title: Sh2d5+/- Striatum female mRNA rep4

description:
ShQ 8-2
ShQ_8_2_GSM3929065
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Sh2d5+/- Striatum female mRNA rep3

status: Public on Oct 19 2022

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:
ShQ 10-1
ShQ_10_1_GSM3929064
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina HiSeq 4000 PE-75.
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: rawCounts_WtHet_Striatum_6m.csv: Comma-separated text file includes Count values for each Sample.
Supplementary_files_format_and_content: FPKM_WtHet_Striatum_6m.csv: Comma-separated text file includes FPKM values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Corpus Striatum

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded libraries preparation protocol (Illumina Inc).

tag: tissue

value: Corpus Striatum

tag: genotype

tag: background

tag: age

value: 6 months

tag: Sex

value: Female

tag: well address

tag: batch

value: Sh2d5 group


title: Sh2d5+/- Striatum female mRNA rep5

description:
ShQ 7-1
ShQ_7_1_GSM3929066
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Sh2d5+/- Striatum female mRNA rep1

description:
ShQ 8-3
ShQ_8_3_GSM3929062
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Scn4b+/- Striatum male mRNA rep4

description:
11-1-59393395
X11_1_GSM3861370
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Male

value: Scn4b group


title: Tbc1d8+/- Striatum male mRNA rep2

description:
TbcQ 1-3
TbcQ_1_3_GSM3972537
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Tbc1d8 group


title: Scn4b+/- Striatum male mRNA rep3

description:
8-2-59395373
X8_2_GSM3861369
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Sh2d5+/- Striatum male mRNA rep1

description:
ShQ 13-2
ShQ_13_2_GSM3929068
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Tbc1d8+/- Striatum female mRNA rep2

description:
TbcQ 4-1
TbcQ_4_1_GSM3972533
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Scn4b+/- Striatum female mRNA rep4

description:
10-2-59384504
X10_2_GSM3861366
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Scn4b+/- Striatum male mRNA rep2

description:
3-1-59384513
X3_1_GSM3861368
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Sh2d5+/- Striatum female mRNA rep2

description:
ShQ 9-2
ShQ_9_2_GSM3929063
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Scn4b+/- Striatum female mRNA rep1

description:
2-4-59388431
X2_4_GSM3861363
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Scn4b+/- Striatum female mRNA rep2

description:
4-2-59382561
X4_2_GSM3861364
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Scn4b+/- Striatum female mRNA rep3

description:
7-3-59389401
X7_3_GSM3861365
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Syndig1l+/- Striatum female mRNA rep3

description:
SynQ 4-1
SynQ_4_1_GSM3885044
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Syndig1l group


title: Ryr1+/- Striatum male mRNA rep4

description:
RyrQ14-4-103714690
RyrQ14_4_GSM3898891
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Ryr1 group


title: Ryr1+/- Striatum male mRNA rep3

description:
RyrQ6-3-103729630
RyrQ6_3_GSM3898890
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ryr1+/- Striatum female mRNA rep1

description:
RyrQ15-1-103728626
RyrQ15_1_GSM3898885
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ryr1+/- Striatum male mRNA rep1

description:
RyrQ1-5-103720670
RyrQ1_5_GSM3898888
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ryr1+/- Striatum male mRNA rep5

description:
RyrQ16-2-103722673
RyrQ16_2_GSM3898892
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Sh2d5+/- Striatum male mRNA rep2

description:
ShQ 5-1
ShQ_5_1_GSM3929069
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ryr1+/- Striatum female mRNA rep3

description:
RyrQ17-5-103727626
RyrQ17_5_GSM3898887
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ryr1+/- Striatum female mRNA rep2

description:
RyrQ17-3-103729628
RyrQ17_3_GSM3898886
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rgs9+/- Striatum male mRNA rep2

description:
RgsQ 5-3
RgsQ_5_3_GSM3909895
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Rgs9 group


title: Scn4b+/- Striatum male mRNA rep1

description:
1-1-59394389
X1_1_GSM3861367
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rgs9+/- Striatum female mRNA rep3

description:
RgsQ 11-1
RgsQ_11_1_GSM3909892
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum male mRNA rep4

description:
12-1-85882799
X12_1_GSM3995112
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Rest+/-

value: Rest group


title: Rgs9+/- Striatum female mRNA rep2

description:
RgsQ 8-3
RgsQ_8_3_GSM3909891
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rgs9+/- Striatum female mRNA rep4

description:
RgsQ 13-3
RgsQ_13_3_GSM3909893
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum male mRNA rep2

description:
8-3-85890815
X8_3_GSM3995110
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum male mRNA rep3

description:
10-4-85886822
X10_4_GSM3995111
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rgs9+/- Striatum female mRNA rep1

description:
RgsQ 2-2
RgsQ_2_2_GSM3909890
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ryr1+/- Striatum male mRNA rep2

description:
RyrQ4-4-103723691
RyrQ4_4_GSM3898889
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum male mRNA rep1

description:
8-1-85884826
X8_1_GSM3995109
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum female mRNA rep3

description:
26-3-85895814
X26_3_GSM3995107
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum female mRNA rep2

description:
19-4-85888827
X19_4_GSM3995106
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rasgef1a+/- Striatum male mRNA rep3

description:
RasQ 6-5
RasQ_6_5_GSM3929036
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Rasgef1a group


title: Rasgef1a+/- Striatum male mRNA rep4

description:
RasQ 10-1
RasQ_10_1_GSM3929037
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum female mRNA rep1

description:
13-3-85886824
X13_3_GSM3995105
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rest+/- Striatum female mRNA rep4

description:
26-4-85892827
X26_4_GSM3995108
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rgs9+/- Striatum male mRNA rep1

description:
RgsQ 3-2
RgsQ_3_2_GSM3909894
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rasgef1a+/- Striatum male mRNA rep2

description:
RasQ 6-4
RasQ_6_4_GSM3929035
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rasgef1a+/- Striatum female mRNA rep3

description:
RasQ 9-4
RasQ_9_4_GSM3929032
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rarb+/- Striatum male mRNA rep2

description:
5-2-85893826
X5_2_GSM3995035
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Rarb+/-

value: Rarb group


title: Rarb+/- Striatum male mRNA rep3

description:
5-4-85893828
X5_4_GSM3995036
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rasgef1a+/- Striatum male mRNA rep1

description:
RasQ 3-3
RasQ_3_3_GSM3929034
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rgs9+/- Striatum male mRNA rep4

description:
RgsQ 9-3
RgsQ_9_3_GSM3909897
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rasgef1a+/- Striatum female mRNA rep1

description:
RasQ 2-2
RasQ_2_2_GSM3929030
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rasgef1a+/- Striatum female mRNA rep4

description:
RasQ 15-3
RasQ_15_3_GSM3929033
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rasgef1a+/- Striatum female mRNA rep2

description:
RasQ 4-1
RasQ_4_1_GSM3929031
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rarb+/- Striatum male mRNA rep1

description:
3-2-85883810
X3_2_GSM3995034
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rgs9+/- Striatum male mRNA rep3

description:
RgsQ 9-1
RgsQ_9_1_GSM3909896
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rarb+/- Striatum female mRNA rep3

description:
16-4-85878804
X16_4_GSM3995032
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rarb+/- Striatum male mRNA rep4

description:
3-5-85885819
X3_5_GSM3995037
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rarb+/- Striatum female mRNA rep1

description:
14-4-85886803
X14_4_GSM3995030
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rarb+/- Striatum female mRNA rep2

description:
14-5-85886805
X14_5_GSM3995031
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pxdn+/- Striatum male mRNA rep3

description:
PxdQ 3-1
PxdQ_3_1_GSM3929004
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Pxdn+/-

value: Pxdn group


title: Pxdn+/- Striatum male mRNA rep4

description:
PxdQ 5-4
PxdQ_5_4_GSM3929005
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Corpus Striatum


title: Pxdn+/- Striatum male mRNA rep2

description:
PxdQ 1-2
PxdQ_1_2_GSM3929003
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: 6 months


title: Pxdn+/- Striatum male mRNA rep1

description:
PxdQ 1-1
PxdQ_1_1_GSM3929002
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pxdn+/- Striatum female mRNA rep4

description:
PxdQ 8-2
PxdQ_8_2_GSM3929001
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Female


title: Pxdn+/- Striatum female mRNA rep3

description:
PxdQ 7-1
PxdQ_7_1_GSM3929000
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pxdn+/- Striatum female mRNA rep2

description:
PxdQ 13-1
PxdQ_13_1_GSM3928999
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pxdn+/- Striatum female mRNA rep1

description:
PxdQ 2-1
PxdQ_2_1_GSM3928998
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Rarb+/- Striatum female mRNA rep4

description:
21-4-85881807
X21_4_GSM3995033
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ptpn7+/- Striatum male mRNA rep4

description:
PtpnQ 9-3
PtpnQ_9_3_GSM3928965
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Ptpn7 group


title: Ptpn7+/- Striatum male mRNA rep3

description:
PtpnQ 7-3
PtpnQ_7_3_GSM3928964
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Male


title: Ptpn7+/- Striatum female mRNA rep2

description:
PtpnQ 6-2
PtpnQ_6_2_GSM3928959
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ptpn7+/- Striatum male mRNA rep2

description:
PtpnQ 5-4
PtpnQ_5_4_GSM3928963
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ptpn7+/- Striatum female mRNA rep3

description:
PtpnQ 6-4
PtpnQ_6_4_GSM3928960
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ptpn7+/- Striatum male mRNA rep1

description:
PtpnQ 3-1
PtpnQ_3_1_GSM3928962
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ptpn7+/- Striatum female mRNA rep4

description:
PtpnQ 13-2
PtpnQ_13_2_GSM3928961
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ptpn7+/- Striatum female mRNA rep1

description:
PtpnQ 4-1
PtpnQ_4_1_GSM3928958
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Prkcq+/- Striatum male mRNA rep1

description:
5-3-85876817
X5_3_GSM3994962
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Prkcq+/-

value: Prkcq group


title: Prkcq+/- Striatum male mRNA rep4

description:
14-3-85875818
X14_3_GSM3994965
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum male mRNA rep4

description:
PppQ 11-3
PppQ_11_3_GSM3972507
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Ppp1ca group


title: Prkcq+/- Striatum male mRNA rep3

description:
14-2-85878799
X14_2_GSM3994964
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Prkcq+/- Striatum female mRNA rep3

description:
4-3-85884811
X4_3_GSM3994960
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Prkcq+/- Striatum male mRNA rep2

description:
12-1-85882799
X12_1_GSM3994963
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum male mRNA rep2

description:
PppQ 12-2
PppQ_12_2_GSM3972505
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Prkcq+/- Striatum female mRNA rep4

description:
4-4-85882811
X4_4_GSM3994961
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Prkcq+/- Striatum female mRNA rep2

description:
2-3-85883801
X2_3_GSM3994959
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Prkcq+/- Striatum female mRNA rep1

description:
2-1-85881798
X2_1_GSM3994958
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum male mRNA rep3

description:
PppQ 3-1
PppQ_3_1_GSM3972506
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum female mRNA rep4

description:
PppQ 10-2
PppQ_10_2_GSM3972503
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum male mRNA rep1

description:
PppQ 1-2
PppQ_1_2_GSM3972504
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum female mRNA rep2

description:
PppQ 8-1
PppQ_8_1_GSM3972501
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum female mRNA rep3

description:
PppQ 8-4
PppQ_8_4_GSM3972502
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ppp1ca+/- Striatum female mRNA rep1

description:
PppQ 8-2
PppQ_8_2_GSM3972500
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde1b+/- Striatum male mRNA rep4

description:
14-1-87850780
X14_1_GSM3861300
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Pde1b group


title: Pde1b+/- Striatum male mRNA rep3

description:
12-3-87856773
X12_3_GSM3861299
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde1b+/- Striatum male mRNA rep2

description:
2-3-87849778
X2_3_GSM3861298
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde1b+/- Striatum male mRNA rep1

description:
1-3-87845774
X1_3_GSM3861297
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde1b+/- Striatum female mRNA rep4

description:
15-3-87845776
X15_3_GSM3861296
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde1b+/- Striatum female mRNA rep3

description:
13-1-87847770
X13_1_GSM3861295
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde1b+/- Striatum female mRNA rep2

description:
11-2-87856772
X11_2_GSM3861294
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde10a+/- Striatum female mRNA rep4

description:
10-1_2-59080171
X10_1_GSM3861481
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Pde10a group


title: Pde10a+/- Striatum male mRNA rep3

description:
5-3_1-59088075
X5_3_GSM3861484
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde1b+/- Striatum female mRNA rep1

description:
9-3-87864778
X9_3_GSM3861293
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde10a+/- Striatum male mRNA rep4

description:
5-4_1-59095053
X5_4_GSM3861485
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pcdh20+/- Striatum male mRNA rep1

description:
P20Q 8-1
P20Q_8_1_GSM3885006
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Pcdh20 group


title: Pde10a+/- Striatum female mRNA rep3

description:
8-4_2-59088079
X8_4_GSM3861480
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pcdh20+/- Striatum female mRNA rep3

description:
P20Q 11-3
P20Q_11_3_GSM3885004
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde10a+/- Striatum male mRNA rep2

description:
5-1_1-59095052
X5_1_GSM3861483
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pcdh20+/- Striatum male mRNA rep2

description:
P20Q 8-2
P20Q_8_2_GSM3885007
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde10a+/- Striatum female mRNA rep1

description:
6-2_2-59095055
X6_2_GSM3861478
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pcdh20+/- Striatum female mRNA rep2

description:
P20Q 5-2
P20Q_5_2_GSM3885003
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pcdh20+/- Striatum male mRNA rep4

description:
P20Q 14-1
P20Q_14_1_GSM3885009
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum male mRNA rep4

description:
P4hQ 12-4
P4hQ_12_4_GSM3928933
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: P4ha1 group


title: Pcdh20+/- Striatum male mRNA rep3

description:
P20Q 8-3
P20Q_8_3_GSM3885008
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde10a+/- Striatum female mRNA rep2

description:
6-3_2-59098041
X6_3_GSM3861479
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pcdh20+/- Striatum female mRNA rep4

description:
P20Q 11-4
P20Q_11_4_GSM3885005
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum male mRNA rep2

description:
P4hQ 8-4
P4hQ_8_4_GSM3928931
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum female mRNA rep3

description:
P4hQ 7-4
P4hQ_7_4_GSM3928928
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum female mRNA rep2

description:
P4hQ 15-3
P4hQ_15_3_GSM3928927
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum female mRNA rep1

description:
P4hQ 5-3
P4hQ_5_3_GSM3928926
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum male mRNA rep1

description:
P4hQ 12-1
P4hQ_12_1_GSM3928930
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum male mRNA rep3

description:
P4hQ 6-3
P4hQ_6_3_GSM3928932
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Nagk+/- Striatum male mRNA rep2

description:
NagQ 4-2
NagQ_4_2_GSM3884967
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Nagk+/-

value: Nagk group


title: Nagk+/- Striatum male mRNA rep4

description:
NagQ 7-4
NagQ_7_4_GSM3884969
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pde10a+/- Striatum male mRNA rep1

description:
3-2_1-59093057
X3_2_GSM3861482
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Nagk+/- Striatum male mRNA rep3

description:
NagQ 7-3
NagQ_7_3_GSM3884968
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Pcdh20+/- Striatum female mRNA rep1

description:
P20Q 3-1
P20Q_3_1_GSM3885002
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Nagk+/- Striatum male mRNA rep1

description:
NagQ 1-2
NagQ_1_2_GSM3884966
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Nagk+/- Striatum female mRNA rep3

description:
NagQ 10-2
NagQ_10_2_GSM3884964
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Nagk+/- Striatum female mRNA rep1

description:
NagQ 3-5
NagQ_3_5_GSM3884962
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Morf4l1+/- Striatum male mRNA rep2

description:
MorQ 11-3
MorQ_11_3_GSM3909846
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Morf4l1 group


title: Morf4l1+/- Striatum male mRNA rep4

description:
MorQ 13-1
MorQ_13_1_GSM3909848
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Morf4l1+/- Striatum male mRNA rep3

description:
MorQ 6-2
MorQ_6_2_GSM3909847
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Morf4l1+/- Striatum female mRNA rep3

description:
MorQ 15-3
MorQ_15_3_GSM3909844
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: P4ha1+/- Striatum female mRNA rep4

description:
P4hQ 5-5
P4hQ_5_5_GSM3928929
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Morf4l1+/- Striatum male mRNA rep1

description:
MorQ 7-1
MorQ_7_1_GSM3909845
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Nagk+/- Striatum female mRNA rep2

description:
NagQ 10-1
NagQ_10_1_GSM3884963
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum male mRNA rep2

description:
Kd4Q 5-1
Kd4Q_5_1_GSM3907508
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Kdm4b group


title: Morf4l1+/- Striatum female mRNA rep1

description:
MorQ 12-4
MorQ_12_4_GSM3909842
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum male mRNA rep3

description:
Kd4Q 15-2
Kd4Q_15_2_GSM3907509
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum male mRNA rep1

description:
Kd4Q 18-2
Kd4Q_18_2_GSM3907507
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum male mRNA rep4

description:
Kd4Q 13-3
Kd4Q_13_3_GSM3907510
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum female mRNA rep1

description:
Kd4Q 4-2
Kd4Q_4_2_GSM3907501
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum female mRNA rep4

description:
Kd4Q 1-3
Kd4Q_1_3_GSM3907504
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3b+/- Striatum male mRNA rep4

description:
Kd3Q 4-2
Kd3Q_4_2_GSM3972475
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Kdm3b group


title: Kdm4b+/- Striatum female mRNA rep6

description:
Kd4Q 1-2
Kd4Q_1_2_GSM3907506
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Corpus Striatum


title: Kdm4b+/- Striatum female mRNA rep3

description:
Kd4Q 7-3
Kd4Q_7_3_GSM3907503
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: 6 months


title: Kdm3b+/- Striatum male mRNA rep3

description:
Kd3Q 2-2
Kd3Q_2_2_GSM3972474
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3b+/- Striatum male mRNA rep1

description:
Kd3Q 4-4
Kd3Q_4_4_GSM3972472
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Nagk+/- Striatum female mRNA rep4

description:
NagQ 12-2
NagQ_12_2_GSM3884965
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Female


title: Kdm3b+/- Striatum female mRNA rep4

description:
Kd3Q 14-2
Kd3Q_14_2_GSM3972471
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3b+/- Striatum female mRNA rep3

description:
Kd3Q 7-3
Kd3Q_7_3_GSM3972470
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3b+/- Striatum female mRNA rep2

description:
Kd3Q 8-2
Kd3Q_8_2_GSM3972469
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Morf4l1+/- Striatum female mRNA rep2

description:
MorQ 8-2
MorQ_8_2_GSM3909843
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3b+/- Striatum male mRNA rep2

description:
Kd3Q 4-1
Kd3Q_4_1_GSM3972473
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Morf4l1+/- Striatum male mRNA rep5

description:
MorQ 7-2
MorQ_7_2_GSM3909849
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3b+/- Striatum female mRNA rep1

description:
Kd3Q 10-2
Kd3Q_10_2_GSM3972468
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum female mRNA rep5

description:
Kd4Q 9-1
Kd4Q_9_1_GSM3907505
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3a+/- Striatum male mRNA rep2

description:
KdmQ7-3-107240174
KdmQ7_3_GSM3861059
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Kdm3a group


title: Kdm3a+/- Striatum male mRNA rep1

description:
KdmQ5-2-107244174
KdmQ5_2_GSM3861058
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Male


title: Kdm3a+/- Striatum male mRNA rep4

description:
KdmQ16-1-107238186
KdmQ16_1_GSM3861061
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm4b+/- Striatum female mRNA rep2

description:
Kd4Q 1-1
Kd4Q_1_1_GSM3907502
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3a+/- Striatum female mRNA rep2

description:
KdmQ4-3-107233182
KdmQ4_3_GSM3861055
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kcnh4+/- Striatum male mRNA rep1

description:
KcnQ_1-3-112855756
KcnQ_1_3_GSM3860625
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Kcnh4 group


title: Kcnh4+/- Striatum male mRNA rep3

description:
KcnQ_8-2-112850765
KcnQ_8_2_GSM3860627
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kcnh4+/- Striatum male mRNA rep4

description:
KcnQ_11-1-112846767
KcnQ_11_1_GSM3860628
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kcnh4+/- Striatum female mRNA rep4

description:
KcnQ_7-2-112854764
KcnQ_7_2_GSM3860624
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kcnh4+/- Striatum male mRNA rep2

description:
KcnQ_4-1-112860754
KcnQ_4_1_GSM3860626
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3a+/- Striatum female mRNA rep3

description:
KdmQ6-1-107241179
KdmQ6_1_GSM3861056
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3a+/- Striatum female mRNA rep1

description:
KdmQ4-2-107237194
KdmQ4_2_GSM3861054
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kcnh4+/- Striatum female mRNA rep3

description:
KcnQ_7-1-112857760
KcnQ_7_1_GSM3860623
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kcnh4+/- Striatum female mRNA rep2

description:
KcnQ_5-3-112848776
KcnQ_5_3_GSM3860622
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Itpr1+/- Striatum female mRNA rep2

description:
ItpQ_12-2-114735639
ItpQ_12_2_GSM3860598
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Itpr1 group


title: Itpr1+/- Striatum male mRNA rep3

description:
ItpQ_1-4-114723662
ItpQ_1_4_GSM3860603
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Itpr1+/- Striatum male mRNA rep2

description:
ItpQ_5-1-114735655
ItpQ_5_1_GSM3860602
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Itpr1+/- Striatum male mRNA rep4

description:
ItpQ_7-4-114734646
ItpQ_7_4_GSM3860604
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Itpr1+/- Striatum female mRNA rep3

description:
ItpQ_8-4-114729684
ItpQ_8_4_GSM3860599
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum male mRNA rep3

description:
InfQ_6-5-112851762
InfQ_6_5_GSM3860460
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Inf2 group


title: Itpr1+/- Striatum female mRNA rep4

description:
ItpQ_3-4-114726676
ItpQ_3_4_GSM3860600
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Itpr1+/- Striatum male mRNA rep1

description:
ItpQ_7-3-114731649
ItpQ_7_3_GSM3860601
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum male mRNA rep2

description:
InfQ_3-1-112842762
InfQ_3_1_GSM3860459
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum male mRNA rep1

description:
InfQ_1-1-112852751
InfQ_1_1_GSM3860458
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Itpr1+/- Striatum female mRNA rep1

description:
ItpQ_6-4-114737646
ItpQ_6_4_GSM3860597
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3a+/- Striatum female mRNA rep4

description:
KdmQ6-2-107249151
KdmQ6_2_GSM3861057
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum female mRNA rep4

description:
InfQ_5-2-112849755
InfQ_5_2_GSM3860456
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum female mRNA rep5

description:
InfQ_5-3-112859747
InfQ_5_3_GSM3860457
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum female mRNA rep3

description:
InfQ_4-2-112850752
InfQ_4_2_GSM3860455
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum female mRNA rep2

description:
InfQ_2-3-112842761
InfQ_2_3_GSM3860454
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Htr2c+/- Striatum female mRNA rep7

description:
15-1--87838772
X15_1_GSM3860411
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Htr2c group


title: Htr2c+/- Striatum female mRNA rep6

description:
14-3--87852769
X14_3_GSM3860410
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Htr2c+/- Striatum female mRNA rep4

description:
10-4--87849764
X10_4_GSM3860408
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Htr2c+/- Striatum female mRNA rep8

description:
15-2--87844766
X15_2_GSM3860412
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Inf2+/- Striatum female mRNA rep1

description:
InfQ_2-2-112856748
InfQ_2_2_GSM3860453
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Htr2c+/- Striatum female mRNA rep2

description:
9-3--87845770
X9_3_GSM3860406
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kcnh4+/- Striatum female mRNA rep1

description:
KcnQ_5-1-112860758
KcnQ_5_1_GSM3860621
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Htr2c+/- Striatum female mRNA rep5

description:
12-3--87854769
X12_3_GSM3860409
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Htr2c+/- Striatum female mRNA rep3

description:
9-4--87846774
X9_4_GSM3860407
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hrk+/- Striatum male mRNA rep3

description:
HrkQ 8-3
HrkQ_8_3_GSM3907565
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Hrk+/-

value: Hrk group


title: Hrk+/- Striatum female mRNA rep4

description:
HrkQ 16-1
HrkQ_16_1_GSM3907562
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Htr2c+/- Striatum female mRNA rep1

description:
6-1--87838776
X6_1_GSM3860405
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hrk+/- Striatum male mRNA rep1

description:
HrkQ 7-3
HrkQ_7_3_GSM3907563
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hrk+/- Striatum female mRNA rep1

description:
HrkQ 3-2
HrkQ_3_2_GSM3907559
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hipk4+/- Striatum male mRNA rep4

description:
9-1_9222-59285339
X9_1_GSM3834257
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Hipk4 group


title: Hipk4+/- Striatum male mRNA rep1

description:
1-1_9222-59284318
X1_1_GSM3834254
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hipk4+/- Striatum male mRNA rep3

description:
6-2_9222-59287334
X6_2_GSM3834256
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hipk4+/- Striatum female mRNA rep3

description:
5-1_9222-59285319
X5_1_GSM3834252
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hipk4+/- Striatum female mRNA rep2

description:
2-5_9222-59287312
X2_5_GSM3834251
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hipk4+/- Striatum male mRNA rep2

description:
6-1_9222-59273352
X6_1_GSM3834255
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hipk4+/- Striatum female mRNA rep4

description:
8-2_9222-59273355
X8_2_GSM3834253
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hrk+/- Striatum male mRNA rep4

description:
HrkQ 4-3
HrkQ_4_3_GSM3907566
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hipk4+/- Striatum female mRNA rep1

description:
2-2_9222-59273338
X2_2_GSM3834250
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gsg1l+/- Striatum male mRNA rep4

description:
GsgQ 3-5
GsgQ_3_5_GSM3928901
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Gsg1l group


title: Hrk+/- Striatum male mRNA rep2

description:
HrkQ 9-4
HrkQ_9_4_GSM3907564
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gsg1l+/- Striatum male mRNA rep3

description:
GsgQ 3-4
GsgQ_3_4_GSM3928900
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum male mRNA rep4

description:
11-2-85886842
X11_2_GSM3814700
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Gpx6 group


title: Gsg1l+/- Striatum female mRNA rep1

description:
GsgQ 2-3
GsgQ_2_3_GSM3928894
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gsg1l+/- Striatum female mRNA rep4

description:
GsgQ 17-1
GsgQ_17_1_GSM3928897
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gsg1l+/- Striatum female mRNA rep3

description:
GsgQ 15-1
GsgQ_15_1_GSM3928896
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum male mRNA rep2

description:
9-4-85883827
X9_4_GSM3814698
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum male mRNA rep3

description:
9-5-85883828
X9_5_GSM3814699
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gsg1l+/- Striatum male mRNA rep1

description:
GsgQ 1-1
GsgQ_1_1_GSM3928898
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gsg1l+/- Striatum female mRNA rep2

description:
GsgQ 4-2
GsgQ_4_2_GSM3928895
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hrk+/- Striatum female mRNA rep3

description:
HrkQ 5-3
HrkQ_5_3_GSM3907561
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum female mRNA rep4

description:
14-3-85882830
X14_3_GSM3814696
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Hrk+/- Striatum female mRNA rep2

description:
HrkQ 5-2
HrkQ_5_2_GSM3907560
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum male mRNA rep1

description:
1-4-85881819
X1_4_GSM3814697
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum female mRNA rep2

description:
12-1-85886801
X12_1_GSM3814694
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum female mRNA rep3

description:
12-2-85889851
X12_2_GSM3814695
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Gpx6+/- Striatum female mRNA rep1

description:
10-4-85891840
X10_4_GSM3814693
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Foxp1+/- Striatum male mRNA rep2

description:
FoxQ_13-3-118907904
FoxQ_13_3_GSM3834223
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Foxp1 group


title: Gsg1l+/- Striatum male mRNA rep2

description:
GsgQ 3-2
GsgQ_3_2_GSM3928899
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Foxp1+/- Striatum male mRNA rep1

description:
FoxQ_7-2-118915846
FoxQ_7_2_GSM3834222
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Foxp1+/- Striatum male mRNA rep3

description:
FoxQ_20-2-118914844
FoxQ_20_2_GSM3834224
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Foxp1+/- Striatum female mRNA rep4

description:
FoxQ_12-3-118913829
FoxQ_12_3_GSM3834221
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Foxp1+/- Striatum female mRNA rep3

description:
FoxQ_9-4-118919835
FoxQ_9_4_GSM3834220
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Foxp1+/- Striatum female mRNA rep2

description:
FoxQ_2-2-118914843
FoxQ_2_2_GSM3834219
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Fbxl16+/- Striatum male mRNA rep5

description:
FbxQ 13-1
FbxQ_13_1_GSM3884891
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Fbxl16 group


title: Fbxl16+/- Striatum male mRNA rep2

description:
FbxQ 9-1
FbxQ_9_1_GSM3884888
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Foxp1+/- Striatum female mRNA rep1

description:
FoxQ_2-1-118911846
FoxQ_2_1_GSM3834218
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Fbxl16+/- Striatum male mRNA rep1

description:
FbxQ 7-2
FbxQ_7_2_GSM3884887
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Fbxl16+/- Striatum male mRNA rep3

description:
FbxQ 11-1
FbxQ_11_1_GSM3884889
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Fbxl16+/- Striatum female mRNA rep3

description:
FbxQ 8-1
FbxQ_8_1_GSM3884886
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Fbxl16+/- Striatum female mRNA rep1

description:
FbxQ 2-2
FbxQ_2_2_GSM3884884
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Fbxl16+/- Striatum female mRNA rep2

description:
FbxQ 6-4
FbxQ_6_4_GSM3884885
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: ips8

city: Nanjing

first: Aiwen

last: Jiang

state: Jiangsu

address: Weigang

country: China

institute: Nanjing Agricultural University

library_source: genomic

data_processing:
Raw data was stored in FASTQ format, including the base sequence and corresponding quality  information. Trimmomatic (v0.36) was used to remove adaptor-polluted or low-quality bases, and  reads too short ( < 36 nt) were filtered out to get the clean data.
Clean data was mapped to reference  genome by Bowtie2, and visualized by IGV
Peaks corresponding  to the open region in genome were detected by MACS2
significantly different peaks between  samples were acquired using Manorm
he enrichment analysis of GO term  (http://geneontology.org/) or KEGG pathway (http://www.kegg.jp/) was based on hypergeometric  test with the threshold q < 0.05, to find the significant enrichment of detected genes
Genome_build: Sus_scrofa.Sscrofa11.1.90.chr

molecule: genomic DNA

organism: Sus scrofa

source_name: tip of ear of E90

extract_protocol:
PEF cell lines were transfected with OSKM plasmid, and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al and Jingyi Wu et al. with slightly modification

tag: developmental stage

value: embryo

value: tip of ear of E90

tag: cell type

value: pluripotent cells derived from PEF


title: Ezh2+/- Striatum male mRNA rep2

description:
EzhQ_5-3-114735622
EzhQ_5_3_GSM3834199
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Corpus Striatum

value: 6 months

value: Ezh2 group


title: ips7


title: Ezh2+/- Striatum male mRNA rep4

description:
EzhQ_5-5-114738625
EzhQ_5_5_GSM3834201
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Male


title: Ezh2+/- Striatum female mRNA rep3

description:
EzhQ_20-5-114732634
EzhQ_20_5_GSM3834196
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Female


title: Foxp1+/- Striatum male mRNA rep4

description:
FoxQ_20-3-118921821
FoxQ_20_3_GSM3834225
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ezh2+/- Striatum male mRNA rep1

description:
EzhQ_5-2-114725652
EzhQ_5_2_GSM3834198
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ezh2+/- Striatum female mRNA rep4

description:
EzhQ_22-2-114719666
EzhQ_22_2_GSM3834197
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: ips5


title: Ezh2+/- Striatum female mRNA rep2

description:
EzhQ_20-3-114725650
EzhQ_20_3_GSM3834195
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: PEF5

value: somatic cells


title: PEF7


title: Ezh2+/- Striatum female mRNA rep1

description:
EzhQ_8-2-114734629
EzhQ_8_2_GSM3834194
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Fbxl16+/- Striatum male mRNA rep4

description:
FbxQ 11-2
FbxQ_11_2_GSM3884890
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: PEF8


title: Ferret lung_Smoke_6Months_rep5 [smoke_833_F1]

city: Birmingham

first: Dr Steven

middle: M.

last: Rowe

state: AL

address: 1720 2nd Avenue South, MCLM 804

department: Professor and Director, Cystic Fibrosis Research Center

institute: University of Alabama at Birmingham

data_processing:
RNA-seq data for 12 samples (six biological replicates each for air and smoke experimental conditions) were sequenced using an Illumina NextSeq 500 System. Pre-alignment quality assessments of the raw fastq sequences were carried out using FastQC (v0.11.7) (Andrews, 2010). The number of paired ends reads for the twelve samples range from 35M to 57M. The raw fastq sequences were aligned to the Mustela putorius furo reference genome (GenBank assembly accession: GCA_000215625.1) (Peng X et al 2014 Nat Biotechnol 32:1250-1255). The alignments were carried out using STAR (v2.7.1a) ( Dobin et al 2013 Bioinformatics 29: 15-21). The ENCODE parameter options for RNA-seq were used (see STAR manual). Gene expression was quantified as gene level counts using the htseq-count function (v0.12.3) (Anders S et al 2015 Bioinformatics 31:166-169).
The Ensembl gene annotations for Mustela putorius furo (genebuild-last-updated 2016-05) was used (Yates AD et al  2020 Nucleic Acids Res 48:D682-D688). The htseq-count default parameters were used except for the strand parameter which was set to reverse to consider the strandedness of library. Differentially expressed genes (DEGs) were identified using DESeq2 (v1.28) (Love MI et al 2014 Genome Biol 15:550). DESeq2 was configured by adding batch and sex to the design to control for these factor whilst DESeq2 tests for association due to the condition (see DESeq2 vignette). Other than including batch and sex in the design, DESeq2 was run with default parameters (Love MI et al 2014 Genome Biol 15:550). Genes were differentially expressed if the absolute log2Fold change was > 1, and the adjusted p-value was < 0.1.
The DESeq2 vs function computes a variance stabilizing transformation of the sample data like putting the data on the log2 scale. To remove shifts in the log2 scale expression data explained by the batch effect, the remove Batch Effect function from limma (v3.44.0) (Ritchie ME et al 2015 Nucleic Acids Res, 43: e4) was used; sex was also included as a factor (see vignettes for DESeq2 and limma).
Genome_build: GenBank assembly accession: GCA_000215625.1) (Peng X et al 2014 Nat Biotechnol 32:1250-1255).
Supplementary_files_format_and_content: excel, DESEQ2, Limma

organism: Mustela putorius furo

source_name: Ferret lung_Smoke_6Months

extract_protocol:
RNA isolated from snap frozen lung tissue using Qiagen miRNeasy Mini Kit  Cat No./ID: 217004 and later we did ribosome reduction for samples.  We used the NEBNext rRNA Depletion kit (Human/Mouse/Rat), cat E7400.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: female

tag: treatment

value: exposed to cigarette smoke

value: Lung tissue


title: Ferret lung_Smoke_6Months_rep6 [smoke_837_M1]

value: male


title: Ddit4l+/- Striatum male mRNA rep4

description:
DdiQ5-4-103722672
DdiQ5_4_GSM3833959
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Ddit4l group


title: Ddit4l+/- Striatum male mRNA rep3

description:
DdiQ5-3-103713707
DdiQ5_3_GSM3833958
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ddit4l+/- Striatum male mRNA rep2

description:
DdiQ4-1-103714689
DdiQ4_1_GSM3833957
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ferret lung_Smoke_6Months_rep3 [smoke_691_M2]


title: Ferret lung_Smoke_6Months_rep4 [smoke_828_F1]


title: Ezh2+/- Striatum male mRNA rep3

description:
EzhQ_5-4-114731630
EzhQ_5_4_GSM3834200
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ddit4l+/- Striatum male mRNA rep1

description:
DdiQ3-1-103727625
DdiQ3_1_GSM3833956
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ferret lung_Smoke_6Months_rep2 [smoke_680_F2]


title: Ddit4l+/- Striatum female mRNA rep4

description:
DdiQ11-3-103725658
DdiQ11_3_GSM3833955
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ferret lung_Smoke_6Months_rep1 [smoke_422_M2]


title: Ddit4l+/- Striatum female mRNA rep3

description:
DdiQ6-3-103714691
DdiQ6_3_GSM3833954
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ferret lung_air control_rep5 [air_871_F1]

source_name: Ferret lung_air control

value: exposed to room air


title: Ferret lung_air control_rep4 [air_859_M2]


title: Ferret lung_air control_rep3 [air_853_M1]


title: Ddit4l+/- Striatum female mRNA rep2

description:
DdiQ2-3-103727624
DdiQ2_3_GSM3833953
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ddit4l+/- Striatum female mRNA rep1

description:
DdiQ2-1-103723688
DdiQ2_1_GSM3833952
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Dach1+/- Striatum male mRNA rep5

description:
DachQ 3-4
DachQ_3_4_GSM3907534
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Dach1 group


title: Ferret lung_air control_rep2 [air_447_M2]


title: Dach1+/- Striatum male mRNA rep4

description:
DachQ 5-2
DachQ_5_2_GSM3907533
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Dach1+/- Striatum male mRNA rep2

description:
DachQ 4-1
DachQ_4_1_GSM3907531
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Dach1+/- Striatum male mRNA rep1

description:
DachQ 3-3
DachQ_3_3_GSM3907530
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Dach1+/- Striatum female mRNA rep3

description:
DachQ 12-4
DachQ_12_4_GSM3907529
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Dach1+/- Striatum female mRNA rep2

description:
DachQ 8-4
DachQ_8_4_GSM3907528
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Dach1+/- Striatum female mRNA rep1

description:
DachQ 12-5
DachQ_12_5_GSM3907527
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 24h_manZ_2DG_rep1

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
Fastq reads were demultiplex to their respective sample by using fastq-multx (version 1.3.1) and aligned to a composite genome of S.Tm 14028S and mouse (mm10) using STAR (version 2.5.3a).
For the host, read counts were calculated using STAR. For S.Tm read counts, R2 reads were calculated by HTSeq.
Data of each organism was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log2 scale. Host minimal expression threshold was set to 4.5 and bacteria minimal expression threshold was set to 2.
Genome_build: composite genome of S.Tm 14028S and mouse (mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads (log2 scale) for each sample

organism:
Mus musculus
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: BMDMs

growth_protocol: Bone marrow was extracted from 6-8 week old female C57BL/6 mice as previously described (Falk et al., 1988). In brief, 6-8 week old female C57BL/6 mice were euthanized and femurs and tibias were harvested. Bone marrow was flushed from the cells, resuspended in DMEM, and plated in non-tissue culture treated dishes in DMEM media containing 5% sodium pyruvate, 20% fetal bovine serum, and 25 ng/ml recombinant mouse M-CSF. Cells were harvested at day 6 after bone marrow isolation and were frozen untill use. All bone marrows extractions were performed in accordance with the Institutional Animal Care and Use Committee at the Weizmann Institute. (IACUC Approval number 27410516-3)

extract_protocol:
Gentle bead beating was done using OmniLyse (disposable cell disruptors) to break the bacterial cell envelope without harming the macrophage RNA. miRNeasy kit (QIAGEN) was used for further RNA extraction
RNAtag-seq cDNA libraries for simultaneous detection of host and intracellular bacterial transcripts was done as previously described in Avraham et al (2016) (Avraham et al., 2016). In brief, samples contain murine RNA transcripts (uninfected controls) or a mix of bacterial and murine RNA transcripts (infected) were barcoded by ligation with RNA adaptors and pooled together. Murine rRNA was depleted using the RiboZero Gold (Human/Mouse/Rat) kit (Illumina) according to the manufacturer’s guidelines. Strand-specific cDNA libraries were prepared and sequenced as Paired-end (R1: 30, R2: 50) using Nextseq machine and 75 high throughput kit with total coverage of ~1.1B reads and a mean of ~19.5M reads per library, ranges from ~4.5M to ~45.5M. For each condition, biological triplicates were analyzed

treatment_protocol: 800,000 cells/well of BMDM cells were plated in non-tissue culture treated 6 well plates supplemented with DMEM with 20% FBS and 25ng/ml rmM-CSF. Infected BMDMs samples were infected with WT or the ∆manZ mutant strains harboring a GFP expressing plasmid (pFPV25.1; Addgene) at MOI of 10:1. In the 2-DG treated samples, 2-DG (Sigma D8375-5G) in a concentration of 1mM was supplemented to the media containing 15 μg/ml gentamicin after the wash of the uninternalized bacteria. Uninfected samples were treated under the same conditions.                                                                                20,000 cells per sample of uninfected controls or infected (GFP positive) cells were sorted under continuous cooling to 4°C by a BD FACS Aria III into a low bind eppendorfs contained 700μl QIAzol Lysis reagent, over a time curse of 0.5h, 6h and 24h post-infection.

tag: bacteria status

value: manZ

tag: 2-dg status

value: with 2-DG

tag: time post-infection (hours)

tag: replicate


title: 24h_manZ_2DG_rep2


title: 24h_manZ_2DG_rep3


title: Chrm4+/- Striatum male mRNA rep2

description:
7-52795819
X7_GSM3814667
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Chrm4 group


title: Chrm4+/- Striatum male mRNA rep3

description:
8-52796810
X8_GSM3814668
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ferret lung_air control_rep6 [air_877_F1]


title: 24h_manZ_no_2DG_rep1

value: without 2-DG


title: 24h_manZ_no_2DG_rep2


title: 24h_WT_2DG_rep3

value: WT


title: 24h_WT_2DG_rep2


title: Chrm4+/- Striatum female mRNA rep5

description:
27-52792797
X27_GSM3814665
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Corpus Striatum

value: 6 months


title: Ferret lung_air control_rep1 [air_209_F2]


title: Chrm4+/- Striatum male mRNA rep1

description:
4-52789828
X4_GSM3814666
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Male


title: 24h_WT_2DG_rep1


title: 24h_WT_no_2DG_rep2


title: 24h_WT_no_2DG_rep3


title: Chrm4+/- Striatum female mRNA rep4

description:
23-52784842
X23_GSM3814664
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Female


title: Chrm4+/- Striatum female mRNA rep3

description:
21-52783842
X21_GSM3814663
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Dach1+/- Striatum male mRNA rep3

description:
DachQ 7-1
DachQ_7_1_GSM3907532
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chrm4+/- Striatum female mRNA rep2

description:
20-52797786
X20_GSM3814662
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chrm4+/- Striatum female mRNA rep1

description:
16-52780860
X16_GSM3814661
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 24h_manZ_no_2DG_rep3


title: 6h_manZ_2DG_rep3


title: 24h_WT_no_2DG_rep1


title: 6h_manZ_2DG_rep2


title: Cd4+/- Striatum male mRNA rep2

description:
Cd4Q1-3-107243152
Cd4Q1_3_GSM3833050
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Cd4 group


title: Cd4+/- Striatum male mRNA rep1

description:
Cd4Q1-2-107238176
Cd4Q1_2_GSM3833049
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Cd4+/- Striatum male mRNA rep3

description:
Cd4Q14-3-107236173
Cd4Q14_3_GSM3833051
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Cd4+/- Striatum female mRNA rep4

description:
Cd4Q8-1-107243156
Cd4Q8_1_GSM3833047
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Cd4+/- Striatum female mRNA rep3

description:
Cd4Q6-4-107244161
Cd4Q6_4_GSM3833046
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Cd4+/- Striatum female mRNA rep5

description:
Cd4Q8-5-107242176
Cd4Q8_5_GSM3833048
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 6h_manZ_no_2DG_rep3


title: 6h_manZ_no_2DG_rep1


title: 6h_WT_2DG_rep3


title: 6h_WT_2DG_rep2


title: Cd4+/- Striatum female mRNA rep2

description:
Cd4Q6-3-107239164
Cd4Q6_3_GSM3833045
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 6h_WT_no_2DG_rep2


title: Bcr+/- Striatum male mRNA rep3

description:
14-3_B-59085160
X14_3_GSM3814623
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Bcr+/-

value: FVB/NJ

value: Bcr group


title: 6h_WT_no_2DG_rep1


title: 0.5h_manZ_2DG_rep3


title: 0.5h_manZ_2DG_rep2


title: Bcr+/- Striatum female mRNA rep4

description:
17-3_B-59089089
X17_3_GSM3814620
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Bcr+/- Striatum female mRNA rep3

description:
9-2_A-59092078
X9_2_GSM3814619
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Bcr+/- Striatum female mRNA rep2

description:
9-1_A-59086131
X9_1_GSM3814618
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 0.5h_manZ_2DG_rep1


title: Bcr+/- Striatum male mRNA rep4

description:
24-4_B-59088095
X24_4_GSM3814624
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 0.5h_manZ_no_2DG_rep3


title: Cd4+/- Striatum female mRNA rep1

description:
Cd4Q6-2-107248145
Cd4Q6_2_GSM3833044
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Bcr+/- Striatum male mRNA rep1

description:
5-1_A-59094071
X5_1_GSM3814621
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 6h_WT_2DG_rep1


title: Bcr+/- Striatum female mRNA rep1

description:
6-4_A-59090073
X6_4_GSM3814617
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kdm3a+/- Striatum male mRNA rep3

description:
KdmQ12-3-107243159
KdmQ12_3_GSM3861060
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Kdm3a group


title: 0.5h_manZ_no_2DG_rep2


title: 0.5h_manZ_no_2DG_rep1


title: Bcl11b+/- Striatum male mRNA rep4

description:
20-2_9219-59288270
X20_2_GSM3898845
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Bcl11b group


title: 6h_WT_no_2DG_rep3


title: 0.5h_WT_2DG_rep3


title: 0.5h_WT_2DG_rep2


title: Bcl11b+/- Striatum male mRNA rep2

description:
11-3_9219-59288258
X11_3_GSM3898841
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Bcl11b+/- Striatum male mRNA rep3

description:
11-5_9219-59280280
X11_5_GSM3898842
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Bcr+/- Striatum male mRNA rep2

description:
12-2_B-59101044
X12_2_GSM3814622
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 6h_manZ_no_2DG_rep2


title: 0.5h_WT_2DG_rep1


title: 0.5h_WT_no_2DG_rep3


title: Bcl11b+/- Striatum female mRNA rep2

description:
6-1_9219-59273326
X6_1_GSM3898857
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Bcl11b+/- Striatum male mRNA rep5

description:
20-3_9219-59290240
X20_3_GSM3898846
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Bcl11b+/- Striatum female mRNA rep1

description:
10-1_9219-59286251
X10_1_GSM3898837
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Na_H1_5

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

data_processing:
The raw reads of bacteria samples were cleaned by Trimimomatic (version 0.36). After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
The cleaned reads were mapped to the Aeromonas.spp H1 genome sequence by HISAT with default parameters
Genome_build: Aeromonas.spp H1 gemome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Aeromonas sp. H1

growth_protocol: Bacteria were grown on LB plate overnight under 28℃ first， then single colone was picked and continue growing in liquid LB containing different chemicals.

extract_protocol:
Bacteria were first harvested by centrifuging with 3000 rpm for 10 minutes,then lysis with lysozyme, and RNA was  extracted by RNA extraction kit from QIAGEN. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100μM Naringenin was added into liquid LB, while the same volume of methonal was used for mock. After 7 hours treatment, bacteria were colllected for RNA extration.

value: bacterial cell

value: Naringenin treatment


title: 0.5h_WT_no_2DG_rep1


title: Atf6+/- Striatum male mRNA rep2

description:
AteQ_6-1-118917831
AteQ_6_1_GSM3832960
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Atf6 group


title: mock_H1_5


title: Atf6+/- Striatum male mRNA rep3

description:
AteQ_19-4-118914824
AteQ_19_4_GSM3832961
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Atf6+/- Striatum female mRNA rep5

description:
AteQ_27-1-118910846
AteQ_27_1_GSM3832958
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: mock_H1_2


title: Atf6+/- Striatum male mRNA rep1

description:
AteQ_19-1-118913820
AteQ_19_1_GSM3832959
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Atf6+/- Striatum female mRNA rep1

description:
AteQ_18-3-118915823
AteQ_18_3_GSM3832954
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Na_H1_2


title: Na_H1_4


title: D50_7d

city: Jinan

first: yuwei

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

data_processing:
CLC Genomics Workbench v 21.0.1
RNA-seq data were processed quality control (QC), trimming and mapping to the human reference genome hg38 using CLC Genomics Workbench.
Gene expression level was measured based on the transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files includeTPM values for each Sample

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Total RNA was extracted from PBMCs by using the RNeasy Mini Kit.
A total amount of 100 ng total RNA per sample was used to prepare for the rRNA-depleted cDNA library by Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina, USA)

value: PBMC

value: Protein Subunit Vaccine

tag: time

value: Day 7


title: Atf6+/- Striatum female mRNA rep3

description:
AteQ_18-1-118917818
AteQ_18_1_GSM3832956
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D50_28d

value: Day 28


title: Atf6+/- Striatum female mRNA rep2

description:
AteQ_12-3-118906884
AteQ_12_3_GSM3832955
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Corpus Striatum


title: D50_14d

value: Day 14


title: D50_0d

value: Day 0


title: Atf6+/- Striatum female mRNA rep4

description:
AteQ_25-4-118920823
AteQ_25_4_GSM3832957
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: 6 months

value: Female


title: D44_28d


title: 0.5h_WT_no_2DG_rep2

value: WT

value: without 2-DG


title: D44_14d


title: Asl+/- Striatum male mRNA rep2

description:
AslQ8-2-104502515
AslQ8_2_GSM3832875
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Asl+/-

value: Male

value: Asl group


title: D44_0d


title: Bcl11b+/- Striatum female mRNA rep3

description:
8-1_9219-59279327
X8_1_GSM3898864
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Bcl11b group


title: Asl+/- Striatum male mRNA rep1

description:
AslQ5-1-104502504
AslQ5_1_GSM3832874
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D44_7d


title: mock_H1_4

value: bacterial cell


title: Asl+/- Striatum male mRNA rep3

description:
AslQ11-1-104502507
AslQ11_1_GSM3832876
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Asl+/- Striatum female mRNA rep3

description:
AslQ9-1-104502516
AslQ9_1_GSM3832872
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Asl+/- Striatum female mRNA rep4

description:
AslQ9-2-104502520
AslQ9_2_GSM3832873
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D33_28d


title: Asl+/- Striatum male mRNA rep4

description:
AslQ11-2-104502508
AslQ11_2_GSM3832877
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D33_7d


title: Asl+/- Striatum female mRNA rep2

description:
AslQ6-1-104502510
AslQ6_1_GSM3832871
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D33_14d


title: Asl+/- Striatum female mRNA rep1

description:
AslQ4-2-104502518
AslQ4_2_GSM3832870
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D33_0d


title: Arpp21+/- Striatum male mRNA rep3

description:
ArpQ15-4-103726656
ArpQ15_4_GSM3814432
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Arpp21 group


title: Arpp21+/- Striatum male mRNA rep2

description:
ArpQ15-3-103721662
ArpQ15_3_GSM3814431
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 6h_manZ_2DG_rep1

value: manZ

value: with 2-DG


title: D08_0d

value: PBMC

value: Protein Subunit Vaccine


title: D08_7d

value: Day 7


title: D08_28d

value: Day 28


title: D08_14d

value: Day 14


title: Arpp21+/- Striatum male mRNA rep1

description:
ArpQ13-1-103716665
ArpQ13_1_GSM3814429
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Corpus Striatum

value: 6 months


title: Bcl11b+/- Striatum male mRNA rep1

description:
11-2_9219-59278273
X11_2_GSM3898840
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Arpp21+/- Striatum female mRNA rep4

description:
ArpQ10-2-103715666
ArpQ10_2_GSM3814426
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Female


title: Arpp21+/- Striatum female mRNA rep5

description:
ArpQ16-1-103714678
ArpQ16_1_GSM3814428
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Arpp21+/- Striatum female mRNA rep3

description:
ArpQ9-3-103711701
ArpQ9_3_GSM3814425
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Arpp21+/- Striatum female mRNA rep2

description:
ArpQ8-3-103715684
ArpQ8_3_GSM3814423
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D06_14d


title: D06_28d


title: D06_7d


title: Arpp21+/- Striatum female mRNA rep1

description:
ArpQ2-3-103711691
ArpQ2_3_GSM3814422
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Arpp19+/- Striatum male mRNA rep4

description:
A19Q 4-2
A19Q_4_2_GSM3972411
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Arpp19 group


title: Arpp19+/- Striatum male mRNA rep3

description:
A19Q 7-1
A19Q_7_1_GSM3972410
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D06_0d

value: Day 0


title: D05_28d


title: Arpp19+/- Striatum male mRNA rep2

description:
A19Q 10-2
A19Q_10_2_GSM3972409
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Male


title: D05_14d


title: Arpp19+/- Striatum male mRNA rep1

description:
A19Q 10-4
A19Q_10_4_GSM3972408
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D05_7d


title: Arpp19+/- Striatum female mRNA rep4

description:
A19Q 15-2
A19Q_15_2_GSM3972407
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: D05_0d


title: A37_14d

value: Inactivated Vaccine


title: A37_28d


title: A19_7d


title: A37_0d


title: A19_28d


title: A19_14d


title: A37_7d


title: Abi3bp+/- Striatum male mRNA rep1

description:
6-1-72975967
X6_1_GSM3791492
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Abi3bp group


title: Abi3bp+/- Striatum female mRNA rep4

description:
9-2-72975972
X9_2_GSM3791491
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Abi3bp+/- Striatum male mRNA rep2

description:
15-3-72986931
X15_3_GSM3791493
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Abi3bp+/- Striatum male mRNA rep4

description:
18-2-72980947
X18_2_GSM3791495
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Arpp19+/- Striatum female mRNA rep3

description:
A19Q 15-3
A19Q_15_3_GSM3972406
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Arpp19+/- Striatum female mRNA rep1

description:
A19Q 8-1
A19Q_8_1_GSM3972404
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Arpp19+/- Striatum female mRNA rep2

description:
A19Q 5-5
A19Q_5_5_GSM3972405
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A19_0d


title: A11_28d


title: A11_7d


title: Chn1+/- Striatum male mRNA rep5

description:
ChnQ 14-2
ChnQ_14_2_GSM4387027
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Chn1 group


title: A11_0d


title: A11_14d


title: Abi3bp+/- Striatum female mRNA rep1

description:
2-4-72990921
X2_4_GSM3791488
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chn1+/- Striatum male mRNA rep4

description:
ChnQ 11-4
ChnQ_11_4_GSM4387026
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chn1+/- Striatum male mRNA rep3

description:
ChnQ 11-1
ChnQ_11_1_GSM4387025
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chn1+/- Striatum male mRNA rep2

description:
ChnQ 8-2
ChnQ_8_2_GSM4387024
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A09_28d


title: Abi3bp+/- Striatum female mRNA rep2

description:
3-3-72975965
X3_3_GSM3791489
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A09_14d


title: Abi3bp+/- Striatum female mRNA rep3

description:
3-5-72984940
X3_5_GSM3791490
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chn1+/- Striatum male mRNA rep1

description:
ChnQ 8-1
ChnQ_8_1_GSM4387023
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A09_0d


title: Abi3bp+/- Striatum male mRNA rep3

description:
16-2-72986933
X16_2_GSM3791494
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chn1+/- Striatum female mRNA rep1

description:
ChnQ 3-4
ChnQ_3_4_GSM4387020
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A03_28d


title: A02_14d


title: Chn1+/- Striatum female mRNA rep2

description:
ChnQ 7-2
ChnQ_7_2_GSM4387021
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A03_14d


title: Kifap3+/- Striatum male mRNA rep1

description:
KifQ 1-3
KifQ_1_3_GSM4287179
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Kifap3 group


title: A03_7d


title: A03_0d


title: Kifap3+/- Striatum male mRNA rep2

description:
KifQ 5-1
KifQ_5_1_GSM4287180
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Chn1+/- Striatum female mRNA rep3

description:
ChnQ 7-3
ChnQ_7_3_GSM4387022
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A02_7d


title: Kifap3+/- Striatum male mRNA rep3

description:
KifQ 3-1
KifQ_3_1_GSM4287181
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: A02_28d


title: Kifap3+/- Striatum female mRNA rep4

description:
KifQ 12-4
KifQ_12_4_GSM4287178
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Kifap3+/- Striatum female mRNA rep3

description:
KifQ 2-3
KifQ_2_3_GSM4287177
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ece2+/- Striatum male mRNA rep5

description:
EceQ 11-1
EceQ_11_1_GSM3972443
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Ece2 group


title: A09_7d


title: Kifap3+/- Striatum female mRNA rep1

description:
KifQ 14-3
KifQ_14_3_GSM4287175
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ece2+/- Striatum male mRNA rep4

description:
EceQ 11-2
EceQ_11_2_GSM3972442
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: W7

city: Gainesville

first: Peter

middle: James

last: Hansen

state: FL

address: 2250 SW Shealy Drive

department: Animal Sciences

institute: University of Florida

description: pool of 10 morulae

data_processing:
The quality of fastq files of sequences data was checked with a FastQC tool
Illumina adapters were trimmed
Reads were mapped to the bovine reference genome using the Hisat2
Read counts were determined using FeatureCounts program
Differentially expressed genes (DEGs) between sample groups were determined by edgeR-robust
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: preimplantation embryo- pool of 10

growth_protocol: in vitro embryo development

extract_protocol:
Qiagen  (RNAeasy micro kit)
TruSeq® mRNA Stranded Sample preparation kit

treatment_protocol: addition of recombinant Wnt5A

value: preimplantation embryo

value: Wnt5A treated

value: morulae


title: W12

description: pool of 10 morulae


title: W10

description: pool of 10 morulae


title: Kifap3+/- Striatum male mRNA rep4

description:
KifQ 3-3
KifQ_3_3_GSM4287182
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: W14

description: pool of 10 morulae


title: Kifap3+/- Striatum female mRNA rep2

description:
KifQ 6-1
KifQ_6_1_GSM4287176
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: W11

description: pool of 10 morulae


title: Ece2+/- Striatum male mRNA rep3

description:
EceQ 3-1
EceQ_3_1_GSM3972441
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: Ece2+/- Striatum male mRNA rep2

description:
EceQ 8-2
EceQ_8_2_GSM3972440
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: W2

description: pool of 10 morulae


title: Ece2+/- Striatum male mRNA rep1

description:
EceQ 9-2
EceQ_9_2_GSM3972439
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: C13

description: pool of 10 morulae

value: control


title: W1

description: pool of 10 morulae


title: C10

description: pool of 10 morulae


title: A02_0d

value: PBMC


title: C06

description: pool of 10 morulae


title: C09

description: pool of 10 morulae


title: 42hpf, pax3 mut, rep3

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet

data_processing:
FastQC was used for quality control of the fastq.gz files
STAR was used for mapping and read counts with the following options: options: -genome Load NoSharedMemory --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 --outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantMode GeneCounts
Assembly: GRCz11, ensemble.org
Supplementary files format and content: Processed files are in a tab delimited format and they include the raw read counts for each sample

molecule: polyA RNA

organism: Danio rerio

source_name: whole embryo at 42hpf

extract_protocol:
Total RNA was extracted using TRizole and treated with TURBO DNase for 15 minutes at 37ºC to remove genomic DNA. Purity and integrity of the RNA samples was confirmed using Agilent 2100 bioanalyzer
poly-A selection libraries were prepared by SciLifeLab

value: whole embryo at 42hpf

value: pax3 mutant


title: Ece2+/- Striatum female mRNA rep1

description:
EceQ 10-1
EceQ_10_1_GSM3972436
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Corpus Striatum

value: 6 months


title: C05

description: pool of 10 morulae


title: Ece2+/- Striatum female mRNA rep2

description:
EceQ 10-2
EceQ_10_2_GSM3972437
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv

value: Female


title: Ece2+/- Striatum female mRNA rep3

description:
EceQ 7-2
EceQ_7_2_GSM3972438
mRNA
processed data file: rawCounts_WtHet_Striatum_6m.csv
processed data file: FPKM_WtHet_Striatum_6m.csv


title: 42hpf, pax3 mut, rep2


title: 42hpf, pax3 mut, rep1


title: C04

description: pool of 10 morulae


title: W4

description: pool of 10 morulae


title: 42hpf, WT, rep3

value: WT


title: C3

description: pool of 10 morulae


title: C2

description: pool of 10 morulae


title: C1

description: pool of 10 morulae


title: miaMB rep mia3

city: Poznan

first: Barbara

last: Uszczyńska-Ratajczak

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry, Polish Academy of Sciences

description:
processed data file:
matrix.MBFvsHSF.mia40.tsv

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were  mapped to the transcriptome (Ensembl annotation v 101) using salmon v1.4.0 with default  parameters (Patro et al.)
Reads mapping to the genes and transcripts were also counted using salmon v 1.4.0
The wild type and mia40a-/- HSF samples were used as a reference in wild type and mia40a-/- MBF comparisons, respectively.
Genome_build: danrer11
Supplementary_files_format_and_content: tab-delimited text files including raw gene counts for each sample

source_name: mia40a -/-_MBF

growth_protocol: Embryos were collected from pair or group incross spawning ofmia40a+/+in theTg(Xla.Eef1a1:mlsEGFP)cms1background (in case ofmia40aWT) or mia40a+/-in theTg(Xla.Eef1a1:mlsEGFP)cms1background (in case ofmia40amutants) and kept in an incubator at 28° C temperature until 5 days post fertilization (dpf). Additionaly, in case ofmia40amutant the embryos was sorted under the fluorescent microscope at 4 dpf to getmia40-/- individuals for biochemical fractionation and further RNA isolation.

extract_protocol:
5dpf zebrafish larvae ( wild typeor mia40-/-) were anaesthetized using Tricaine, washed with Ringer's solution and homogenized. The homogenate (Whole) was centrifuged twice at 1500 Xg for 10 min to remove nuclei and debris which resulted in obtaining the post-nuclear supernatant (PNS). The PNS was centrifuged at 14,000 Xg for 15 min to pellet down Membrane Bound Fraction (MBF). Subsequently, the ultra-centrifugation of the supernatant at 100,000 X g for 60 min was performed to obtain the High-Speed Fraction (HSF).  RNA was extracted from Whole, MBF and HSF using the TRI Reagent solutionand isolated using isopropanol precipitation. The samples were treated with RNase-Free DNase (Qiagen, 79254) to avoid gDNA contamination and cleaned and concentrated using Agencourt RNAClean XP beads (Beckman Coulter, A63987). The RNA concentration was estimated by Quantus Fluorometer (Promega) or Nanodrop Spectrophotometer (ThermoFisher Scientific) and the integrity of RNA was verified by 2200 Tapestation system (Agilent Technologies). The RNA samples were stored in -80º C until further use.
2 μg ofRNA from each sample was spiked in with ERCC ExFold RNA Spike-In mixes (Thermofisher Scientific,4456739) following the manufacturer’s guideline and subjected to mRNA enrichment by Poly (A) capture coupled with library preparation by using KAPA Stranded mRNA -Seq Kit with KAPA mRNA capture Kit (Kapa biosystems, KK8420) and following manufacturer's protocol.  Library fragment size distribution was confirmed by electrophoresis in Tapestation (Agilent Technologies). Library concentration was determined by both Quantus and qPCR. Sequencing was performed on the NextSeq500 instrument (Illumina) using the v2 chemistry, resulting in an average of 100 M of 2 x 75 bp paired-end reads per library.

tag: strain

value: AB

tag: fraction

value: membrane-bound fraction (MBF)


title: 42hpf, WT, rep2

tag: tissue


title: miaMB rep mia1

tag: genotype


title: miaMB rep mia2


title: miaHS rep mia3

source_name: mia40a -/-_HSF

value: high speed fraction (HSF)


title: miaHS rep mia2


title: miaHS rep mia1


title: MB rep 2

description:
processed data file:
matrix.MBFvsHSF.wt.tsv

source_name: wild type_MBF

value: wild type


title: MB rep 3


title: HS rep 2

source_name: wild type_HSF


title: ORC2_2_KD_ORC2_ChIP

city: Nashville

first: Logan

last: Richards

state: Tennessee

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

description: anti-ORC2 ChIP-Seq performed on Drosophila S2 cells RNAi treated for ORC2 for 5 days

data_processing:
Sequencing reads were aligned to genome assembly dm6 using Bowtie2 (version 2.4.2) with defuallt setting and "--very sensitive local"
Aligned reads were flagged using Picard: MarkDuplicates (version 2.18.2.2)
Coverage files were generated using deeptools: bamcoverage (version 3.3.2.0.0) with deafult settings. For ATAC-seq, coverage was normalized to counts per million. For ChIP-Seq, coverage was normalized to background. For CUT&RUN, coverage was normalized to 1X.
Peak calling was performed with MACS2 (version 2.1.1.20160309.6) with default settings using the option "-- no model"
Assembly: dm6
Supplementary files format and content: Processed data files are in bigwig format for coverage visualization using the UCSC genome browser.

organism: Drosophila melanogaster

source_name: embryonic cells

extract_protocol:
RNAi treated cells were lysed, cleared by centrifugation, and sonciated
Libraries contructed following NEBNext Ultra II Library Prep Kit for Illumina

tag: cell line

value: Embryonic cells

value: 5 day RNAi against ORC2

tag: method/antibody

value: ChIP-seq with ORC2 antibody (Richards et al., 2022)


title: HS rep 3


title: MB rep 1


title: ORC2_2_KD_ATAC

description: ATAC-Seq performed on Drosophila S2 cells RNAi treated for ORC2 for 5 days

extract_protocol:
RNAi treated cells were lysed and treated with Tn5 transposase.
Libraries constructed following Active Motif kit instructions

value: ATAC-seq (Active Motif 53150)


title: Elys_2_KD_ATAC

description: ATAC-Seq performed on Drosophila S2 cells RNAi treated for Elys for 5 days

value: 5 day RNAi against Elys


title: Elys_2_KD_ORC2_ChIP

description: anti-ORC2 ChIP-Seq performed on Drosophila S2 cells RNAi treated for Elys for 5 days


title: GFP_2_KD_ATAC

description: ATAC-Seq performed on Drosophila S2 cells RNAi treated for GFP for 5 days

value: 5 day RNAi against GFP


title: Nup98_2_KD_ATAC

description: ATAC-Seq performed on Drosophila S2 cells RNAi treated for Nup98 for 5 days

value: 5 day RNAi against Nup98


title: GFP_2_KD_ORC2_ChIP

description: anti-ORC2 ChIP-Seq performed on Drosophila S2 cells RNAi treated for GFP for 5 days


title: 42hpf, WT, rep1

value: whole embryo at 42hpf


title: HS rep 1


title: Nup98_1_KD_ORC2_ChIP

description: anti-ORC2 ChIP-Seq performed on Drosophila S2 cells RNAi treated for Nup98 for 5 days


title: Elys_1_KD_ORC2_ChIP


title: ORC2_1_KD_ORC2_ChIP


title: WT_CUTNRUN_mab414

description: CUT&RUN performed on wild type Drosophila S2 cells with mab414 antibody

data_processing:
Library strategy: CUT&RUN
Sequencing reads were aligned to genome assembly dm6 using Bowtie2 (version 2.4.2) with defuallt setting and "--very sensitive local"
Aligned reads were flagged using Picard: MarkDuplicates (version 2.18.2.2)
Coverage files were generated using deeptools: bamcoverage (version 3.3.2.0.0) with deafult settings. For ATAC-seq, coverage was normalized to counts per million. For ChIP-Seq, coverage was normalized to background. For CUT&RUN, coverage was normalized to 1X.
Peak calling was performed with MACS2 (version 2.1.1.20160309.6) with default settings using the option "-- no model"
Assembly: dm6
Supplementary files format and content: Processed data files are in bigwig format for coverage visualization using the UCSC genome browser.

extract_protocol:
Wild type cells were attached to ConA beads and permabilized with digitonin.
Libraries contructed following NEBNext Ultra II Library Prep Kit for Illumina

value: no treatment

value: CUT&RUN with mam414 antibody (BioLegend)


title: GFP_1_KD_ORC2_ChIP


title: Nup98_2_KD_ORC2_ChIP


title: GFP_1_KD_ATAC