title: T433F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s090_T433F.wk0d3_S3


title: T433F-wk0d1

status: Public on Sep 29 2023

type: SRA

city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

country: USA

institute: Beth Israel Deaconess Medical Center

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s089_T433F.wk0d1_S2

library_source: transcriptomic

data_processing:
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing are suitable for further analysis.
Adapter sequences, other contaminant sequences such as polyA tails and low-quality sequences with PHRED quality scores less than five were trimmed from reads using atropos (https://github.com/jdidion/atropos).
Trimmed reads were aligned to the Macaca mulatta genome using STAR. Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap and other custom tools.
Transcript abundance estimates was calculated internal to the STAR aligner using the algorithm of htseq-count as described previously.
DESeq2 was used for normalization, producing both a raw and normalized read count table. Normalized expression counts were used for visualizations purposes using PCA and heatmaps where indicated.
Assembly: New Rhesus Genome (MacaM version 7.6) (https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome)
Supplementary files format and content: raw_counts_p22321.csv
Supplementary files format and content: normalized_counts_p22321.csv

molecule: total RNA

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Whole-blood was collected from PAXgene tubes at pre and post-challenge timepoints, including necropsy. Whole-blood RNA was extracted and sequenced on an Illumina NovaSeq 6000.
Total RNA was extracted from these samples and libraries were prepared for Next-Gen Sequencing Paired-End 75bp (PE75).
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).

tag: tissue

value: Whole blood


title: T433F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s088_T433F.wk.1_S1


title: T433F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s094_T433F.wk3_S7


title: T460M-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s086_T460M.wk.1_S86


title: T460M-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s087_T460M.wk3_S87


title: T450F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s084_T450F.wk5d35_S84


title: T450F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s082_T450F.wk4d29_S82


title: T450F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s081_T450F.wk4d28_S81


title: T450F-Group-VI-Necropsy

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s085_T450F.Group.VI.Necropsy_S85


title: T450F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s083_T450F.wk4d31_S83


title: T450F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s080_T450F.wk3_S80


title: T450F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s079_T450F.wk.1_S79


title: T438F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s107_T438F.wk2_S20


title: T438F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s103_T438F.wk0d1_S16


title: T433F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s097_T433F.wk4d31_S10


title: T442F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s078_T442F.Day.1.Terminal_S78


title: T433F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s095_T433F.wk4d28_S8


title: T433F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s093_T433F.wk2_S6


title: T442F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s075_T442F.wk5d35_S75


title: T442F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s073_T442F.wk4d29_S73


title: T442F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s074_T442F.wk4d31_S74


title: T442F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s076_T442F.wk5d38_S76


title: T433F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s091_T433F.wk1d7_S4


title: T433F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s092_T433F.wk1d10_S5


title: T442F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s069_T442F.wk1d10_S69


title: T442F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s077_T442F.wk6_S77


title: T442F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s065_T442F.wk.1_S65


title: T442F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s068_T442F.wk1d7_S68


title: T442F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s072_T442F.wk4d28_S72


title: T442F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s071_T442F.wk3_S71


title: T447F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s060_T447F.wk4d31_S60


title: T442F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s067_T442F.wk0d3_S67


title: T447F-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s064_T447F.Day.2.Terminal_S64


title: T447F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s058_T447F.wk4d28_S58


title: T442F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s070_T442F.wk2_S70


title: T447F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s061_T447F.wk5d35_S61


title: T447F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s063_T447F.wk6_S63


title: T447F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s057_T447F.wk3_S57


title: T447F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s062_T447F.wk5d38_S62


title: T447F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s056_T447F.wk2_S56


title: T447F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s055_T447F.wk1d10_S55


title: T447F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s054_T447F.wk1d7_S54


title: T447F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s053_T447F.wk0d3_S53


title: T447F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s051_T447F.wk.1_S51


title: T447F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s052_T447F.wk0d1_S52


title: T439F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s050_T439F.Day.1.Terminal_S50


title: T439F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s049_T439F.wk6_S49


title: T439F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s047_T439F.wk5d35_S47


title: T439F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s045_T439F.wk4d29_S45


title: T439F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s046_T439F.wk4d31_S46


title: T442F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s066_T442F.wk0d1_S66


title: T439F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s042_T439F.wk2_S42


title: T439F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s041_T439F.wk1d10_S41


title: T439F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s044_T439F.wk4d28_S44


title: T447F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s059_T447F.wk4d29_S59


title: T439F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s038_T439F.wk0d1_S38


title: T439F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s037_T439F.wk.1_S37


title: T464M-wk3_S36

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s036_T464M.wk3_S36


title: T464M-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s032_T464M.wk1d7_S32


title: T464M-wk3_S35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s035_T464M.wk3_S35


title: T464M-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s031_T464M.wk0d3_S31


title: T464M-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s034_T464M.wk2_S34


title: T464M-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s033_T464M.wk1d10_S33


title: T464M-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s030_T464M.wk0d1_S30


title: T411F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s028_T411F.Day.1.Terminal_S28


title: T464M-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s029_T464M.wk.1_S29


title: T411F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s027_T411F.wk6_S27


title: T411F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s024_T411F.wk4d31_S24


title: T411F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s022_T411F.wk4d28_S22


title: T411F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s021_T411F.wk3_S21


title: T411F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s020_T411F.wk2_S20


title: T411F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s025_T411F.wk5d35_S25


title: T439F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s043_T439F.wk3_S43


title: T411F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s019_T411F.wk1d10_S19


title: T439F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s048_T439F.wk5d38_S48


title: T411F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s023_T411F.wk4d29_S23


title: T411F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s016_T411F.wk0d1_S16


title: T411F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s015_T411F.wk.1_S15


title: T439F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s039_T439F.wk0d3_S39


title: T411F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s026_T411F.wk5d38_S26


title: T456M-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s014_T456M.Day.2.Terminal_S14


title: T411F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s017_T411F.wk0d3_S17


title: T456M-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s012_T456M.wk5d38_S12


title: T439F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s040_T439F.wk1d7_S40


title: T456M-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s005_T456M.wk1d10_S5


title: T456M-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s004_T456M.wk1d7_S4


title: T456M-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s002_T456M.wk0d1_S2


title: T456M-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s010_T456M.wk4d31_S10


title: T456M-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s009_T456M.wk4d29_S9


title: T456M-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s008_T456M.wk4d28_S8


title: T456M-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s007_T456M.wk3_S7


title: T456M-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s003_T456M.wk0d3_S3


title: T456M-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s006_T456M.wk2_S6


title: T456M-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s001_T456M.wk.1_S1


title: M6522, Lymph Nodes, Day 3

status: Public on Aug 30 2023

data_processing:
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing are suitable for further analysis.
Adapter sequences, other contaminant sequences such as polyA tails and low-quality sequences with PHRED quality scores less than five were trimmed from reads using atropos (https://github.com/jdidion/atropos).
Trimmed reads were aligned to the Macaca mulatta genome using STAR. Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap and other custom tools.
Transcript abundance estimates was calculated internal to the STAR aligner using the algorithm of htseq-count as described previously.
DESeq2 was used for normalization, producing both a raw and normalized read count table. Normalized expression counts were used for visualizations purposes using PCA and heatmaps where indicated.
Assembly: New Rhesus Genome (MacaM version 7.6) (https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome)
Supplementary files format and content: CSV file (read count matrix), geo_1511_may19_PBMC_countMatrix.csv, md5: ce95b4b9ab3f959a82c4097ea956ab5e
Supplementary files format and content: CSV file (read count matrix), geo_1511_may19_LN_countMatrix.csv, md5: 2bec57edf8a2704046e620229a69b8e1

source_name: Lymph Nodes

extract_protocol:
Cell-associated RNA was collected from PBMCs and tissue biopsied LNMCs two weeks prior to infection as a baseline control, the timepoints that each group of monkeys-initiated ART (6 hours for group I, day 1 for group II, day 2 for group III and day 3 for group IV) and week 24 before ART discontinuation.
Total RNA was extracted from these samples and libraries were prepared for Illumina NextSeq 500 Next-Gen Sequencing Paired-End 75bp (PE75).
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).

value: Lymph Nodes

tag: time

value: Day 3

tag: cell type

value: LNMC

tag: virus

tag: group

value: Rebound

tag: treatment

value: ART


title: T411F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s018_T411F.wk1d7_S18


title: M6521, Lymph Nodes, Day 3

description:
X20180531_d3_6521_PTL5537.2of3_S9
geo_1511_may19_LN_countMatrix.csv


title: M6518, Lymph Nodes, Day 3

description:
X20180531_d3_6518_PTL5537.2of3_S6
geo_1511_may19_LN_countMatrix.csv


title: M6516, Lymph Nodes, Day 2

description:
X20180531_d2_6516_PTL5537.2of3_S4
geo_1511_may19_LN_countMatrix.csv

value: Day 2

value: No Rebound


title: M6517, Lymph Nodes, Day 2

description:
X20180531_d2_6517_PTL5537.2of3_S5
geo_1511_may19_LN_countMatrix.csv


title: M6513, Lymph Nodes, Day 2

description:
X20180531_d2_6513_PTL5537.2of3_S1
geo_1511_may19_LN_countMatrix.csv


title: M6515, Lymph Nodes, Day 2

description:
X20180531_d2_6515_PTL5537.2of3_S3
geo_1511_may19_LN_countMatrix.csv


title: T456M-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s011_T456M.wk5d35_S11


title: M6506, Lymph Nodes, Week 24

description:
X180531_Wk24_6506_PTL5537.2of3_S14
geo_1511_may19_LN_countMatrix.csv

value: Week 24

value: ART (Stopped at Week 24)


title: M6503, Lymph Nodes, Week 24

description:
X180531_Wk24_6503_PTL5537.2of3_S11
geo_1511_may19_LN_countMatrix.csv


title: M6522, Lymph Nodes, Week 24

description:
X180527_Wk24_6522_PTL5537_3of3_S15
geo_1511_may19_LN_countMatrix.csv


title: M6507, Lymph Nodes, Week 24

description:
X180531_Wk24_6507_PTL5537.2of3_S15
geo_1511_may19_LN_countMatrix.csv


title: M6505, Lymph Nodes, Week 24

description:
X180531_Wk24_6505_PTL5537.2of3_S13
geo_1511_may19_LN_countMatrix.csv


title: M6514, Lymph Nodes, Day 2

description:
X20180531_d2_6514_PTL5537.2of3_S2
geo_1511_may19_LN_countMatrix.csv


title: M6521, Lymph Nodes, Week 24

description:
X180527_Wk24_6521_PTL5537_3of3_S14
geo_1511_may19_LN_countMatrix.csv


title: M6504, Lymph Nodes, Week 24

description:
X180531_Wk24_6504_PTL5537.2of3_S12
geo_1511_may19_LN_countMatrix.csv


title: M6520, Lymph Nodes, Week 24

description:
X180527_Wk24_6520_PTL5537_3of3_S13
geo_1511_may19_LN_countMatrix.csv


title: M6517, Lymph Nodes, Week 24

description:
X180527_Wk24_6517_PTL5537_3of3_S10
geo_1511_may19_LN_countMatrix.csv


title: M6516, Lymph Nodes, Week 24

description:
X180527_Wk24_6516_PTL5537_3of3_S9
geo_1511_may19_LN_countMatrix.csv


title: M6514, Lymph Nodes, Week 24

description:
X180527_Wk24_6514_PTL5537_3of3_S7
geo_1511_may19_LN_countMatrix.csv


title: M6519, Lymph Nodes, Week 24

description:
X180527_Wk24_6519_PTL5537_3of3_S12
geo_1511_may19_LN_countMatrix.csv


title: M6519, Lymph Nodes, Day 3

description:
X20180531_d3_6519_PTL5537.2of3_S7
geo_1511_may19_LN_countMatrix.csv


title: M6513, Lymph Nodes, Week 24

description:
X180527_Wk24_6513_PTL5537_3of3_S6
geo_1511_may19_LN_countMatrix.csv


title: M6520, Lymph Nodes, Day 3

description:
X20180531_d3_6520_PTL5537.2of3_S8
geo_1511_may19_LN_countMatrix.csv


title: M6512, Lymph Nodes, Week 24

description:
X180527_Wk24_6512_PTL5537_3of3_S5
geo_1511_may19_LN_countMatrix.csv


title: M6510, Lymph Nodes, Week 24

description:
X180527_Wk24_6510_PTL5537_3of3_S3
geo_1511_may19_LN_countMatrix.csv


title: M6508, Lymph Nodes, Week 24

description:
X180527_Wk24_6508_PTL5537_3of3_S1
geo_1511_may19_LN_countMatrix.csv


title: M6509, Lymph Nodes, Week 24

description:
X180527_Wk24_6509_PTL5537_3of3_S2
geo_1511_may19_LN_countMatrix.csv


title: M6511, Lymph Nodes, Week 24

description:
X180527_Wk24_6511_PTL5537_3of3_S4
geo_1511_may19_LN_countMatrix.csv


title: ShamG877, Lymph Nodes, Baseline

description:
X052718_Naive_G877_PTL5537_1of3_S5
geo_1511_may19_LN_countMatrix.csv

value: Baseline

value: NA (Sham)


title: Sham666, Lymph Nodes, Baseline

description:
X052718_Naive_666_PTL5537_1of3_S2
geo_1511_may19_LN_countMatrix.csv


title: ShamG66M, Lymph Nodes, Baseline

description:
X052718_Naive_G66M_PTL5537_1of3_S4
geo_1511_may19_LN_countMatrix.csv


title: Sham239, Lymph Nodes, Baseline

description:
X052718_Naive_239x_PTL5537_1of3_S3
geo_1511_may19_LN_countMatrix.csv


title: M6511, Lymph Nodes, Day 1

description:
X052718_d1_6511_PTL5537_1of3_S14
geo_1511_may19_LN_countMatrix.csv

value: Day 1


title: M6512, Lymph Nodes, Day 1

description:
X052718_d1_6512_PTL5537_1of3_S15
geo_1511_may19_LN_countMatrix.csv


title: M6509, Lymph Nodes, Day 1

description:
X052718_d1_6509_PTL5537_1of3_S12
geo_1511_may19_LN_countMatrix.csv


title: M6510, Lymph Nodes, Day 1

description:
X052718_d1_6510_PTL5537_1of3_S13
geo_1511_may19_LN_countMatrix.csv


title: M6508, Lymph Nodes, Day 1

description:
X052718_d1_6508_PTL5537_1of3_S11
geo_1511_may19_LN_countMatrix.csv


title: M6506, Lymph Nodes, 6 Hours

description:
X052718_d0_6506_PTL5537_1of3_S9
geo_1511_may19_LN_countMatrix.csv

value: 6 Hours


title: M6518, Lymph Nodes, Week 24

description:
X180527_Wk24_6518_PTL5537_3of3_S11
geo_1511_may19_LN_countMatrix.csv


title: M6505, Lymph Nodes, 6 Hours

description:
X052718_d0_6505_PTL5537_1of3_S8
geo_1511_may19_LN_countMatrix.csv


title: M6515, Lymph Nodes, Week 24

description:
X180527_Wk24_6515_PTL5537_3of3_S8
geo_1511_may19_LN_countMatrix.csv


title: M6522, Blood, Week 24

description:
X20171218_6522.wk24.RNALater_PTL5036.4of4_S15
geo_1511_may19_PBMC_countMatrix.csv

source_name: Blood

value: Blood

value: PBMC


title: M6521, Blood, Week 24

description:
X20171218_6521.wk24.RNALater_PTL5036.4of4_S14
geo_1511_may19_PBMC_countMatrix.csv


title: M6518, Blood, Week 24

description:
X20171218_6518.wk24.RNALater_PTL5036.4of4_S11
geo_1511_may19_PBMC_countMatrix.csv


title: M6519, Blood, Week 24

description:
X20171218_6519.wk24.RNALater_PTL5036.4of4_S12
geo_1511_may19_PBMC_countMatrix.csv


title: M6517, Blood, Week 24

description:
X20171218_6517.wk24.RNALater_PTL5036.4of4_S10
geo_1511_may19_PBMC_countMatrix.csv


title: M6516, Blood, Week 24

description:
X20171218_6516.wk24.RNALater_PTL5036.4of4_S9
geo_1511_may19_PBMC_countMatrix.csv


title: M6515, Blood, Week 24

description:
X20171218_6515.wk24.RNALater_PTL5036.4of4_S8
geo_1511_may19_PBMC_countMatrix.csv


title: M6513, Blood, Week 24

description:
X20171218_6513.wk24.RNALater_PTL5036.4of4_S6
geo_1511_may19_PBMC_countMatrix.csv


title: M6511, Blood, Week 24

description:
X20171218_6511.wk24.RNALater_PTL5036.4of4_S4
geo_1511_may19_PBMC_countMatrix.csv


title: M6520, Blood, Week 24

description:
X20171218_6520.wk24.RNALater_PTL5036.4of4_S13
geo_1511_may19_PBMC_countMatrix.csv


title: M6510, Blood, Week 24

description:
X20171218_6510.wk24.RNALater_PTL5036.4of4_S3
geo_1511_may19_PBMC_countMatrix.csv


title: M6512, Blood, Week 24

description:
X20171218_6512.wk24.RNALater_PTL5036.4of4_S5
geo_1511_may19_PBMC_countMatrix.csv


title: M6509, Blood, Week 24

description:
X20171218_6509.wk24.RNALater_PTL5036.4of4_S2
geo_1511_may19_PBMC_countMatrix.csv


title: Sham665, Lymph Nodes, Baseline

description:
X052718_Naive_665_PTL5537_1of3_S1
geo_1511_may19_LN_countMatrix.csv


title: M6508, Blood, Week 24

description:
X20171218_6508.wk24.RNALater_PTL5036.4of4_S1
geo_1511_may19_PBMC_countMatrix.csv


title: M6521, Blood, Day 3

description:
X20171215_6521.d3.RNALater_PTL5036.3of4_S9
geo_1511_may19_PBMC_countMatrix.csv


title: M6522, Blood, Day 3

description:
X20171215_6522.d3.RNALater_PTL5036.3of4_S10
geo_1511_may19_PBMC_countMatrix.csv


title: M6520, Blood, Day 3

description:
X20171215_6520.d3.RNALater_PTL5036.3of4_S8
geo_1511_may19_PBMC_countMatrix.csv


title: M6514, Blood, Week 24

description:
X20171218_6514.wk24.RNALater_PTL5036.4of4_S7
geo_1511_may19_PBMC_countMatrix.csv


title: M6504, Lymph Nodes, 6 Hours

description:
X052718_d0_6504_PTL5537_1of3_S7
geo_1511_may19_LN_countMatrix.csv


title: M6518, Blood, Day 3

description:
X20171215_6518.d3.RNALater_PTL5036.3of4_S6
geo_1511_may19_PBMC_countMatrix.csv


title: M6516, Blood, Day 2

description:
X20171215_6516.d2.RNALater_PTL5036.3of4_S4
geo_1511_may19_PBMC_countMatrix.csv


title: M6513, Blood, Day 2

description:
X20171215_6513.d2.RNALater_PTL5036.3of4_S1
geo_1511_may19_PBMC_countMatrix.csv


title: M6515, Blood, Day 2

description:
X20171215_6515.d2.RNALater_PTL5036.3of4_S3
geo_1511_may19_PBMC_countMatrix.csv


title: M6503, Lymph Nodes, 6 Hours

description:
X052718_d0_6503_PTL5537_1of3_S6
geo_1511_may19_LN_countMatrix.csv


title: M6514, Blood, Day 2

description:
X20171215_6514.d2.RNALater_PTL5036.3of4_S2
geo_1511_may19_PBMC_countMatrix.csv


title: M6507, Blood, Week 24

description:
X20171215_6507.wk24.RNALater_PTL5036.3of4_S15
geo_1511_may19_PBMC_countMatrix.csv


title: M6506, Blood, Week 24

description:
X20171215_6506.wk24.RNALater_PTL5036.3of4_S14
geo_1511_may19_PBMC_countMatrix.csv


title: M6505, Blood, Week 24

description:
X20171215_6505.wk24.RNALater_PTL5036.3of4_S13
geo_1511_may19_PBMC_countMatrix.csv


title: M6504, Blood, Week 24

description:
X20171215_6504.wk24.RNALater_PTL5036.3of4_S12
geo_1511_may19_PBMC_countMatrix.csv


title: M6503, Blood, Week 24

description:
X20171215_6503.wk24.RNALater_PTL5036.3of4_S11
geo_1511_may19_PBMC_countMatrix.csv


title: M6522, Blood, Baseline

description:
X20171214_6522.wk.2_PBMC_PTL5036.2of4_S5
geo_1511_may19_PBMC_countMatrix.csv


title: M6521, Blood, Baseline

description:
X20171214_6521.wk.2_PBMC_PTL5036.2of4_S4
geo_1511_may19_PBMC_countMatrix.csv


title: M6520, Blood, Baseline

description:
X20171214_6520.wk.2_PBMC_PTL5036.2of4_S3
geo_1511_may19_PBMC_countMatrix.csv


title: M6519, Blood, Baseline

description:
X20171214_6519.wk.2_PBMC_PTL5036.2of4_S2
geo_1511_may19_PBMC_countMatrix.csv


title: M6512, Blood, Day 1

description:
X20171214_6512.d1.RNALater_PTL5036.2of4_S15
geo_1511_may19_PBMC_countMatrix.csv


title: M6519, Blood, Day 3

description:
X20171215_6519.d3.RNALater_PTL5036.3of4_S7
geo_1511_may19_PBMC_countMatrix.csv


title: M6511, Blood, Day 1

description:
X20171214_6511.d1.RNALater_PTL5036.2of4_S14
geo_1511_may19_PBMC_countMatrix.csv


title: M6510, Blood, Day 1

description:
X20171214_6510.d1.RNALater_PTL5036.2of4_S13
geo_1511_may19_PBMC_countMatrix.csv


title: M6504, Blood, 6 Hours

description:
X20171214_6504.d0.RNALater_PTL5036.2of4_S7
geo_1511_may19_PBMC_countMatrix.csv


title: M6517, Blood, Day 2

description:
X20171215_6517.d2.RNALater_PTL5036.3of4_S5
geo_1511_may19_PBMC_countMatrix.csv


title: M6505, Blood, 6 Hours

description:
X20171214_6505.d0.RNALater_PTL5036.2of4_S8
geo_1511_may19_PBMC_countMatrix.csv


title: M6503, Blood, 6 Hours

description:
X20171214_6503.d0.RNALater_PTL5036.2of4_S6
geo_1511_may19_PBMC_countMatrix.csv


title: M6507, Blood, 6 Hours

description:
X20171214_6507.d0.RNALater_PTL5036.2of4_S10
geo_1511_may19_PBMC_countMatrix.csv


title: M6508, Blood, Day 1

description:
X20171214_6508.d1.RNALater_PTL5036.2of4_S11
geo_1511_may19_PBMC_countMatrix.csv


title: M6509, Blood, Day 1

description:
X20171214_6509.d1.RNALater_PTL5036.2of4_S12
geo_1511_may19_PBMC_countMatrix.csv


title: M6506, Blood, 6 Hours

description:
X20171214_6506.d0.RNALater_PTL5036.2of4_S9
geo_1511_may19_PBMC_countMatrix.csv


title: M6515, Blood, Baseline

description:
X20171213_6515.wk.2PBMC_PTL5036_S13
geo_1511_may19_PBMC_countMatrix.csv


title: M6517, Blood, Baseline

description:
X20171213_6517.wk.2PBMC_PTL5036_S15
geo_1511_may19_PBMC_countMatrix.csv


title: M6512, Blood, Baseline

description:
X20171213_6512.wk.2PBMC_PTL5036_S10
geo_1511_may19_PBMC_countMatrix.csv


title: M6514, Blood, Baseline

description:
X20171213_6514.wk.2PBMC_PTL5036_S12
geo_1511_may19_PBMC_countMatrix.csv


title: M6513, Blood, Baseline

description:
X20171213_6513.wk.2PBMC_PTL5036_S11
geo_1511_may19_PBMC_countMatrix.csv


title: M6511, Blood, Baseline

description:
X20171213_6511.wk.2PBMC_PTL5036_S9
geo_1511_may19_PBMC_countMatrix.csv


title: M6510, Blood, Baseline

description:
X20171213_6510.wk.2PBMC_PTL5036_S8
geo_1511_may19_PBMC_countMatrix.csv


title: M6507, Blood, Baseline

description:
X20171213_6507.wk.2PBMC_PTL5036_S5
geo_1511_may19_PBMC_countMatrix.csv


title: M6509, Blood, Baseline

description:
X20171213_6509.wk.2PBMC_PTL5036_S7
geo_1511_may19_PBMC_countMatrix.csv


title: M6508, Blood, Baseline

description:
X20171213_6508.wk.2PBMC_PTL5036_S6
geo_1511_may19_PBMC_countMatrix.csv


title: M6506, Blood, Baseline

description:
X20171213_6506.wk.2PBMC_PTL5036_S4
geo_1511_may19_PBMC_countMatrix.csv


title: M6505, Blood, Baseline

description:
X20171213_6505.wk.2PBMC_PTL5036_S3
geo_1511_may19_PBMC_countMatrix.csv


title: M6518, Blood, Baseline

description:
X20171214_6518.wk.2_PBMC_PTL5036.2of4_S1
geo_1511_may19_PBMC_countMatrix.csv


title: M6504, Blood, Baseline

description:
X20171213_6504.wk.2PBMC_PTL5036_S2
geo_1511_may19_PBMC_countMatrix.csv


title: M6503, Blood, Baseline

description:
X20171213_6503.wk.2PBMC_PTL5036_S1
geo_1511_may19_PBMC_countMatrix.csv


title: endothelial cells pulmonary artery dog B

status: Public on Aug 22 2023

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

data_processing:
RNA-seq reads were aligned to the reference genome using STAR version 2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1, using the union mode.
Genome_build: canfam3.1
Supplementary_files_format_and_content: raw counts

organism: Canis lupus familiaris

source_name: endothelial cells pulmonary artery

extract_protocol:
cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

value: endothelial cells


title: endothelial cells pulmonary artery dog A


title: endothelial cells femoral artery dog C

source_name: endothelial cells femoral artery


title: endothelial cells pulmonary artery dog C


title: M6516, Blood, Baseline

description:
X20171213_6516.wk.2PBMC_PTL5036_S14
geo_1511_may19_PBMC_countMatrix.csv


title: endothelial cells femoral artery dog B


title: Purified R. rickettsii st. Iowa, Rep3

status: Public on Jul 06 2023

city: Hamilton

first: Ted

last: Hackstadt

state: MT

address: 903 S. Forth St

institute: NIAID

data_processing:
RNA-Seek (https://github.com/OpenOmics/RNA-seek)
A custom hybrid reference genome database was built with Chlorocebus sabaeus (Green Monkey) reference genome (GCA_000409795.2) – background of Vero cells, and R. rickettsii str. Iowa genome (GCA_000017445.3) using ‘build’ function in RNA-Seek pipeline.
Initial data preprocessing included read quality check with FASTQC v0.11.5, screening for sources of contamination (FQScreen v0.9.3, Kraken v2.0.8), removal of adapters and short sequences, and quality trimming with Cutadapt v1.18.
Preprocessed reads were then mapped to the hybrid genome reference using STAR v2.7.6a aligner, and reads mapping to C. sabaeus and R. rickettsia genes were quantified using RSEM v1.3.0.
The gene quantification data was split between C. sabaeus and R. rickettsia genes. The R. rickettsia gene expression data was further differential gene expression analyses.
Assembly: Hybrid genome (Chlorocebus sabaeus + R. rickettsii str. Iowa)
Supplementary files format and content: tab-delimited text files include RPKM counts (non-normalized) for R. rickettesia strain Iowa genes

organism: Rickettsia rickettsii

source_name: st. Iowa

growth_protocol: Vero76 cells (ATCC® CCL-81™) were grown in RPMI medium plus 5 % heat-inactivated fetal bovine serum (FBS) at 37˚C in a 5% CO2 atmosphere.

extract_protocol:
RNA containing aqueous phase was extracted using Qiagen AllPrep DNA/RNA 96-well system (Valencia, CA). The RNA yield was determined by spectrophotometry at 260 nm and 280nm and the integrity was assessed using the Agilent 2100 Bioanalyzer using RNA 6000 Pico kit (Agilent Technologies, Santa Clara, Ca).   The average RNA Integrity Number (RIN) was 9.2.
Ribo-Zero Epidemiology kits (Illumina, Inc, San Deigo, CA) were used to deplete the samples of ribosomal RNAs prior to library preparation with the TruSeq Total RNA-Seq Library Prep Kit (Illumina), starting at the Elute-Frag-Prime step without further modification. Final libraries were assessed on a BioAnalyzer DNA1000 chip (Agilent Technologies, Santa Clara, CA) and quantified using the Kapa Quantification Kit for Illumina MiSeq (v3 chemistry )Sequencing (Roche, Basel, Switzerland).

treatment_protocol:
Vero76 cells in 6-well plates (2/replicate) were infected with R. rickettsii Morgan or Iowa at a multiplicity of infection (MOI) of 30 for a 4 hr time point and MOI of 1 for 24 and 48 hr time points.
Cultures were centrifuged at 2000 RPM for 5 min at room temperature to synchronize infections, and were incubated at 34ºC for 4, 24, or 48 hr prior to harvesting by scraping into Trizol. Purified rickettsiae of each strain were also extracted into Trizol. All conditions were performed in triplicate.

tag: strain

value: st. Iowa

tag: agent

value: no infection


title: endothelial cells femoral artery dog A


title: Purified R. rickettsii st. Morgan, Rep3

source_name: st. Morgan

value: st. Morgan


title: Purified R. rickettsii st. Iowa, Rep1


title: Purified R. rickettsii st. Morgan, Rep2


title: Purified R. rickettsii st. Morgan, Rep1


title: Vero76 cells, R. rickettsii st. Iowa, 48hpi, Rep3

organism: Chlorocebus aethiops

source_name: Vero76 (ATCC CCL-81)

tag: cell line

value: Vero76 (ATCC CCL-81)

value: R. rickettsii st. Iowa

value: 48 hour post infection


title: Purified R. rickettsii st. Iowa, Rep2


title: Vero76 cells, R. rickettsii st. Iowa, 48hpi, Rep1


title: Vero76 cells, R. rickettsii st. Morgan, 48hpi, Rep3

value: R. rickettsii st. Morgan


title: Vero76 cells, R. rickettsii st. Iowa, 48hpi, Rep2


title: Vero76 cells, R. rickettsii st. Morgan, 48hpi, Rep2


title: Vero76 cells, R. rickettsii st. Morgan, 48hpi, Rep1


title: Vero76 cells, R. rickettsii st. Iowa, 24hpi, Rep3

value: 24 hour post infection


title: Vero76 cells, R. rickettsii st. Iowa, 24hpi, Rep1


title: Vero76 cells, R. rickettsii st. Iowa, 24hpi, Rep2


title: Vero76 cells, R. rickettsii st. Morgan, 24hpi, Rep2


title: Vero76 cells, R. rickettsii st. Iowa, 4hpi, Rep3

value: 4 hour post infection


title: Vero76 cells, R. rickettsii st. Morgan, 24hpi, Rep3


title: Vero76 cells, R. rickettsii st. Iowa, 4hpi, Rep2


title: Vero76 cells, R. rickettsii st. Iowa, 4hpi, Rep1


title: Vero76 cells, R. rickettsii st. Morgan, 4hpi, Rep3


title: Vero76 cells, R. rickettsii st. Morgan, 4hpi, Rep1


title: Vero76 cells, R. rickettsii st. Morgan, 4hpi, Rep2


title: P30 wildtype harvested following 3h of sleep deprivation, replicate 2 [WTSD3_P30_PFC_2]

status: Public on Jan 16 2023

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

data_processing:
Raw sequencing reads in FASTQ files  were processed with Salmon v1.8 using the ‘mapping mode’. To prepare the index, Gencode (release M28) reference genome (‘GRCm39.primary_assembly.genome.fa.gz’) and reference transcriptome (‘gencode.vM28.transcripts.fa.gz)’ were downloaded, along with GTF coordinates (‘gencode.vM28.annotation.gtf.gz’). To improve the accuracy of quantification estimates from Salmon, an index was built that incorporated a set of genome targets as decoys. Using the concatenated list of transcriptome targets along with genome targets, the `salmon index` function was used to build the index with the flags: `--gencode`, `--threads 4`, and  `-k 31`.
`salmon quant` was used to perform quantification with the flags `--threads 6` and `--numBootstraps 30`. To create the final SummarizedExperiment object at the gene level, the summarizeToGene()` function from the tximeta (v1.14) R/Bioconductor package was used.
Assembly: GRCm39
Supplementary files format and content: text file, summarized experiment with gene counts (Tximeta) for gene level analysis

organism: Mus musculus

source_name: Pre Frontal Cortex

growth_protocol: Timed breeding pairs were established to obtain wild type (WT) at specific postnatal ages. Mice were house in standard cages on a 12:12 h light:dark cycle with food and water ad libitum. P16 mice were housed with the littermates and parents until the experiment. P24 mice were weaned and single housed at P18. P30 and P90 animals were weaned at P21 and single housed for a week before SD.

extract_protocol:
RNA was extracted from thawed tissue using the Qiagen RNAeasy Microarray Tissue kit with RWT buffer. The tissue was lysed and homogenized using a TissueLyzer. Briefly, 1ml of Qiazol was added to the pre-sterilized 2ml round bottom tubes with one 5mm steel bead inside,before adding the frozen tissue. The tissue was liyed for 2x 2min at 30Hz. Samples were spun down and the clear lysate was transfere to a clean tube. RNA was isolated through phase separation. For this, 200 µl of water saturated chloroform with isoamylalcohol (ChCl3:IAA 24:1) was added followed by vigorous shaking, incubated at rorom temparature of 3 min and then centrifuged at 12,000 g for 15 min at 4C. The aqueous phase was transfered to a new tube and 600ul of 100% EtOH was added. The ethanol-lysate mix was then loaded on a RNAeasy mini spin column and centrifuged at max speed for 30sec at room temparature. The loaded colums were washed using 500 µl of RWT (Qiagen), centrifuged again for 30s at max speed at room temparature. The flowthrough was discarded. The membrane was washed twice with 500 µl of RPE buffer (Qiagen) followed by a 30s (first wash) or 2min (second wash) spin at max speed at room temparature. RNA was eluted from the membrane with 30ul of RNase free water. The RNase free water was loaded directly onto the semi dry membran, centrifuged for one min at max speed at RT. This step was reapeated once by re-loading the eluat and centrigation again for 1min at room temparature. 1ul of the RNA eluat was used to measure concentrations in the Nanodrop. The extraced RNA sampel was aliquoted in 2x15ul aliquots and stored at -80C until further processing.
The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity RNA Analysis Kit.  RNA Quality Numbers (RQNs) from 1 to 10 were assigned to each sample to indicate its integrity or quality.  RNA samples with RQNs ranging from 7 to 10 were used for RNA library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).  Briefly, mRNA was isolated from 2.5 µg of total RNA using poly-T oligo attached to magnetic beads and then subjected to fragmentation, followed by cDNA synthesis, dA-tailing, adaptor ligation and PCR enrichment.  The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit.  The concentrations of RNA libraries were measured by StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA).  The libraries were diluted to 2 nM with RSB (10 mM Tris-HCl, pH8.5) and denatured with 0.1 N NaOH.  Eighteen pM libraries were clustered in a high-output flow cell using HiSeq Cluster Kit v4 on a cBot (Illumina).  After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using HiSeq SBS kit v4 (Illumina).  DNA was sequenced from both ends (paired-end) with a read length of 100 bp.

treatment_protocol: Begining at light onset, sleep deprived mice were kept awake for 3 or 5 hours via gentle handling. P16 animals for SD or homecage control were separated from the dam and housed in groups of 2 or 3 in a prewarmed cage. Prefrontal cortex tissue was collected at the conclusion of sleep deprivation (SD) and immediately flash frozen in liquid nitrogen. Control animals that were left in their home cage to sleep were dissected at the same time of day (HC).

value: Pre Frontal Cortex

value: Brain Tissue Homogenate

tag: genotype

value: wild type

value: Sleepdeprivation

tag: age


title: P30 wildtype homecage control harvested at ZT hour 3, replicate 5 [WTHC3_P30_PFC_5]

value: control


title: P30 wildtype harvested following 3h of sleep deprivation, replicate 3 [WTSD3_P30_PFC_3]


title: Ventral skin 2

status: Public on Feb 08 2023

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

data_processing:
Basecall data generated by the NextSeq 1000/2000 Control Software (Version 1.4.1.39716)
cellranger mkfastq was used go generated fastq
cellranger count (--include-introns --expect-cells=10,000) was used for generating the processed data files
Genome_build: GRCh38 (version 2020-A; pre-built index provided by 10x Genomics)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx

organism: Homo sapiens

source_name: Finger

extract_protocol:
Collected tissue was flash frozen and stored at -80C. Nuclei were isolated by homogenization in EZ Nuclei Lysis Buffer, washed, and prepared for cDNA library generation.
NextSeq 1000/2000 P3 Reagents (100 cycles) v3 Kit (#20040559)
Libraries were pooled  in equimolar quantities and PhiX Control v3 (#FC-110-3001) library was spiked in to the run  at a concentration of ~1% to help with cluster resolution and facilitate troubleshooting in case  of any problems with the run. Sequencing was run on NextSeq 2000 platform (Illumina Inc, #SY-415-1002)

tag: tissue type

value: skin

tag: tissue location

value: Finger

value: Ventral


title: Ventral skin 1


title: P30 wildtype harvested following 3h of sleep deprivation, replicate 5 [WTSD3_P30_PFC_5]


title: P30 wildtype homecage control harvested at ZT hour 3, replicate 3 [WTHC3_P30_PFC_3]


title: P30 wildtype homecage control harvested at ZT hour 3, replicate 4 [WTHC3_P30_PFC_4]


title: P30 wildtype harvested following 3h of sleep deprivation, replicate 4 [WTSD3_P30_PFC_4]


title: P30 wildtype harvested following 3h of sleep deprivation, replicate 1 [WTSD3_P30_PFC_1]


title: P24 wildtype harvested following 3h of sleep deprivation, replicate 8 [WTSD3_P24_PFC_8]


title: P24 wildtype harvested following 3h of sleep deprivation, replicate 6 [WTSD3_P24_PFC_6]


title: P24 wildtype harvested following 3h of sleep deprivation, replicate 7 [WTSD3_P24_PFC_7]


title: P30 wildtype homecage control harvested at ZT hour 3, replicate 2 [WTHC3_P30_PFC_2]


title: Vero76 cells, R. rickettsii st. Morgan, 24hpi, Rep1


title: P30 wildtype homecage control harvested at ZT hour 3, replicate 1 [WTHC3_P30_PFC_1]


title: P24 wildtype homecage control harvested at ZT hour 3, replicate 6 [WTHC3_P24_PFC_6]


title: P24 wildtype homecage control harvested at ZT hour 3, replicate 7 [WTHC3_P24_PFC_7]


title: P24 wildtype homecage control harvested at ZT hour 3, replicate 5 [WTHC3_P24_PFC_5]


title: P24 wildtype homecage control harvested at ZT hour 3, replicate 8 [WTHC3_P24_PFC_8]


title: MB002_T0

status: Public on Nov 09 2022

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
PACE_115
gRNA amplicon

library_source: genomic

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequences using a bespoke Perl script
Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:  -p 16 -v 3 -l 18 --chunkmbs 256 -t TKOv3 --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was then enumerated for each .sam file, and alignment statistics were recorded.  Guide IDs and counts were then written to individual count files, and subsequently merged into a full read count matrix with library annotations using R.
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPRseq

molecule: genomic DNA

source_name: brain cancer

extract_protocol:
Genomic DNA was extracted using Puregene Cell and Tissue kit (Qiagen) as per manufacturer’s instructions and quantified using spectrophotometry
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harbouring Illumina TruSeq adaptors with i5 and i7 barcodes.  The resulting sequencign libraries were pooled and gel purified.

tag: time point

value: brain cancer

value: medulloblastoma


title: Col0_XVE-ROS1_Estradiol_Nanopore-seq

status: Public on Nov 07 2022

city: Sheffield

first: Jurriaan

last: Ton

state: South Yorkshire

address: Western Bank

department: Animal and Plant Sciences

institute: University of Sheffield

description: Col-0 plants transformed with an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were spray-induced with 25 µM estradiol on day 14 and 25 µM on day 18. On day 20, aerial tissue from ~100 seedlings was harvested for DNA extraction and long-read sequencing (Oxford Nanopore Technologies).

data_processing:
Raw .fast5 files were basecalled and filtered using Guppy v6.0.1 (‘guppy_basecaller --config dna_r9.4.1_450bps_hac.cfg’)
Basecalled sequences were annotated onto raw .fast5 files (‘tombo preprocess annotate_raw_with_fastqs’) and resquiggled (‘tombo resquiggle --signal-length-range 0 1000000 --sequence-length-range 0 100000’) using Tombo v1.5.1. Mapped against the Arabidopsis reference genome TAIR v10.
Methylation predictions for all cytosines in the genome were called using DeepSignal-plant v0.1.4 (‘deepsignal_plant call_mods’), with the model ‘model.dp2.CNN.arabnrice2-1_120m_R9.4plus_tem.bn13_sn16.both_bilstm.epoch6.ckpt’.
The frequency of methylation at each CG, CHG, and CHH site was called using DeepSignal-plant v0.1.4 (‘deepsignal_plant call_freq’).
Assembly: TAIR10
Supplementary files format and content: Methylation frequency files (.tsv) output from DeepSignal-plant pipeline. Columns are: <chrom> <0-based genomic coordinate><position in strand><prob unmethylated><prob methylated><reads methylated><reads unmethylated><coverage><methylation frequency><k-mer around targeted base>

organism: Arabidopsis thaliana

source_name: Aerial tissue from 20-day-old seedlings

growth_protocol: Homozygous XVE:ROS1-YFP seeds sown onto soil containing a 2:1 (v/v) mixture of Levington Advance Pot & Bedding M3 compost and sand after suspension in dH2O for 4 days in the dark at 4 ℃. Plants were cultivated under the following conditions: 8.5:15.5 hr day:night, 21 °C, 45-70% relative humidity (RH) and 100-250 μE m−2 s−1.

extract_protocol:
On day 20 and 48 hrs after the second spray treatment, aerial tissue from c. 100 seedlings (c. 500 mg FW) were harvested and extracted for DNA using the NucleoBond® HMW DNA kit (Macherey Nagel, 740160.20) according to the manufacturer's instructions
Library preparation was conducted using the Oxford Nanopore Technologies (ONT) Rapid Barcoding kit (SQK-RBK004). The prepared libary was loaded into the Flow Cell (ONT, FLO-MIN106) of a MinION sequencer. The Flow Cell was washed using Flow Cell Wash Kit (ONT, EXP-WSH004) after 2 days of sequencing, and then ran to exhaustation.

treatment_protocol: For the estradiol treatment, seedlings were sprayed with dH2O containing 10 µM estradiol 14 days after sowing and 25 µM estradiol 18 days after sowing (estradiol sample). For the DMSO treatment, plants were sprayed with dH2O supplemented with the same percentage (v/v) DMSO as the estradiol treatment on days 14 and 18 (DMSO sample).

value: Aerial tissue from 20-day-old seedlings

tag: background

tag: generation

value: Homozygous T3

value: 10 µM Beta-Estradiol (estradiol) spray-induction at 14 days followed by 25 uM estradiol spray-induction at 18 days.

tag: plant age

value: 20 days


title: Col0_XVE-ROS1_DMSO_Nanopore-seq

description: Col-0 plants transformed with an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were spray-induced with 0.02% DMSO on day 14 and 0.05% on day 18. On day 20, aerial tissue from ~100 seedlings was harvested for DNA extraction and long-read sequencing (Oxford Nanopore Technologies).

tag: tissue

value: 0.02% dimethyl sulfoxide (DMSO) spray-induction at 14 days followed by 0.05% DMSO spray-induction at 18 days.


title: nrpe1-11_rep4_Bisulfite-seq

data_processing:
Reads were trimmed using Trimmomatic (v0.38) with the parameters: ‘SLIDINGWINDOW:4:25’, ‘HEADCROP:6’, MINLEN:36’.
Trimmed reads were aligned to the TAIR10 genome assembly using Bismark (v0.22.3) and Bowtie2 (v2.3.4.3) with default parameters.
Read deduplication was performed using the 'deduplicate_bismark' tool from the Bismark suite (v0.22.3) with the setting: "--paired".
Methylated and unmethylated read counts per cytosine (C) position were generated using the Bismark (v0.22.3) tool ‘bismark_methylation_extractor’ with the parameters: ‘--paired-end’, ‘--no_overlap’, ‘--ignore_3prime_r2 90’, ‘--comprehensive’, ‘--bedGraph’, ‘--CX’, ‘--cytosine_report’.
Assembly: TAIR10
Supplementary files format and content: Genome-wide cytosine reports output by the 'bismark_methylation_extractor' tool. The column headers in the text files are as follows: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>.

source_name: Aerial tissue from two- to three-week-old plants.

growth_protocol: Seeds were stored at 4 °C, in the dark and suspended in deionised H2O (dH2O) for 4 days to break dormancy, after which they were sown onto soil consisting of Levington Advance Pot & Bedding M3 compost (ICL) and sand in a 3:1 ratio and cultivated under the following conditions: 16:8 hr day:night, 22 °C, 60% relative humidity (RH) and 150 μmol m−2 s−1.

extract_protocol:
28-35 seedlings were pooled for each replicate, flash frozen and ground to a powder. Genomic DNA was extracted using the GenElute Plant Genomic DNA Miniprep Kit (Sigma-Aldrich).
Bisulfite treatment, library preparation and 150 bp paired-end sequencing was performed by BGI genomics.

treatment_protocol: Plants were grown under stress free conditions.

value: Aerial tissue

value: 2-3 weeks old


title: nrpe1-11_rep3_Bisulfite-seq


title: T456M-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s013_T456M.wk6_S13

value: Whole blood


title: Esophagus Sample 46

status: Public on Aug 17 2022

city: Ann Arbor

first: Laura

middle: A

last: Kresty

state: MI

address: 1500 E Medical Center Dr

department: Surgery

institute: University of Michigan

data_processing:
QC and trimming were performed using FastQC and Trimmomatic.
RNA quantification was performed using Kallisto (version 0.46.2) with parameter -g --pseudobam -t 8 -b 100.
Isoform switching analysis was performed using isoformSwitchAnalyzeR package (version 1.14.1) in R (version 4.1.1) with default parameter.
Genome_build: Gencode Human Release 34 (GRCh38.p13)
Supplementary_files_format_and_content: Table with transcripts that show significant isoform switching events.

source_name: Esophagus

extract_protocol:
RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Esophagus

tag: histopathology


title: Esophagus Sample 44


title: Esophagus Sample 45


title: Col0_rep2_Bisulfite-seq


title: nrpe1-11_rep1_Bisulfite-seq


title: Col0_rep3_Bisulfite-seq


title: Esophagus Sample 41


title: Esophagus Sample 43


title: nrpe1-11_rep2_Bisulfite-seq


title: Esophagus Sample 40


title: P24 wildtype harvested following 3h of sleep deprivation, replicate 4 [WTSD3_P24_PFC_4]

value: Pre Frontal Cortex

tag: cell type

value: Brain Tissue Homogenate

value: wild type


title: Col0_rep4_Bisulfite-seq


title: Esophagus Sample 36


title: Col0_rep1_Bisulfite-seq


title: Esophagus Sample 34


title: Esophagus Sample 32


title: Esophagus Sample 37


title: Esophagus Sample 42


title: P24 wildtype homecage control harvested at ZT hour 3, replicate 4 [WTHC3_P24_PFC_4]

value: control


title: P24 wildtype harvested following 3h of sleep deprivation, replicate 5 [WTSD3_P24_PFC_5]

value: Sleepdeprivation


title: Esophagus Sample 33


title: Esophagus Sample 38


title: Esophagus Sample 39


title: Esophagus Sample 31


title: Esophagus Sample 30


title: Esophagus Sample 29


title: Esophagus Sample 27


title: Esophagus Sample 28


title: Esophagus Sample 26


title: Esophagus Sample 25


title: Esophagus Sample 23


title: Esophagus Sample 24


title: Esophagus Sample 21


title: Esophagus Sample 20


title: Esophagus Sample 35


title: Esophagus Sample 18


title: Esophagus Sample 22


title: Esophagus Sample 19


title: Esophagus Sample 10


title: Esophagus Sample 16


title: Esophagus Sample 17


title: Esophagus Sample 12


title: Esophagus Sample 13


title: Esophagus Sample 15


title: Esophagus Sample 14


title: Esophagus Sample 9


title: Esophagus Sample 5


title: Esophagus Sample 2


title: Esophagus Sample 8


title: Esophagus Sample 1


title: Esophagus Sample 6


title: Esophagus Sample 4


title: Esophagus Sample 7


title: BM-UPN12 scRNA-seq

status: Public on Jul 30 2022

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
scRNA-seq libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina). scRNA-seq libraries were sequenced using a NextSeq 500 150-cycle flow cell (Illumina).
For scATAC-seq, reads were aligned to the  human genomes (hg38), and peaks were called using the cellranger-atac count pipeline. Individual samples were merged using the cellranger-atac pipeline to generate the transcription factor activity matrix.
For scRNA-seq,  raw reads were aligned to the  human genomes (hg38), and the digital expression matrix was generated using cellranger count. Individual samples were merged to generate the digital expression matrix using cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: Transcription factor activity matrix for scATAC-seq and raw count expression matrix for scRNA-seq.

molecule: polyA RNA

source_name: primary BM cells from SF3B1-mutant MDS-RS samples

growth_protocol: MACS-purified CD34+ cells were subjected to a 3-phase in vitro culture. Cells were maintained in phase 1 from the day of collection until day 8, at which time the cells underwent ribonucleoprotein-based gene editing and were transitioned to phase 2 medium. On day 13 of culture, the cells were transitioned to phase 3 medium. Samples for Western blot and cytospin analyses, and sample for flow cytometry were harvested on day 13 or 15 of culture, respectively.

extract_protocol:
BM MNCs were isolated from each sample using the standard gradient separation approach with Ficoll-Paque PLUS (GE Healthcare Lifesciences, Marlborough, MA). For cell sorting applications, MNCs were enriched in CD34+ cells using magnetic sorting (MACS) with the CD34 Microbead Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) and further purified by fluorescence-activated cell sorting as described below.
For scATAC-seq, the scATAC Low Cell Input Nuclei Isolation protocol (10X Genomics) was used to isolate nuclei from FACS-purified cells. The trypan blue exclusion assay was performed to check for intact nuclei. The remaining extracted nuclei were used for the consecutive steps of the scATAC-seq library preparation protocol following 10X Genomics guidelines. Equal molar concentrations of uniquely indexed samples were pooled together. For scRNA-seq, sample preparation and sequencing were performed at MD Anderson Cancer Center’s Advanced Technology Genomics Core. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10X Genomics, Pleasanton, CA), and single cells were lysed and barcoded for reverse transcription. Equal amounts of each uniquely indexed sample library were pooled together.

tag: disease state

value: myelodysplastic syndrome with ringed sideroblasts (MDS-RS)

value: bone marrow mononuclear cells

value: SF3B1 mutant

value: bone marrow


title: tot_7_RNA-seq_S51A_veh_3

status: Public on Jul 15 2022

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Reads were demultiplexed with Fastq Multx, trimmed using rfastp, and aligned to the mm10 reference genome using bowtie2
For expression analysis of ribosome profiling data only reads in the CDS were included and reads coming from the first 15 codons (45bp) and last 5 codons (15bp) were excluded. Additionally, only reads of size between 20-23bp or 26-32bp were counted. Counting of reads over these regions was done with featureCounts (Liao et al., 2014) followed by differential analysis with DESeq2 (Love et al., 2014).
Gene lists were generated by first by filtering genes with significant differences in RPF-read counts (RPF_FC>1.5 and padj <0.05), and then genes that changed specifically at the translation level were identified as the subset of filtered  genes with translational efficiency (TE=normalized RPF/normalized total RNA) fold changes greater than 1.5.
Genome_build: mm10
Supplementary_files_format_and_content: Counts tables contain the raw counts quantified by featureCounts and DESeq2.

growth_protocol: Cells were maintened in Elow media

extract_protocol:
Cells were quickly washed twice in ice-cold PBS, and harvested in 400uL polysome lysis buffer by scraping on ice
Ribo-seq libraries were constructed as previously described (McGlincy, 2017). rRNA was depleted using RiboCop following manufacturer's instructions (Lexogen). Total RNA libraries were built with Illumina TrySeq kit using rRNA depletion.
Novaseq S1 1x100bp

treatment_protocol: Cells were treated for 4.5h with either DMSO (vehicle) or 100nM bortezomib

value: Squamous cell carcinoma

value: Vehicle


title: M6507, Lymph Nodes, 6 Hours

description:
X052718_d0_6507_PTL5537_1of3_S10
geo_1511_may19_LN_countMatrix.csv

value: Lymph Nodes

tag: time

value: 6 Hours

value: LNMC

tag: virus

tag: group

value: No Rebound

value: ART


title: tot_5_RNA-seq_S51A_veh_1

tag: treatment


title: tot_10_RNA-seq_Ctrl_Bort_2

value: Bortezomib (100nM, 4.5h)


title: tot_9_RNA-seq_Ctrl_Bort_1


title: Esophagus Sample 11

value: Esophagus


title: tot_6_RNA-seq_S51A_veh_2


title: tot_12_RNA-seq_Ctrl_Bort_4


title: Sample_6_Ribo-Seq S51A_veh_2

tag: molecule subtype


title: Sample_11_Ribo-Seq Ctrl_Bort_3

tag: genotype


title: Sample_10_Ribo-Seq Ctrl_Bort_2


title: Sample_12_Ribo-Seq Ctrl_Bort_4


title: Esophagus Sample 3


title: M-M01-40

status: Public on Jul 01 2022

city: OSLO

first: Knut

middle: Tomas

last: Dalen

state: OSLO

address: Sognsvannsveien 9

department: Department of Nutriton

country: Norway

institute: University of Oslo

data_processing:
50 bp paired end reads were sequenced on an Illumina Novaseq 600 intrument
BBDuk (BBMap v34.56) was used to remove/trim low-quality reads and adapter sequences
Reads were  mapped to a human reference genome/transcriptome (ENSEMBL release 101, GRCh38.101) using HiSat2 v.1.2.1
Read counting was done with FeatureCounts v1.4.6-p1
Genome_build: GRCh38.101
Supplementary_files_format_and_content: Normalized_gene_counts_TPM.csv is a csv file that containes normalised counts (TPM), for all samples, annotated to ensembl/entrez/hgnc. Unnormalised_feature_counts.csv is a csv file containing unnormalised counts for all samples, annotated to ensembl, generated in HiSat2 v.1.2.1

source_name: Liver tissue

growth_protocol: Female 8-week old C57BL/6J mice were fed chow or a high fat. The high-fat fed mice were then given controlled, isocaloric diets where 50% of the dietary protein was from fishmeal from salmon by-products, salmon filet or beef for 10 weeks

extract_protocol:
RNA was isolated with a NucleoSpin RNA mini kit (Machery-Nagel), according to the manufacturer’s instructions.
Strand-Specific TruSeqTM mRNA-seq library preparation

value: liver

tag: sample group

value: Beef

tag: strain

tag: Sex

value: female

tag: timepoint

value: 28-week old


title: Sample_5_Ribo-Seq S51A_veh_1


title: M-M01-35


title: M-M01-31

value: Salmon


title: M-M01-32


title: M-M01-39


title: M-M01-26


title: M-M01-27


title: M-M01-25


title: M-M01-22


title: M-M01-23


title: M-M01-20

value: Fishmeal


title: tot_11_RNA-seq_Ctrl_Bort_3


title: Sample_8_Ribo-Seq S51A_veh_4


title: M-M01-16


title: M-M01-13


title: M-M01-14


title: M-M01-12


title: M-M01-10

value: Chow


title: M-M01-5


title: M-M01-7


title: Sample_9_Ribo-Seq Ctrl_Bort_1


title: M-M01-1


title: M-M01-2


title: SR_6

status: Public on Apr 25 2022

city: Jyväskylä

first: Tero

last: Sievänen

address: Rautpohjankatu 8

country: Finland

institute: University of Jyväskylä

data_processing:
Illumina bcl2 was to convert data to fastq-format
FastQC was used to check data quality. Samples with <1 M reads were excluded. Samples with Phred scrore <25 were excluded. FastX-toolkit was used for adapter trimming (AACTGTAGGCACCATCAAT) and clipping (-l 20, -M 19), trimming (-f 1, -l 22) and filtering (-q 25, -p 90) and conversion of hsa_mir_rna.fa to hsa_mir_dna.fa (-d, -i). Individual lane files were merged before alignment. Bowtie was used to build indexes (-f) and for alignment (-v 2, -k 1, --best, -p 1, -q, -S).
Data filtering was conducted using edgeR R-package (c-miR had to have 1> count per million in 70% of samples in a sample group) and normalization was done with DESeq2 R-package with median of ratios method.
Assembly: hsa_mir_rna.fa (miRbase v. 22)
Supplementary files format and content: Matrix table with raw counts for every c-miR and every sample
Supplementary files format and content: Tab-delimited file for phenotypic information for each sample

source_name: Serum

extract_protocol:
Qiaqen advanced serum/plasma kit, starting volume 500 ul, affinity column based extraction of enriched miRs
QIASeq miRNA Library Kit (96)

tag: type

value: SRME

tag: ngs

value: two

value: Sporadic rectal cancer

tag: health

value: Cancer

value: male

tag: variant

tag: previous cancers

tag: batch


title: WT1_P46 Lepr-Cre;mTmG (Rep 1)

status: Public on May 16 2022

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
Raw FASTQs from sorted, GFP-positive cells were aligned to mouse mm10 reference genome (GRCm38.93.dna/GRCm38.93.gtf) using Cell Ranger version 2.1.1. The reference was modified to include a eGFP sequence. Raw FASTQs from unsorted, whole backskin were aligned to mouse mm10 reference genome (GRCm38.84.dna/GRCm38.84.gtf) and Cell Ranger version 3.1.0. The reference was modified to include a GFP, tdTomato, and YFP sequences.
Quality control of all data sets was performed using Seurat version 3.2.2 and Scrublet version 0.2.1
Processed files were analyzed with Scrublet Seurat V3.2.2,  scanpy V1.6.0. and CellChat V0.0.1
Genome_build: mm10
Genome_build: GRCm38.93.dna and GRCm.38.84.dna; GRCm38.93.gtf and GRCm.38.84.gtf
Supplementary_files_format_and_content: tsv and mtx

source_name: Backskin

growth_protocol: N/A. Primary cells were used in this study.

extract_protocol:
Dorsal skin from P46 Lepr-Cre;mTmG;Smo (n=2 technical replicates) and Lepr-Cre;mTmG;Smo+/- (n=2 technical replicates)  female mice were isolated and processed into single cells as previously described in Guerrero-Juarez, CF, et al. Nat Commun. 2019 with minor modifications.
Dorsal skin from P50 Lepr-Cre;mTmG female mice were isolated and processed into single cells as previously described in Guerrero-Juarez, CF, et al. Nat Commun. 2019 with minor modifications. Viable, GFP-positive cells were physicially sorted via FACS.
Single cells were captured using the Chromium Platform (10X Genomics) and cDNA libraries were generated using Single Cell 3’ v2 (sorted GFP-positive cells) and v3 chemistries (unsorted, whole dorsal skin cells). Single cells were quantified using a hemocytometer. Cell capture, cDNA library preparation, quality control, and sequencing was performed at UC Irvine Genomic High Throughput Facility.
Single Cell 3’ v2 Chemistry - 10X Genomics

tag: age

tag: genotype/variation

value: Lepr-Cre;mTmG

tag: tissue

value: Backskin

tag: cell type

value: dorsal skin cells

value: Unsorted cells


title: SR_9

tag: group


title: SR_1

value: three


title: SR_2


title: SR_3


title: SR_4


title: SR_8


title: SR_7


title: SR_15


title: SR_14


title: SR_12


title: SR_22


title: SR_20

value: one


title: SR_17


title: tot_8_RNA-seq_S51A_veh_4

value: Squamous cell carcinoma

tag: treatment

value: Vehicle


title: SR_5

value: female


title: SR_24


title: SR_18


title: SR_21


title: SR_10


title: SR_19


title: SR_13


title: SR_16


title: WT2_P46 Lepr-Cre;mTmG (Rep 2)

treatment_protocol: N/A. Primary cells were used in this study.


title: SR_11


title: LS_32

value: LS

value: Healthy

value: Lynch syndrome


title: LS_38


title: LS_31


title: LS_61


title: SR_23

value: SRME


title: LS_65

value: two


title: LS_58


title: LS_63


title: LS_43


title: LS_48


title: LS_55


title: LS_53


title: LS_49


title: LS_89


title: LS_80


title: LS_66


title: LS_19


title: LS_24


title: LS_74


title: LS_39


title: LS_30


title: LS_83


title: LS_72


title: LS_81


title: LS_20


title: LS_90


title: LS_29


title: LS_6


title: LS_1


title: LS_21


title: LS_88


title: LS_93


title: LS_84


title: LS_71


title: LS_26


title: LS_17


title: LS_70


title: LS_2


title: LS_9


title: LS_13


title: LS_79


title: LS_10


title: LS_27


title: LS_16


title: LS_76


title: LS_86


title: LS_87


title: LS_4


title: LS_8


title: LS_77


title: LS_15


title: LS_78


title: LS_75


title: LS_69


title: LS_85


title: LS_33


title: LS_67


title: LS_92


title: LS_57


title: LS_45


title: LS_7


title: LS_51


title: LS_42


title: LS_50


title: LS_91


title: LS_37


title: LS_52


title: LS_40


title: LS_35


title: LS_68


title: LS_64


title: LS_34


title: LS_46


title: LS_28


title: Sample_7_Ribo-Seq S51A_veh_3

tag: genotype

tag: molecule subtype


title: LS_41


title: LS_54


title: LS_3


title: LS_23


title: LS_11


title: LS_60


title: LS_56


title: LS_18


title: LS_73


title: LS_47


title: LS_62


title: LS_82


title: LS_22


title: LS_59


title: LS_12


title: LS_44


title: CT_27

value: CTRL

value: Control


title: LS_25


title: LS_36


title: LS_14


title: CT_26


title: CT_9


title: CT_32


title: LS_94

value: male


title: CT_35


title: CT_22


title: CT_3


title: CT_23


title: CT_1


title: CT_36


title: CT_7


title: CT_25


title: CT_20


title: CT_18


title: CT_31


title: CT_14


title: CT_24


title: LS_5


title: CT_8


title: CT_10


title: CT_28


title: CT_12


title: CT_6


title: CT_30


title: CT_5


title: CT_16


title: CT_15


title: CT_19


title: CT_29


title: CT_21


title: CT_37


title: CT_33


title: CT_2


title: X53

status: Public on Mar 26 2022

data_processing:
Alignment was performed using STAR version 2.7.3a with the MesAur1.0 (GCF_000349665.1) assembly and annotation of the hamster downloaded from NCBI. Transcript abundance estimates was calculated internal to the STAR aligner using the algorithm of htseq-count as described previously.
DESeq2 was used for normalization, producing both a raw and normalized read count table. Differential expression at the gene level were performed by DESeq2 implemented in the DESeq2 R package.
A corrected p-value cut-off of 0.05 was used to assess significant genes that were upregulated or down regulated by SARS-CoV-2 at day 4 post challenge in sham and vaccinated animals compared to naïve controls and in vaccinated compared to sham animals using Benjamini-Hochberg (BH) method.
Genome_build: MesAur1.0 (GCF_000349665.1)
Supplementary_files_format_and_content: Raw, and normalized read count tables. File format is .csv.

organism: Mesocricetus auratus

source_name: Golden hamster 53 (S98)

growth_protocol: Seventy male and female Syrian golden hamsters (Envigo), 10–12 weeks old, were randomly allocated to groups. All animals were housed at Bioqual. Animals received Ad26 vectors expressing S.dTM.PP or S.PP or sham controls (n = 10 per group). Animals received a single immunization of 1010 or 109 vp Ad26 vectors by the intramuscular route without adjuvant at week 0. At week 4, all animals were challenged with 5.0 × 105 TCID50 or 5.0 × 104 TCID50 SARS-CoV-2, which was derived with one passage from USA-WA1/2020 (NR-52281, BEI Resources).

extract_protocol:
Lung tissue was homogenized in 700 L of QIAzol (Qiagen) and stored at -80°C until being extracted using the miRNeasy Micro kit (Qiagen) with on-column DNase digestion.
RNA quality was assessed using an Agilent Bioanalyzer and ten nanograms of total RNA used as input for library preparation using the SMARTer Stranded Total RNA-Seq V2 Pico Input Mammalian kit (Takara Bio) according to the manufacturer’s instructions. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, targeting 25-30 million reads per sample.

treatment_protocol: Virus was administered as 100 μl by the intranasal route (50 μl in each nare). Body weights were assessed daily. All immunologic and virologic assays were performed blinded. All animal studies were conducted in compliance with all relevant local, state and federal regulations and were approved by the Bioqual Institutional Animal Care and Use Committee. On day 4, a subset of animals was euthanized for tissue viral loads, pathology and transcriptomics profiling.

value: Lung (snap frozen)

tag: virus

value: None (PBS control)

tag: vaccine

value: Unvaccinated (PBS control)

tag: volume

tag: dose (vp)

value: Control group


title: X52

description: Syrian golden hamsters (Envigo), 10–12 weeks old

source_name: Golden hamster 52 (S97)


title: X54

source_name: Golden hamster 54 (S99)


title: X281

source_name: Golden hamster 281 (S95)

value: TCID50 SARS-CoV-2

value: Unvaccinated (Sham)

value: Sham group


title: X277

source_name: Golden hamster 277 (S94)


title: X282

source_name: Golden hamster 282 (S96)


title: CT_17

tag: type

tag: ngs

value: three

tag: Sex


title: X272

source_name: Golden hamster 272 (S93)

value: Ad26.S.PP (Ad26.COV2.S)


title: X267

source_name: Golden hamster 267 (S91)


title: X271

source_name: Golden hamster 271 (S92)


title: X262

source_name: Golden hamster 262 (S90)


title: X248

source_name: Golden hamster 248 (S88)


title: CT_11

tag: health

tag: variant

tag: previous cancers


title: X244

source_name: Golden hamster 244 (S87)


title: X261

source_name: Golden hamster 261 (S89)


title: X238

source_name: Golden hamster 238 (S86)


title: X234

source_name: Golden hamster 234 (S85)


title: MBS32

status: Public on Feb 10 2022

data_processing:
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing are suitable for further analysis. Reads were aligned using STAR v2.7.3. Reads were aligned to Macaca mulatta genome . We used the macaques genome reference Macaca mulatta - MacaM (https://www.unmc.edu/rhesusgenechip/index.htm). The counts of reads aligning to annotated genes was obtained from STAR ReadsPerGene files. We used DESeq2 (Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2) internal filtering algorithm called "independentFiltering" that sets a threshold on the mean of normalized counts of all samples (baseMean > 10) in order to maximize the number of tests that pass multiple test correction. DESeq2 was used to generate the normalized read count table based on their estimateSizeFactors() function with default parameters by calculating a pseudo-reference sample of the geometric means for each gene across all samples and then use the "median ratio" of each sample to the pseudo-reference as the sizeFactor for that sample. The sizeFactor is then applied to each gene's raw count to get the normalized count for that gene. Differential expression at the gene level were performed by DESeq2 implemented in the DESeq2 R package, using counts per gene generated by a custom script that pulls out the library prep abundance estimation column into files, and read those files into DESeq2 with the DESeqDataSetFromHTSeqCount() function. A corrected p value cut-off of 0.05 was used to assess significant genes that were upregulated or down regulated at days 2, 7, 14 and 28 compared to baseline using Benjamini-Hochberg (BH) method.
Gene set enrichment analysis and a compendium of databases of biological and immunological pathways were used to test the longitudinal enrichment of pathways on days 2, 7, 14 and 28 post vaccination compared to baseline. Genes were pre-ranked by fold change from the highest to the lowest and GSEA was used to assess the enrichment of selected gene sets. Cytokines signaling, immune cell signatures, and molecular pathways were compiled from the MSigDB Hallmark, C2, C7 and C3 gene sets
(https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp), and the blood transcriptional modules (BTMs) (25). The GSEA Java desktop program was downloaded from the Broad Institute (http://www.broadinstitute.org/gsea/index.jsp) and used with GSEA Pre-Ranked module parameters (number of permutations: 1,000; enrichment statistic: weighted; 10≤ gene set size ≤5,000). Sample-level enrichment analysis (26) was used to investigate the enrichment of pathways in each individual animal. Briefly, the expression of all the genes in a specific pathway was averaged across samples and compared to the average expression of 1,000 randomly generated gene sets of the same size. The resulting Z score was then used to reflect the overall perturbation of each pathway in each individual sample. Pathways SLE scores were correlated with binding and neutralizing titers and B cell responses elicited by Ad26 days following vaccination, using Spearman correlation method.
Pharmacokinetics.  To estimate antibody decay rate, the antibody median values for 1x1011 and 5x1010 dose groups were plotted as a function of time post-vaccination, and the data were fitted to a biphasic decaying (27) exponential model using the Curve Fitting Tool in MATLAB (version R_2021a). The half-life of the fast and slow phases of each decay model are indicated on the graphs.
Genome_build: MacaM (https://www.unmc.edu/rhesusgenechip/index.htm)

source_name: Whole blood

extract_protocol: RNA was isolated from blood samples stored in Paxgene tubes at the Yerkes National Primate Center for library preparation (http://www.yerkes.emory.edu/nhp_genomics_core/). RNA quality was assessed using an Agilent 4200 TapeStation and concentration via the RNA HS assay on the Qubit. Globin transcripts in the blood RNA were blocked with the FastSelect Globin Reagent (Qiagen) prior to library preparation. Libraries were prepared using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) in combination with the NexteraXT DNA Library Preparation kit to append dual-indexed adapter sequences (Illumina).  Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 25-30 million reads per sample.

treatment_protocol: 20 outbred Indian-origin adult male and female rhesus macaques (Macaca mulatta) ages 6-10 years old were randomly allocated to groups. All animals were housed at Bioqual, Inc. (Rockville, MD).  Animals were immunized with 1011 vp (N=10) or 5x1010 vp (N=10) Ad26.COV2.S and were followed for either 230 or 315 days.  Animals were then boosted with 5x1010 vp Ad26.COV2.S (N=10) or Ad26.COV2.S.351 (N=10).  Half of animals in each original dose group were immunized by each booster vaccine.  All immunologic studies were performed blinded. Animal studies were conducted in compliance with all relevant local, state, and federal regulations and were approved by the Bioqual Institutional Animal Care and Use Committee (IACUC).

tag: vaccine administered

tag: ad26.cov. dose

tag: time post-vaccination


title: CT_13

source_name: Serum

tag: group

value: female

tag: batch


title: MBH31


title: M15.147


title: MBE00


title: CT_34

value: Healthy


title: MBE75


title: M16.144


title: M16.04


title: M16.138


title: CT_4


title: RSr15_d264

status: Public on Feb 09 2022

data_processing:
RNA-Seq data was collected at the Yerkes Nonhuman Primate Genomics Core laboratory.
Alignment was performed using STAR version 2.3.0e; parameters were set using the annotation as a splice junction reference, and unannotated, noncanonical splice junction mappings and nonunique mappings were removed from downstream analysis. Transcripts were annotated using MacaM assembly and annotation, version 7.6. Transcript assembly, abundance estimates, and differential expression analysis were performed using Cufflinks, version 2.1.1, and Cuffdiff. RNA-seq data are expressed as fragments per kilobase mapped (FPKM), which is the default output by Cufflinks/Cuffdiff, in which reads and fragments mapping to an individual gene are normalized by the total number of kilobases that map to the reference genome for an individual sample; this calculation minimizes bias due to differences in sequencing depth between samples.
Genome_build: New Rhesus Genome (MacaM version 7.6) (https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome)
Supplementary_files_format_and_content: Read counts for animals at different timepoints (across different replicates). Format is a csv table (.csv).

source_name: Rhesus macaque RSr15

growth_protocol: PBMCs at pre-infection (d-20 p.i.) were stored in RLT buffer (QIAGEN) at -80°C.

extract_protocol:
Total RNA was prepared using QIAGEN RNeasy kits. Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers, and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform.
Libraries were validated by microelectrophoresis and quantified, pooled, and clustered on Illumina TruSeq v3 flow cells. Clustered flow cells were sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

treatment_protocol: A neutralizing anti-IL-10 monoclonal antibody (mAb) was administered in vivo to SIV-infected, ART-treated RMs. Six RMs were i.v. infected with SIVmac239 and at d35 post-infection began a daily ART regimen. At d211 post-infection, all RMs were i.v. administered 10 mg/kg of a rhesus-recombinant anti-IL-10 mAb. Four weeks later (d238 post-infection), all RMs received a second infusion of the anti-IL-10 mAb, which was dose-escalated to 20 mg/kg.

tag: cell type

value: PBMC

tag: disease state

value: Necropsy

tag: treatment

tag: time

value: 264 days post-infection

tag: animal

value: Indian-origin, specific-pathogen-free rhesus macaques


title: RSr15_d252

value: SIV+

value: ART, aIL10 (two doses)

value: 252 days post-infection


title: RSr15_d230

value: ART, aIL10 (first dose)

value: 230 days post-infection


title: RSr15_d-10

value: SIV-

value: 10 days pre-infection


title: RSr15_d167

value: ART

value: 167 days post-infection


title: RSr15_d35

value: 35 days post-infection


title: RSr15_d209

value: 209 days post-infection


title: RRs15_d264

source_name: Rhesus macaque RRs15


title: RRs15_d230


title: RRs15_d252


title: M15.133


title: MBH69


title: RRs15_d-10


title: RRs15_d35


title: RRs15_d209


title: RQv15_d252

source_name: Rhesus macaque RQv15


title: RQv15_d230


title: RQv15_d209


title: RQv15_d167


title: RQv15_d-10


title: RPz15_d252

source_name: Rhesus macaque RPz15


title: RPz15_d264


title: RQv15_d35


title: RPz15_d230


title: RPz15_d167


title: RPz15_d209


title: RPz15_d35


title: RPz15_d-10


title: RNw15_d264

source_name: Rhesus macaque RNw15


title: RNw15_d252


title: RNw15_d230


title: RNw15_d209


title: RNw15_d167


title: RNw15_d35


title: RNw15_d-10


title: RBf16_d264

source_name: Rhesus macaque RBf16


title: RBf16_d252

value: ART, Neutralizing anti-IL-10 monoclonal antibody (aIL10) [two doses]


title: RBf16_d35

value: Antiretroviral therapy (ART)


title: RRs15_d167

value: PBMC


title: RBf16_d167


title: RBf16_d209


title: 1508-3_S8_L002

status: Public on Feb 08 2022

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

description:
passage 106; cell line's former name: DT15/08
1508-3_S8

data_processing:
Bases were called with Illumina Casava bcl2fastq (version 2.15.0.4).
Sequencing reads were trimmed and filtered using trimmomatic (v0.36) with parameters "-phred33, HEADCROP:11 LEADING:20 TRAILING:20 AVGQUAL:20 MINLEN:25". Reads were mapped to the dog reference genome (Ensembl CanFam 3.1) and corresponding gene model annotation (v94) using STAR (v2.5.3) with parameters: "--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts". RSEM (v.1.3.0) was used to quantify gene expression with parameters "--bam --no-bam-output". Finally, for each library, read counts derived from multiple lanes were added together.
Genome_build: Ensembl CanFam 3.1
Supplementary_files_format_and_content: Tab-delimited text including raw gene counts for every gene Ensembl gene identifier

source_name: Adcarc1508 rep3

growth_protocol: Culturing conditions were Medium 199 (Life Technologies GmbH, Darmstadt, Germany) containing 10% fetal calf serum (FBS Superior, Biochrom GmbH, Berlin, Germany), 200 IU/ml penicillin and 200 mg/ml streptomycin (Biochrom GmbH) at 37°C in humidified air.

extract_protocol:
RNA from cell pellets was isolated using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany), in accordance with the manufacturer’s protocols. For tissue samples, the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen GmbH) was utilized.
Samples with RNA integrity numbers ≥ 5.2 measured with RNA 6000 Nano LabChip on an Agilent Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA) were further processed for library preparation using the NEBNext Ultra RNA preparation kit (New England Biolabs Inc., Ipswich, MA, USA).

treatment_protocol: Each cell line was seeded in T25 flasks in triplicate beyond passage 60. At 70-80% confluency, cells were detached with TrypLE™Express (Life Technologies GmbH, Darmstadt, Germany), pelleted, fresh frozen in liquid nitrogen and stored at ‑80°C until further use.

tag: cell line

tag: breed

value: Mixed breed

tag: description

value: male neutered

tag: age

value: 11 years

tag: cell line short name

tag: histopathological classification

value: prostate adenocarcinoma

tag: patient id

tag: original tumor tissue, from which the cell line was established


title: RBf16_d-10

value: Indian-origin, specific-pathogen-free rhesus macaques


title: 1508-3_S8_L001


title: 1508-1_S1_L004

description:
passage 97; cell line's former name: DT15/08
1508-1_S1

source_name: Adcarc1508 rep1


title: 1508-3_S8_L003


title: 1508-1_S1_L001


title: 1506-3_S6_L004

description:
passage 107; cell line's former name: DT15/06
1506-3_S6

source_name: TCC1506 rep3

value: Labrador Retriever

value: female

value: 10 years

value: transitional cell carcinoma


title: 1508-2_S7_L004

description:
passage 105; cell line's former name: DT15/08
1508-2_S7

source_name: Adcarc1508 rep2


title: 1508-2_S7_L001


title: 1508-1_S1_L002


title: 1506-3_S6_L001


title: 1508-1_S1_L003


title: 1506-2_S11_L004

description:
passage 106; cell line's former name: DT15/06
1506-2_S11

source_name: TCC1506 rep2


title: 1506-2_S11_L003


title: 1506-3_S6_L002


title: 1506-1_S3_L004

description:
passage 98; cell line's former name: DT15/06
1506-1_S3

source_name: TCC1506 rep1


title: 1506-2_S11_L002


title: 1506-1_S3_L003


title: 1506-1_S3_L001


title: 1508-2_S7_L003


title: 1508-3_S8_L004


title: 1508-2_S7_L002


title: is_129_010

status: Public on Dec 11 2021

data_processing:
Sequencing was performed on an Ion S5™ XL Sequencer (Thermo Scientific, Waltham, MA).
Data had read lengths with average between 98 and 110 bp and high mapping (95% of aligned bases). The expression values were generated by using software Torrent Suite™ (version 5.10.1).
The expression values were generated by using software Torrent Suite™ (version 5.10.1).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Epidydimal white adipose tissue

extract_protocol:
Total RNA was isolated from eWAT (n=5) using the Direct-zol RNA MiniPrep column kit (The Epigenetics Company, Irvine, CA).
cDNA libraries were prepared and amplified with the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (Life Technologies, Carlsbad, CA), following the manufacturer`s instructions. Sequencing was performed on an Ion S5™ XL Sequencer (Thermo Scientific, Waltham, MA).

tag: strain

tag: tissue

value: Epidydimal white adipose tissue

value: 18-week old

tag: genotype

value: Srgn-/-

value: high sucrose/high fat diet for 8 weeks


title: is_129_007


title: is_129_009


title: is_129_005

value: Srgn+/+


title: is_129_004


title: is_129_006


title: is_129_008


title: is_129_003


title: is_129_001


title: MCF10Ca1h cells, RNA.NT

status: Public on Jan 11 2021

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
Sequencing libraries were generated according to Illumina’s TruSeq® Stranded mRNA Sample Preparation protocol and run on Illumina HiSeq platform PE 125bp cycle
Estimating gene expression levels from RNA-Seq data with RSEM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: human breast cell lines

growth_protocol: Cells were cultured in DMEM/F12 media supplemented with 5% horse serum.

extract_protocol:
RNA was extracted using TRIzol reagent (Ambion).
Sequencing libraries were generated using Illumina TruSeq Stranded Total RNA kit RS-122-2201 protocol.
Sequencing libraries were run on Illumina HiSeq platform with HiSeq 3000/4000 seequencing chemistry for paired-end 125bp cycle runs.

treatment_protocol: Cells were treated with PADI4 inhibitor (GSK484) or control compound (GSK107) for 72 hours.

value: MCF10Ca1h human breast cancer cell line

value: No treatment (NT)

tag: in vivo timepoint


title: MCF10Ca1h cells, RNA.CON

value: CON

value: 72 hrs


title: HMPOS parental rep 3

status: Public on Jan 05 2021

city: Raleigh

first: Hiroyuki

last: Mochizuki

state: NC

address: 1060 William Moore Dr

institute: North Carolina State University

description: HMPOS parental cell line

data_processing:
standard RNA data processing used
The software package Real Time Analysis (RTA), was used to generate raw bcl, or base call files, which were then de-multiplexed by sample into fastq files.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic-0.38 with parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50.
The trimmed sequence reads were mapped to CanFam3.1 using TopHat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks and compared using cuffdiff.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: CSV files of comparison of differences in FPKM between samples.

source_name: Osteosarcoma

extract_protocol:
Total RNA was extracted from tissue samples using an RNeasy mini kit (Qiagen, USA) and assessed for RNA sample integrity using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies, USA).
Purification of messenger RNA (mRNA) was performed using oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA). Complementary DNA (cDNA) libraries for Illumina sequencing were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Mulitplex Oligos for Illumina (NEB) using the manufacturer-specified protocol. Briefly, the mRNA was chemically fragmented and primed with random oligos for first strand cDNA synthesis. Second strand cDNA synthesis was then carried out with dUTPs to preserve strand orientation information. The double-stranded cDNA was then purified, end repaired and “a-tailed” for adaptor ligation. Following ligation, the samples were selected a final library size (adapters included) of 400-550 bp using sequential AMPure XP bead isolation (Beckman Coulter, USA). Library enrichment was performed and specific indexes for each sample were added during the protocol-specified PCR amplification. The amplified library fragments were purified and checked for quality and final concentration using an Agilent 2200 Tapestation (D1000 chip, Agilent Technologies, USA) combined with a Qubit fluorometer (ThermoFisher, USA).

value: Osteosarcoma cell line

tag: phenotype

value: parental cell line


title: HMPOS parental rep 2

description: HMPOS parental cell line


title: is_129_002


title: MCF10Ca1h cells, RNA.GSK484


title: 1506-3_S6_L003


title: 1506-1_S3_L002


title: 8-week mouse kidney bulk ATAC-seq sample 2

status: Public on Aug 29 2020

city: Philadelphia

first: Katalin

last: Susztak

state: Pennsylvania

address: 3400 Civic Center Boulevard, 12th floor

institute: University of Pennsylvania

description: P56-2-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig

data_processing:
snATAC raw fastq files were aligned to the mm10 (GRCm38) reference genome and quantified using Cell Ranger ATAC (v. 1.1.0). We only kept valid barcodes with number of fragments ranging from 1,000 to 40,000, mitochondria ratio less than 10%, and promoter ratio more than 20%. clustering was conducted using snapATAC.
snATAC peak calling was conducted for each cell type separately using MACS2 with parameters “--nomodel --keep-dup all --shift 100 --ext 200 --qval 1e-2 -B --SPMR --call-summits”.
Bulk ATAC-seq raw fastq files were processed using the end-to-end tool ENCODE ATAC-seq pipeline
scRNA raw fastq files were aligned to the mm10 (Ensembl GRCm38.93) reference genome and quantified using CellRanger v3.1.0. Seurat R package v3.0 was used for data quality control, preprocessing and dimensional reduction analysis. After gene-cell data matrix generation of both P0 and adult datasets, matrices were merged and poor-quality cells with <200 or >3,000 expressed genes and mitochondrial gene percentages >50 were excluded
Genome_build: mm10

source_name: 8-week mouse kidney

extract_protocol:
50,000 nuclei/sample were tagmented with Tn5 transposase (Illumina) in 50 ml reaction volume including Tween-20 (0.1%) (Sigma) and digitonin (0.01%) (Promega). The reaction was carried out at 37 °C for 30 min in a thermomixer at 1,000 RPM. After purification of DNA with Qiagen Minelute Reaction Cleanup kit (Qiagen), samples were subjected to library amplification (8-10 cycles).
Libraries were purified with AmpureXP beads (Beckman Coulter) and their quality was assessed by Agilent High sensitivity DNA Bioanalysis chip (Agilent).

tag: developmental stages


title: HMPOS parental rep 1

description: HMPOS parental cell line


title: D17 parental rep 2

description: D17 parental cell line


title: 1506-2_S11_L001


title: 8-week mouse kidney bulk ATAC-seq sample 1

description: P56-1-50_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig


title: D17 parental rep 3

description: D17 parental cell line


title: H1 [re-analyzed]

status: Public on Jun 07 2020

city: Fort Worth

first: Kejin

last: Hu

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

description:
hESC_GAGTGG_L005
This is duplicated sample record of GSM1632428 for the convenient retrieval of the complete raw data from SRA.

data_processing:
Initial QC was performed with FastQC and low-quality bases were removed with Trim Galore (v. 0.4.5).
Reads were quasi-mapped and quantified with Salmon (v0.12.0, with `--gencode` and `-k 21` flags for index generation and `-l A, `--gcBias` and `--validateMappings` flags for quasi-mapping).
Gene-level summarization was performed with tximport (v1.10.0). Count normalization and differential expression were performed with DESeq2 (v1.16.1).
Genome_build: hg38
Supplementary_files_format_and_content: Comma delimited file which contain the normalized gene-level counts for each biological sample.

source_name: Embryonic stem cells

growth_protocol: We culture human embryonic stem cells (H1 and H9) in the chemically defined E8 media. Human foreskin BJ fibroblasts (ATCC, CRL-2522) were cultured in fibroblast medium: DMEM, 10% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 100 U ml−1 penicillin, 100 μg ml−1 streptomycin, 0.1 mM MEM NEAA and 4 ng ml−1 human bFGF.

extract_protocol:
Cells were harvested with Trizol reagent and stored at -80 °C until use. Total RNA was extracted using the Direct-zolTM Miniprep kit (R2052).
The standard Agilent SureSelect Strand-Specific RNA sequencing protocol was followed. Briefly, the polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers in the presence of Actinomycin D using standard techniques. The resulting first stand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques. The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. PCR amplification was done in the presence of uracil DNA glycosylase to generate strand specificity. A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment. The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).

tag: cell type

value: human embryonic stem cells

tag: passage number

value: passage 40

tag: harvest time

value: 80% confluence


title: BJ_4

source_name: Fibroblast, BJ

tag: cell line

value: BJ

value: Human foreskin BJ fibroblasts

value: passage 5

value: 72 hours post seeding


title: BJ_1 [re-analyzed]

description:
BJ_48h_CACTTC_L004
This is duplicated sample record of GSM1632430 for the convenient retrieval of the complete raw data from SRA.

value: passage 8

value: 48 hours post seeding


title: H1_2

value: passage 41


title: H9 [re-analyzed]

description:
H9_ESC_P43_AGTGGT_L001
This is duplicated sample record of GSM1632429 for the convenient retrieval of the complete raw data from SRA.

value: passage 43


title: BJ_3 [re-analyzed]

description:
BJ72_ATCACG_L004
This is duplicated sample record of GSM1632432 for the convenient retrieval of the complete raw data from SRA.


title: BJ_2 [re-analyzed]

description:
BJ48_ATCACG_L001
This is duplicated sample record of GSM1632431 for the convenient retrieval of the complete raw data from SRA.


title: D17 parental rep 1

description: D17 parental cell line


title: Q7: SHH MB

status: Public on Apr 10 2020

type: genomic

city: Omaha

first: Pranita

last: Atri

state: NE

address: S 42nd and Emile St

department: Biochemistry

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

hyb_protocol: Bisulfite converted D was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC (850K) Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Rnbeads Version 2.0.0

label: Cy3, Cy5

source_name: SHH MB

label_protocol: Standard Illumina Protocol

extract_protocol: Isolated genomic D using the RecoverAll kit

value: SHH Medulloblastoma

tag: age (years)

tag: Sex

value: M

tag: subgroup

value: SHH MB


title: Q35: Grp3 MB

source_name: Grp3 MB

value: Grp3 Medulloblastoma

value: Grp3 MB


title: Q5: SHH MB

value: F


title: Q29: Grp3 MB


title: Q31: Grp4 MB

source_name: Grp4 MB

value: Grp4 Medulloblastoma

value: Grp4 MB


title: Q14: Grp4 MB


title: Q37: SHH MB


title: Q15: Grp3 MB


title: Q8: Grp4 MB


title: Q27: SHH MB


title: Q30: Grp4 MB


title: Q6: Grp4 MB


title: Q18: Grp3 MB


title: Q34: Grp3 MB


title: Q28: WNT MB

source_name: WNT MB

value: WNT Medulloblastoma

value: WNT MB


title: Q39: Grp3 MB


title: Q25: Grp4 MB


title: Q24: Grp3 MB


title: Q2: Grp4 MB


title: Q21: SHH MB


title: Q32: Grp3 MB


title: Q3: Grp4 MB


title: Q26: Grp4 MB


title: Q4: SHH MB


title: Q22: SHH MB


title: Q23: Grp4 MB


title: Q40: Grp4 MB


title: Q11: Grp3 MB