. RNA on beads was resuspended in RNase-free water, heated 5 min at 70°C and used for first-strand cDNA synthesis with random hexamers and Superscript Vilo master mix (Life technologies, 11755050) as described by the supplier. After heating the beads 5 min at 85°C, the supernatant containing single strand cDNA was column purified.
Libraries were prepared starting from single strand cDNA with the TruSeq RNA sample prep v2 kit (Illumina, RS-122-2001) according to manufacturer’s instructions, but using Nucleospin columns and NTC buffer when required instead of AmpureXP beads.

tag: experiment

value: neusRNA_seq (NC, negative control)

tag: cell line

value: Cells serum starved (5 hrs) + DMSO for 5h


title: neusRNA-seq mock(DMSO)-labeled IMR90hTert cells, (SS) rep2

description:
NC_SS_rep2
small RNAs
neusRNA-seq


title: neusRNA-seq EU-labeled IMR90hTert cells, (SS) rep3

description:
EU_SS_rep3
small RNAs
neusRNA-seq

value: Cells serum starved (5 hrs) +  0.25 mM 5-ethynyl uridine (Life Technologies, E-10345) for 5h


title: HET (Q111) 6 month Female cortex microRNA rep2

description:
23483_1_524L_cortex_Q111_HET_F_L3.LB2.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex

value: Female


title: neusRNA-seq EU-labeled IMR90hTert cells, (SS) rep2

description:
EU_SS_rep2
small RNAs
neusRNA-seq


title: neusRNA-seq mock(DMSO)-labeled IMR90hTert cells, (SS) rep3

description:
NC_SS_rep3
small RNAs
neusRNA-seq


title: 01-27_V5

value: patient 01-27


title: 01-28_V5

value: patient 01-28


title: HET (Q111) 2 month Male cortex microRNA rep3

description:
322956_Q111B0017_10_L2.LB6.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q111) Knock-In

value: 2 month

value: Male


title: HET (Q111) 2 month Male cortex microRNA rep2

description:
322923_Q111B0017_08_L1.LB9.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: housed with HET (Q111) mice


title: neusRNA-seq EU-labeled IMR90hTert cells, (SS) rep1

description:
EU_SS_rep1
small RNAs
neusRNA-seq


title: HET (Q111) 6 month Female cortex microRNA rep1

description:
23457_1_522L_cortex_Q111_HET_F_L3.LB1.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: 6 month


title: 01-26_V5

value: patient 01-26

value: Lyme disease


title: 01-29_V5

value: patient 01-29

value: 6 months following treatment completion (V5)


title: neusRNA-seq mock(DMSO)-labeled IMR90hTert cells, (FBS) rep2

description:
NC_FBS_rep2
small RNAs
neusRNA-seq

value: Cells grown in fetal bovine serum + DMSO for 5h


title: HET (Q111) 2 month Male cortex microRNA rep1

description:
322922_Q111B0017_06_L1.LB8.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-25_V5

value: patient 01-25

value: PBMC


title: neusRNA-seq mock(DMSO)-labeled IMR90hTert cells, (FBS) rep3

description:
NC_FBS_rep3
small RNAs
neusRNA-seq

value: neusRNA_seq (NC, negative control)


title: HET (Q111) 6 month Male cortex microRNA rep2

description:
23379_1_516L_cortex_Q111_HET_M_L40.V40.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: cortex


title: HET (Q111) 6 month Male cortex microRNA rep1

description:
23353_1_514L_cortex_Q111_HET_M_L45.V45.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: HET (Q111) 2 month Female cortex microRNA rep4

description:
322964_Q111B0021_10_L7.LB15.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Female


title: 01-31_V5

value: patient 01-31


title: neusRNA-seq mock(DMSO)-labeled IMR90hTert cells, (FBS) rep1

description:
NC_FBS_rep1
small RNAs
neusRNA-seq


title: HET (Q111) 2 month Female cortex microRNA rep3

description:
322957_Q111B0021_02_L3.LB7.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000


title: 01-23_V5

value: patient 01-23


title: neusRNA-seq EU-labeled IMR90hTert cells, (FBS) rep3

description:
EU_FBS_rep3
small RNAs
neusRNA-seq

value: Cells grown in fetal bovine serum + 0.25 mM 5-ethynyl uridine (Life Technologies, E-10345) for 5h


title: 01-20_V5

value: patient 01-20


title: HET (Q111) 2 month Male cortex microRNA rep4

description:
322959_Q111B0017_04_L3.LB9.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: Het (Q111) Knock-In

value: 2 month

value: Male


title: 01-54_V2

value: patient 01-54

value: 3 weeks later, immediately following completion of a standard course of antibiotics (V2)


title: HET (Q111) 2 month Female cortex microRNA rep1

description:
322918_Q111B0021_06_L1.LB4.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

value: housed with HET (Q111) mice


title: neusRNA-seq EU-labeled IMR90hTert cells, (FBS) rep2

description:
EU_FBS_rep2
small RNAs
neusRNA-seq


title: 01-53_V2

value: patient 01-53

value: Lyme disease


title: 01-52_V2

value: patient 01-52


title: DamIP-seq in IMR90hTert cells expressing EGFPB_DamK9A, (SS) rep1

description:
EGFP_pooled_DamIP_SS.bedgraph
EGFPB_DamIP_SS_rep1

data_processing:
library strategy: DamIP-seq
Tags were first trimmed using Cutadapt
Alignment : Tags with perfect matches were directly extracted from the eland_extended mode of ELAND (v2e in the Illumina CASSAVA pipeline version 1.82) output.
Alignment : Tags with multiple matches were mapped onto the Human genome build hg19 using the fetchGWI software and allowing 500 repeats on the genome. The tags mapping more than once onto the genome were then attributed a weight corresponding to the number of times the tag was sequenced divided by the number of genomic matches.
Pol III scores were calculated for bins including the annotated gene body ±150bp as the mean log2 (IPtag count/INPUTtag count) of two replicates per condition.
For de novo enriched regions discovery, the whole genome was split into 400 bp bins and bin scores were calculated as the mean log2 (MAF1tag count/EGFPtag count) for each condition. Bins having 1) more than 8 tags in the MAF1-expressing clones and 2) a positive score, were considered as potentially occupied
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: bedgraph

extract_protocol:
DamIP-seq was performed as described (Xiao et al., 2010, 2012) with modifications. In brief, 10 µg of gDNA were sheared to 100-300bp with a Covaris S220 Focused-Ultrasonicator in 6x16mm µTUBE (Covaris, Cat. 520045). DNA was boiled 10’ at 98°C, cooled 10’ in ice, diluted with 1 volume of ice-cold 2X DamIP buffer (20 mM Tris-Cl pH 7.4, 300 mM NaCl and 0.2% NP40) and incubated O/N at 4°C under rotation with 4 µg of Anti-N6-methyladenosine antibody (Millipore, 1 µg/µl, ABE572). Antibody-DNA complexes were pulled-down with 25 µl of Dynabeads protein-A (Life technologies, 10002D) by 1h incubation at room temperature. Beads were washed four times in 1X DamIP buffer and resuspended in 300 µl of Elution buffer (50 mM Tris-Cl pH 8, 10 mM EDTA and 0.5% SDS) with 40 µg of Proteinase K. After 3h incubation at 48°C, immunoprecipitated single stranded DNA (ssDNA) was extracted with phenol chloroform, ethanol precipitated and resuspended in 17 µl of EB buffer.
Libraries were prepared starting from single strand cDNA with the TruSeq RNA sample prep v2 kit (Illumina, RS-122-2001) according to manufacturer’s instructions, but using Nucleospin columns and NTC buffer when required instead of AmpureXP beads.

value: DamIP-seq

tag: expressing

value: Cells serum starved (8 hrs)

tag: damip antibody

value: anti-N6-methyladenosine antibody (Millipore, catalog# ABE572, lot# 2377410)


title: HET (Q111) 2 month Female cortex microRNA rep2

description:
322942_Q111B0021_08_L2.LB28.clipped
Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000

tag: strain

value: cortex

value: Female


title: DamIP-seq in IMR90hTert cells expressing EGFPB_DamK9A, (SS) rep2

description:
EGFP_pooled_DamIP_SS.bedgraph
EGFPB_DamIP_SS_rep2


title: neusRNA-seq EU-labeled IMR90hTert cells, (FBS) rep1

description:
EU_FBS_rep1
small RNAs
neusRNA-seq


title: DamIP-seq in IMR90hTert cells expressing EGFPA_DamK9A, (SS) rep2

description:
EGFP_pooled_DamIP_SS.bedgraph
EGFPA_DamIP_SS_rep2


title: 01-51_V2

value: patient 01-51

value: PBMC


title: 01-24_V5

value: patient 01-24

value: 6 months following treatment completion (V5)


title: 01-49_V2

value: patient 01-49


title: 01-50_V2

value: patient 01-50


title: DamIP-seq in IMR90hTert cells expressing EGFPA_DamK9A, (SS) rep1

description:
EGFP_pooled_DamIP_SS.bedgraph
EGFPA_DamIP_SS_rep1


title: DamIP-seq in IMR90hTert cells expressing EGFPB_DamK9A, (FBS) rep1

description:
EGFP_pooled_DamIP_FBS.bedgraph
EGFPB_DamIP_FBS_rep1

value: Cells grown in fetal bovine serum


title: DamIP-seq in IMR90hTert cells expressing EGFPA_DamK9A, (FBS) rep2

description:
EGFP_pooled_DamIP_FBS.bedgraph
EGFPA_DamIP_FBS_rep2


title: DamIP-seq in IMR90hTert cells expressing EGFPB_DamK9A, (FBS) rep2

description:
EGFP_pooled_DamIP_FBS.bedgraph
EGFPB_DamIP_FBS_rep2


title: 01-47_V2

value: patient 01-47

value: 3 weeks later, immediately following completion of a standard course of antibiotics (V2)


title: 01-46_V2

value: patient 01-46


title: 01-45_V2

value: patient 01-45

value: Lyme disease


title: DamIP-seq in IMR90hTert cells expressing MAF1B_DamK9A, (SS) rep2

description:
MAF1_pooled_DamIP_SS.bedgraph
MAF1B_DamIP_SS_rep2

value: DamIP-seq

value: HA-tagged MAF1-DamK9A


title: DamIP-seq in IMR90hTert cells expressing EGFPA_DamK9A, (FBS) rep1

description:
EGFP_pooled_DamIP_FBS.bedgraph
EGFPA_DamIP_FBS_rep1

value: anti-N6-methyladenosine antibody (Millipore, catalog# ABE572, lot# 2377410)


title: 01-44_V2

value: patient 01-44


title: DamIP-seq in IMR90hTert cells expressing MAF1A_DamK9A, (SS) rep2

description:
MAF1_pooled_DamIP_SS.bedgraph
MAF1A_DamIP_SS_rep2

value: Cells serum starved (8 hrs)


title: 01-40_V2

value: patient 01-40


title: 01-39_V2

value: patient 01-39

value: PBMC


title: DamIP-seq in IMR90hTert cells expressing MAF1A_DamK9A, (SS) rep1

description:
MAF1_pooled_DamIP_SS.bedgraph
MAF1A_DamIP_SS_rep1


title: DamIP-seq in IMR90hTert cells expressing MAF1B_DamK9A, (FBS) rep2

description:
MAF1_pooled_DamIP_FBS.bedgraph
MAF1B_DamIP_FBS_rep2


title: 01-37_V2

value: patient 01-37


title: 01-34_V2

value: patient 01-34


title: 01-33_V2

value: patient 01-33


title: 01-48_V2

value: patient 01-48


title: DamIP-seq in IMR90hTert cells expressing MAF1A_DamK9A, (FBS) rep2

description:
MAF1_pooled_DamIP_FBS.bedgraph
MAF1A_DamIP_FBS_rep2

value: Cells grown in fetal bovine serum


title: DamIP-seq in IMR90hTert cells expressing MAF1B_DamK9A, (FBS) rep1

description:
MAF1_pooled_DamIP_FBS.bedgraph
MAF1B_DamIP_FBS_rep1


title: 01-31_V2

value: patient 01-31

value: 3 weeks later, immediately following completion of a standard course of antibiotics (V2)


title: 01-32_V2

value: patient 01-32


title: DamIP-seq in IMR90hTert cells expressing MAF1A_DamK9A, (FBS) rep1

description:
MAF1_pooled_DamIP_FBS.bedgraph
MAF1A_DamIP_FBS_rep1


title: 01-29_V2

value: patient 01-29

value: Lyme disease


title: INPUT DNA IMR90hTert cells, #1MAF1_siRNA

data_processing:
Alignment : Tags with perfect matches were directly extracted from the eland_extended mode of ELAND (v2e in the Illumina CASSAVA pipeline version 1.82) output.
Alignment : Tags with multiple matches were mapped onto the Human genome build hg19 using the fetchGWI software and allowing 500 repeats on the genome. The tags mapping more than once onto the genome were then attributed a weight corresponding to the number of times the tag was sequenced divided by the number of genomic matches.
Pol III scores were calculated for bins including the annotated gene body ±150bp as the mean log2 (IPtag count/INPUTtag count) of two replicates per condition.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: bedgraph

extract_protocol:
ChiP-seq was performed as described (Canella et al., 2010)
Libraries were prepared with 12 ng of ChIP DNA (ChIP-seq) or genomic DNA (INPUT) according to manufacturer's's instruction with the ChIP-seq DNA Sample prep kit” (Illumina, 1003473)

value: ChIP-seq (INPUT)

value: Cells treated with #2MAF1 siRNA (Ambion 427037, id s38691), 36hrs; then serum starved (8 hrs)

tag: chip antibody


title: 01-28_V2

value: patient 01-28


title: ChIP-seq Rpc4 IMR90hTert cells, #2MAF1_siRNA

value: ChIP-seq

value: Cells treated with #1MAF1 siRNA (Ambion 427037, id s38693), 36hrs; then serum starved (8 hrs)

value: anti-Rpc4 (Canella et al, 2010; homemade antibody raised in rabbit against peptide CSPDFESLLDHKHR of the RNA polymerase III subunit POLR3D (Rpc4))


title: INPUT DNA IMR90hTert cells, #NEG_siRNA

value: Cells treated with #NEG siRNA (Ambion 4390843), 36hrs; then serum starved (8 hrs)


title: 01-26_V2

value: patient 01-26

value: PBMC


title: DamIP-seq in IMR90hTert cells expressing MAF1B_DamK9A, (SS) rep1

description:
MAF1_pooled_DamIP_SS.bedgraph
MAF1B_DamIP_SS_rep1

value: DamIP-seq

value: HA-tagged MAF1-DamK9A

value: Cells serum starved (8 hrs)

value: anti-N6-methyladenosine antibody (Millipore, catalog# ABE572, lot# 2377410)


title: 01-24_V2

value: patient 01-24

value: 3 weeks later, immediately following completion of a standard course of antibiotics (V2)


title: 01-25_V2

value: patient 01-25


title: ChIP-seq Rpc4 IMR90hTert cells, #NEG_siRNA


title: INPUT DNA IMR90hTert cells, (SS_I) rep2

value: Cells serum starved (8 hrs) + 10 µM Insulin (90 min)


title: INPUT DNA IMR90hTert cells, (SS_R_I) rep2

value: ChIP-seq (INPUT)

value: Cells serum starved (8 hrs) + 2 nM rapamycin (45 min) + 10 µM Insulin (90 min)


title: INPUT DNA IMR90hTert cells, (SS_R_I) rep1


title: 01-23_V2

value: patient 01-23

value: Lyme disease


title: INPUT DNA IMR90hTert cells, (SS) rep2


title: 01-20_V2

value: patient 01-20


title: INPUT DNA IMR90hTert cells, (SS_I) rep1


title: 01-54_V1

value: patient 01-54

value: acute Lyme pre-treatment (V1)


title: 01-53_V1

value: patient 01-53


title: INPUT DNA IMR90hTert cells, #2MAF1_siRNA

value: Cells treated with #1MAF1 siRNA (Ambion 427037, id s38693), 36hrs; then serum starved (8 hrs)


title: INPUT DNA IMR90hTert cells, (SS) rep1


title: 01-52_V1

value: patient 01-52

value: PBMC


title: 01-30_V2

value: patient 01-30


title: 01-50_V1

value: patient 01-50


title: INPUT DNA IMR90hTert cells, (FBS) rep2

value: Cells grown in fetal bovine serum


title: 01-49_V1

value: patient 01-49


title: INPUT DNA IMR90hTert cells, (FBS) rep1


title: ChIP-seq Rpc4 IMR90hTert cells, (SS_R_I) rep2

value: ChIP-seq

value: anti-Rpc4 (Canella et al, 2010; homemade antibody raised in rabbit against peptide CSPDFESLLDHKHR of the RNA polymerase III subunit POLR3D (Rpc4))


title: 01-27_V2

value: patient 01-27

value: 3 weeks later, immediately following completion of a standard course of antibiotics (V2)


title: ChIP-seq Rpc4 IMR90hTert cells, (SS_R_I) rep1

value: Cells serum starved (8 hrs) + 2 nM rapamycin (45 min) + 10 µM Insulin (90 min)


title: 01-47_V1

value: patient 01-47

value: Lyme disease


title: ChIP-seq Rpc4 IMR90hTert cells, #1MAF1_siRNA

value: Cells treated with #2MAF1 siRNA (Ambion 427037, id s38691), 36hrs; then serum starved (8 hrs)


title: ChIP-seq Rpc4 IMR90hTert cells, (SS) rep1

value: Cells serum starved (8 hrs)


title: 01-44_V1

value: patient 01-44

value: acute Lyme pre-treatment (V1)


title: ChIP-seq Rpc4 IMR90hTert cells, (SS_I) rep2

value: Cells serum starved (8 hrs) + 10 µM Insulin (90 min)


title: 01-40_V1

value: patient 01-40

value: PBMC


title: ChIP-seq Rpc4 IMR90hTert cells, (SS) rep2


title: ChIP-seq Rpc4 IMR90hTert cells, (SS_I) rep1


title: 01-45_V1

value: patient 01-45


title: ChIP-seq Rpc4 IMR90hTert cells, (FBS) rep1

value: Cells grown in fetal bovine serum


title: 01-37_V1

value: patient 01-37


title: 01-39_V1

value: patient 01-39


title: ChIP-seq Rpc4 IMR90hTert cells, (FBS) rep2

value: ChIP-seq

value: anti-Rpc4 (Canella et al, 2010; homemade antibody raised in rabbit against peptide CSPDFESLLDHKHR of the RNA polymerase III subunit POLR3D (Rpc4))


title: NSC-U5 Day 21 Rep 2

city: Seattle

first: Patrick

last: Paddison

state: WA

address: 1100 Fairview Ave N, C3-187

institute: Fred Hutchinson Cancer Research Center

description:
sgRNA
U5212

data_processing:
Base calling was performed using Illumina's RTA software, v1.17.21.3
Bcl to fastq conversion was conducted using Illumina's CASAVA v1.8.2
Demultiplexing of in line indices was performed using fastx-toolkit
Reads were aligned to the GECKO v1 human sgRNA reference via bowtie 1.0.0, allowing for 0 mismatches
Normalization and significance testing were done using the Bioconductor package edgeR
Genome_build: GECKO v1 human sgRNAs
Supplementary_files_format_and_content: tab delimited text file with annotation and raw counts for each sgRNA across all samples

source_name: Neural stem cells

growth_protocol: GSC and NSC lines were grown in N2B27 neural basal media (StemCell Technologies) supplemented with EGF and FGF-2 (20ng/mL each) (Peprotech) on laminin (Sigma) coated polystyrene plates and passaged as previously described.  Cells were detached from their plates using Accutase (Millipore).  Cells were split every 3-4 days.

extract_protocol:
Genomic DNA was extracted using QiaAmp blood purification Midi kit (Qiagen).
A two-step PCR procedure was employed to amplify sgRNA sequences (first PCR:12 cycles) and then to incorporate deep sequencing primer sites onto sgRNA amplicons (second PCR:20 cycles).  For the first PCR, the amount of genomic DNA for each sample was calculated in order to achieve 500-fold coverage over the library (~6.6 μg of gDNA for 106 cells), which resulted in ~213 μg DNA per sample. For each sample, ~100 separate PCR reactions were performed with 2 μg genomic DNA in each reaction using Herculase II Fusion DNA Polymerase (Agilent). Afterwards, a second PCR was performed to add on Illumina adaptors and to barcode samples, using 5ul of the product from the first PCR. We used a primer set to include both a variable 1-6 bp sequence to increase library complexity and 6 bp Illumina barcodes for multiplexing of different biological samples. Resulting amplicons from the second PCR were column purified using the combination of PureLink PCR purification kit (Life Technologies) and MinElute PCR purification kit (Qiagen) to remove genomic DNA and first round PCR product. Purified products were quantified, and mixed.

treatment_protocol: For large-scale transduction, ~ 220 million GSC or NSC cells were plated into T225 flasks at an appropriate density per biological replicate.  Each replicate was transduced such that ~500 fold representation of the library was achieved (at MOI~1 and 30% infection efficiency).  2 days after transduction, puromycin was added (1-4μg/ml) and maintained for 3 days.  A portion of cells were harvested as Day 0 time point.  The remaining cells were then passaged into T225 flasks maintaining 500 fold representation and cultured for an additional 21-23 days or ~8-10 cell doublings.

tag: isolate

value: Day 21

value: Neural stem cells

tag: source

value: Primary patient-derived isolates

value: Fetal


title: 01-42_V1

value: patient 01-42

value: Lyme disease


title: NSC-U5 Day 21  Rep 1

description:
sgRNA
U5211

tag: age


title: 01-36_V1

value: patient 01-36


title: 01-33_V1

value: patient 01-33

value: acute Lyme pre-treatment (V1)


title: NSC-U5 Day 0 Rep 1

description:
sgRNA
U5001

value: Day 0


title: 01-48_V1

value: patient 01-48

value: PBMC


title: NSC-U5 Day 0 Rep 2

description:
sgRNA
U5002


title: NSC-CB660 Day 23 Rep 2

description:
sgRNA
CB660232

value: Day 23


title: NSC-CB660 Day 23  Rep 1

description:
sgRNA
CB660231


title: 01-46_V1

value: patient 01-46


title: 01-34_V1

value: patient 01-34


title: CB-020  PND 0

city: New Brunswick

first: Caroll

last: Bagnell

address: 59 Dudley Road

department: Animal Sciences

institute: Rutgers University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed using bcl2fastq conversion software v1.8.3 (Illumina, Inc., San Diego, CA, USA) with default settings. Raw reads were mapped to the latest pig Sscrofa10.2 build (NCBI). Further, downstream analysis was done on the Avadis NGS (Strand Scientifics) platform.
Mapped reads were filtered based on their read quality (Quality threshold > 30, Alignment score threshold > 95, Mapping quality threshold > 40) and then on duplicates. Quantification was accomplished using TMM normalization.
Genome_build: NCBI Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include TMM normalized Expression values for each Sample.

organism: Sus scrofa

source_name: no nursing_PND 0_uterus

extract_protocol:
Total RNA was isolated using Rneasy kit (Qiagen) following the manufacturer's protocol.  RNA quality was assessed using Agilent Bioanalyzer and Qbit Fluorometer.
RNA libraries were prepared for sequencing using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England BioLabs Inc., Ipswich, MA, USA) according to the manufacturer's instructions

treatment_protocol: Pigs were euthanized within 1 h of birth (PND 0) or at 50 h of age (PND 2N and PND 2R).  Uteri were trimmed of connective tissue, immersed in RNALater and stored at -80C until RNA extraction.

tag: breed

value: Crossbred (Landrace, Yorkshire, Duroc, Hampshire)

tag: feeding

value: no nursing

tag: age (days)

value: PND 0

tag: tissue

value: uterus


title: 01-32_V1

value: patient 01-32

tag: cell type


title: CB-017  PND 0


title: 01-30_V1

tag: individual

value: patient 01-30


title: 01-31_V1

value: patient 01-31

tag: disease state


title: 01-29_V1

value: patient 01-29

value: Lyme disease

tag: time


title: RiboSeq WT rep 2

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence unsing perl script
Unique mapping using Bowtie v0.12.7 with parameters -q -S -m 1 –un (unique mapping mode)
Measuring differential gene expression by assigning reads with Htseq-count version 0.5.3p3 using intersection-nonempty mode
Differential expression analysis with DESeq version 1.6.1 using default parameters
Genome_build: Saccer3
Supplementary_files_format_and_content: Count file from Htseq-count

organism: Saccharomyces cerevisiae

source_name: ribosome protected fragments

growth_protocol: OD600 of 0.6-0.8 at 30°C in YPD medium

extract_protocol:
As previously published by Ingolia et al, Science 324, 218-223 (2009).
Directional RNA-Seq library preparation was carried out with the Small RNA Sample Prep Kit and the v1.5 sRNA 3' Adaptor (Illumina), according to the manufacturer’s protocol.

treatment_protocol: Cells are treated with cycloheximide

tag: genotype/variaion

value: wild type


title: NSC-CB660 Day 0 Rep 2

description:
sgRNA
CB660002

value: Neural stem cells

value: Primary patient-derived isolates

value: Fetal


title: CB-016  PND 0


title: RiboSeq WT rep 1


title: NSC-CB660 Day 0 Rep 1

description:
sgRNA
CB660001

value: Day 0


title: CB-014  PND 0


title: CB-008  PND 2R

source_name: replacer-fed_PND 2_uterus

value: replacer-fed

value: PND 2


title: 01-27_V1

value: patient 01-27

value: acute Lyme pre-treatment (V1)

value: PBMC


title: GSC-0827 Day 23 Rep 2

description:
sgRNA
827232

source_name: GBM stem-like cells

value: Day 23

value: GBM stem-like cells

value: Adult

tag: gbm subtype

value: Proneural


title: CB-009  PND 2R

value: Crossbred (Landrace, Yorkshire, Duroc, Hampshire)

value: uterus


title: GSC-0827 Day 0 Rep 2

description:
sgRNA
827002


title: CB-005  PND 2R


title: 01-25_V1

value: patient 01-25

value: Lyme disease


title: 01-28_V1

value: patient 01-28


title: GSC-0827 Day 0 Rep 1

description:
sgRNA
827001

value: Primary patient-derived isolates


title: CB-004  PND 2N

source_name: nursed_PND 2_uterus

value: nursed


title: RiboSeq tcs2∆ rep 2


title: 01-26_V1

value: patient 01-26


title: RiboSeq tcs2∆ rep 1


title: CB-007  PND 2R

value: replacer-fed


title: GSC-0131 Day 23 Rep 2

description:
sgRNA
131232

value: Mesenchymal


title: 01-24_V1

value: patient 01-24


title: GSC-0131 Day 0 Rep 2

description:
sgRNA
131002

value: Day 0