title: HDT2_S#G2_11:00

description: Gene expression of participant S#G2, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT2, at 11:00 hr


title: HC_M1P2_J3

status: Public on Mar 09 2024

type: SRA

city: Stanford

first: Wenfei

last: Sun

address: 318 Campus Dr.

country: USA

institute: Stanford University

description:
Smartseq
cell by gene matrix

library_source: transcriptomic

data_processing:
Fastq reads were mapped with STAR(2.7.9a)
Assembly: mm10
Supplementary files format and content: Cell by gene matrix format

molecule: polyA RNA

organism: Mus musculus

source_name: posteromedial nucleus of the cortical amygdala

extract_protocol:
OligodT primers were used to enrich mRNA
Brain tissues were dissociated with Worthington Papain Digestion Kit RNA libraries were prepared using smart seq 2

treatment_protocol: Food Transmitted Food Preference paradigm

tag: tissue


title: HDT3_S#C2_19:00

type: RNA

city: Guildford

first: Simon

last: Archer

address: Stag Hill

country: United Kingdom

institute: University of Surrey

description: Gene expression of participant S#C2, sampling session HDT3, at 19:00 hr

hyb_protocol: Labeled cRNA (1.65 μg) was hy- bridized on a Whole Human Genome SurePrint G3 8x60k custom oligonucleotide microarray (G4102A, AMADID 085218; Agilent). Standard manufacturer’s in- structions for one-color gene-expression analysis were followed for labeling, hybridization and washing steps. Microarrays were hybridized at 65 °C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, prewarmed Wash Buffer 2 (37 °C), and acetonitrile, according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 s.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide were scanned at 10% and 100% PMT and imported into the Agilent Feature Extraction software (v4.0.1.2.1) for image analysis.

data_processing: Log 2 values were quantile- normalized using the normalizeBetweenArrays function from R package limma (v3.46.0). Non-control 44k probes (all probes in microarray with GEO accession no. GPL15331) were were extracted resulting in a Gene Expression Matrix (GEM) of 41,619 transcripts in 637 samples. Transcripts flagged in any of the FE QC variables in less than 20% of the samples were retained for all analyses (n=27,154).

molecule: total RNA

organism: Homo sapiens

source_name: Peripherial_blood, participant S#C2, sampling session HDT3, at 19:00 hr

label_protocol: cRNA was synthesized and fluorescently labeled with Cy3-CTP from 100 ng of total RNA using the Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Whole blood was collected via an indwelling cannula

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: Whole peripheral blood (2.5 mL) was collected using PAXgene Blood RNA tubes (BD Biosciences) at selected time points.

tag: melatonin offset (decimal time)


title: HC_M1P2_K22

description:
Smartseq
cell by gene matrix

value: posteromedial nucleus of the cortical amygdala


title: HC_M1P2_J6

description:
Smartseq
cell by gene matrix


title: HDT3_S#G2_15:00

description: Gene expression of participant S#G2, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT3, at 15:00 hr


title: HDT3_S#C2_11:00

description: Gene expression of participant S#C2, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT3, at 11:00 hr


title: HDT2_S#C2_11:00

description: Gene expression of participant S#C2, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT2, at 11:00 hr


title: HDT2_S#G2_07:00

description: Gene expression of participant S#G2, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT2, at 07:00 hr


title: HC_M1P2_J24

description:
Smartseq
cell by gene matrix


title: HC_M1P2_J10

description:
Smartseq
cell by gene matrix


title: HC_M1P2_I8

description:
Smartseq
cell by gene matrix


title: HC_M1P2_J20

description:
Smartseq
cell by gene matrix


title: HDT2_S#G2_23:00

description: Gene expression of participant S#G2, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT2, at 23:00 hr


title: HC_M1P2_I7

description:
Smartseq
cell by gene matrix


title: HC_M1P2_J13

description:
Smartseq
cell by gene matrix


title: HC_M1P2_I5

description:
Smartseq
cell by gene matrix


title: HC_M1P2_J12

description:
Smartseq
cell by gene matrix


title: HC_M1P2_I4

description:
Smartseq
cell by gene matrix


title: HDT2_S#C2_03:00

description: Gene expression of participant S#C2, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT2, at 03:00 hr


title: HDT2_S#C2_23:00

description: Gene expression of participant S#C2, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT2, at 23:00 hr


title: HDT2_S#C2_07:00

description: Gene expression of participant S#C2, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT2, at 07:00 hr


title: HC_M1P2_J11

description:
Smartseq
cell by gene matrix


title: HC_M1P2_I9

description:
Smartseq
cell by gene matrix


title: BDC2_S#C2_07:00

description: Gene expression of participant S#C2, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC2, at 07:00 hr


title: HC_M1P2_I6

description:
Smartseq
cell by gene matrix


title: BDC2_S#G2_07:00

description: Gene expression of participant S#G2, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC2, at 07:00 hr


title: BDC2_S#G2_03:00

description: Gene expression of participant S#G2, sampling session BDC2, at 03:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC2, at 03:00 hr


title: BDC2_S#G2_23:00

description: Gene expression of participant S#G2, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC2, at 23:00 hr


title: HC_M1P2_I10

description:
Smartseq
cell by gene matrix


title: HDT2_S#G2_15:00

description: Gene expression of participant S#G2, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT2, at 15:00 hr


title: HC_M1P2_H6

description:
Smartseq
cell by gene matrix


title: BDC2_S#C2_15:00

description: Gene expression of participant S#C2, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC2, at 15:00 hr


title: BDC2_S#G2_11:00

description: Gene expression of participant S#G2, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC2, at 11:00 hr


title: HC_M1P2_I12

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P2_I17

description:
Smartseq
cell by gene matrix


title: HC_M1P2_H2

description:
Smartseq
cell by gene matrix


title: BDC2_S#C2_23:00

description: Gene expression of participant S#C2, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC2, at 23:00 hr


title: HDT2_S#G2_19:00

description: Gene expression of participant S#G2, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT2, at 19:00 hr


title: HDT2_S#C2_19:00

description: Gene expression of participant S#C2, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT2, at 19:00 hr


title: HC_M1P2_H9

description:
Smartseq
cell by gene matrix


title: HDT1_S#G2_11:00

description: Gene expression of participant S#G2, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT1, at 11:00 hr


title: BDC2_S#G2_19:00

description: Gene expression of participant S#G2, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC2, at 19:00 hr


title: HC_M1P2_H12

description:
Smartseq
cell by gene matrix


title: HDT2_S#C2_15:00

description: Gene expression of participant S#C2, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT2, at 15:00 hr


title: HC_M1P2_I11

description:
Smartseq
cell by gene matrix


title: HDT1_S#G2_23:00

description: Gene expression of participant S#G2, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT1, at 23:00 hr


title: HC_M1P2_H8

description:
Smartseq
cell by gene matrix


title: HC_M1P2_G8

description:
Smartseq
cell by gene matrix


title: HC_M1P2_H4

description:
Smartseq
cell by gene matrix


title: BDC2_S#G2_15:00

description: Gene expression of participant S#G2, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC2, at 15:00 hr


title: BDC2_S#C2_19:00

description: Gene expression of participant S#C2, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC2, at 19:00 hr


title: HDT1_S#C2_11:00

description: Gene expression of participant S#C2, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT1, at 11:00 hr


title: HC_M1P2_H14

description:
Smartseq
cell by gene matrix


title: HDT1_S#C2_07:00

description: Gene expression of participant S#C2, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT1, at 07:00 hr


title: BDC2_S#C2_03:00

description: Gene expression of participant S#C2, sampling session BDC2, at 03:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC2, at 03:00 hr


title: HC_M1P2_H5

description:
Smartseq
cell by gene matrix


title: HDT1_S#C2_23:00

description: Gene expression of participant S#C2, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT1, at 23:00 hr


title: HDT1_S#G2_07:00

description: Gene expression of participant S#G2, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT1, at 07:00 hr


title: HDT1_S#G2_03:00

description: Gene expression of participant S#G2, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT1, at 03:00 hr


title: HC_M1P2_H10

description:
Smartseq
cell by gene matrix


title: BDC1_S#G2_07:00

description: Gene expression of participant S#G2, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC1, at 07:00 hr


title: BDC1_S#G2_03:00

description: Gene expression of participant S#G2, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC1, at 03:00 hr


title: HC_M1P2_G1

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P2_G5

description:
Smartseq
cell by gene matrix


title: HC_M1P2_G6

description:
Smartseq
cell by gene matrix


title: BDC1_S#G2_23:00

description: Gene expression of participant S#G2, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC1, at 23:00 hr


title: HDT1_S#C2_03:00

description: Gene expression of participant S#C2, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT1, at 03:00 hr


title: HC_M1P2_G22

description:
Smartseq
cell by gene matrix


title: HC_M1P2_F8

description:
Smartseq
cell by gene matrix


title: HC_M1P2_G18

description:
Smartseq
cell by gene matrix


title: BDC1_S#C2_03:00

description: Gene expression of participant S#C2, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC1, at 03:00 hr


title: HC_M1P2_F6

description:
Smartseq
cell by gene matrix


title: HDT1_S#G2_19:00

description: Gene expression of participant S#G2, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT1, at 19:00 hr


title: HC_M1P2_F2

description:
Smartseq
cell by gene matrix


title: HC_M1P2_G12

description:
Smartseq
cell by gene matrix


title: HC_M1P2_G10

description:
Smartseq
cell by gene matrix


title: BDC1_S#C2_07:00

description: Gene expression of participant S#C2, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC1, at 07:00 hr


title: HC_M1P2_F12

description:
Smartseq
cell by gene matrix


title: HC_M1P2_E9

description:
Smartseq
cell by gene matrix


title: HC_M1P2_F5

description:
Smartseq
cell by gene matrix


title: BDC1_S#C2_23:00

description: Gene expression of participant S#C2, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC1, at 23:00 hr


title: HC_M1P2_E5

description:
Smartseq
cell by gene matrix


title: HDT1_S#C2_19:00

description: Gene expression of participant S#C2, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT1, at 19:00 hr


title: HDT1_S#G2_15:00

description: Gene expression of participant S#G2, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session HDT1, at 15:00 hr


title: BDC1_S#C2_11:00

description: Gene expression of participant S#C2, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC1, at 11:00 hr


title: BDC1_S#C2_15:00

description: Gene expression of participant S#C2, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC1, at 15:00 hr


title: R_S#J1_07:00

description: Gene expression of participant S#J1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session R, at 07:00 hr


title: HC_M1P2_E12

description:
Smartseq
cell by gene matrix


title: HDT1_S#C2_15:00

description: Gene expression of participant S#C2, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session HDT1, at 15:00 hr


title: BDC1_S#G2_19:00

description: Gene expression of participant S#G2, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC1, at 19:00 hr


title: HC_M1P2_F19

description:
Smartseq
cell by gene matrix


title: BDC1_S#G2_15:00

description: Gene expression of participant S#G2, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#G2, sampling session BDC1, at 15:00 hr


title: HC_M1P2_F16

description:
Smartseq
cell by gene matrix


title: HC_M1P2_E10

description:
Smartseq
cell by gene matrix


title: HC_M1P2_D8

description:
Smartseq
cell by gene matrix


title: HDT3_S#J1_03:00

description: Gene expression of participant S#J1, sampling session HDT3, at 03:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT3, at 03:00 hr


title: HC_M1P2_E7

description:
Smartseq
cell by gene matrix


title: HC_M1P2_E6

description:
Smartseq
cell by gene matrix


title: BDC1_S#C2_19:00

description: Gene expression of participant S#C2, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#C2, sampling session BDC1, at 19:00 hr


title: HC_M1P2_D7

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P2_F3

description:
Smartseq
cell by gene matrix


title: HC_M1P2_D6

description:
Smartseq
cell by gene matrix


title: HC_M1P2_E3

description:
Smartseq
cell by gene matrix


title: HC_M1P2_D4

description:
Smartseq
cell by gene matrix


title: R_S#J1_23:00

description: Gene expression of participant S#J1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session R, at 23:00 hr


title: R_S#J1_11:00

description: Gene expression of participant S#J1, sampling session R, at 11:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session R, at 11:00 hr


title: R_S#J1_15:00

description: Gene expression of participant S#J1, sampling session R, at 15:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session R, at 15:00 hr


title: R_S#J1_19:00

description: Gene expression of participant S#J1, sampling session R, at 19:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session R, at 19:00 hr


title: R_S#I1_07:00

description: Gene expression of participant S#I1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session R, at 07:00 hr


title: R_S#I1_11:00

description: Gene expression of participant S#I1, sampling session R, at 11:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session R, at 11:00 hr


title: HC_M1P2_E15

description:
Smartseq
cell by gene matrix


title: HC_M1P2_D12

description:
Smartseq
cell by gene matrix


title: HC_M1P2_D9

description:
Smartseq
cell by gene matrix


title: R_S#I1_19:00

description: Gene expression of participant S#I1, sampling session R, at 19:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session R, at 19:00 hr


title: HC_M1P2_D10

description:
Smartseq
cell by gene matrix


title: HDT3_S#I1_23:00

description: Gene expression of participant S#I1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT3, at 23:00 hr


title: R_S#I1_23:00

description: Gene expression of participant S#I1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session R, at 23:00 hr


title: R_S#I1_15:00

description: Gene expression of participant S#I1, sampling session R, at 15:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session R, at 15:00 hr


title: HDT3_S#I1_03:00

description: Gene expression of participant S#I1, sampling session HDT3, at 03:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT3, at 03:00 hr


title: HC_M1P2_C2

description:
Smartseq
cell by gene matrix


title: HC_M1P2_C16

description:
Smartseq
cell by gene matrix


title: HC_M1P2_D2

description:
Smartseq
cell by gene matrix


title: HC_M1P2_D16

description:
Smartseq
cell by gene matrix


title: HDT3_S#J1_19:00

description: Gene expression of participant S#J1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT3, at 19:00 hr


title: HC_M1P2_B8

description:
Smartseq
cell by gene matrix


title: HC_M1P2_B7

description:
Smartseq
cell by gene matrix


title: HDT3_S#J1_23:00

description: Gene expression of participant S#J1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT3, at 23:00 hr


title: HC_M1P2_C12

description:
Smartseq
cell by gene matrix


title: HC_M1P2_A9

description:
Smartseq
cell by gene matrix


title: HDT2_S#J1_23:00

description: Gene expression of participant S#J1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT2, at 23:00 hr


title: HDT3_S#I1_19:00

description: Gene expression of participant S#I1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT3, at 19:00 hr


title: HC_M1P2_C11

description:
Smartseq
cell by gene matrix


title: HDT2_S#I1_11:00

description: Gene expression of participant S#I1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT2, at 11:00 hr


title: HC_M1P1_P7

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HDT3_S#I1_15:00

description: Gene expression of participant S#I1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT3, at 15:00 hr


title: HDT1_S#J1_07:00

description: Gene expression of participant S#J1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT1, at 07:00 hr


title: HDT3_S#J1_15:00

description: Gene expression of participant S#J1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT3, at 15:00 hr


title: HDT1_S#J1_23:00

description: Gene expression of participant S#J1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT1, at 23:00 hr


title: HDT2_S#I1_07:00

description: Gene expression of participant S#I1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT2, at 07:00 hr


title: HC_M1P2_B6

description:
Smartseq
cell by gene matrix


title: HDT2_S#J1_03:00

description: Gene expression of participant S#J1, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT2, at 03:00 hr


title: HC_M1P2_B4

description:
Smartseq
cell by gene matrix


title: HDT2_S#I1_03:00

description: Gene expression of participant S#I1, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT2, at 03:00 hr


title: HC_M1P2_B22

description:
Smartseq
cell by gene matrix


title: HDT1_S#I1_03:00

description: Gene expression of participant S#I1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT1, at 03:00 hr


title: HDT2_S#J1_11:00

description: Gene expression of participant S#J1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT2, at 11:00 hr


title: HDT1_S#J1_11:00

description: Gene expression of participant S#J1, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT1, at 11:00 hr


title: HC_M1P1_P19

description:
Smartseq
cell by gene matrix


title: HC_M1P2_I2

description:
Smartseq
cell by gene matrix


title: HC_M1P2_C10

description:
Smartseq
cell by gene matrix


title: HDT1_S#J1_03:00

description: Gene expression of participant S#J1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT1, at 03:00 hr


title: BDC2_S#J1_07:00

description: Gene expression of participant S#J1, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC2, at 07:00 hr


title: HC_M1P1_P15

description:
Smartseq
cell by gene matrix


title: HC_M1P1_P3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_P5

description:
Smartseq
cell by gene matrix


title: HC_M1P1_P16

description:
Smartseq
cell by gene matrix


title: HDT1_S#I1_11:00

description: Gene expression of participant S#I1, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT1, at 11:00 hr


title: HC_M1P1_O5

description:
Smartseq
cell by gene matrix


title: HC_M1P1_O4

description:
Smartseq
cell by gene matrix


title: HC_M1P2_A19

description:
Smartseq
cell by gene matrix


title: HDT1_S#I1_07:00

description: Gene expression of participant S#I1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT1, at 07:00 hr


title: HC_M1P1_P24

description:
Smartseq
cell by gene matrix


title: HC_M1P1_P23

description:
Smartseq
cell by gene matrix


title: HDT2_S#I1_19:00

description: Gene expression of participant S#I1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT2, at 19:00 hr


title: HDT2_S#I1_23:00

description: Gene expression of participant S#I1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT2, at 23:00 hr


title: BDC2_S#J1_19:00

description: Gene expression of participant S#J1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC2, at 19:00 hr


title: HC_M1P1_O24

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P1_P18

description:
Smartseq
cell by gene matrix


title: HDT1_S#I1_23:00

description: Gene expression of participant S#I1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT1, at 23:00 hr


title: BDC2_S#J1_03:00

description: Gene expression of participant S#J1, sampling session BDC2, at 03:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC2, at 03:00 hr


title: BDC2_S#I1_15:00

description: Gene expression of participant S#I1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC2, at 15:00 hr


title: HC_M1P1_P17

description:
Smartseq
cell by gene matrix


title: BDC2_S#I1_19:00

description: Gene expression of participant S#I1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC2, at 19:00 hr


title: BDC1_S#J1_11:00

description: Gene expression of participant S#J1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC1, at 11:00 hr


title: BDC1_S#J1_07:00

description: Gene expression of participant S#J1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC1, at 07:00 hr


title: HC_M1P1_O23

description:
Smartseq
cell by gene matrix


title: BDC2_S#J1_23:00

description: Gene expression of participant S#J1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC2, at 23:00 hr


title: BDC2_S#J1_15:00

description: Gene expression of participant S#J1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC2, at 15:00 hr


title: HC_M1P1_O11

description:
Smartseq
cell by gene matrix


title: BDC1_S#J1_03:00

description: Gene expression of participant S#J1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC1, at 03:00 hr


title: HC_M1P1_P12

description:
Smartseq
cell by gene matrix


title: HC_M1P1_O1

description:
Smartseq
cell by gene matrix


title: HC_M1P1_P1

description:
Smartseq
cell by gene matrix


title: BDC2_S#I1_11:00

description: Gene expression of participant S#I1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC2, at 11:00 hr


title: HC_M1P1_N7

description:
Smartseq
cell by gene matrix


title: HDT2_S#J1_15:00

description: Gene expression of participant S#J1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT2, at 15:00 hr


title: HDT2_S#J1_19:00

description: Gene expression of participant S#J1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT2, at 19:00 hr


title: HC_M1P1_N3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_O16

description:
Smartseq
cell by gene matrix


title: HDT1_S#J1_19:00

description: Gene expression of participant S#J1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT1, at 19:00 hr


title: HC_M1P1_O3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_O21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_N2

description:
Smartseq
cell by gene matrix


title: HC_M1P1_N19

description:
Smartseq
cell by gene matrix


title: HC_M1P1_O19

description:
Smartseq
cell by gene matrix


title: HC_M1P1_N18

description:
Smartseq
cell by gene matrix


title: HC_M1P1_O17

description:
Smartseq
cell by gene matrix


title: HDT2_S#I1_15:00

description: Gene expression of participant S#I1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT2, at 15:00 hr


title: HDT1_S#J1_15:00

description: Gene expression of participant S#J1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT1, at 15:00 hr


title: HDT1_S#I1_19:00

description: Gene expression of participant S#I1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT1, at 19:00 hr


title: HC_M1P1_N14

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: BDC2_S#I1_07:00

description: Gene expression of participant S#I1, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC2, at 07:00 hr


title: HC_M1P1_N13

description:
Smartseq
cell by gene matrix


title: BDC1_S#I1_19:00

description: Gene expression of participant S#I1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC1, at 19:00 hr


title: HDT1_S#I1_15:00

description: Gene expression of participant S#I1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session HDT1, at 15:00 hr


title: BDC1_S#I1_11:00

description: Gene expression of participant S#I1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC1, at 11:00 hr


title: HC_M1P1_N22

description:
Smartseq
cell by gene matrix


title: HC_M1P1_N20

description:
Smartseq
cell by gene matrix


title: BDC1_S#I1_07:00

description: Gene expression of participant S#I1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC1, at 07:00 hr


title: HC_M1P1_M9

description:
Smartseq
cell by gene matrix


title: BDC1_S#J1_19:00

description: Gene expression of participant S#J1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC1, at 19:00 hr


title: R_S#G1_23:00

description: Gene expression of participant S#G1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session R, at 23:00 hr


title: R_S#G1_07:00

description: Gene expression of participant S#G1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session R, at 07:00 hr


title: HC_M1P1_N17

description:
Smartseq
cell by gene matrix


title: HC_M1P1_N15

description:
Smartseq
cell by gene matrix


title: HC_M1P1_N12

description:
Smartseq
cell by gene matrix


title: BDC1_S#J1_15:00

description: Gene expression of participant S#J1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session BDC1, at 15:00 hr


title: HDT2_S#J1_07:00

description: Gene expression of participant S#J1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#J1, sampling session HDT2, at 07:00 hr


title: HDT3_S#H1_03:00

description: Gene expression of participant S#H1, sampling session HDT3, at 03:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT3, at 03:00 hr


title: BDC1_S#I1_15:00

description: Gene expression of participant S#I1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#I1, sampling session BDC1, at 15:00 hr


title: HC_M1P1_M5

description:
Smartseq
cell by gene matrix


title: R_S#H1_03:00

description: Gene expression of participant S#H1, sampling session R, at 03:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session R, at 03:00 hr


title: HC_M1P1_M2

description:
Smartseq
cell by gene matrix


title: HC_M1P1_N11

description:
Smartseq
cell by gene matrix


title: R_S#H1_23:00

description: Gene expression of participant S#H1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session R, at 23:00 hr


title: R_S#H1_11:00

description: Gene expression of participant S#H1, sampling session R, at 11:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session R, at 11:00 hr


title: HDT3_S#H1_19:00

description: Gene expression of participant S#H1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT3, at 19:00 hr


title: HDT3_S#G1_23:00

description: Gene expression of participant S#G1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT3, at 23:00 hr


title: R_S#G1_15:00

description: Gene expression of participant S#G1, sampling session R, at 15:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session R, at 15:00 hr


title: HDT3_S#H1_15:00

description: Gene expression of participant S#H1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT3, at 15:00 hr


title: HDT3_S#G1_19:00

description: Gene expression of participant S#G1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT3, at 19:00 hr


title: HC_M1P1_M15

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P1_M21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_M3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_M13

description:
Smartseq
cell by gene matrix


title: HDT2_S#H1_03:00

description: Gene expression of participant S#H1, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT2, at 03:00 hr


title: HDT2_S#H1_23:00

description: Gene expression of participant S#H1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT2, at 23:00 hr


title: HDT3_S#G1_11:00

description: Gene expression of participant S#G1, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT3, at 11:00 hr


title: HDT3_S#G1_03:00

description: Gene expression of participant S#G1, sampling session HDT3, at 03:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT3, at 03:00 hr


title: HC_M1P1_M23

description:
Smartseq
cell by gene matrix


title: HDT3_S#H1_11:00

description: Gene expression of participant S#H1, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT3, at 11:00 hr


title: HC_M1P1_M22

description:
Smartseq
cell by gene matrix


title: HC_M1P1_L4

description:
Smartseq
cell by gene matrix


title: HDT1_S#H1_03:00

description: Gene expression of participant S#H1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT1, at 03:00 hr


title: HDT1_S#H1_23:00

description: Gene expression of participant S#H1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT1, at 23:00 hr


title: HC_M1P1_L24

description:
Smartseq
cell by gene matrix


title: HDT3_S#G1_15:00

description: Gene expression of participant S#G1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT3, at 15:00 hr


title: HC_M1P1_M14

description:
Smartseq
cell by gene matrix


title: HC_M1P1_M20

description:
Smartseq
cell by gene matrix


title: HC_M1P1_L21

description:
Smartseq
cell by gene matrix


title: HDT2_S#H1_11:00

description: Gene expression of participant S#H1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT2, at 11:00 hr


title: HDT1_S#G1_07:00

description: Gene expression of participant S#G1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT1, at 07:00 hr


title: HDT1_S#G1_23:00

description: Gene expression of participant S#G1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT1, at 23:00 hr


title: HC_M1P1_M19

description:
Smartseq
cell by gene matrix


title: HDT1_S#G1_03:00

description: Gene expression of participant S#G1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT1, at 03:00 hr


title: HDT2_S#G1_11:00

description: Gene expression of participant S#G1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT2, at 11:00 hr


title: HC_M1P1_M12

description:
Smartseq
cell by gene matrix


title: HC_M1P1_L17

description:
Smartseq
cell by gene matrix


title: HDT2_S#G1_07:00

description: Gene expression of participant S#G1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT2, at 07:00 hr


title: BDC2_S#H1_23:00

description: Gene expression of participant S#H1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC2, at 23:00 hr


title: HC_M1P1_L18

description:
Smartseq
cell by gene matrix


title: HDT1_S#H1_11:00

description: Gene expression of participant S#H1, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT1, at 11:00 hr


title: HC_M1P1_M11

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P1_L14

description:
Smartseq
cell by gene matrix


title: HC_M1P1_M10

description:
Smartseq
cell by gene matrix


title: HDT2_S#G1_23:00

description: Gene expression of participant S#G1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT2, at 23:00 hr


title: BDC2_S#G1_03:00

description: Gene expression of participant S#G1, sampling session BDC2, at 03:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC2, at 03:00 hr


title: HC_M1P1_L13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_L9

description:
Smartseq
cell by gene matrix


title: HDT1_S#H1_07:00

description: Gene expression of participant S#H1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT1, at 07:00 hr


title: HDT2_S#H1_19:00

description: Gene expression of participant S#H1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT2, at 19:00 hr


title: HC_M1P1_L3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_L12

description:
Smartseq
cell by gene matrix


title: HDT2_S#H1_15:00

description: Gene expression of participant S#H1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT2, at 15:00 hr


title: HC_M1P1_L11

description:
Smartseq
cell by gene matrix


title: BDC2_S#G1_23:00

description: Gene expression of participant S#G1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC2, at 23:00 hr


title: HC_M1P1_L7

description:
Smartseq
cell by gene matrix


title: HDT1_S#G1_11:00

description: Gene expression of participant S#G1, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT1, at 11:00 hr


title: HC_M1P1_L10

description:
Smartseq
cell by gene matrix


title: HC_M1P1_L22

description:
Smartseq
cell by gene matrix


title: BDC2_S#H1_15:00

description: Gene expression of participant S#H1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC2, at 15:00 hr


title: HC_M1P1_L19

description:
Smartseq
cell by gene matrix


title: HC_M1P1_L16

description:
Smartseq
cell by gene matrix


title: BDC2_S#G1_19:00

description: Gene expression of participant S#G1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC2, at 19:00 hr


title: HC_M1P1_L15

description:
Smartseq
cell by gene matrix


title: BDC2_S#G1_11:00

description: Gene expression of participant S#G1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC2, at 11:00 hr


title: HC_M1P1_M24

description:
Smartseq
cell by gene matrix


title: BDC2_S#H1_11:00

description: Gene expression of participant S#H1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC2, at 11:00 hr


title: BDC1_S#H1_23:00

description: Gene expression of participant S#H1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC1, at 23:00 hr


title: HC_M1P1_K7

description:
Smartseq
cell by gene matrix


title: HC_M1P1_K8

description:
Smartseq
cell by gene matrix


title: BDC1_S#H1_03:00

description: Gene expression of participant S#H1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC1, at 03:00 hr


title: HC_M1P1_K5

description:
Smartseq
cell by gene matrix


title: BDC2_S#H1_19:00

description: Gene expression of participant S#H1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC2, at 19:00 hr


title: HDT2_S#G1_15:00

description: Gene expression of participant S#G1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT2, at 15:00 hr


title: BDC1_S#G1_11:00

description: Gene expression of participant S#G1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC1, at 11:00 hr


title: BDC1_S#G1_07:00

description: Gene expression of participant S#G1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC1, at 07:00 hr


title: HC_M1P1_K4

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P1_K20

description:
Smartseq
cell by gene matrix


title: BDC1_S#H1_07:00

description: Gene expression of participant S#H1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC1, at 07:00 hr


title: HC_M1P1_K14

description:
Smartseq
cell by gene matrix


title: HDT2_S#G1_19:00

description: Gene expression of participant S#G1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT2, at 19:00 hr


title: BDC1_S#H1_11:00

description: Gene expression of participant S#H1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC1, at 11:00 hr


title: HC_M1P1_K21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_K24

description:
Smartseq
cell by gene matrix


title: HC_M1P1_K2

description:
Smartseq
cell by gene matrix


title: BDC1_S#G1_23:00

description: Gene expression of participant S#G1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC1, at 23:00 hr


title: HC_M1P1_K19

description:
Smartseq
cell by gene matrix


title: HDT1_S#H1_19:00

description: Gene expression of participant S#H1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT1, at 19:00 hr


title: HC_M1P1_K10

description:
Smartseq
cell by gene matrix


title: BDC1_S#G1_03:00

description: Gene expression of participant S#G1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC1, at 03:00 hr


title: BDC2_S#G1_15:00

description: Gene expression of participant S#G1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC2, at 15:00 hr


title: HC_M1P1_K17

description:
Smartseq
cell by gene matrix


title: HC_M1P1_M17

description:
Smartseq
cell by gene matrix


title: HC_M1P1_K16

description:
Smartseq
cell by gene matrix


title: HC_M1P1_J3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_J24

description:
Smartseq
cell by gene matrix


title: BDC1_S#G1_15:00

description: Gene expression of participant S#G1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC1, at 15:00 hr


title: HC_M1P1_K13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_J21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_K12

description:
Smartseq
cell by gene matrix


title: HDT1_S#H1_15:00

description: Gene expression of participant S#H1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session HDT1, at 15:00 hr


title: HC_M1P1_K11

description:
Smartseq
cell by gene matrix


title: HC_M1P1_K15

description:
Smartseq
cell by gene matrix


title: HC_M1P1_J7

description:
Smartseq
cell by gene matrix


title: BDC1_S#H1_15:00

description: Gene expression of participant S#H1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC1, at 15:00 hr


title: HC_M1P1_J19

description:
Smartseq
cell by gene matrix


title: BDC1_S#H1_19:00

description: Gene expression of participant S#H1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#H1, sampling session BDC1, at 19:00 hr


title: HC_M1P1_K1

description:
Smartseq
cell by gene matrix


title: HC_M1P1_J5

description:
Smartseq
cell by gene matrix


title: R_S#E1_07:00

description: Gene expression of participant S#E1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session R, at 07:00 hr


title: HC_M1P1_J14

description:
Smartseq
cell by gene matrix


title: HDT1_S#G1_15:00

description: Gene expression of participant S#G1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT1, at 15:00 hr


title: R_S#F1_03:00

description: Gene expression of participant S#F1, sampling session R, at 03:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session R, at 03:00 hr


title: HDT1_S#G1_19:00

description: Gene expression of participant S#G1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session HDT1, at 19:00 hr


title: HC_M1P1_J22

description:
Smartseq
cell by gene matrix


title: BDC1_S#G1_19:00

description: Gene expression of participant S#G1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#G1, sampling session BDC1, at 19:00 hr


title: HDT3_S#E1_23:00

description: Gene expression of participant S#E1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT3, at 23:00 hr


title: R_S#E1_03:00

description: Gene expression of participant S#E1, sampling session R, at 03:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session R, at 03:00 hr


title: R_S#E1_23:00

description: Gene expression of participant S#E1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session R, at 23:00 hr


title: HC_M1P1_J10

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P1_J1

description:
Smartseq
cell by gene matrix


title: HDT3_S#F1_23:00

description: Gene expression of participant S#F1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT3, at 23:00 hr


title: HC_M1P1_J16

description:
Smartseq
cell by gene matrix


title: R_S#E1_19:00

description: Gene expression of participant S#E1, sampling session R, at 19:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session R, at 19:00 hr


title: HDT3_S#E1_11:00

description: Gene expression of participant S#E1, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT3, at 11:00 hr


title: HDT3_S#E1_07:00

description: Gene expression of participant S#E1, sampling session HDT3, at 07:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT3, at 07:00 hr


title: HC_M1P1_J13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I4

description:
Smartseq
cell by gene matrix


title: HDT3_S#E1_19:00

description: Gene expression of participant S#E1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT3, at 19:00 hr


title: HDT3_S#F1_11:00

description: Gene expression of participant S#F1, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT3, at 11:00 hr


title: R_S#F1_15:00

description: Gene expression of participant S#F1, sampling session R, at 15:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session R, at 15:00 hr


title: R_S#F1_23:00

description: Gene expression of participant S#F1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session R, at 23:00 hr


title: HC_M1P1_J11

description:
Smartseq
cell by gene matrix


title: HDT3_S#F1_07:00

description: Gene expression of participant S#F1, sampling session HDT3, at 07:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT3, at 07:00 hr


title: HC_M1P1_I21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_J12

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I9

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I16

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I7

description:
Smartseq
cell by gene matrix


title: HDT2_S#E1_07:00

description: Gene expression of participant S#E1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT2, at 07:00 hr


title: HC_M1P1_I5

description:
Smartseq
cell by gene matrix


title: R_S#E1_15:00

description: Gene expression of participant S#E1, sampling session R, at 15:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session R, at 15:00 hr


title: HDT2_S#F1_07:00

description: Gene expression of participant S#F1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT2, at 07:00 hr


title: HDT3_S#E1_15:00

description: Gene expression of participant S#E1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT3, at 15:00 hr


title: HC_M1P1_I11

description:
Smartseq
cell by gene matrix


title: HDT2_S#E1_23:00

description: Gene expression of participant S#E1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT2, at 23:00 hr


title: HC_M1P1_J15

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I22

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I24

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H9

description:
Smartseq
cell by gene matrix


title: HDT3_S#F1_19:00

description: Gene expression of participant S#F1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT3, at 19:00 hr


title: HDT2_S#E1_11:00

description: Gene expression of participant S#E1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT2, at 11:00 hr


title: HDT1_S#E1_07:00

description: Gene expression of participant S#E1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT1, at 07:00 hr


title: HDT3_S#F1_15:00

description: Gene expression of participant S#F1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT3, at 15:00 hr


title: HC_M1P1_H5

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HDT1_S#F1_11:00

description: Gene expression of participant S#F1, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT1, at 11:00 hr


title: HDT2_S#E1_03:00

description: Gene expression of participant S#E1, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT2, at 03:00 hr


title: HC_M1P1_I20

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I18

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I14

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_I10

description:
Smartseq
cell by gene matrix


title: HDT1_S#F1_23:00

description: Gene expression of participant S#F1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT1, at 23:00 hr


title: HC_M1P1_H3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H24

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H23

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H19

description:
Smartseq
cell by gene matrix


title: HDT2_S#F1_11:00

description: Gene expression of participant S#F1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT2, at 11:00 hr


title: HDT1_S#F1_03:00

description: Gene expression of participant S#F1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT1, at 03:00 hr


title: HDT1_S#E1_03:00

description: Gene expression of participant S#E1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT1, at 03:00 hr


title: HDT1_S#F1_07:00

description: Gene expression of participant S#F1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT1, at 07:00 hr


title: HC_M1P1_H18

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H2

description:
Smartseq
cell by gene matrix


title: BDC2_S#E1_07:00

description: Gene expression of participant S#E1, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC2, at 07:00 hr


title: HC_M1P1_H17

description:
Smartseq
cell by gene matrix


title: HDT1_S#E1_23:00

description: Gene expression of participant S#E1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT1, at 23:00 hr


title: BDC2_S#E1_23:00

description: Gene expression of participant S#E1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC2, at 23:00 hr


title: BDC2_S#F1_11:00

description: Gene expression of participant S#F1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC2, at 11:00 hr


title: BDC2_S#F1_07:00

description: Gene expression of participant S#F1, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC2, at 07:00 hr


title: BDC2_S#F1_23:00

description: Gene expression of participant S#F1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC2, at 23:00 hr


title: HDT2_S#E1_19:00

description: Gene expression of participant S#E1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT2, at 19:00 hr


title: HDT2_S#E1_15:00

description: Gene expression of participant S#E1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session HDT2, at 15:00 hr


title: HC_M1P1_H13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H14

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H22

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G9

description:
Smartseq
cell by gene matrix


title: HC_M1P1_H1

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G8

description:
Smartseq
cell by gene matrix


title: HDT2_S#F1_15:00

description: Gene expression of participant S#F1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT2, at 15:00 hr


title: HC_M1P1_H12

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: BDC2_S#E1_11:00

description: Gene expression of participant S#E1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC2, at 11:00 hr


title: BDC2_S#E1_19:00

description: Gene expression of participant S#E1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC2, at 19:00 hr


title: HC_M1P1_G23

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G24

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G2

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G22

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G19

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G18

description:
Smartseq
cell by gene matrix


title: BDC1_S#E1_11:00

description: Gene expression of participant S#E1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC1, at 11:00 hr


title: BDC1_S#E1_23:00

description: Gene expression of participant S#E1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC1, at 23:00 hr


title: BDC2_S#F1_15:00

description: Gene expression of participant S#F1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC2, at 15:00 hr


title: BDC2_S#F1_19:00

description: Gene expression of participant S#F1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC2, at 19:00 hr


title: BDC1_S#E1_07:00

description: Gene expression of participant S#E1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC1, at 07:00 hr


title: BDC1_S#E1_03:00

description: Gene expression of participant S#E1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC1, at 03:00 hr


title: BDC1_S#F1_11:00

description: Gene expression of participant S#F1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC1, at 11:00 hr


title: HC_M1P1_G15

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G14

description:
Smartseq
cell by gene matrix


title: BDC1_S#F1_07:00

description: Gene expression of participant S#F1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC1, at 07:00 hr


title: HDT1_S#F1_19:00

description: Gene expression of participant S#F1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT1, at 19:00 hr


title: BDC1_S#F1_23:00

description: Gene expression of participant S#F1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC1, at 23:00 hr


title: HC_M1P1_G12

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_G1

description:
Smartseq
cell by gene matrix


title: HC_M1P1_F7

description:
Smartseq
cell by gene matrix


title: HC_M1P1_F9

description:
Smartseq
cell by gene matrix


title: BDC1_S#F1_19:00

description: Gene expression of participant S#F1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC1, at 19:00 hr


title: BDC1_S#F1_15:00

description: Gene expression of participant S#F1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session BDC1, at 15:00 hr


title: HC_M1P1_F5

description:
Smartseq
cell by gene matrix


title: BDC1_S#E1_19:00

description: Gene expression of participant S#E1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC1, at 19:00 hr


title: HC_M1P1_F4

description:
Smartseq
cell by gene matrix


title: R_S#D1_11:00

description: Gene expression of participant S#D1, sampling session R, at 11:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session R, at 11:00 hr


title: HC_M1P1_F6

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HDT1_S#F1_15:00

description: Gene expression of participant S#F1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#F1, sampling session HDT1, at 15:00 hr


title: HC_M1P1_F21

description:
Smartseq
cell by gene matrix


title: cmdTAC_ripseq_rep2

city: Cambridge

first: Christopher

middle: Ross

last: Doering

state: MA

address: 31 Ames St

department: Biology

institute: MIT

description:
Singular G4 sequencer
Complete Genomics

data_processing:
Remaining adapter sequences were trimmed from reads using cudadapt. Paired-end reads were mapped to the MG1655 (NC_00913.2) and T4 (NC_000866) genomes using bowtie2 and default settings. Mapped reads were converted into python operable numpy arrays using the python package genomearray3. TPM calculations were performed using the custom made jupyter notebooks available at https://github.com/chrisdoering8197/CmdTAC.
Assembly: NC_00913.2, NC_000866
Supplementary files format and content: TPM values for each gene in addition to the gene name are listed for both the MG1655 genome (ripseq_invivo_host_tpm.csv) and T4 genome (ripseq_invivo_t4_tpm.csv). Each column corresponds to a different sample.

organism:
Escherichia coli
Escherichia phage T4

source_name: str. K12 substr. MG1655

growth_protocol: Overnight cultures of +cmdTAC and -cmdTAC cells were grown at 37C in LB + chloramphenicol. The day of the experiment cultures were back-diluted to an OD600 = 0.05 and allowed to grow for an additional 1.5 hours in LB + chloramphenicol at 37C until reaching an OD600 between 0.2 and 0.3.

extract_protocol:
RNA was extracted with two rounds of acidic phenol heated to 67C followed by one extraction with acidic phenol chloroform at room temperature. RNA was precipitated using isopropanol precipitation at -80C and DNA was removed with DNAse treatment using Turbo DNAse. rRNA was depleted using biotinylated capture probes specific to the E. coli 5S, 16S, and 23S rRNA. RIP-seq samples subjected to IP with an ADP-ribose antibody to enrich for modified transcripts
cDNA library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer's protocol fro use with rRNA depleted RNA.

treatment_protocol: Cultures at an OD600 between 0.2 and 0.3 were infected with bacteriophage T4 at a multiplicity of infection (MOI) of 10 and continued to grow at 37C with shaking at 200rpm until sample collection. Samples were collected by mixing 1 mL of cells with 1 mL of of boiling lysis buffer (2% SDS, 4 mM EDTA) before flash freezing in liquid nitrogen.

value: str. K12 substr. MG1655

tag: genotype

tag: treatment

value: T4 infection


title: cmdTAC_rnaseq_rep2

description:
Singular G4 sequencer
Complete Genomics


title: HC_M1P1_F22

description:
Smartseq
cell by gene matrix


title: HC_M1P1_F2

description:
Smartseq
cell by gene matrix


title: HC_M1P1_F20

description:
Smartseq
cell by gene matrix


title: cmdTAC_ripseq_rep1

description:
Singular G4 sequencer
Complete Genomics


title: R_S#D1_07:00

description: Gene expression of participant S#D1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session R, at 07:00 hr


title: R_S#B1_07:00

description: Gene expression of participant S#B1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session R, at 07:00 hr


title: R_S#D1_03:00

description: Gene expression of participant S#D1, sampling session R, at 03:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session R, at 03:00 hr


title: R_S#B1_11:00

description: Gene expression of participant S#B1, sampling session R, at 11:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session R, at 11:00 hr


title: R_S#B1_03:00

description: Gene expression of participant S#B1, sampling session R, at 03:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session R, at 03:00 hr


title: cmdT_treated_rna

description:
Singular G4 sequencer
Complete Genomics

data_processing:
Remaining adapter sequences were trimmed from reads using cudadapt. Paired-end reads were mapped to the MG1655 (NC_00913.2) and T4 (NC_000866) genomes using bowtie2 and default settings. Mapped reads were converted into python operable numpy arrays using the python package genomearray3. TPM calculations were performed Geneious.
Assembly: NC_00913.2, NC_000866
Supplementary files format and content: TPM values for each gene in addition to the gene name are listed for both the MG1655 genome (ripseq_invitro_host_tpm.csv) and T4 genome (ripseq_invitro_t4_tpm.csv) with each column denoted a different sample.

growth_protocol: Cultures at an OD600 between 0.2 and 0.3 were infected with bacteriophage T4 at a multiplicity of infection (MOI) of 10 and continued to grow at 37C with shaking at 200rpm until sample collection. Samples were collected by mixing 1 mL of cells with 1 mL of of boiling lysis buffer (2% SDS, 4 mM EDTA) before flash freezing in liquid nitrogen.

extract_protocol:
RNA was extracted with two rounds of acidic phenol heated to 67C followed by one extraction with acidic phenol chloroform at room temperature. RNA was precipitated using isopropanol precipitation at -80C and DNA was removed with DNAse treatment using Turbo DNAse. Extracted RNA was ADP-ribosylated with CmdT with 0.25 mM 6-Biotin-17-NAD+ for 4 hours at 37 °C and then continued at 4 °C overnight. 10 µg of each reaction was kept at -80 °C as the pre-pulldown sample. The remaining 10 µg were incubated with streptavidin conjugated superparamagnetic beads following the manufacturer’s protocol. RNA was stripped from the beads by addition of 0.5 mL Trizol and incubation at 25 °C for 15 minutes on a thermomixer at 1000 rpm. Beads were then precipitated with a magnet and 100 µL of chloroform were added. The phases were separated by centrifugation at 14,000 g for 15 minutes. Finally, the aqueous phase was purified using the RNA Clean and Concentrate Kit (Zymogen).
cDNA library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer's protocol.


title: HC_M1P1_F24

description:
Smartseq
cell by gene matrix


title: HC_M1P1_F16

description:
Smartseq
cell by gene matrix


title: HC_M1P1_F15

description:
Smartseq
cell by gene matrix


title: cmdT_pulldown

description:
Singular G4 sequencer
Complete Genomics


title: R_S#B1_23:00

description: Gene expression of participant S#B1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session R, at 23:00 hr


title: HC_M1P1_F12

description:
Smartseq
cell by gene matrix


title: R_S#D1_23:00

description: Gene expression of participant S#D1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session R, at 23:00 hr


title: cmdTAC_rnaseq_rep1

description:
Singular G4 sequencer
Complete Genomics


title: HDT3_S#D1_11:00

description: Gene expression of participant S#D1, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT3, at 11:00 hr


title: HC_M1P1_F11

description:
Smartseq
cell by gene matrix


title: BDC2_S#E1_15:00

description: Gene expression of participant S#E1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#E1, sampling session BDC2, at 15:00 hr


title: HC_M1P1_F19

description:
Smartseq
cell by gene matrix


title: Rice Osmads32 mutant

city: Shanghai

first: Xuelian

last: Zhang

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

data_processing:
The raw sequencing data are evaluated by FAST-QC including quality distribution of nucleotides, position specific sequencing quality, GC content, the proportion of PCR duplication, kmer frequency etc.
Mapsplice was used for RNA-seq alignment.
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

organism: Oryza sativa

growth_protocol: All rice plants were grown in the paddy ﬁeld of Shanghai Jiao Tong University, located in Shanghai (31.03ºN, 121.45ºE).

extract_protocol:
RNA was harvested using RNAeasy kit (Qiagen).
Libraries were prepared from 2-5μg of total RNA, and mRNA was enriched with Dynabeads mRNA Purification Kit (Thermo Fisher).

value: palea

value: Rice Osmads32 mutant

value: T-DNA insertion mutant


title: HC_M1P1_F1

description:
Smartseq
cell by gene matrix


title: HC_M1P1_F18

description:
Smartseq
cell by gene matrix


title: HDT3_S#D1_07:00

description: Gene expression of participant S#D1, sampling session HDT3, at 07:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT3, at 07:00 hr


title: Rice Osmads6 mutant

source_name: Nipponbare

value: Rice Osmads6 mutant

value: Tos17 retrotransposon insertion mutant


title: HC_M1P1_F17

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E7

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E9

description:
Smartseq
cell by gene matrix


title: HDT3_S#D1_03:00

description: Gene expression of participant S#D1, sampling session HDT3, at 03:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT3, at 03:00 hr


title: Rice Wild type

source_name: O. sativa L. ssp. japonica

value: Rice Wild type

value: wild type


title: Rice rep1 mutant

value: Rice rep1 mutant

value: deletion mutant


title: HDT3_S#D1_23:00

description: Gene expression of participant S#D1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT3, at 23:00 hr


title: HC_M1P1_E6

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: HC_M1P1_E5

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E3

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E4

description:
Smartseq
cell by gene matrix


title: HDT3_S#B1_11:00

description: Gene expression of participant S#B1, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT3, at 11:00 hr


title: HDT3_S#B1_07:00

description: Gene expression of participant S#B1, sampling session HDT3, at 07:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT3, at 07:00 hr


title: HC_M1P1_E24

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E8

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 3 days post Drosophila C virus infection, rep4

city: Edinburgh

first: Pedro

last: Vale

state: Edinburgh

address: Ashworth Labs, Charlotte Auerbach Road

department: School of Biological Sciences

institute: University of Edinburgh

data_processing:
Reads were trimmed using Cutadapt1 (version cutadapt-1.18-venv). Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA kit (AGATCGGAAGAGC). Reads after trimming were required to have a minimum length of 50.
Reads were aligned to the reference genome using STAR2 (version 2.7.3a) specifying paired-end reads
Reads were normalised using the weighted trimmed mean of M-values method5, passing ‘TMM’ as the method to the calcNormFactors method of edgeR.
Assembly: The reference used for mapping was the Drosophila melanogaster (BDGP6_ens107) combined with S. aureus (GCA_000013425.1), P. rettgeri (GCF_003204135.1) and DCV (NC_001834.1). The annotation used for counting was the standard GTF-format annotation for that reference.
Supplementary files format and content: Text file containing normalized read counts for genes in all samples (CPMs)

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Drosophila melanogaster flies were grown from egg to adults at 25°C at LD12:12

extract_protocol:
RNA was extracted using TRI reagent (MRC, Fisher Scientific), according to manufacturer's protocol
Sequencing and initial bioinformatics analysis was carried out by Edinburgh Genomics, The University of Edinburgh, which is partly supported with core funding from the Natural Environment Research Council (UKSBS PR18037) and BBSRC (BB/T017864/1)
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep kits

treatment_protocol: 1-4 days old, mated females and males were infected with Staphylococcus aureus (PIG1) or  Providencia rettgeri (DSM4542) by pricking the flies with a tungsten needle dipped in bacterial solution (OD600=0.1). Samples were collected 8 and 20 hours after infecting the flies. Systemic infection with DCV was introduced to 2-5 days old, mated females and males by pricking as described with the bacterial infections. DCV inoculum of 10^8 viral particles was used. Samples were collected 3 days after the infection with DCV. As controls, uninfected flies of similar age were collected.

value: whole fly

tag: gender

value: male


title: min_cmdTAC_30min_rep2

data_processing:
Remaining adapter sequences were trimmed from reads using cudadapt. Paired-end reads were mapped to the MG1655 (NC_00913.2) and T4 (NC_000866) genomes using bowtie2 and default settings. Mapped reads were converted into python operable numpy arrays using the python package genomearray3. TPM calculations were performed using the custom made jupyter notebooks available at https://github.com/chrisdoering8197/CmdTAC.
Assembly: NC_00913.2, NC_000866
Supplementary files format and content: TPM values for each gene in addition to the gene name are listed for both the MG1655 genome (rnaseq_host_tpm.csv) and T4 genome (rnaseq_t4_tpm.csv)

source_name: str. K12 substr. MG1655

extract_protocol:
RNA was extracted with two rounds of acidic phenol heated to 67C followed by one extraction with acidic phenol chloroform at room temperature. RNA was precipitated using isopropanol precipitation at -80C and DNA was removed with DNAse treatment using Turbo DNAse. rRNA was depleted using biotinylated capture probes specific to the E. coli 5S, 16S, and 23S rRNA
cDNA library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer's protocol fro use with rRNA depleted RNA.

value: pKVS45 empty vector


title: HC_M1P1_E23

description:
Smartseq
cell by gene matrix


title: R_S#D1_19:00

description: Gene expression of participant S#D1, sampling session R, at 19:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session R, at 19:00 hr


title: KSA2 male flies, 3 days post Drosophila C virus infection, rep3


title: minus_cmdTAC_15min_rep2


title: HDT3_S#D1_15:00

description: Gene expression of participant S#D1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT3, at 15:00 hr


title: KSA2 male flies, 3 days post Drosophila C virus infection, rep2


title: KSA2 male flies, 3 days post Drosophila C virus infection, rep1


title: plus_cmdTAC_30min_rep2


title: HC_M1P1_E21

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E19

description:
Smartseq
cell by gene matrix


title: min_cmdTAC_30min_rep1


title: plus_cmdTAC_15min_rep2


title: HDT3_S#D1_19:00

description: Gene expression of participant S#D1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT3, at 19:00 hr


title: minus_cmdTAC_15min_rep1


title: Unassigned

description: Unassigned


title: HDT3_S#B1_19:00

description: Gene expression of participant S#B1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT3, at 19:00 hr


title: plus_cmdTAC_30min_rep1


title: KSA2 female flies, 3 days post Drosophila C virus infection, rep3

value: female


title: KSA2 female flies, 3 days post Drosophila C virus infection, rep2


title: HC_M1P1_E22

description:
Smartseq
cell by gene matrix


title: R_S#B1_19:00

description: Gene expression of participant S#B1, sampling session R, at 19:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session R, at 19:00 hr


title: KSA2 female flies, 3 days post Drosophila C virus infection, rep1


title: plus_cmdTAC_15min_rep1


title: HDT3_S#B1_15:00

description: Gene expression of participant S#B1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT3, at 15:00 hr


title: HDT2_S#D1_11:00

description: Gene expression of participant S#D1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT2, at 11:00 hr


title: HC_M1P1_E16

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E15

description:
Smartseq
cell by gene matrix


title: KSA2 female flies, 3 days post Drosophila C virus infection, rep4


title: OR male flies, 3 days post Drosophila C virus infection, rep4

value: OR


title: Extended aged donors, BMMCs_HSPCs, Cell Hash, sample 18

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

description: Cell Hash library (Cell barcodes are matchable with ATAC, and mRNA in sample 18): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains Hashing barcode.

library_source: other

data_processing:
ReDeeM. For each sample, all three libraries were sequenced on Illumina NovaSeq S4 300 cycle kit. The sequencing length was as below. Read1: 149nt, i7: 8nt, i5: 24nt, Read2: 149nt. We expected to sequence 20,000~30,000 raw reads per cell for RNA libraries and ATAC libraries, while 50,000~60,000 raw reads for enrich mtDNA libraries.
The data preprocessing for the joint single-cell RNA and ATAC data was performed using 10X Genomics data preprocessing software Cell-ranger-arc.  The basic quality control analysis was as follows: RNA UMI: 1,000~25,000 transcripts per cell, unique ATAC fragment: 1,000 ~ 70,000, Fragment on peak minimum percentage: 10%, minimum mtDNA copies per position per cell: 10X. Finally, the possible doublets are removed by Amulet (using default parameter). Unsupervised community detection-based clustering was performed on weighted nearest neighbour (WNN) using Seurat. Cell types are firstly annotated by gene expression using the latest signature (van Galen under review) which was further validated by sorted bulk RNA-seq data (https://sankaranlab.shinyapps.io/geneExpression/). The ATAC unique fragments for each clustered cell type were further aggregated to generate pseudo-bulk ATAC tracks. The single cell motif analysis was performed using ChromVar using the JASPAR human transcription factor (TF) database. The deviation of the TF frequency was computed for each cell for the downstream analysis.
The mutation calling pipeline is in following steps using package redeemV: 1, Data Preprocessing and eUMI grouping. 2, Consensus filtering. 3, Strand bias removal. 4, Lineage informative variants identification
Assembly: hg38
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv
Library strategy: HTO-seq

molecule: other

source_name: Bone Marrow

extract_protocol:
Bone marrow was collected from healthy young or aged donors. Bone marrow aspirate was diluted with an equal volume of Wash Buffer (PBS, 2% FBS, 1mM EDTA). Ficoll medium was added to SepMateTM (Catalog #85460) tubes and then the diluted bone marrow sample was layered on top followed by centrifuging at 1200 g for 20 minutes at room temperature. The top layer, containing the mononuclear cells, was transferred to a new tube, which was then filled up by Wash Buffer. The mononuclear cells were centrifuged at 300 g for 8 minutes. The supernatant was discarded, and the cells were washed twice and resuspended in Wash Buffer for further enrichment or in Freezing buffer (10% DMSO in FBS). Starting with the BMMCs isolated from the previous step, we enriched CD34+ cells following EasySep™ Human Cord Blood CD34 Positive Selection Kit II (Catalog #17896). Briefly, EasySep™ Human CD34 Positive Selection Cocktail (Catalog #18096C) was added to BMMCs suspension to 100 ul/ml and incubated at room temperature for 10 minutes. EasySep™ Dextran RapidSpheres™ (Catalog #50100) was vortexed and added to each sample to 50 µl/ml.  The mix was incubated for 3 minutes at room temperature. Next, Wash Buffer (7 ml) was added to the tube, The cells were then washed 4 times in "The Big Easy" EasySep™ Magnet (Catalog #18001). Finally, cells were resuspended in Wash Buffer and were centrifuged at 300g for 10 min. The CD34+ positive cell pellet was then resuspended in a freezing buffer (10% DMSO in FBS).  To further enrich the hematopoietic stem cells (HSCs), an aliquot of the enriched CD34+ cells were stained by one of the following two antibody panels. 1) CD34 PerCP-Cy5.5 (Catalog #347222); CD45RA Alexa Fluor 488 (Catalog #304114); CD90 PE-Cy7 (Catalog #561558); and  DAPI (Catalog #D1306) as viability dye. Or 2) CD34 BV421 (Catalog #562577); CD45RA-APC-H7 (Catalog #560674); CD90 PE-Cy7 (Catalog #561558), and 7-AAD as viability dye(Catalog #559925). The cells were further sorted using BD FACSAriaTM for CD34+CD45RA-CD90+ to enrich HSCs. BMMCs, as well as enriched CD34+ and CD34+CD45RA-CD90+ cells were cryopreserved. After thawing, cells were immediately processed for experiment as soon as possible without any culturing. Different donors are hashed and pooled together for ReDeeM experiments
RNA lib and ATAC lib prep:  After tagmentation, cells were immediately processed for GEM generation & barcoding following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Manual (version CG000338 Rev A, 10x Genomics) with Step 2. Next, the Post GEM Incubation Cleanup and Pre-Amplification PCR were performed following the same User Manual with Step 3 and Step 4. The pre-amplified library was eluted in 100ul EB buffer instead of 160ul. For RNA library prep, we took an aliquot of 35 ul pre-amplified library and followed the same User Manual (version CG000338 Rev A, 10x Genomics) from Step 6 and Step 7. We developed an in-house protocol to generate the massive ATAC library with enough material for both direct sequencing and mtDNA hybridization. For each sample, 8 reactions of the following were performed (each in 50 ul). 5 μl pre-amplified product, 25 μl NEBnext mix (Catalog M0541L), 2.4 μl 10 μM Nextera N70X primer (Supplementary Data 2), 2.4 μl 10X SI PCR primer B (Catalog #PN2000128), 0.5 μl 100X SYBR Green (Catalog #S7563), and 14.7 μl water. The thermocycler program started with 98°C 45 s., followed by the 6-12 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s.; The actual cycle numbers are determined using the amplification curve and the qPCR was stopped when the curve started to reach plateau. The qPCR products (50ul * 8 wells) were combined and purified using SPRI beads (Catalog #B23318) with size selection 0.4X~1.55X. The expected yield is 2,000 ng to 4,000 ng.
mtDNA lib prep: We designed 4 sets of DNA probes, with each probe set covering the whole mitochondrial genome and containing 138 biotinylated oligos that are 120 bp long. The 4 sets of probes ((v1, v2, v3, and v4) are staggered by 30 bp with each other and ensure good coverage on junction areas (Supplementary Data 2). The hybridization started with 500 ng ATAC library products for each probe set. In total, 4 independent reactions were performed in parallel and combined at the end (2,000ng input in total). The detailed incubation and wash methods largely followed the Tube Protocol in IDT xGen Hybridization Capture of DNA Libraries protocol.  Briefly, 500 ng input was combined with Cot DNA and purified by SPRI beads, which was eluted by hybridization mix that contains hybridization buffer, hybridization buffer enhancer, one of the probe set, as well as xGen™ Universal Blockers NXT (Catalog #1079584). The hybridization reaction was performed as below: 95C 30 seconds followed by 65C overnight.  The biotin-streptavidin Dynabeads purification was carried out on Day 2 using xGen Hybridization and Wash Kit. The Dynabeads after capturing and washing were used for final quick qPCR amplification (3-5 cycles). The reaction mix is as below: 20ul beads, 25ul KAPA HiFi HotStart ReadyMix (Catalog #KK2601), Primer 2.4ul P5 (Supplementary Data 2), Primer P7 (Supplementary Data 2), 0.5ul 100X SYBR Green (Catalog #S7563). The PCR program started with 98°C 45 s, followed by the 3-5 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s. The final enriched mtDNA was purified by SPRI beads (1.6X)

value: Bone Marrow

tag: cell type

value: Bone Marrow Mononuclear Cells (BMMCs)

tag: group

value: aged donor

tag: library type

value: Hash


title: HC_M1P1_E14

description:
Smartseq
cell by gene matrix

value: posteromedial nucleus of the cortical amygdala


title: HDT2_S#D1_07:00

description: Gene expression of participant S#D1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT2, at 07:00 hr


title: OR male flies, 3 days post Drosophila C virus infection, rep3


title: HC_M1P1_E13

description:
Smartseq
cell by gene matrix


title: OR male flies, 3 days post Drosophila C virus infection, rep2


title: Extended aged donors, BMMCs_HSPCs, ATAC(enriched mito included), sample 18

description: Combined ATAC library and enriched mtDNA library(Cell barcodes are matchable with mRNA and CellHash lib in sample 18): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

library_source: genomic single cell

data_processing:
ReDeeM. For each sample, all three libraries were sequenced on Illumina NovaSeq S4 300 cycle kit. The sequencing length was as below. Read1: 149nt, i7: 8nt, i5: 24nt, Read2: 149nt. We expected to sequence 20,000~30,000 raw reads per cell for RNA libraries and ATAC libraries, while 50,000~60,000 raw reads for enrich mtDNA libraries.
The data preprocessing for the joint single-cell RNA and ATAC data was performed using 10X Genomics data preprocessing software Cell-ranger-arc.  The basic quality control analysis was as follows: RNA UMI: 1,000~25,000 transcripts per cell, unique ATAC fragment: 1,000 ~ 70,000, Fragment on peak minimum percentage: 10%, minimum mtDNA copies per position per cell: 10X. Finally, the possible doublets are removed by Amulet (using default parameter). Unsupervised community detection-based clustering was performed on weighted nearest neighbour (WNN) using Seurat. Cell types are firstly annotated by gene expression using the latest signature (van Galen under review) which was further validated by sorted bulk RNA-seq data (https://sankaranlab.shinyapps.io/geneExpression/). The ATAC unique fragments for each clustered cell type were further aggregated to generate pseudo-bulk ATAC tracks. The single cell motif analysis was performed using ChromVar using the JASPAR human transcription factor (TF) database. The deviation of the TF frequency was computed for each cell for the downstream analysis.
The mutation calling pipeline is in following steps using package redeemV: 1, Data Preprocessing and eUMI grouping. 2, Consensus filtering. 3, Strand bias removal. 4, Lineage informative variants identification
Assembly: hg38
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv

molecule: genomic DNA

value: ATAC


title: OR male flies, 3 days post Drosophila C virus infection, rep1


title: HC_M1P1_E11

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E10

description:
Smartseq
cell by gene matrix


title: OR female flies, 3 days post Drosophila C virus infection, rep4

description:
OR_M2_UI
The Read2 file of one of the two runs was corrupt and could not be uploaded.


title: Extended young donors, HSPCs, Cell Hash, sample 17

description: Cell Hash library (Cell barcodes are matchable with ATAC, and mRNA lib in sample 17): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains Hashing barcode.

value: young donor


title: Extended young donors, HSPCs, mRNA-derived cDNA, sample 17

description: 3' mRNA library (Cell barcodes are matchable with ATAC, and CellHash lib in sample 17): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.

library_source: transcriptomic single cell

value: mRNA


title: HDT2_S#B1_11:00

description: Gene expression of participant S#B1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT2, at 11:00 hr


title: OR female flies, 3 days post Drosophila C virus infection, rep3


title: Extended young donors, HSPCs, ATAC(enriched mito included), sample 17

description: Combined ATAC library and enriched mtDNA library(Cell barcodes are matchable with mRNA and CellHash lib in sample 17): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.


title: HC_M1P1_D9

description:
Smartseq
cell by gene matrix


title: Extended aged donors, BMMCs_HSPCs, mRNA-derived cDNA, sample 18

description: 3' mRNA library (Cell barcodes are matchable with ATAC, and CellHash lib in sample 18): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: HDT2_S#B1_07:00

description: Gene expression of participant S#B1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT2, at 07:00 hr


title: HC_M1P1_D8

description:
Smartseq
cell by gene matrix


title: OR female flies, 3 days post Drosophila C virus infection, rep2


title: HDT2_S#B1_03:00

description: Gene expression of participant S#B1, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT2, at 03:00 hr


title: HDT2_S#D1_03:00

description: Gene expression of participant S#D1, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT2, at 03:00 hr


title: HC_M1P1_D7

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: Extended young donors, BMMC, Cell Hash, sample 16

description: Cell Hash library (Cell barcodes are matchable with ATAC, and mRNA lib in sample 16): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains Hashing barcode.


title: HDT2_S#B1_23:00

description: Gene expression of participant S#B1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT2, at 23:00 hr


title: OR female flies, 3 days post Drosophila C virus infection, rep1

source_name: whole fly


title: HDT2_S#D1_23:00

description: Gene expression of participant S#D1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT2, at 23:00 hr


title: Extended young donors, BMMCs, mRNA-derived cDNA, sample 16

description: 3' mRNA library (Cell barcodes are matchable with ATAC, and CellHash lib in sample 16): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: HC_M1P1_D6

description:
Smartseq
cell by gene matrix


title: HDT1_S#D1_07:00

description: Gene expression of participant S#D1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT1, at 07:00 hr


title: HC_M1P1_D4

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 20 h post Staphylococcus aureus infection, rep4


title: HDT1_S#B1_11:00

description: Gene expression of participant S#B1, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT1, at 11:00 hr


title: HDT1_S#D1_23:00

description: Gene expression of participant S#D1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT1, at 23:00 hr


title: Extended young donors, BMMCs, ATAC(enriched mito included), sample 16

description: Combined ATAC library and enriched mtDNA library(Cell barcodes are matchable with mRNA and CellHash lib in sample 16): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.


title: rapamycin-6.IP

city: Luzhou

first: Kai

last: Wang

address: No. 1, Section 1, Xianglin Road, Longmatan District

institute: Southwest Medical University

data_processing:
First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Assembly: hg19
Supplementary files format and content: excel and bed format file includs number of raw junction read for each sample
Library strategy: MeRIP-seq

growth_protocol: H460 cells were routinely cultured with DMEM medium containing 1% streptomycin/penicillin and 10% fetal bovine serum (FBS) in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from H460 cells using an ultrapure total RNA extraction kit (Simgen, Hangzhou, China). 1.3ug total RNA was used for the construction of sequencing libraries.
The GenSeq® rRNA Removal Kit (GenSeq, Inc.) was used to remove ribosomal RNA (rRNA) from the sample. After the removal of rRNA, sequencing libraries were constructed using the GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) kit according to the manufacturer's instructions.

treatment_protocol: Autophagy was induced by treatment with 100nM rapamycin for 24h.

tag: cell line

value: Human large cell lung cancer cell

value: wild-type

value: 100nM rapamycin


title: HC_M1P1_D3

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 20 h post Staphylococcus aureus infection, rep3


title: HC_M1P1_D24

description:
Smartseq
cell by gene matrix


title: rapamycin-5.IP


title: rapamycin-6.Input

data_processing:
First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Assembly: hg19
Supplementary files format and content: excel and bed format file includs number of raw junction read for each sample


title: KSA2 male flies, 20 h post Staphylococcus aureus infection, rep1


title: KSA2 female flies, 20 h post Staphylococcus aureus infection, rep4


title: HC_M1P1_D22

description:
Smartseq
cell by gene matrix


title: rapamycin-5.Input


title: rapamycin-4.IP


title: R_S#B1_15:00

description: Gene expression of participant S#B1, sampling session R, at 15:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session R, at 15:00 hr


title: KSA2 female flies, 20 h post Staphylococcus aureus  infection, rep3


title: BDC2_S#D1_11:00

description: Gene expression of participant S#D1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC2, at 11:00 hr


title: HC_M1P1_D21

description:
Smartseq
cell by gene matrix


title: BDC2_S#D1_07:00

description: Gene expression of participant S#D1, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC2, at 07:00 hr


title: BDC2_S#D1_23:00

description: Gene expression of participant S#D1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC2, at 23:00 hr


title: HC_M1P1_D20

description:
Smartseq
cell by gene matrix


title: KSA2 female flies, 20 h post Staphylococcus aureus  infection, rep2


title: KSA2 female flies, 20 h post Staphylococcus aureus  infection, rep1


title: OR male flies, 20 h post Staphylococcus aureus  infection, rep4


title: con-3.IP

value: without any treatment


title: con-3.Input


title: con-2.IP


title: HC_M1P1_D19

description:
Smartseq
cell by gene matrix


title: HC_M1P1_D23

description:
Smartseq
cell by gene matrix


title: HC_M1P1_E17

description:
Smartseq
cell by gene matrix


title: BDC2_S#B1_11:00

description: Gene expression of participant S#B1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC2, at 11:00 hr


title: KSA2 male flies, 20 h post Staphylococcus aureus infection, rep2

value: whole fly


title: HC_M1P1_D18

description:
Smartseq
cell by gene matrix


title: con-2.Input


title: OR male flies, 20 h post Staphylococcus aureus infection, rep3

value: male


title: HDT1_S#B1_23:00

description: Gene expression of participant S#B1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT1, at 23:00 hr


title: BDC2_S#B1_07:00

description: Gene expression of participant S#B1, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC2, at 07:00 hr


title: HC_M1P1_D17

description:
Smartseq
cell by gene matrix


title: OR male flies, 20 h post Staphylococcus aureus infection, rep2


title: OR male flies, 20 h post Staphylococcus aureus  infection, rep1


title: HC_M1P1_D16

description:
Smartseq
cell by gene matrix


title: con-1.IP


title: BDC2_S#B1_03:00

description: Gene expression of participant S#B1, sampling session BDC2, at 03:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC2, at 03:00 hr


title: HDT2_S#D1_19:00

description: Gene expression of participant S#D1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT2, at 19:00 hr