title: WT Striatum male ZT6 miRNA rep5

description:
561590_CRM4
561590_CRM4_WT_STRR_26WKS_M_ZT6_L5.LB13
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT21 miRNA rep1

status: Public on Jul 14 2020

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:
561532_CRM106
561532_CRM106_WT_STRR_26WKS_M_ZT21_L3.LB27
miRNA
processed data file: Striatum-counts.csv

library_source: transcriptomic

data_processing:
Libraries for miRNA-seq were sequenced using an Illumina HiSeq 2000.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.3a with default parameter settings.
Raw counts were obtained with HTSeq 0.10.0 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38 (mm10)
Supplementary_files_format_and_content: *-counts.csv: Comma-separated text files include count values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Striatum right hemisphere

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

tag: tissue

value: Corpus Striatum

tag: genotype

value: Wild type

tag: strain/background

tag: age

value: 26 weeks

tag: Sex

value: male

tag: zt group

value: 21 hrs

tag: time point


title: Vhc3

city: Montreal

first: Hadla

last: Hariri

state: Quebec

address: 1003 Decarie Boulevard, Shriners Hospital For Children

department: Human Genetics

country: Canada

institute: Shriners Hospital for Children, Canada-Montreal, Department of Human Genetics, McGill University, Montreal,Quebec,Canada

description: Extracted by TRIzol method

data_processing:
The Cufflinks program was used to assemble aligned RNA-Seq reads into transcripts and to estimate their abundance (FPKM).
Pair-end reads of 100 base pairs were obtained by Illumina HiSeq 2000 PE100 sequncing.Sequenced reads were trimmed for adaptor sequence and mapped to whole mouse genome mm10.
Illumina TrueSeq RNA adaptor was used.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

source_name: MC3T3-E1 cells

growth_protocol: MC3T3-E1 cells (subclone 4) were mantained in minimumessential medium alpha (αMEM;Invitrogen, Waltham, MAsupplemented with 10% fetal bovine serum (FBS) from HyClone (Logan, UT).

extract_protocol:
Prior to RNA isolation, cells were washed 3 times with cold PBS. RNA was isolated using 1 ml of TRIzol reagent following the manufacturer's instructions(Thermo Fisher Scientific, Mississauga, ON).
RNA-Seq libraries were built with TruSeq Stranded mRNA Library Prep Kit from Illumina following the manufacturer's instructions. Pair-end reads of 100 base pairs were obtained on a HiSeq 2000 sequencing system (Illumina). The Cufflinks program was used to assemble aligned RNA-Seq reads into transcripts and to estimate their abundance (FPKM).

treatment_protocol: Cells were treated with Vehicle or parathyroid hormone PTH(1-34) recombinant protein for 2 h prior to extraction. PTH(1–34) (catalog no. H4835) was purchased from Bachem (Torrance, CA)

tag: cell line

value: MC3T3-E1 cells

tag: source

value: Calvaria

tag: cell type

value: Osteoblast-like cells

tag: treatment

value: Vehicle, 30min


title: WT Striatum male ZT12 miRNA rep9

description:
561679_CRM92
561679_CRM92_WT_STRR_26WKS_M_ZT12_L7.LB1
miRNA
processed data file: Striatum-counts.csv

value: 12 hrs

value: 36 hrs


title: WT Striatum male ZT12 miRNA rep8

description:
561677_CRM84
561677_CRM84_WT_STRR_26WKS_M_ZT12_L7.LB35
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT18 miRNA rep1

description:
561628_CRM80
561628_CRM80_WT_STRR_26WKS_M_ZT18_L3.LB21
miRNA
processed data file: Striatum-counts.csv

value: 18 hrs


title: WT Striatum male ZT12 miRNA rep2

description:
561585_CRM75
561585_CRM75_WT_STRR_26WKS_M_ZT12_L5.LB8
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT0 miRNA rep6

description:
561621_CRM63
561621_CRM63_WT_STRR_26WKS_M_ZT0_L3.LB14
miRNA
processed data file: Striatum-counts.csv

value: 0 hr

value: 0 hrs


title: WT Liver male ZT9 miRNA rep6

description:
561737_CRM88
561737_CRM88_WT_L_26WKS_M_ZT9_L1.LB23
miRNA
processed data file: Liver-counts.csv

source_name: Liver

value: Liver

value: 9 hrs

value: 33 hrs


title: WT Liver male ZT6 miRNA rep12

description:
561771_CRM93
561771_CRM93_WT_L_26WKS_M_ZT6_L3.LB22
miRNA
processed data file: Liver-counts.csv

value: 6 hrs

value: 30 hrs


title: WT Striatum male ZT0 miRNA rep5

description:
561602_CRM113
561602_CRM113_WT_STRR_26WKS_M_ZT0_L2.LB31
miRNA
processed data file: Striatum-counts.csv

value: Corpus Striatum

value: Wild type

value: 26 weeks

value: 24 hrs


title: WT Liver male ZT9 miRNA rep5

description:
561730_CRM95
561730_CRM95_WT_L_26WKS_M_ZT9_L1.LB16
miRNA
processed data file: Liver-counts.csv

value: male


title: WT Liver male ZT9 miRNA rep8

description:
561756_CRM57
561756_CRM57_WT_L_26WKS_M_ZT9_L2.LB7
miRNA
processed data file: Liver-counts.csv


title: WT Striatum male ZT0 miRNA rep3

description:
561549_CRM55
561549_CRM55_WT_STRR_26WKS_M_ZT0_L3.LB8
miRNA
processed data file: Striatum-counts.csv


title: WT Liver male ZT9 miRNA rep9

description:
561768_CRM96
561768_CRM96_WT_L_26WKS_M_ZT9_L3.LB19
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT9 miRNA rep1

description:
561703_CRM35
561703_CRM35_WT_L_26WKS_M_ZT9_L8.LB25
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT9 miRNA rep3

description:
561726_CRM90
561726_CRM90_WT_L_26WKS_M_ZT9_L8.LB12
miRNA
processed data file: Liver-counts.csv


title: WT Striatum male ZT0 miRNA rep1

description:
561523_CRM118
561523_CRM118_WT_STRR_26WKS_M_ZT0_L2.LB18
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 miRNA rep3

description:
561586_CRM67
561586_CRM67_WT_STRR_26WKS_M_ZT12_L5.LB9
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT0 miRNA rep4

description:
561559_CRM102
561559_CRM102_WT_STRR_26WKS_M_ZT0_L4.LB18
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 miRNA rep4

description:
561608_CRM119
561608_CRM119_WT_STRR_26WKS_M_ZT12_L2.LB1
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT0 miRNA rep7

description:
561622_CRM101
561622_CRM101_WT_STRR_26WKS_M_ZT0_L3.LB15
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 miRNA rep1

description:
561509_CRM117
561509_CRM117_WT_STRR_26WKS_M_ZT12_L2.LB4
miRNA
processed data file: Striatum-counts.csv


title: WT Liver male ZT9 miRNA rep7

description:
561740_CRM36
561740_CRM36_WT_L_26WKS_M_ZT9_L1.LB27
miRNA
processed data file: Liver-counts.csv


title: WT Striatum male ZT12 miRNA rep5

description:
561620_CRM87
561620_CRM87_WT_STRR_26WKS_M_ZT12_L3.LB13
miRNA
processed data file: Striatum-counts.csv


title: WT Liver male ZT9 miRNA rep10

description:
561772_CRM1
561772_CRM1_WT_L_26WKS_M_ZT9_L3.LB23
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT9 miRNA rep2

description:
561719_CRM86
561719_CRM86_WT_L_26WKS_M_ZT9_L8.LB5
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT9 miRNA rep4

description:
561728_CRM5
561728_CRM5_WT_L_26WKS_M_ZT9_L1.LB14
miRNA
processed data file: Liver-counts.csv


title: WT Striatum male ZT0 miRNA rep2

description:
561548_CRM46
561548_CRM46_WT_STRR_26WKS_M_ZT0_L3.LB7
miRNA
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 miRNA rep6

description:
561637_CRM56
561637_CRM56_WT_STRR_26WKS_M_ZT12_L3.LB30
miRNA
processed data file: Striatum-counts.csv


title: WT Liver male ZT6 miRNA rep11

description:
561763_CRM89
561763_CRM89_WT_L_26WKS_M_ZT6_L3.LB14
miRNA
processed data file: Liver-counts.csv


title: WT Striatum male ZT12 miRNA rep7

description:
561671_CRM52
561671_CRM52_WT_STRR_26WKS_M_ZT12_L6.LB29
miRNA
processed data file: Striatum-counts.csv


title: WT Liver male ZT9 miRNA rep11

description:
561773_CRM10
561773_CRM10_WT_L_26WKS_M_ZT9_L4.LB24
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep5

description:
561723_CRM4
561723_CRM4_WT_L_26WKS_M_ZT6_L8.LB9
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep10

description:
561762_CRM14
561762_CRM14_WT_L_26WKS_M_ZT6_L3.LB13
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep9

description:
561746_CRM98
561746_CRM98_WT_L_26WKS_M_ZT6_L2.LB33
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep8

description:
561745_CRM91
561745_CRM91_WT_L_26WKS_M_ZT6_L2.LB32
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep3

description:
561714_CRM13
561714_CRM13_WT_L_26WKS_M_ZT6_L8.LB36
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep4

description:
561722_CRM31
561722_CRM31_WT_L_26WKS_M_ZT6_L8.LB8
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep2

description:
561709_CRM34
561709_CRM34_WT_L_26WKS_M_ZT6_L8.LB31
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep12

description:
561765_CRM62
561765_CRM62_WT_L_26WKS_M_ZT3_L3.LB16
miRNA
processed data file: Liver-counts.csv

value: 3 hrs

value: 27 hrs


title: WT Liver male ZT6 miRNA rep6

description:
561727_CRM97
561727_CRM97_WT_L_26WKS_M_ZT6_L1.LB13
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep10

description:
561754_CRM59
561754_CRM59_WT_L_26WKS_M_ZT3_L2.LB5
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep1

description:
561707_CRM94
561707_CRM94_WT_L_26WKS_M_ZT6_L8.LB29
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep8

description:
561749_CRM38
561749_CRM38_WT_L_26WKS_M_ZT3_L2.LB36
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep6

description:
561738_CRM15
561738_CRM15_WT_L_26WKS_M_ZT3_L1.LB25
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep4

description:
561732_CRM42
561732_CRM42_WT_L_26WKS_M_ZT3_L1.LB18
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep7

description:
561741_CRM110
561741_CRM110_WT_L_26WKS_M_ZT3_L2.LB28
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep3

description:
561710_CRM3
561710_CRM3_WT_L_26WKS_M_ZT3_L8.LB32
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep1

description:
561704_CRM112
561704_CRM112_WT_L_26WKS_M_ZT3_L8.LB26
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT21 miRNA rep4

description:
561767_CRM73
561767_CRM73_WT_L_26WKS_M_ZT21_L3.LB18
miRNA
processed data file: Liver-counts.csv

value: 21 hrs


title: WT Liver male ZT3 miRNA rep5

description:
561734_CRM120
561734_CRM120_WT_L_26WKS_M_ZT3_L1.LB20
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT21 miRNA rep6

description:
561778_CRM106
561778_CRM106_WT_L_26WKS_M_ZT21_L4.LB29
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT21 miRNA rep5

description:
561774_CRM103
561774_CRM103_WT_L_26WKS_M_ZT21_L4.LB25
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT21 miRNA rep3

description:
561739_CRM72
561739_CRM72_WT_L_26WKS_M_ZT21_L1.LB26
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep2

description:
561708_CRM16
561708_CRM16_WT_L_26WKS_M_ZT3_L8.LB30
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT21 miRNA rep2

description:
561733_CRM44
561733_CRM44_WT_L_26WKS_M_ZT21_L1.LB19
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT18 miRNA rep5

description:
561744_CRM76
561744_CRM76_WT_L_26WKS_M_ZT18_L2.LB31
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT6 miRNA rep7

description:
561735_CRM66
561735_CRM66_WT_L_26WKS_M_ZT6_L1.LB21
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT18 miRNA rep6

description:
561757_CRM80
561757_CRM80_WT_L_26WKS_M_ZT18_L3.LB8
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep11

description:
561760_CRM2
561760_CRM2_WT_L_26WKS_M_ZT3_L3.LB11
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT18 miRNA rep3

description:
561720_CRM48
561720_CRM48_WT_L_26WKS_M_ZT18_L8.LB6
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT18 miRNA rep4

description:
561743_CRM25
561743_CRM25_WT_L_26WKS_M_ZT18_L2.LB30
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT18 miRNA rep2

description:
561716_CRM71
561716_CRM71_WT_L_26WKS_M_ZT18_L8.LB2
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT21 miRNA rep1

description:
561724_CRM83
561724_CRM83_WT_L_26WKS_M_ZT21_L8.LB10
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT3 miRNA rep9

description:
561750_CRM114
561750_CRM114_WT_L_26WKS_M_ZT3_L2.LB1
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT18 miRNA rep1

description:
561711_CRM81
561711_CRM81_WT_L_26WKS_M_ZT18_L8.LB33
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT15 miRNA rep4

description:
561766_CRM18
561766_CRM18_WT_L_26WKS_M_ZT15_L3.LB17
miRNA
processed data file: Liver-counts.csv

value: 15 hrs


title: WT Liver male ZT15 miRNA rep5

description:
561770_CRM70
561770_CRM70_WT_L_26WKS_M_ZT15_L3.LB21
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep12

description:
561775_CRM56
561775_CRM56_WT_L_26WKS_M_ZT12_L4.LB26
miRNA
processed data file: Liver-counts.csv

value: 12 hrs


title: WT Liver male ZT12 miRNA rep9

description:
561758_CRM107
561758_CRM107_WT_L_26WKS_M_ZT12_L3.LB9
miRNA
processed data file: Liver-counts.csv

value: 36 hrs


title: WT Liver male ZT12 miRNA rep10

description:
561759_CRM67
561759_CRM67_WT_L_26WKS_M_ZT12_L3.LB10
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep3

description:
561713_CRM111
561713_CRM111_WT_L_26WKS_M_ZT12_L8.LB35
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep7

description:
561747_CRM49
561747_CRM49_WT_L_26WKS_M_ZT12_L2.LB34
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT15 miRNA rep1

description:
561742_CRM22
561742_CRM22_WT_L_26WKS_M_ZT15_L2.LB29
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep6

description:
561736_CRM52
561736_CRM52_WT_L_26WKS_M_ZT12_L1.LB22
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT15 miRNA rep6

description:
561776_CRM30
561776_CRM30_WT_L_26WKS_M_ZT15_L4.LB27
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep1

description:
561702_CRM117
561702_CRM117_WT_L_26WKS_M_ZT12_L8.LB24
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep2

description:
561706_CRM75
561706_CRM75_WT_L_26WKS_M_ZT12_L8.LB28
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep4

description:
561717_CRM92
561717_CRM92_WT_L_26WKS_M_ZT12_L8.LB3
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT0 miRNA rep11

description:
561769_CRM55
561769_CRM55_WT_L_26WKS_M_ZT0_L3.LB20
miRNA
processed data file: Liver-counts.csv

value: 0 hr

value: 0 hrs


title: WT Liver male ZT0 miRNA rep8

description:
561748_CRM61
561748_CRM61_WT_L_26WKS_M_ZT0_L2.LB35
miRNA
processed data file: Liver-counts.csv

value: Liver


title: WT Liver male ZT0 miRNA rep9

description:
561752_CRM46
561752_CRM46_WT_L_26WKS_M_ZT0_L2.LB3
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT15 miRNA rep2

description:
561753_CRM27
561753_CRM27_WT_L_26WKS_M_ZT15_L2.LB4
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT0 miRNA rep10

description:
561761_CRM63
561761_CRM63_WT_L_26WKS_M_ZT0_L3.LB12
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT0 miRNA rep6

description:
561725_CRM54
561725_CRM54_WT_L_26WKS_M_ZT0_L8.LB11
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT15 miRNA rep3

description:
561755_CRM45
561755_CRM45_WT_L_26WKS_M_ZT15_L2.LB6
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT12 miRNA rep8

description:
561751_CRM119
561751_CRM119_WT_L_26WKS_M_ZT12_L2.LB2
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT0 miRNA rep3

description:
561715_CRM47
561715_CRM47_WT_L_26WKS_M_ZT0_L8.LB1
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT0 miRNA rep7

description:
561731_CRM115
561731_CRM115_WT_L_26WKS_M_ZT0_L1.LB17
miRNA
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT9 miRNA rep10

description:
561666_CRM10
561666_CRM10_WT_HY_26WKS_M_ZT9_L6.LB24
miRNA
processed data file: Hypothalamus-counts.csv

source_name: Hypothalamus

value: Hypothalamus

value: 9 hrs


title: WT Liver male ZT0 miRNA rep2

description:
561712_CRM101
561712_CRM101_WT_L_26WKS_M_ZT0_L8.LB34
miRNA
processed data file: Liver-counts.csv


title: WT Liver male ZT0 miRNA rep1

description:
561705_CRM118
561705_CRM118_WT_L_26WKS_M_ZT0_L8.LB27
miRNA
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT9 miRNA rep6

description:
561595_CRM86
561595_CRM86_WT_HY_26WKS_M_ZT9_L5.LB18
miRNA
processed data file: Hypothalamus-counts.csv

value: 33 hrs


title: WT Liver male ZT0 miRNA rep4

description:
561718_CRM105
561718_CRM105_WT_L_26WKS_M_ZT0_L8.LB4
miRNA
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT9 miRNA rep7

description:
561629_CRM35
561629_CRM35_WT_HY_26WKS_M_ZT9_L3.LB22
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Liver male ZT0 miRNA rep5

description:
561721_CRM113
561721_CRM113_WT_L_26WKS_M_ZT0_L8.LB7
miRNA
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT9 miRNA rep9

description:
561648_CRM57
561648_CRM57_WT_HY_26WKS_M_ZT9_L5.LB6
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 miRNA rep5

description:
561576_CRM99
561576_CRM99_WT_HY_26WKS_M_ZT9_L4.LB35
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep12

description:
561668_CRM89
561668_CRM89_WT_HY_26WKS_M_ZT6_L6.LB26
miRNA
processed data file: Hypothalamus-counts.csv

value: 6 hrs

value: 30 hrs


title: WT Hypothalamus male ZT9 miRNA rep4

description:
561572_CRM36
561572_CRM36_WT_HY_26WKS_M_ZT9_L4.LB31
miRNA
processed data file: Hypothalamus-counts.csv

value: Wild type

value: 26 weeks


title: WT Hypothalamus male ZT9 miRNA rep1

description:
561531_CRM88
561531_CRM88_WT_HY_26WKS_M_ZT9_L2.LB26
miRNA
processed data file: Hypothalamus-counts.csv

value: male


title: WT Hypothalamus male ZT9 miRNA rep8

description:
561639_CRM96
561639_CRM96_WT_HY_26WKS_M_ZT9_L3.LB32
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Liver male ZT12 miRNA rep5

description:
561729_CRM87
561729_CRM87_WT_L_26WKS_M_ZT12_L1.LB15
miRNA
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep11

description:
561665_CRM97
561665_CRM97_WT_HY_26WKS_M_ZT6_L6.LB23
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 miRNA rep3

description:
561565_CRM95
561565_CRM95_WT_HY_26WKS_M_ZT9_L4.LB24
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 miRNA rep2

description:
561555_CRM90
561555_CRM90_WT_HY_26WKS_M_ZT9_L3.LB14
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Liver male ZT0 miRNA rep12

description:
561777_CRM102
561777_CRM102_WT_L_26WKS_M_ZT0_L4.LB28
miRNA
processed data file: Liver-counts.csv

value: 24 hrs


title: WT Hypothalamus male ZT6 miRNA rep10

description:
561663_CRM98
561663_CRM98_WT_HY_26WKS_M_ZT6_L6.LB21
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep9

description:
561636_CRM31
561636_CRM31_WT_HY_26WKS_M_ZT6_L3.LB29
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep8

description:
561606_CRM93
561606_CRM93_WT_HY_26WKS_M_ZT6_L2.LB35
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep7

description:
561593_CRM14
561593_CRM14_WT_HY_26WKS_M_ZT6_L5.LB16
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep6

description:
561581_CRM91
561581_CRM91_WT_HY_26WKS_M_ZT6_L4.LB4
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep5

description:
561567_CRM66
561567_CRM66_WT_HY_26WKS_M_ZT6_L4.LB26
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep4

description:
561553_CRM13
561553_CRM13_WT_HY_26WKS_M_ZT6_L3.LB12
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep2

description:
561535_CRM34
561535_CRM34_WT_HY_26WKS_M_ZT6_L3.LB30
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep10

description:
561673_CRM62
561673_CRM62_WT_HY_26WKS_M_ZT3_L6.LB31
miRNA
processed data file: Hypothalamus-counts.csv

value: 3 hrs

value: 27 hrs


title: WT Hypothalamus male ZT6 miRNA rep3

description:
561542_CRM94
561542_CRM94_WT_HY_26WKS_M_ZT6_L3.LB1
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep9

description:
561626_CRM38
561626_CRM38_WT_HY_26WKS_M_ZT3_L3.LB19
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep8

description:
561594_CRM2
561594_CRM2_WT_HY_26WKS_M_ZT3_L5.LB17
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 miRNA rep1

description:
561533_CRM4
561533_CRM4_WT_HY_26WKS_M_ZT6_L3.LB28
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep3

description:
561556_CRM110
561556_CRM110_WT_HY_26WKS_M_ZT3_L3.LB15
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep7

description:
561580_CRM112
561580_CRM112_WT_HY_26WKS_M_ZT3_L4.LB3
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT21 miRNA rep4

description:
561676_CRM83
561676_CRM83_WT_HY_26WKS_M_ZT21_L7.LB34
miRNA
processed data file: Hypothalamus-counts.csv

value: 21 hrs


title: WT Hypothalamus male ZT21 miRNA rep3

description:
561646_CRM44
561646_CRM44_WT_HY_26WKS_M_ZT21_L5.LB4
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep1

description:
561530_CRM59
561530_CRM59_WT_HY_26WKS_M_ZT3_L2.LB25
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep11

description:
561688_CRM114
561688_CRM114_WT_HY_26WKS_M_ZT3_L7.LB10
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep4

description:
561558_CRM16
561558_CRM16_WT_HY_26WKS_M_ZT3_L4.LB17
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 miRNA rep4

description:
561627_CRM71
561627_CRM71_WT_HY_26WKS_M_ZT18_L3.LB20
miRNA
processed data file: Hypothalamus-counts.csv

value: 18 hrs


title: WT Hypothalamus male ZT21 miRNA rep1

description:
561524_CRM73
561524_CRM73_WT_HY_26WKS_M_ZT21_L2.LB19
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep2

description:
561538_CRM3
561538_CRM3_WT_HY_26WKS_M_ZT3_L3.LB33
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep5

description:
561573_CRM120
561573_CRM120_WT_HY_26WKS_M_ZT3_L4.LB32
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 miRNA rep2

description:
561564_CRM80
561564_CRM80_WT_HY_26WKS_M_ZT18_L4.LB23
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 miRNA rep6

description:
561577_CRM15
561577_CRM15_WT_HY_26WKS_M_ZT3_L4.LB36
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 miRNA rep3

description:
561571_CRM76
561571_CRM76_WT_HY_26WKS_M_ZT18_L4.LB30
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 miRNA rep1

description:
561557_CRM81
561557_CRM81_WT_HY_26WKS_M_ZT18_L3.LB16
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT21 miRNA rep2

description:
561610_CRM106
561610_CRM106_WT_HY_26WKS_M_ZT21_L2.LB3
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 miRNA rep5

description:
561672_CRM27
561672_CRM27_WT_HY_26WKS_M_ZT15_L6.LB30
miRNA
processed data file: Hypothalamus-counts.csv

value: 15 hrs


title: WT Hypothalamus male ZT18 miRNA rep5

description:
561662_CRM48
561662_CRM48_WT_HY_26WKS_M_ZT18_L6.LB20
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 miRNA rep4

description:
561659_CRM18
561659_CRM18_WT_HY_26WKS_M_ZT15_L6.LB17
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 miRNA rep3

description:
561612_CRM45
561612_CRM45_WT_HY_26WKS_M_ZT15_L2.LB5
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 miRNA rep2

description:
561525_CRM70
561525_CRM70_WT_HY_26WKS_M_ZT15_L2.LB20
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 miRNA rep1

description:
561515_CRM22
561515_CRM22_WT_HY_26WKS_M_ZT15_L2.LB10
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT21 miRNA rep5

description:
561700_CRM103
561700_CRM103_WT_HY_26WKS_M_ZT21_L7.LB22
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep12

description:
561699_CRM52
561699_CRM52_WT_HY_26WKS_M_ZT12_L7.LB21
miRNA
processed data file: Hypothalamus-counts.csv

value: 12 hrs


title: WT Hypothalamus male ZT12 miRNA rep9

description:
561680_CRM67
561680_CRM67_WT_HY_26WKS_M_ZT12_L7.LB2
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep10

description:
561683_CRM111
561683_CRM111_WT_HY_26WKS_M_ZT12_L7.LB5
miRNA
processed data file: Hypothalamus-counts.csv

value: 36 hrs


title: WT Hypothalamus male ZT12 miRNA rep8

description:
561674_CRM87
561674_CRM87_WT_HY_26WKS_M_ZT12_L6.LB32
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep5

description:
561607_CRM107
561607_CRM107_WT_HY_26WKS_M_ZT12_L2.LB36
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep6

description:
561609_CRM84
561609_CRM84_WT_HY_26WKS_M_ZT12_L2.LB2
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep1

description:
561541_CRM75
561541_CRM75_WT_HY_26WKS_M_ZT12_L3.LB36
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep11

description:
561689_CRM55
561689_CRM55_WT_HY_26WKS_M_ZT0_L7.LB11
miRNA
processed data file: Hypothalamus-counts.csv

value: 0 hr

value: 0 hrs


title: WT Hypothalamus male ZT0 miRNA rep10

description:
561682_CRM113
561682_CRM113_WT_HY_26WKS_M_ZT0_L7.LB4
miRNA
processed data file: Hypothalamus-counts.csv

value: Hypothalamus


title: WT Hypothalamus male ZT0 miRNA rep8

description:
561675_CRM105
561675_CRM105_WT_HY_26WKS_M_ZT0_L7.LB33
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep2

description:
561575_CRM92
561575_CRM92_WT_HY_26WKS_M_ZT12_L4.LB34
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep3

description:
561601_CRM119
561601_CRM119_WT_HY_26WKS_M_ZT12_L2.LB30
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep5

description:
561633_CRM102
561633_CRM102_WT_HY_26WKS_M_ZT0_L3.LB26
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep7

description:
561656_CRM54
561656_CRM54_WT_HY_26WKS_M_ZT0_L6.LB14
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep2

description:
561547_CRM47
561547_CRM47_WT_HY_26WKS_M_ZT0_L3.LB6
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep3

description:
561600_CRM101
561600_CRM101_WT_HY_26WKS_M_ZT0_L5.LB23
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep11

description:
561691_CRM49
561691_CRM49_WT_HY_26WKS_M_ZT12_L7.LB13
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep9

description:
561681_CRM63
561681_CRM63_WT_HY_26WKS_M_ZT0_L7.LB3
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep4

description:
561615_CRM118
561615_CRM118_WT_HY_26WKS_M_ZT0_L2.LB8
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Cortex male ZT9 miRNA rep9

description:
561634_CRM96
561634_CRM96_WT_CTXR_26WKS_M_ZT9_L3.LB27
miRNA
processed data file: Cortex-counts.csv

source_name: Cortex right hemisphere

value: Cerebral Cortex

value: 9 hrs

value: 33 hrs


title: WT Cortex male ZT9 miRNA rep12

description:
561697_CRM5
561697_CRM5_WT_CTXR_26WKS_M_ZT9_L7.LB19
miRNA
processed data file: Cortex-counts.csv

value: Wild type


title: WT Cortex male ZT9 miRNA rep11

description:
561684_CRM35
561684_CRM35_WT_CTXR_26WKS_M_ZT9_L7.LB6
miRNA
processed data file: Cortex-counts.csv

value: 26 weeks


title: WT Hypothalamus male ZT0 miRNA rep1

description:
561518_CRM46
561518_CRM46_WT_HY_26WKS_M_ZT0_L2.LB13
miRNA
processed data file: Hypothalamus-counts.csv

value: male


title: WT Hypothalamus male ZT12 miRNA rep7

description:
561660_CRM117
561660_CRM117_WT_HY_26WKS_M_ZT12_L6.LB18
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Cortex male ZT9 miRNA rep10

description:
561661_CRM99
561661_CRM99_WT_CTXR_26WKS_M_ZT9_L6.LB19
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep8

description:
561623_CRM86
561623_CRM86_WT_CTXR_26WKS_M_ZT9_L3.LB16
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep7

description:
561614_CRM36
561614_CRM36_WT_CTXR_26WKS_M_ZT9_L2.LB7
miRNA
processed data file: Cortex-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep12

description:
561701_CRM61
561701_CRM61_WT_HY_26WKS_M_ZT0_L8.LB23
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 miRNA rep4

description:
561605_CRM56
561605_CRM56_WT_HY_26WKS_M_ZT12_L2.LB34
miRNA
processed data file: Hypothalamus-counts.csv


title: WT Cortex male ZT6 miRNA rep7

description:
561599_CRM94
561599_CRM94_WT_CTXR_26WKS_M_ZT6_L5.LB22
miRNA
processed data file: Cortex-counts.csv

value: 6 hrs

value: 30 hrs


title: WT Cortex male ZT6 miRNA rep8

description:
561617_CRM34
561617_CRM34_WT_CTXR_26WKS_M_ZT6_L3.LB10
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep6

description:
561569_CRM10
561569_CRM10_WT_CTXR_26WKS_M_ZT9_L4.LB28
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep3

description:
561546_CRM13
561546_CRM13_WT_CTXR_26WKS_M_ZT6_L3.LB5
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep5

description:
561579_CRM66
561579_CRM66_WT_CTXR_26WKS_M_ZT6_L4.LB2
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep5

description:
561566_CRM90
561566_CRM90_WT_CTXR_26WKS_M_ZT9_L4.LB25
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep12

description:
561696_CRM4
561696_CRM4_WT_CTXR_26WKS_M_ZT6_L7.LB18
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep10

description:
561635_CRM98
561635_CRM98_WT_CTXR_26WKS_M_ZT6_L3.LB28
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep4

description:
561552_CRM93
561552_CRM93_WT_CTXR_26WKS_M_ZT6_L3.LB11
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep1

description:
561507_CRM95
561507_CRM95_WT_CTXR_26WKS_M_ZT9_L2.LB2
miRNA
processed data file: Cortex-counts.csv


title: WT Hypothalamus male ZT0 miRNA rep6

description:
561647_CRM115
561647_CRM115_WT_HY_26WKS_M_ZT0_L5.LB5
miRNA
processed data file: Hypothalamus-counts.csv

value: 24 hrs


title: WT Cortex male ZT6 miRNA rep11

description:
561652_CRM97
561652_CRM97_WT_CTXR_26WKS_M_ZT6_L6.LB10
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep3

description:
561527_CRM57
561527_CRM57_WT_CTXR_26WKS_M_ZT9_L2.LB22
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep1

description:
561506_CRM89
561506_CRM89_WT_CTXR_26WKS_M_ZT6_L2.LB1
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep9

description:
561632_CRM31
561632_CRM31_WT_CTXR_26WKS_M_ZT6_L3.LB25
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep2

description:
561519_CRM88
561519_CRM88_WT_CTXR_26WKS_M_ZT9_L2.LB14
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep6

description:
561598_CRM91
561598_CRM91_WT_CTXR_26WKS_M_ZT6_L5.LB21
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 miRNA rep4

description:
561551_CRM1
561551_CRM1_WT_CTXR_26WKS_M_ZT9_L3.LB10
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep11

description:
561690_CRM42
561690_CRM42_WT_CTXR_26WKS_M_ZT3_L7.LB12
miRNA
processed data file: Cortex-counts.csv

value: 3 hrs


title: WT Cortex male ZT3 miRNA rep10

description:
561651_CRM120
561651_CRM120_WT_CTXR_26WKS_M_ZT3_L6.LB9
miRNA
processed data file: Cortex-counts.csv

value: 27 hrs


title: WT Cortex male ZT3 miRNA rep12

description:
561695_CRM16
561695_CRM16_WT_CTXR_26WKS_M_ZT3_L7.LB17
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep8

description:
561638_CRM38
561638_CRM38_WT_CTXR_26WKS_M_ZT3_L3.LB31
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep9

description:
561640_CRM112
561640_CRM112_WT_CTXR_26WKS_M_ZT3_L3.LB33
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep7

description:
561625_CRM3
561625_CRM3_WT_CTXR_26WKS_M_ZT3_L3.LB18
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 miRNA rep2

description:
561540_CRM14
561540_CRM14_WT_CTXR_26WKS_M_ZT6_L3.LB35
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep3

description:
561544_CRM110
561544_CRM110_WT_CTXR_26WKS_M_ZT3_L3.LB3
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep5

description:
561597_CRM59
561597_CRM59_WT_CTXR_26WKS_M_ZT3_L5.LB20
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep4

description:
561574_CRM114
561574_CRM114_WT_CTXR_26WKS_M_ZT3_L4.LB33
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep1

description:
561511_CRM62
561511_CRM62_WT_CTXR_26WKS_M_ZT3_L2.LB6
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep6

description:
561604_CRM2
561604_CRM2_WT_CTXR_26WKS_M_ZT3_L2.LB33
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT18 miRNA rep3

description:
561578_CRM76
561578_CRM76_WT_CTXR_26WKS_M_ZT18_L4.LB1
miRNA
processed data file: Cortex-counts.csv

value: 18 hrs


title: WT Cortex male ZT21 miRNA rep6

description:
561678_CRM103
561678_CRM103_WT_CTXR_26WKS_M_ZT21_L7.LB36
miRNA
processed data file: Cortex-counts.csv

value: 21 hrs


title: WT Cortex male ZT21 miRNA rep2

description:
561528_CRM73
561528_CRM73_WT_CTXR_26WKS_M_ZT21_L2.LB23
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 miRNA rep2

description:
561512_CRM15
561512_CRM15_WT_CTXR_26WKS_M_ZT3_L2.LB7
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT21 miRNA rep4

description:
561644_CRM44
561644_CRM44_WT_CTXR_26WKS_M_ZT21_L5.LB2
miRNA
processed data file: Cortex-counts.csv


title: LT7 cells - long cells overexpressing SIRT7, rep2

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Gene expression after establishment and expansion of single cell clones of long cells overexpressing SIRT7 (LT7)
LT 7_2

hyb_protocol: 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Genotypic will fill scanned immediately after washing on the Agilent  Microarray Scanner (G2505C)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75thPercentile shift normalization.

source_name: Cell line

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: GFP or SIRT7GFP expressing cells were grown in DMEM with 10% FBS  and 5%CO2.

extract_protocol: RNA isolation was done using Qiagen RNAeasy kit .

value: fibroblast cells NIH3T3

value: overexpressing SIRT7

tag: phenotype

value: long cells


title: LT7 cells - long cells overexpressing SIRT7, rep1

description:
Gene expression after establishment and expansion of single cell clones of long cells overexpressing SIRT7 (LT7)
LT 7_1_R1


title: WT Cortex male ZT21 miRNA rep5

description:
561650_CRM72
561650_CRM72_WT_CTXR_26WKS_M_ZT21_L6.LB8
miRNA
processed data file: Cortex-counts.csv


title: ST7 cells - small cells overexpressing SIRT7, rep2

description:
Gene expression after establishment and expansion of single cell clones of small cells overexpressing SIRT7 (ST7)
Sri 5_2

value: small cells


title: WT Cortex male ZT21 miRNA rep1

description:
561516_CRM83
561516_CRM83_WT_CTXR_26WKS_M_ZT21_L2.LB11
miRNA
processed data file: Cortex-counts.csv

value: Cerebral Cortex


title: WT Cortex male ZT15 miRNA rep2

description:
561570_CRM27
561570_CRM27_WT_CTXR_26WKS_M_ZT15_L4.LB29
miRNA
processed data file: Cortex-counts.csv

value: 15 hrs


title: WT Cortex male ZT18 miRNA rep6

description:
561667_CRM80
561667_CRM80_WT_CTXR_26WKS_M_ZT18_L6.LB25
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT18 miRNA rep2

description:
561561_CRM81
561561_CRM81_WT_CTXR_26WKS_M_ZT18_L4.LB20
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT15 miRNA rep6

description:
561692_CRM30
561692_CRM30_WT_CTXR_26WKS_M_ZT15_L7.LB14
miRNA
processed data file: Cortex-counts.csv


title: ST7 cells - small cells overexpressing SIRT7, rep1

description:
Gene expression after establishment and expansion of single cell clones of small cells overexpressing SIRT7 (ST7)
Sri 5_1


title: WT Cortex male ZT18 miRNA rep4

description:
561603_CRM71
561603_CRM71_WT_CTXR_26WKS_M_ZT18_L2.LB32
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT18 miRNA rep1

description:
561534_CRM48
561534_CRM48_WT_CTXR_26WKS_M_ZT18_L3.LB29
miRNA
processed data file: Cortex-counts.csv


title: NIH3T3 cells expressing GFP, rep2

description:
Gene expression after establishment and expansion of single cell clones of GFP expressing cells
SKGFP_2

value: expressing GFP

value: control


title: WT Cortex male ZT15 miRNA rep5

description:
561669_CRM22
561669_CRM22_WT_CTXR_26WKS_M_ZT15_L6.LB27
miRNA
processed data file: Cortex-counts.csv

value: Wild type

value: 26 weeks


title: NIH3T3 cells expressing GFP, rep1

description:
Gene expression after establishment and expansion of single cell clones of GFP expressing cells
SKGFP_1


title: WT Cortex male ZT21 miRNA rep3

description:
561537_CRM106
561537_CRM106_WT_CTXR_26WKS_M_ZT21_L3.LB32
miRNA
processed data file: Cortex-counts.csv

value: male


title: WT Cortex male ZT15 miRNA rep4

description:
561591_CRM45
561591_CRM45_WT_CTXR_26WKS_M_ZT15_L5.LB14
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT15 miRNA rep1

description:
561539_CRM70
561539_CRM70_WT_CTXR_26WKS_M_ZT15_L3.LB34
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT15 miRNA rep3

description:
561583_CRM18
561583_CRM18_WT_CTXR_26WKS_M_ZT15_L4.LB6
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 miRNA rep12

description:
561685_CRM52
561685_CRM52_WT_CTXR_26WKS_M_ZT12_L7.LB7
miRNA
processed data file: Cortex-counts.csv

value: 12 hrs


title: WT Cortex male ZT12 miRNA rep11

description:
561670_CRM117
561670_CRM117_WT_CTXR_26WKS_M_ZT12_L6.LB28
miRNA
processed data file: Cortex-counts.csv

value: 36 hrs


title: WT Cortex male ZT12 miRNA rep9

description:
561653_CRM56
561653_CRM56_WT_CTXR_26WKS_M_ZT12_L6.LB11
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 miRNA rep2

description:
561514_CRM119
561514_CRM119_WT_CTXR_26WKS_M_ZT12_L2.LB9
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep11

description:
561687_CRM115
561687_CRM115_WT_CTXR_26WKS_M_ZT0_L7.LB9
miRNA
processed data file: Cortex-counts.csv

value: 0 hr

value: 24 hrs


title: WT Cortex male ZT12 miRNA rep8

description:
561611_CRM84
561611_CRM84_WT_CTXR_26WKS_M_ZT12_L2.LB4
miRNA
processed data file: Cortex-counts.csv


title: WT Liver male ZT12 miRNA rep11

description:
561764_CRM84
561764_CRM84_WT_L_26WKS_M_ZT12_L3.LB15
miRNA
processed data file: Liver-counts.csv

value: Liver


title: WT Cortex male ZT12 miRNA rep7

description:
561587_CRM107
561587_CRM107_WT_CTXR_26WKS_M_ZT12_L5.LB10
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 miRNA rep1

description:
561510_CRM87
561510_CRM87_WT_CTXR_26WKS_M_ZT12_L2.LB5
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 miRNA rep4

description:
561554_CRM92
561554_CRM92_WT_CTXR_26WKS_M_ZT12_L3.LB13
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 miRNA rep3

description:
561550_CRM49
561550_CRM49_WT_CTXR_26WKS_M_ZT12_L3.LB9
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep10

description:
561686_CRM46
561686_CRM46_WT_CTXR_26WKS_M_ZT0_L7.LB8
miRNA
processed data file: Cortex-counts.csv

value: 0 hrs


title: WT Cortex male ZT0 miRNA rep12

description:
561693_CRM118
561693_CRM118_WT_CTXR_26WKS_M_ZT0_L7.LB15
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep8

description:
561645_CRM47
561645_CRM47_WT_CTXR_26WKS_M_ZT0_L5.LB3
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep7

description:
561643_CRM63
561643_CRM63_WT_CTXR_26WKS_M_ZT0_L5.LB1
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 miRNA rep10

description:
561654_CRM111
561654_CRM111_WT_CTXR_26WKS_M_ZT12_L6.LB12
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep6

description:
561624_CRM61
561624_CRM61_WT_CTXR_26WKS_M_ZT0_L3.LB17
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep2

description:
561536_CRM101
561536_CRM101_WT_CTXR_26WKS_M_ZT0_L3.LB31
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep1

description:
561508_CRM55
561508_CRM55_WT_CTXR_26WKS_M_ZT0_L2.LB3
miRNA
processed data file: Cortex-counts.csv


title: WT Liver male ZT9 mRNA rep10

description:
331611_CRM1
331611_CRM1_WT_L_26WKS_M_ZT9_L7.D707
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

data_processing:
Libraries for RNA-seq were sequenced using an Illumina HiSeq 2000.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.3a with default parameter settings.
Raw counts were obtained with HTSeq 0.10.0 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38 (mm10)
Supplementary_files_format_and_content: *-FPKM.csv: Comma-separated text files include FPKM values for each Sample.
Supplementary_files_format_and_content: *-counts.csv: Comma-separated text files include count values for each Sample.

value: 9 hrs


title: WT Liver male ZT9 mRNA rep11

description:
331612_CRM10
331612_CRM10_WT_L_26WKS_M_ZT9_L7.D708
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT9 mRNA rep9

description:
331607_CRM96
331607_CRM96_WT_L_26WKS_M_ZT9_L8.D703
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 33 hrs


title: WT Cortex male ZT0 miRNA rep4

description:
561596_CRM105
561596_CRM105_WT_CTXR_26WKS_M_ZT0_L5.LB19
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 miRNA rep6

description:
561568_CRM75
561568_CRM75_WT_CTXR_26WKS_M_ZT12_L4.LB27
miRNA
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 miRNA rep3

description:
561588_CRM102
561588_CRM102_WT_CTXR_26WKS_M_ZT0_L5.LB11
miRNA
processed data file: Cortex-counts.csv


title: WT Liver male ZT9 mRNA rep7

description:
331579_CRM36
331579_CRM36_WT_L_26WKS_M_ZT9_L3.D710
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT9 mRNA rep8

description:
331595_CRM57
331595_CRM57_WT_L_26WKS_M_ZT9_L6.D702
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Cortex male ZT12 miRNA rep5

description:
561563_CRM67
561563_CRM67_WT_CTXR_26WKS_M_ZT12_L4.LB22
miRNA
processed data file: Cortex-counts.csv


title: WT Liver male ZT9 mRNA rep5

description:
331569_CRM95
331569_CRM95_WT_L_26WKS_M_ZT9_L1.D712
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT9 mRNA rep4

description:
331567_CRM5
331567_CRM5_WT_L_26WKS_M_ZT9_L8.D710
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT9 mRNA rep6

description:
331576_CRM88
331576_CRM88_WT_L_26WKS_M_ZT9_L2.D707
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep11

description:
331602_CRM89
331602_CRM89_WT_L_26WKS_M_ZT6_L7.D709
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 6 hrs

value: 30 hrs


title: WT Liver male ZT6 mRNA rep10

description:
331601_CRM14
331601_CRM14_WT_L_26WKS_M_ZT6_L7.D708
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Cortex male ZT0 miRNA rep9

description:
561649_CRM113
561649_CRM113_WT_CTXR_26WKS_M_ZT0_L6.LB7
miRNA
processed data file: Cortex-counts.csv

value: Cerebral Cortex


title: WT Liver male ZT6 mRNA rep7

description:
331574_CRM66
331574_CRM66_WT_L_26WKS_M_ZT6_L2.D705
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep12

description:
331610_CRM93
331610_CRM93_WT_L_26WKS_M_ZT6_L7.D706
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep6

description:
331566_CRM97
331566_CRM97_WT_L_26WKS_M_ZT6_L8.D709
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Cortex male ZT0 miRNA rep5

description:
561619_CRM54
561619_CRM54_WT_CTXR_26WKS_M_ZT0_L3.LB12
miRNA
processed data file: Cortex-counts.csv


title: WT Liver male ZT6 mRNA rep8

description:
331584_CRM91
331584_CRM91_WT_L_26WKS_M_ZT6_L4.D703
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep4

description:
331561_CRM31
331561_CRM31_WT_L_26WKS_M_ZT6_L7.D704
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep3

description:
331552_CRM13
331552_CRM13_WT_L_26WKS_M_ZT6_L6.D708
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep2

description:
331547_CRM34
331547_CRM34_WT_L_26WKS_M_ZT6_L5.D703
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep10

description:
331593_CRM59
331593_CRM59_WT_L_26WKS_M_ZT3_L6.D712
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 3 hrs

value: 27 hrs


title: WT Liver male ZT3 mRNA rep11

description:
331599_CRM2
331599_CRM2_WT_L_26WKS_M_ZT3_L7.D706
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep12

description:
331604_CRM62
331604_CRM62_WT_L_26WKS_M_ZT3_L8.D711
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep9

description:
331589_CRM114
331589_CRM114_WT_L_26WKS_M_ZT3_L5.D708
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Cortex male ZT18 miRNA rep5

description:
561630_CRM25
561630_CRM25_WT_CTXR_26WKS_M_ZT18_L3.LB23
miRNA
processed data file: Cortex-counts.csv

value: 18 hrs


title: WT Liver male ZT3 mRNA rep8

description:
331588_CRM38
331588_CRM38_WT_L_26WKS_M_ZT3_L5.D707
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: Wild type


title: WT Liver male ZT3 mRNA rep6

description:
331577_CRM15
331577_CRM15_WT_L_26WKS_M_ZT3_L2.D708
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 26 weeks


title: WT Liver male ZT9 mRNA rep2

description:
331558_CRM86
331558_CRM86_WT_L_26WKS_M_ZT9_L7.D701
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: male


title: WT Liver male ZT3 mRNA rep4

description:
331571_CRM42
331571_CRM42_WT_L_26WKS_M_ZT3_L1.D702
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT9 mRNA rep3

description:
331565_CRM90
331565_CRM90_WT_L_26WKS_M_ZT9_L8.D708
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep3

description:
331548_CRM3
331548_CRM3_WT_L_26WKS_M_ZT3_L5.D704
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT9 mRNA rep1

description:
331541_CRM35
331541_CRM35_WT_L_26WKS_M_ZT9_L3.D709
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep2

description:
331546_CRM16
331546_CRM16_WT_L_26WKS_M_ZT3_L4.D702
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep5

description:
331573_CRM120
331573_CRM120_WT_L_26WKS_M_ZT3_L2.D704
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep1

description:
331542_CRM112
331542_CRM112_WT_L_26WKS_M_ZT3_L4.D710
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep9

description:
331585_CRM98
331585_CRM98_WT_L_26WKS_M_ZT6_L4.D704
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT21 mRNA rep5

description:
331613_CRM103
331613_CRM103_WT_L_26WKS_M_ZT21_L8.D709
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 21 hrs


title: WT Liver male ZT6 mRNA rep5

description:
331562_CRM4
331562_CRM4_WT_L_26WKS_M_ZT6_L7.D705
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT21 mRNA rep6

description:
331617_CRM106
331617_CRM106_WT_L_26WKS_M_ZT21_L8.D701
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT21 mRNA rep4

description:
331606_CRM73
331606_CRM73_WT_L_26WKS_M_ZT21_L8.D702
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT21 mRNA rep3

description:
331578_CRM72
331578_CRM72_WT_L_26WKS_M_ZT21_L3.D709
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT21 mRNA rep1

description:
331563_CRM83
331563_CRM83_WT_L_26WKS_M_ZT21_L8.D706
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT18 mRNA rep6

description:
331596_CRM80
331596_CRM80_WT_L_26WKS_M_ZT18_L6.D703
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT18 mRNA rep5

description:
331583_CRM76
331583_CRM76_WT_L_26WKS_M_ZT18_L4.D702
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT21 mRNA rep2

description:
331572_CRM44
331572_CRM44_WT_L_26WKS_M_ZT21_L1.D703
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT18 mRNA rep4

description:
331582_CRM25
331582_CRM25_WT_L_26WKS_M_ZT18_L3.D701
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT6 mRNA rep1

description:
331545_CRM94
331545_CRM94_WT_L_26WKS_M_ZT6_L4.D701
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT18 mRNA rep3

description:
331559_CRM48
331559_CRM48_WT_L_26WKS_M_ZT18_L7.D702
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT3 mRNA rep7

description:
331580_CRM110
331580_CRM110_WT_L_26WKS_M_ZT3_L3.D711
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT18 mRNA rep2

description:
331554_CRM71
331554_CRM71_WT_L_26WKS_M_ZT18_L6.D710
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT18 mRNA rep1

description:
331549_CRM81
331549_CRM81_WT_L_26WKS_M_ZT18_L5.D705
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT15 mRNA rep5

description:
331609_CRM70
331609_CRM70_WT_L_26WKS_M_ZT15_L7.D705
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 15 hrs


title: WT Liver male ZT15 mRNA rep6

description:
331615_CRM30
331615_CRM30_WT_L_26WKS_M_ZT15_L8.D711
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT15 mRNA rep1

description:
331581_CRM22
331581_CRM22_WT_L_26WKS_M_ZT15_L3.D712
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT15 mRNA rep3

description:
331594_CRM45
331594_CRM45_WT_L_26WKS_M_ZT15_L6.D701
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep11

description:
331603_CRM84
331603_CRM84_WT_L_26WKS_M_ZT12_L8.D710
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 12 hrs


title: WT Liver male ZT12 mRNA rep10

description:
331598_CRM67
331598_CRM67_WT_L_26WKS_M_ZT12_L7.D705
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT15 mRNA rep2

description:
331592_CRM27
331592_CRM27_WT_L_26WKS_M_ZT15_L5.D711
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep8

description:
331590_CRM119
331590_CRM119_WT_L_26WKS_M_ZT12_L5.D709
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 36 hrs


title: WT Liver male ZT12 mRNA rep7

description:
331586_CRM49
331586_CRM49_WT_L_26WKS_M_ZT12_L4.D705
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: Liver


title: WT Liver male ZT12 mRNA rep12

description:
331614_CRM56
331614_CRM56_WT_L_26WKS_M_ZT12_L8.D710
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT15 mRNA rep4

description:
331605_CRM18
331605_CRM18_WT_L_26WKS_M_ZT15_L8.D712
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep4

description:
331556_CRM92
331556_CRM92_WT_L_26WKS_M_ZT12_L6.D711
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep9

description:
331597_CRM107
331597_CRM107_WT_L_26WKS_M_ZT12_L6.D704
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep6

description:
331575_CRM52
331575_CRM52_WT_L_26WKS_M_ZT12_L2.D706
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep3

description:
331551_CRM111
331551_CRM111_WT_L_26WKS_M_ZT12_L5.D707
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep2

description:
331544_CRM75
331544_CRM75_WT_L_26WKS_M_ZT12_L4.D712
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep11

description:
331608_CRM55
331608_CRM55_WT_L_26WKS_M_ZT0_L7.D704
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 0 hr

value: 0 hrs


title: WT Liver male ZT0 mRNA rep12

description:
331616_CRM102
331616_CRM102_WT_L_26WKS_M_ZT0_L8.D712
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv

value: 24 hrs


title: WT Liver male ZT0 mRNA rep9

description:
331591_CRM46
331591_CRM46_WT_L_26WKS_M_ZT0_L5.D710
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep8

description:
331587_CRM61
331587_CRM61_WT_L_26WKS_M_ZT0_L4.D706
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep10

description:
331600_CRM63
331600_CRM63_WT_L_26WKS_M_ZT0_L7.D707
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT12 mRNA rep1

description:
331540_CRM117
331540_CRM117_WT_L_26WKS_M_ZT12_L3.D708
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep6

description:
331564_CRM54
331564_CRM54_WT_L_26WKS_M_ZT0_L8.D707
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep7

description:
331570_CRM115
331570_CRM115_WT_L_26WKS_M_ZT0_L14
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep5

description:
331560_CRM113
331560_CRM113_WT_L_26WKS_M_ZT0_L7.D703
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep3

description:
331553_CRM47
331553_CRM47_WT_L_26WKS_M_ZT0_L6.D709
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep1

description:
331543_CRM118
331543_CRM118_WT_L_26WKS_M_ZT0_L4.D711
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Liver male ZT0 mRNA rep2

description:
331550_CRM101
331550_CRM101_WT_L_26WKS_M_ZT0_L5.D706
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep11

description:
331490_CRM10
331490_CRM10_WT_HY_26WKS_M_ZT9_L3.D712
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: Hypothalamus

value: 9 hrs


title: WT Hypothalamus male ZT9 mRNA rep9

description:
331454_CRM96
331454_CRM96_WT_HY_26WKS_M_ZT9_L5.D704
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 33 hrs


title: WT Hypothalamus male ZT9 mRNA rep10

description:
331464_CRM57
331464_CRM57_WT_HY_26WKS_M_ZT9_L7.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Liver male ZT12 mRNA rep5

description:
331568_CRM87
331568_CRM87_WT_L_26WKS_M_ZT12_L1.D711
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep7

description:
331405_CRM86
331405_CRM86_WT_HY_26WKS_M_ZT9_L11
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Liver male ZT0 mRNA rep4

description:
331557_CRM105
331557_CRM105_WT_L_26WKS_M_ZT0_L6.D712
mRNA
processed data file: Liver-FPKM.csv
processed data file: Liver-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep6

description:
331389_CRM5
331389_CRM5_WT_HY_26WKS_M_ZT9_L8.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep5

description:
331382_CRM99
331382_CRM99_WT_HY_26WKS_M_ZT9_L7.D704
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep2

description:
331356_CRM90
331356_CRM90_WT_HY_26WKS_M_ZT9_L2.D704
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep4

description:
331377_CRM36
331377_CRM36_WT_HY_26WKS_M_ZT9_L6.D712
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep12

description:
331494_CRM89
331494_CRM89_WT_HY_26WKS_M_ZT6_L4.D703
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 6 hrs

value: 30 hrs


title: WT Hypothalamus male ZT9 mRNA rep1

description:
331331_CRM88
331331_CRM88_WT_HY_26WKS_M_ZT9_L6.D703
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep11

description:
331489_CRM97
331489_CRM97_WT_HY_26WKS_M_ZT6_L3.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep10

description:
331487_CRM98
331487_CRM98_WT_HY_26WKS_M_ZT6_L2.D709
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep8

description:
331416_CRM93
331416_CRM93_WT_HY_26WKS_M_ZT6_L5.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep9

description:
331451_CRM31
331451_CRM31_WT_HY_26WKS_M_ZT6_L4.D701
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep7

description:
331403_CRM14
331403_CRM14_WT_HY_26WKS_M_ZT6_L3.D712
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep4

description:
331354_CRM13
331354_CRM13_WT_HY_26WKS_M_ZT6_L2.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep5

description:
331372_CRM66
331372_CRM66_WT_HY_26WKS_M_ZT6_L5.D707
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep6

description:
331388_CRM91
331388_CRM91_WT_HY_26WKS_M_ZT6_L8.D710
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep2

description:
331336_CRM34
331336_CRM34_WT_HY_26WKS_M_ZT6_L7.D708
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep1

description:
331333_CRM4
331333_CRM4_WT_HY_26WKS_M_ZT6_L1
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep8

description:
331440_CRM35
331440_CRM35_WT_HY_26WKS_M_ZT9_L2.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep11

description:
331510_CRM42
331510_CRM42_WT_HY_26WKS_M_ZT3_L6.D705
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 3 hrs


title: WT Hypothalamus male ZT3 mRNA rep10

description:
331504_CRM62
331504_CRM62_WT_HY_26WKS_M_ZT3_L5.D710
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: Wild type

value: 27 hrs


title: WT Hypothalamus male ZT3 mRNA rep12

description:
331524_CRM114
331524_CRM114_WT_HY_26WKS_M_ZT3_L8.D704
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 26 weeks

value: male


title: WT Hypothalamus male ZT3 mRNA rep9

description:
331437_CRM38
331437_CRM38_WT_HY_26WKS_M_ZT3_L1.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep7

description:
331387_CRM112
331387_CRM112_WT_HY_26WKS_M_ZT3_L15
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep8

description:
331404_CRM2
331404_CRM2_WT_HY_26WKS_M_ZT3_L10
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep3

description:
331358_CRM110
331358_CRM110_WT_HY_26WKS_M_ZT3_L3.D706
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep4

description:
331360_CRM16
331360_CRM16_WT_HY_26WKS_M_ZT3_L3.D708
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep1

description:
331330_CRM59
331330_CRM59_WT_HY_26WKS_M_ZT3_L19
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT9 mRNA rep3

description:
331369_CRM95
331369_CRM95_WT_HY_26WKS_M_ZT9_L5.D705
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep2

description:
331339_CRM3
331339_CRM3_WT_HY_26WKS_M_ZT3_L7.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT3 mRNA rep5

description:
331379_CRM120
331379_CRM120_WT_HY_26WKS_M_ZT3_L6.D701
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT21 mRNA rep5

description:
331507_CRM83
331507_CRM83_WT_HY_26WKS_M_ZT21_L5.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 21 hrs


title: WT Hypothalamus male ZT21 mRNA rep4

description:
331479_CRM72
331479_CRM72_WT_HY_26WKS_M_ZT21_L1.D701
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 mRNA rep6

description:
331486_CRM48
331486_CRM48_WT_HY_26WKS_M_ZT18_L2.D708
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 18 hrs


title: WT Hypothalamus male ZT21 mRNA rep6

description:
331537_CRM103
331537_CRM103_WT_HY_26WKS_M_ZT21_L3.D705
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT21 mRNA rep1

description:
331324_CRM73
331324_CRM73_WT_HY_26WKS_M_ZT21_L4.D708
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT6 mRNA rep3

description:
331343_CRM94
331343_CRM94_WT_HY_26WKS_M_ZT6_L8.D703
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT21 mRNA rep3

description:
331462_CRM44
331462_CRM44_WT_HY_26WKS_M_ZT21_L6.D712
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT21 mRNA rep2

description:
331421_CRM106
331421_CRM106_WT_HY_26WKS_M_ZT21_L6.D707
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 mRNA rep5

description:
331438_CRM71
331438_CRM71_WT_HY_26WKS_M_ZT18_L31
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 mRNA rep2

description:
331367_CRM80
331367_CRM80_WT_HY_26WKS_M_ZT18_L4.D703
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 mRNA rep3

description:
331376_CRM76
331376_CRM76_WT_HY_26WKS_M_ZT18_L6.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 mRNA rep6

description:
331503_CRM27
331503_CRM27_WT_HY_26WKS_M_ZT15_L5.D709
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 15 hrs


title: WT Hypothalamus male ZT18 mRNA rep4

description:
331420_CRM25
331420_CRM25_WT_HY_26WKS_M_ZT18_L1.D703
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 mRNA rep3

description:
331423_CRM45
331423_CRM45_WT_HY_26WKS_M_ZT15_L7.D709
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 mRNA rep4

description:
331447_CRM30
331447_CRM30_WT_HY_26WKS_M_ZT15_L3.D709
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT18 mRNA rep1

description:
331359_CRM81
331359_CRM81_WT_HY_26WKS_M_ZT18_L3.D707
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 mRNA rep2

description:
331325_CRM70
331325_CRM70_WT_HY_26WKS_M_ZT15_L13
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep12

description:
331536_CRM52
331536_CRM52_WT_HY_26WKS_M_ZT12_L30
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 12 hrs


title: WT Hypothalamus male ZT3 mRNA rep6

description:
331383_CRM15
331383_CRM15_WT_HY_26WKS_M_ZT3_L7.D705
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep6

description:
331419_CRM84
331419_CRM84_WT_HY_26WKS_M_ZT12_L1.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep7

description:
331484_CRM117
331484_CRM117_WT_HY_26WKS_M_ZT12_L2.D706
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 36 hrs


title: WT Hypothalamus male ZT12 mRNA rep8

description:
331505_CRM87
331505_CRM87_WT_HY_26WKS_M_ZT12_L5.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep10

description:
331518_CRM111
331518_CRM111_WT_HY_26WKS_M_ZT12_L7.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT15 mRNA rep1

description:
331315_CRM22
331315_CRM22_WT_HY_26WKS_M_ZT15_L2.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep9

description:
331513_CRM67
331513_CRM67_WT_HY_26WKS_M_ZT12_L6.D707
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep2

description:
331381_CRM92
331381_CRM92_WT_HY_26WKS_M_ZT12_L6
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep3

description:
331411_CRM119
331411_CRM119_WT_HY_26WKS_M_ZT12_L4.D709
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep1

description:
331342_CRM75
331342_CRM75_WT_HY_26WKS_M_ZT12_L8.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 mRNA rep11

description:
331525_CRM55
331525_CRM55_WT_HY_26WKS_M_ZT0_L8.D705
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 0 hr

value: 0 hrs


title: WT Hypothalamus male ZT12 mRNA rep4

description:
331415_CRM56
331415_CRM56_WT_HY_26WKS_M_ZT12_L5.D701
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: Hypothalamus


title: WT Hypothalamus male ZT0 mRNA rep12

description:
331539_CRM61
331539_CRM61_WT_HY_26WKS_M_ZT0_L3.D707
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 mRNA rep9

description:
331514_CRM63
331514_CRM63_WT_HY_26WKS_M_ZT0_L7.D708
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 mRNA rep8

description:
331506_CRM105
331506_CRM105_WT_HY_26WKS_M_ZT0_L5.D712
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 24 hrs


title: WT Hypothalamus male ZT0 mRNA rep3

description:
331410_CRM101
331410_CRM101_WT_HY_26WKS_M_ZT0_L4.D708
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 mRNA rep6

description:
331463_CRM115
331463_CRM115_WT_HY_26WKS_M_ZT0_L6.D701
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 mRNA rep5

description:
331444_CRM102
331444_CRM102_WT_HY_26WKS_M_ZT0_L3.D706
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT0 mRNA rep1

description:
331318_CRM46
331318_CRM46_WT_HY_26WKS_M_ZT0_L3.D702
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep11

description:
331527_CRM49
331527_CRM49_WT_HY_26WKS_M_ZT12_L1.D707
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Striatum male ZT9 mRNA rep7

description:
331480_CRM36
331480_CRM36_WT_STRR_26WKS_M_ZT9_L1.D702
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: Corpus Striatum

value: 9 hrs


title: WT Striatum male ZT9 mRNA rep8

description:
331530_CR88
331530_CR88_WT_STRR_26WKS_M_ZT9_L1.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 33 hrs


title: WT Hypothalamus male ZT0 mRNA rep2

description:
331348_CRM47
331348_CRM47_WT_HY_26WKS_M_ZT0_L1.D708
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Striatum male ZT9 mRNA rep9

description:
331538_CRM90
331538_CRM90_WT_STRR_26WKS_M_ZT9_L3.D706
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 mRNA rep5

description:
331364_CRM57
331364_CRM57_WT_STRR_26WKS_M_ZT9_L4.D712
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 mRNA rep4

description:
331346_CRM35
331346_CRM35_WT_STRR_26WKS_M_ZT9_L8.D706
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 mRNA rep2

description:
331322_CRM95
331322_CRM95_WT_STRR_26WKS_M_ZT9_L4.D706
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 mRNA rep3

description:
331329_CRM99
331329_CRM99_WT_STRR_26WKS_M_ZT9_L5.D701
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 mRNA rep11

description:
331498_CRM14
331498_CRM14_WT_STRR_26WKS_M_ZT6_L4.D706
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 6 hrs


title: WT Hypothalamus male ZT15 mRNA rep5

description:
331481_CRM18
331481_CRM18_WT_HY_26WKS_M_ZT15_L1.D703
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: Wild type


title: WT Striatum male ZT9 mRNA rep1

description:
331320_CRM96
331320_CRM96_WT_STRR_26WKS_M_ZT9_L3.D704
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 mRNA rep10

description:
331488_CRM94
331488_CRM94_WT_STRR_26WKS_M_ZT6_L3.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 30 hrs


title: WT Hypothalamus male ZT0 mRNA rep10

description:
331516_CRM113
331516_CRM113_WT_HY_26WKS_M_ZT0_L7.D710
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: 26 weeks


title: WT Hypothalamus male ZT0 mRNA rep7

description:
331477_CRM54
331477_CRM54_WT_HY_26WKS_M_ZT0_L8.D711
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv

value: male


title: WT Striatum male ZT6 mRNA rep9

description:
331457_CRM98
331457_CRM98_WT_STRR_26WKS_M_ZT6_L5.D707
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Hypothalamus male ZT12 mRNA rep5

description:
331417_CRM107
331417_CRM107_WT_HY_26WKS_M_ZT12_L1.D712
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Striatum male ZT6 mRNA rep8

description:
331446_CRM31
331446_CRM31_WT_STRR_26WKS_M_ZT6_L1.D706_503
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Hypothalamus male ZT0 mRNA rep4

description:
331426_CRM118
331426_CRM118_WT_HY_26WKS_M_ZT0_L7.D712
mRNA
processed data file: Hypothalamus-FPKM.csv
processed data file: Hypothalamus-counts.csv


title: WT Striatum male ZT6 mRNA rep7

description:
331445_CRM91
331445_CRM91_WT_STRR_26WKS_M_ZT6_L1.D705
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 mRNA rep6

description:
331429_CRM34
331429_CRM34_WT_STRR_26WKS_M_ZT6_L4
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 mRNA rep5

description:
331400_CRM4
331400_CRM4_WT_STRR_26WKS_M_ZT6_L2.D709
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 mRNA rep4

description:
331393_CRM93
331393_CRM93_WT_STRR_26WKS_M_ZT6_L1.D702
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 mRNA rep3

description:
331362_CRM97
331362_CRM97_WT_STRR_26WKS_M_ZT6_L4.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT6 mRNA rep2

description:
331326_CRM89
331326_CRM89_WT_STRR_26WKS_M_ZT6_L5.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep8

description:
331478_CRM59
331478_CRM59_WT_STRR_26WKS_M_ZT3_L1.D712
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 3 hrs

value: 27 hrs


title: WT Striatum male ZT6 mRNA rep1

description:
331321_CRM66
331321_CRM66_WT_STRR_26WKS_M_ZT6_L4.D705
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep6

description:
331474_CRM42
331474_CRM42_WT_STRR_26WKS_M_ZT3_L1.D707_503
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep7

description:
331476_CRM112
331476_CRM112_WT_STRR_26WKS_M_ZT3_L8.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep5

description:
331461_CRM38
331461_CRM38_WT_STRR_26WKS_M_ZT3_L6.D711
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep3

description:
331335_CRM110
331335_CRM110_WT_STRR_26WKS_M_ZT3_L6.D707
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep4

description:
331368_CRM114
331368_CRM114_WT_STRR_26WKS_M_ZT3_L5.D704
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep1

description:
331313_CRM2
331313_CRM2_WT_STRR_26WKS_M_ZT3_L2.D709
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT9 mRNA rep6

description:
331456_CRM86
331456_CRM86_WT_STRR_26WKS_M_ZT9_L5.D706
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT3 mRNA rep2

description:
331317_CRM62
331317_CRM62_WT_STRR_26WKS_M_ZT3_L22
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT21 mRNA rep5

description:
331424_CRM73
331424_CRM73_WT_STRR_26WKS_M_ZT21_L7.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 21 hrs


title: WT Striatum male ZT21 mRNA rep4

description:
331397_CRM44
331397_CRM44_WT_STRR_26WKS_M_ZT21_L2.D706
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT21 mRNA rep2

description:
331344_CRM103
331344_CRM103_WT_STRR_26WKS_M_ZT21_L1.D707
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT21 mRNA rep3

description:
331390_CRM83
331390_CRM83_WT_STRR_26WKS_M_ZT21_L1.D712
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT21 mRNA rep6

description:
331535_CRM72
331535_CRM72_WT_STRR_26WKS_M_ZT21_L2.D703
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT18 mRNA rep4

description:
331533_CRM48
331533_CRM48_WT_STRR_26WKS_M_ZT18_L2.D701
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 18 hrs


title: WT Striatum male ZT21 mRNA rep1

description:
331332_CRM106
331332_CRM106_WT_STRR_26WKS_M_ZT21_L6.D704
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT18 mRNA rep1

description:
331439_CRM80
331439_CRM80_WT_STRR_26WKS_M_ZT18_L2.D701
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT18 mRNA rep2

description:
331442_CRM76
331442_CRM76_WT_STRR_26WKS_M_ZT18_L2.D704
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT15 mRNA rep2

description:
331386_CRM70
331386_CRM70_WT_STRR_26WKS_M_ZT15_L16
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 15 hrs


title: WT Striatum male ZT15 mRNA rep1

description:
331357_CRM27
331357_CRM27_WT_STRR_26WKS_M_ZT15_L3.D705
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep9

description:
331508_CRM84
331508_CRM84_WT_STRR_26WKS_M_ZT12_L6.D703
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 12 hrs


title: WT Striatum male ZT12 mRNA rep11

description:
331515_CRM49
331515_CRM49_WT_STRR_26WKS_M_ZT12_L18
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep8

description:
331502_CRM52
331502_CRM52_WT_STRR_26WKS_M_ZT12_L4.D708
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep10

description:
331511_CRM92
331511_CRM92_WT_STRR_26WKS_M_ZT12_L6.D706
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 36 hrs


title: WT Striatum male ZT12 mRNA rep6

description:
331452_CRM56
331452_CRM56_WT_STRR_26WKS_M_ZT12_L4.D702
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep5

description:
331431_CRM87
331431_CRM87_WT_STRR_26WKS_M_ZT12_L8.D705
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep7

description:
331491_CRM111
331491_CRM111_WT_STRR_26WKS_M_ZT12_L3.D701
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep4

description:
331418_CRM119
331418_CRM119_WT_STRR_26WKS_M_ZT12_L32
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep2

description:
331394_CRM75
331394_CRM75_WT_STRR_26WKS_M_ZT12_L33
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT12 mRNA rep3

description:
331395_CRM67
331395_CRM67_WT_STRR_26WKS_M_ZT12_L1.D704
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT0 mRNA rep8

description:
331448_CRM54
331448_CRM54_WT_STRR_26WKS_M_ZT0_L3.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: 0 hr

value: 0 hrs


title: WT Striatum male ZT0 mRNA rep7

description:
331433_CRM101
331433_CRM101_WT_STRR_26WKS_M_ZT0_L1.D704
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: Corpus Striatum

value: 24 hrs


title: RNAseq_ddH2O_2

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description: mRNA

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
The fastq files are checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Fastq files are mapped to hg19 reference genome (from igenomes) using STAR
Read counts are then generated using featureCounts
TMM normalization and differential expression analysis is performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: a table of edgeR analysis of these RNA-seq data

organism: Homo sapiens

source_name: HCT116 colon cancer cell line

growth_protocol: HCT116 NMD reporter cells were treated with ddH2O or 200 μM paraquat for 96 hours

extract_protocol:
RNA was isolated using the RNeasy Mini kit (Qiagen) and gDNA contamination was removed using the TURBO DNA-Free kit (ThermoFisher Scientific)
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced using the 75 bp single-read protocol on a NextSeq 500 platform (Illumina).

tag: sgrna received

value: no

tag: sample type

value: NMD reporter


title: WT Striatum male ZT0 mRNA rep5

description:
331412_CRM113
331412_CRM113_WT_STRR_26WKS_M_ZT0_L4.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv

value: Wild type


title: RNAseq_ddH2O_1

description: mRNA


title: WT Striatum male ZT12 mRNA rep1

description:
331309_CRM117
331309_CRM117_WT_STRR_26WKS_M_ZT12_L1.D705
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT0 mRNA rep4

description:
331361_CRM102
331361_CRM102_WT_STRR_26WKS_M_ZT0_L3.D709
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT0 mRNA rep6

description:
331432_CRM63
331432_CRM63_WT_STRR_26WKS_M_ZT0_L3
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Striatum male ZT0 mRNA rep3

description:
331350_CRM55
331350_CRM55_WT_STRR_26WKS_M_ZT0_L1.D710
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: RNAseq_PQ_1

description: mRNA


title: WT Striatum male ZT0 mRNA rep9

description:
331483_CRM47
331483_CRM47_WT_STRR_26WKS_M_ZT0_L2.D705
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: RNAseq_DMSO-2

description: mRNA

growth_protocol: HCT116 NMD reporter cells were treated with DMSO or 5 nM bafilomycin for 48 hours


title: WT Striatum male ZT0 mRNA rep2

description:
331349_CRM46
331349_CRM46_WT_STRR_26WKS_M_ZT0_L1.D709
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Cortex male ZT9 mRNA rep12

description:
331534_CRM5
331534_CRM5_WT_CTXR_26WKS_M_ZT9_L2.D702
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: Cerebral Cortex

value: 9 hrs


title: RNAseq_DMSO-1

description: mRNA


title: WT Cortex male ZT9 mRNA rep10

description:
331485_CRM99
331485_CRM99_WT_CTXR_26WKS_M_ZT9_L2.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 26 weeks

value: male

value: 33 hrs


title: RNAseq_PQ_2

description: mRNA


title: WT Cortex male ZT9 mRNA rep9

description:
331449_CRM96
331449_CRM96_WT_CTXR_26WKS_M_ZT9_L4.D711
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Striatum male ZT18 mRNA rep3

description:
331482_CRM71
331482_CRM71_WT_STRR_26WKS_M_ZT18_L5
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Cortex male ZT9 mRNA rep7

description:
331425_CRM36
331425_CRM36_WT_CTXR_26WKS_M_ZT9_L7.D711
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 mRNA rep8

description:
331434_CRM86
331434_CRM86_WT_CTXR_26WKS_M_ZT9_L1.D708
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: RNAseq_Baf_2

description: mRNA


title: WT Cortex male ZT9 mRNA rep11

description:
331519_CRM35
331519_CRM35_WT_CTXR_26WKS_M_ZT9_L7.D712
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 mRNA rep6

description:
331374_CRM10
331374_CRM10_WT_CTXR_26WKS_M_ZT9_L6.D709
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 mRNA rep5

description:
331370_CRM90
331370_CRM90_WT_CTXR_26WKS_M_ZT9_L17
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: RNA-seq_sgNT2

description: mRNA

growth_protocol: HCT116 cells were infected with lentivirus to deliver Cas9 and sgRNAs targeting ABCE1, or non-target sgRNAs. Successfully transduced cells were selected in puromycin for 4 days, before harvesting for RNA-sequencing.

treatment_protocol: N/A.


title: WT Cortex male ZT9 mRNA rep4

description:
331352_CRM1
331352_CRM1_WT_CTXR_26WKS_M_ZT9_L2.D712
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 mRNA rep3

description:
331327_CRM57
331327_CRM57_WT_CTXR_26WKS_M_ZT9_L5.D711
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 mRNA rep2

description:
331319_CRM88
331319_CRM88_WT_CTXR_26WKS_M_ZT9_L9
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT9 mRNA rep1

description:
331307_CRM95
331307_CRM95_WT_CTXR_26WKS_M_ZT9_L1.D703
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: RNA-seq_sgNT1

description: mRNA


title: WT Cortex male ZT6 mRNA rep12

description:
331532_CRM4
331532_CRM4_WT_CTXR_26WKS_M_ZT6_L2.D712
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 6 hrs


title: WT Striatum male ZT0 mRNA rep1

description:
331323_CRM118
331323_CRM118_WT_STRR_26WKS_M_ZT0_L4.D707
mRNA
processed data file: Striatum-FPKM.csv
processed data file: Striatum-counts.csv


title: WT Cortex male ZT6 mRNA rep10

description:
331450_CRM98
331450_CRM98_WT_CTXR_26WKS_M_ZT6_L4.D712
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 30 hrs


title: RNA-seq_sgABCE1-1

description: mRNA


title: WT Cortex male ZT6 mRNA rep9

description:
331443_CRM31
331443_CRM31_WT_CTXR_26WKS_M_ZT6_L2.D705
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 mRNA rep11

description:
331471_CRM97
331471_CRM97_WT_CTXR_26WKS_M_ZT6_L7.D706
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Ribosome profiling_sgNT2

description: ribosome protected mRNA fragments

data_processing:
For each sample, fastq files from two runs were combined
Adapter was trimmed using custom scripts
Reads that mapped to noncoding RNA were discarded
Reads were mapped to human reference genome using HISAT2.1.0
Uniquely mapped reads between 24 and 31nt were kept
Genome_build: GRCh38
Supplementary_files_format_and_content: a table of ribosome protected fragment counts

growth_protocol: HCT116 cells were infected with lentivirus to deliver Cas9 and sgRNAs targeting ABCE1, or non-target sgRNAs. Successfully transduced cells were selected in puromycin for 4 days, before harvesting for ribosome profiling as described in the manuscript.

extract_protocol:
Ribosome protected fragments were isolated as described in McGlincy and Ingolia, Methods, 2017.
Ribosome profiling libraries were prepared as described in Ingolia et al., Nature Protocols, 2012, and McGlincy and Ingolia, Methods, 2017, and sequenced on a NextSeq500 platform.


title: WT Cortex male ZT6 mRNA rep7

description:
331409_CRM94
331409_CRM94_WT_CTXR_26WKS_M_ZT6_L4.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Ribosome profiling_sgNT1

description: ribosome protected mRNA fragments


title: WT Cortex male ZT6 mRNA rep5

description:
331385_CRM66
331385_CRM66_WT_CTXR_26WKS_M_ZT6_L8.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: RNAseq_Baf_1

description: mRNA


title: WT Cortex male ZT6 mRNA rep4

description:
331353_CRM93
331353_CRM93_WT_CTXR_26WKS_M_ZT6_L2.D701
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Ribosome profiling_sgABCE1-2

description: ribosome protected mRNA fragments


title: WT Cortex male ZT6 mRNA rep3

description:
331347_CRM13
331347_CRM13_WT_CTXR_26WKS_M_ZT6_L1.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 mRNA rep2

description:
331341_CRM14
331341_CRM14_WT_CTXR_26WKS_M_ZT6_L8.D701
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT6 mRNA rep6

description:
331408_CRM91
331408_CRM91_WT_CTXR_26WKS_M_ZT6_L4.D706
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: NMD screen_unsorted_PTC35-2

description: sgRNA sequence amplified out of genomic DNA

library_source: genomic

data_processing:
Reads were mapped to Brunello library sgRNA reference files.
Normalized read counts were calculated as described in Shalem et al., Science, 2014.
MAGeCK (Li et al., Genome Biology, 2014) was used to assign significance to each gene targeted by the sgRNAs in the Brunello library.
Genome_build: Brunello library sgRNA reference files obtained from Addgene
Supplementary_files_format_and_content: A table of normalized read counts for each sgRNA in each sample is provided.

molecule: genomic DNA

growth_protocol: Fluorescent-reporter coupled CRISPR/Cas9-mediated loss of function screening was carried out as described in Golden et al., Nature, 2017, except for the Brunello library (Addgene #73179) but not the GeCKO V2 libarary was used, in both NMD EGFP reporter and control EGFP reporter cell lines. Reporter cell line generation and more information about the screen are described in the manuscript.

extract_protocol:
Genomic DNA was extracted from cell pellets using either a gDNA isolation method that has been previously described Golden et al., Nature, 2017 for the sorted cells or the MasterPureTM Complete DNA Purification Kit (Lucigen) for the unsorted cells.
PCR amplicon libraries were generated as described in the manuscript.
CRISPR/Cas9-mediated loss of function screening.

tag: experiment

value: NMD screen

tag: lentiviral library received

value: Brunello library

tag: reporter cell line

value: Control reporter


title: WT Cortex male ZT6 mRNA rep1

description:
331306_CRM89
331306_CRM89_WT_CTXR_26WKS_M_ZT6_L1.D702
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: tissue


title: WT Cortex male ZT3 mRNA rep11

description:
331526_CRM42
331526_CRM42_WT_CTXR_26WKS_M_ZT3_L1.D706
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: genotype

value: 3 hrs


title: Ribosome profiling_sgABCE1-1

description: ribosome protected mRNA fragments


title: WT Cortex male ZT3 mRNA rep12

description:
331531_CRM16
331531_CRM16_WT_CTXR_26WKS_M_ZT3_L2.D711
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: strain/background


title: RNA-seq_sgABCE1-2

description: mRNA


title: WT Cortex male ZT3 mRNA rep10

description:
331467_CRM120
331467_CRM120_WT_CTXR_26WKS_M_ZT3_L7.D705
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: age

value: 27 hrs


title: WT Cortex male ZT3 mRNA rep9

description:
331455_CRM112
331455_CRM112_WT_CTXR_26WKS_M_ZT3_L5.D705
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: Sex


title: NMD screen_unsorted_PTC231-2


title: WT Cortex male ZT3 mRNA rep8

description:
331453_CRM38
331453_CRM38_WT_CTXR_26WKS_M_ZT3_L4.D703
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: zt group


title: NMD screen_unsorted_PTC231-1


title: WT Cortex male ZT3 mRNA rep7

description:
331436_CRM3
331436_CRM3_WT_CTXR_26WKS_M_ZT3_L1.D710
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: time point


title: WT Cortex male ZT6 mRNA rep8

description:
331428_CRM34
331428_CRM34_WT_CTXR_26WKS_M_ZT6_L7.D702
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: NMD screen_Sorted_PTC35-2


title: NMD screen_sorted_PTC35-1


title: WT Cortex male ZT3 mRNA rep5

description:
331407_CRM59
331407_CRM59_WT_CTXR_26WKS_M_ZT3_L3.D705
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 mRNA rep6

description:
331414_CRM2
331414_CRM2_WT_CTXR_26WKS_M_ZT3_L5.D712
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv