title: MAPT_P301S_male05

type: RNA

description: total RNA was were scanned in the nCounter Digital Analyzer using the Nanostring Mm_AD30_v1.1 cartridge. 2 Cartridges were used, with males on one cartidge, females on the other.

hyb_protocol: isolated RNA was hybridized to the Reporter CodeSet and Capture ProbeSet according to Nanostring manufacture specifications

scan_protocol: Cartridges were scanned in the nCounter Digital Analyzer at 555 fields of view for the maximum level of sensitivity.

data_processing: Raw reads and the Nanostring Mm_AD30_v1.1 probe annotation codeset were imported into the Nanostring proprietary software, nSolver 4.0, and QC was performed following company protocol guidelines.  Counts for target genes were normalized to house-keeping genes included in the panel

source_name: hippocampal tissue

label_protocol: RNA was labelled using a direct molecular barcoding system outlined in the Nanostring Technologies nCounter® XT Assay User Manual

extract_protocol: Hippocampal tissue was isolated and flash frozen in Liquid nitrogen. Frozen tissue was extracted using TRIzol and the PureLink RNA extraction kit (Invitrogen).

value: Hippocampus

tag: age

value: 6 months


title: R0_baseline, 0 hr, ATAC-Seq, rep 2

status: Public on Feb 14 2024

type: SRA

city: La Jolla

first: Shankar

last: Subramaniam

state: California

address: 3223 Voigt Dr

department: Bioengineering

country: USA

institute: University of California San Diego

library_source: genomic

data_processing:
The sequenced fastq files (using Fastqc) indicated Nextera adaptor content and were subsequently processed and cleaned using TrimGalore (v.0.6.6). The cleaned sequences were then mapped to the most current version of NCBI reference human genome, at the time of analysis- hg38 (patch 13) using BBMap, available through the BBTools suite. The mapped reads were then sorted and indexed using SAM tools to allow for the use of Genrich peak caller. In addition to peak calling, Genrich was used on the sorted files, to remove mitochondrial reads and reads mapping to ENCODE black-listed regions.
Assembly: GRCh38.p13
Supplementary files format and content: Genrich peak caller narrow peak files

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Briefly, 50,000 single cells were lysed using cell lysis buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin in resuspension buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, and 3 mM MgCl2 in water) for 3 min on ice.  After washing using resuspension buffer containing 0.1% Tween-20, cells were centrifuged at 500 g for 10 min at 4°C. The transposition reaction was performed using Tagment DNA enzyme and buffer (Illumina, catalog no. 20034197) at 37°C for 30 min in an Eppendorf ThermoMixer (1,000 rpm). DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, catalog no. 28204). Libraries were prepared by amplifying DNA for 5-9 cycles using DNA/RNA UD Indexes Set A (Illumina, catalog no. 20027213) and NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, catalog no. M0541S). AMPure XP bead purification (Beckman Coulter, catalog no. A63880) was used for the PCR product cleanup.
Libraries were prepared by amplifying DNA for 5-9 cycles using DNA/RNA UD Indexes Set A (Illumina, catalog no. 20027213) and NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, catalog no. M0541S). AMPure XP bead purification (Beckman Coulter, catalog no. A63880) was used for the PCR product cleanup. The libraries were validated with Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with qPCR at the IGC

tag: cell line

tag: cell type

value: Breast cancer epithelial cells

tag: time

value: 0 hr


title: suprachiasmatic nucleus, low workload, ZT05, rep1

first: Laura

last: van Rosmalen

address: 10010 N Torrey Pines Rd

department: RBIO-P

institute: Salk Institute for Biological Studies

description:
SCN_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

library_source: transcriptomic

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
TES_L_ZT21_X27 was removed from the analysis because it was an extreme outlier
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: suprachiasmatic nucleus

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 300ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

tag: tissue

value: suprachiasmatic nucleus

tag: strain

value: CBA/CaJ

tag: Sex

value: male

tag: treatment

value: low workload

tag: zeitgeber time


title: MAPT_P301S_male03

city: Los Angeles

first: Constanza

middle: J

last: Cortes

address: 3715 McClintock Ave

institute: University of Southern California

tag: group


title: MAPT_P301S;cTFEB;HSACre_male04


title: MAPT_P301S;cTFEB;HSACre_male02


title: MAPT_P301S_male04


title: MAPT_P301S_female03

value: female


title: MAPT_P301S;cTFEB;HSACre_male03


title: S24_Con, 24 hr, ATAC-Seq, rep 1

value: 24 hr


title: S12_EGF, 12 hr, ATAC-Seq, rep 2

value: 12 hr


title: MAPT_P301S_male02


title: S24_EGF, 24 hr, ATAC-Seq, rep 1


title: S24_EGF, 24 hr, ATAC-Seq, rep 2


title: MAPT_P301S;cTFEB;HSACre_female04


title: suprachiasmatic nucleus, low workload, ZT01, rep2

description:
SCN_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S12_EGF, 12 hr, ATAC-Seq, rep 1


title: suprachiasmatic nucleus, low workload, ZT13, rep1

description:
SCN_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: MAPT_P301S;cTFEB;HSACre_female02


title: MAPT_P301S_female02


title: MAPT_P301S;cTFEB;HSACre_female01


title: suprachiasmatic nucleus, low workload, ZT01, rep1

description:
SCN_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: MAPT_P301S_female01


title: liver from fish fed diet #6 biological rep 9

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using the TrimGalore! software version 0.6.5 running Cutadapt version 2.7. This software was used to trim low-quality ends from reads and for Illumina adapter removal.
Bowtie2 version 2.3.4.1 was used for alignment of reads to the channel catfish transcriptome using the alignment parameters as recommended by the eXpress software.
Alignment files were piped into the eXpress version 1.5.1 software using the default parameters, but including the strand information, to generate read-counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package 1.24.0 in R-base 3.6.2.
Assembly: All RNA transcripts from the white bass transcriptome shotgun assembly GAZY00000000.1 (GAZY01000001-GAZY01183659) in GenBank
Supplementary files format and content: tab-delimited text files of effective read counts, rounded to the nearest whole number

organism: Morone chrysops

source_name: liver

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Total RNA was standardized to 100 ng each sample. Sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcodes used were the NEBNext Multiplex Oligos for Illumina (Index Primers Sets 1 and 2).

value: liver

tag: diet

value: test diet 6

tag: diet description

value: commercial ingredient test

tag: developmental stage

value: Juvenile


title: MAPT_P301S_male01


title: quadriceps, high workload, ZT21, rep2

description:
QUA_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: quadriceps

value: quadriceps

value: high workload


title: S12_HRG, 12 hr, ATAC-Seq, rep 2


title: MAPT_P301S;cTFEB;HSACre_male01

value: Hippocampus


title: liver from fish fed diet #6 biological rep 8


title: MAPT_P301S;cTFEB;HSACre_female03

value: 6 months


title: liver from fish fed diet #6 biological rep 5


title: liver from fish fed diet #6 biological rep 6


title: quadriceps, high workload, ZT21, rep1

description:
QUA_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: quadriceps, high workload, ZT17, rep2

description:
QUA_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #6 biological rep 4


title: liver from fish fed diet #6 biological rep 3


title: S12_Con, 12 hr, ATAC-Seq, rep 2

value: Breast cancer epithelial cells


title: S12_HRG, 12 hr, ATAC-Seq, rep 1


title: liver from fish fed diet #6 biological rep 7


title: S12_Con, 12 hr, ATAC-Seq, rep 1


title: S1_EGF, 1 hr, ATAC-Seq, rep 2

value: 1 hr


title: liver from fish fed diet #6 biological rep 2


title: liver from fish fed diet #6 biological rep 1


title: liver from fish fed diet #5 biological rep 9

value: test diet 5

value: all plant protein


title: quadriceps, high workload, ZT13, rep2

description:
QUA_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ

value: male


title: S1_EGF, 1 hr, ATAC-Seq, rep 1


title: liver from fish fed diet #5 biological rep 8


title: quadriceps, high workload, ZT13, rep1

description:
QUA_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #5 biological rep 7


title: S1_HRG, 1 hr, ATAC-Seq, rep 2


title: liver from fish fed diet #5 biological rep 6


title: quadriceps, high workload, ZT09, rep2

description:
QUA_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S1_HRG, 1 hr, ATAC-Seq, rep 1


title: liver from fish fed diet #5 biological rep 5


title: liver from fish fed diet #5 biological rep 4


title: quadriceps, high workload, ZT17, rep1

description:
QUA_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #5 biological rep 3


title: liver from fish fed diet #5 biological rep 2


title: S1_Con, 1 hr, ATAC-Seq, rep 2


title: liver from fish fed diet #5 biological rep 1


title: quadriceps, high workload, ZT05, rep2

description:
QUA_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: quadriceps, high workload, ZT05, rep1

description:
QUA_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #4 biological rep 9

value: test diet 4

value: fish meal free with poultry meal


title: S0_Baseline, 0hr, ATAC-Seq, rep2

value: 0 hr


title: liver from fish fed diet #4 biological rep 8

value: liver


title: S1_Con, 1 hr, ATAC-Seq, rep 1


title: liver from fish fed diet #4 biological rep 7


title: quadriceps, high workload, ZT01, rep2

description:
QUA_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #4 biological rep 6


title: S0_Baseline, 0hr, ATAC-Seq, rep1


title: liver from fish fed diet #4 biological rep 4


title: quadriceps, high workload, ZT01, rep1

description:
QUA_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: si-NC, rep3

city: Guangzhou

first: Linglong

last: Tang

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
RNA-Seq reads were adaptor trimmed and the data quality was assessed with the fastp (v 0.23.2) software before any data filtering criteria was applied.
Reads were mapped onto the human reference genome (GRCh38.p12 assembly) by using HISAT2 (v 2.0.4). The mapped reads were assembled into transcripts or genes by using StringTie software (v 1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf).
For quantification purpose, the relative abundance of the transcript/gene was measured by a normalized metrics, FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: GRCh38
Supplementary files format and content: a tab-delimited text file including raw counts for all samples
Supplementary files format and content: a tab-delimited text file including FPKM values for all samples

growth_protocol: HONE-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion, Invitrogen, USA) according to the reagent protocols.
A total amount of 1 μg RNA per sample was used as the input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: HONE-1 cells were transfected with si-ATMIN or si-NC(control) for 48h

value: nasopharyngeal carcinoma cell line

tag: genotype

value: WT


title: liver from fish fed diet #4 biological rep 5

value: Juvenile


title: liver from fish fed diet #4 biological rep 3


title: liver from fish fed diet #4 biological rep 2


title: quadriceps, low workload, ZT21, rep2

description:
QUA_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: quadriceps

value: low workload


title: si-NC, rep2


title: quadriceps, low workload, ZT21, rep1

description:
QUA_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #4 biological rep 1


title: liver from fish fed diet #3 biological rep 9

value: test diet 3

value: low fish meal with poultry meal


title: si-NC, rep1


title: quadriceps, high workload, ZT09, rep1

description:
QUA_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: high workload


title: liver from fish fed diet #3 biological rep 8


title: quadriceps, low workload, ZT17, rep2

description:
QUA_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #3 biological rep 7


title: liver from fish fed diet #3 biological rep 6


title: si-ATMIN, rep3

value: ATMIN knockdown


title: si-ATMIN, rep1


title: si-ATMIN, rep2


title: liver from fish fed diet #3 biological rep 5


title: quadriceps, low workload, ZT13, rep2

description:
QUA_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: quadriceps, low workload, ZT13, rep1

description:
QUA_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #3 biological rep 4


title: HONE-1, HA_ATMIN_ChIP

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low quality reads using Cutadapt v1.18 (non-default parameters: --max-n 0 --minimum-length 35) and Trimmomatic v0.38 (non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:35).
Then FastQC (with default parameters) is used to ensure high reads quality. The clean reads were mapped to the human genome (hg38 assembly) using the Bowtie2 v2.3.4.1 (with default parameters) software. Duplicate reads were then removed using picard MarkDuplicates.
Peak detection was performed using the MACS v2.1.2 (non-default parameters: -f BAMPE -g hs/mm -p 0.01) peak finding algorithm with 0.01 set as the p-value cutoff. Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Assembly: hg38
Supplementary files format and content: bigWig files for both input and HA_ATMIN_ChIP samples
Supplementary files format and content: narrowPeak file only for HA_ATMIN_ChIP sample

extract_protocol:
HONE-1 cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti- HA antibodies (ChIP grade) .
After reverse crosslinking, ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with paired-end 2x150 as the sequencing mode.

treatment_protocol: HONE-1 cells were transfected with pSin-EF2-puro-ATMIN-HA plasmids for about 48h

value: ATMIN IP


title: quadriceps, low workload, ZT09, rep2

description:
QUA_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: HONE-1, input

value: none (input)


title: liver from fish fed diet #3 biological rep 2


title: liver from fish fed diet #3 biological rep 3


title: quadriceps, low workload, ZT09, rep1

description:
QUA_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: liver from fish fed diet #2 biological rep 9

value: test diet 2

value: low fish meal high soy


title: quadriceps, low workload, ZT17, rep1

description:
QUA_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: M5 CAR-T cells, Mock, donor # 612, rep 2

city: Philadelphia

first: David

last: Mai

state: PA

address: 8-189 Smilow Center for Translational Research

institute: University of Pennsylvania

data_processing:
Sequence reads were trimmed for adaptor sequence, uncertain nucleotides (>10% of either read), and low quality reads (base quality <5 constitute >50% of read).
Trimmed sequence reads were mapped to GRCh38.p14 using the salmon algorithm.
Supplementary files format and content: GRCh38.p14
Supplementary files format and content: comma-separated values files including average normalized counts values for genes for each experimental condition

source_name: Primary T cells

growth_protocol: Primary human T cells were maintained in R10 media in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were pelleted in RNALater (Invitrogen) and frozen at -20C until processing. Total RNA was harvested using RNeasy mini kit (Qiagen). At least 400ng of total RNA was used for the construction of sequencing libraries, per Novogene's input requirements.
RNA libraries for bulk RNA-seq was outsourced to Novogene, specifying Eukaryotic RNA-Seq as the library type.

treatment_protocol: ZFP36 was genetically disrupted using CRISPR-Cas9 during expansion of CAR-T cells.

value: Primary T cells

value: T cells

value: Baseline


title: M5 CAR-T cells, Mock, donor # 614, rep 2

value: WT


title: quadriceps, low workload, ZT01, rep2

description:
QUA_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #2 biological rep 7

value: liver

value: Juvenile


title: quadriceps, low workload, ZT05, rep1

description:
QUA_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: quadriceps

value: low workload


title: quadriceps, low workload, ZT01, rep1

description:
QUA_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: M5 CAR-T cells, Mock, donor # 612, rep 1


title: Melanoma PT.MM-C8_P

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–PackardGene Array Scanner

data_processing: GCRMA (usingGcrma package from R/Bioconductor).

label: biotin

source_name: patient-derived frozen sections

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subject id

tag: diagnosis

value: Melanoma PT

tag: amplification cycles


title: Melanoma PT.MM-C8_C


title: Melanoma PT.MM-C9_P


title: Melanoma PT.MM-C9_C


title: Melanoma PT.MM-C1_C


title: periventricular zone, high workload, ZT21, rep1

description:
PVZ_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: periventricular zone

value: periventricular zone

value: high workload


title: liver from fish fed diet #2 biological rep 8


title: liver from fish fed diet #2 biological rep 6


title: DysplasticNevus.DN-18

value: DysplasticNevus


title: liver from fish fed diet #3 biological rep 1

value: test diet 3

value: low fish meal with poultry meal


title: M5 CAR-T cells, ZFP36 KO, donor # 614, rep 1

value: ZFP36 KO


title: quadriceps, low workload, ZT05, rep2

description:
QUA_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: liver from fish fed diet #2 biological rep 5

value: test diet 2

value: low fish meal high soy


title: M5 CAR-T cells, ZFP36 KO, donor # 614, rep 2

value: Primary T cells

value: T cells


title: M5 CAR-T cells, Mock, donor # 614, rep 1

value: WT

value: Baseline


title: periventricular zone, high workload, ZT17, rep1

description:
PVZ_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: M5 CAR-T cells, ZFP36 KO, donor # 612, rep 2


title: liver from fish fed diet #2 biological rep 4

value: liver

value: Juvenile


title: periventricular zone, high workload, ZT13, rep2

description:
PVZ_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: M5 CAR-T cells, ZFP36 KO, donor # 612, rep 1


title: periventricular zone, high workload, ZT13, rep1

description:
PVZ_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: periventricular zone, high workload, ZT09, rep1

description:
PVZ_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #1 biological rep 9

value: control diet 1

value: standard fish meal


title: liver from fish fed diet #2 biological rep 2


title: DysplasticNevus.DN-102


title: DysplasticNevus.DN-101


title: ComonNevus.CN-U16

value: ComonNevus


title: Sars-CoV-2 Placenta, 4F, RNA-seq

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

description:
Fetal_filtered_counts.txt
Fetal_Raw_counts.txt

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA).
Sequenced raw FASTQ files were trimmed for Nextera transposase adapters and small RNA adapters.
Trimmed reads were mapped to the reference genome hg38 using STAR aligner for mRNA seqeuncing data and Bowtie 2 for small RNA sequencing with default parameters.
Mapped reads were further filtered and quantified to transcripts and genes using hg38 assembly and Ensemble transcripts release 107 for mRNA data and small RNA data was quantified to miRbase v.22 in the partek software.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include filtered counts for each Sample

source_name: Placenta

extract_protocol:
Total RNA is extracted from the placental samples by zymo quick RNA microprep kit with proteinase K as per the manufacturers protocol
cDNA library were constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014) and  miRNA sequencing was performed as per the Hagemann et al 2018 protocol

value: Placenta

tag: compartment

value: Fetal Placental Compartment

tag: infection

value: immediately after term delivery


title: liver from fish fed diet #2 biological rep 1


title: Control Placenta, 7F, RNA-seq

value: Control


title: Control Placenta, 5F, RNA-seq


title: periventricular zone, high workload, ZT09, rep2

description:
PVZ_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: periventricular zone

value: CBA/CaJ

value: high workload


title: Control Placenta, 9F, RNA-seq


title: liver from fish fed diet #1 biological rep 8


title: periventricular zone, high workload, ZT05, rep1

description:
PVZ_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: periventricular zone, high workload, ZT01, rep2

description:
PVZ_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #1 biological rep 7


title: DysplasticNevus.DN-16

value: DysplasticNevus


title: Control Placenta, 3F, RNA-seq


title: ComonNevus.CN-L16


title: periventricular zone, high workload, ZT01, rep1

description:
PVZ_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Melanoma PT.MM-C1_P

value: Melanoma PT


title: DysplasticNevus.DN-11


title: ComonNevus.CN-20


title: ComonNevus.CN-21


title: liver from fish fed diet #2 biological rep 3

value: test diet 2

value: low fish meal high soy


title: liver from fish fed diet #1 biological rep 6


title: Normal.DER-10

value: Normal


title: ComonNevus.CN-2


title: Normal.DER-9


title: Control Placenta, 2F, RNA-seq


title: periventricular zone, low workload, ZT21, rep1

description:
PVZ_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male

value: low workload


title: periventricular zone, low workload, ZT17, rep2

description:
PVZ_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Sars-CoV-2 Placenta, 1F, RNA-seq


title: liver from fish fed diet #1 biological rep 5

value: liver

value: control diet 1

value: Juvenile


title: liver from fish fed diet #1 biological rep 4

value: standard fish meal


title: liver from fish fed diet #1 biological rep 3


title: Sars-CoV-2 Placenta, 17F, RNA-seq

value: Placenta

value: Fetal Placental Compartment


title: periventricular zone, low workload, ZT17, rep1

description:
PVZ_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: periventricular zone, low workload, ZT13, rep2

description:
PVZ_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver from fish fed diet #1 biological rep 2


title: Sars-CoV-2 Placenta, 16F, RNA-seq

value: immediately after term delivery


title: periventricular zone, low workload, ZT13, rep1

description:
PVZ_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: periventricular zone


title: Normal.DER-8


title: Normal.DER-7


title: Normal.DER-6


title: Control Placenta, 12F, RNA-seq

value: Control


title: liver from fish fed diet #1 biological rep 1


title: Sars-CoV-2 Placenta, 14F, RNA-seq


title: periventricular zone, low workload, ZT09, rep2

description:
PVZ_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: Normal.DER-4


title: Normal.DER-3


title: periventricular zone, low workload, ZT09, rep1

description:
PVZ_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Normal.DER-5


title: Control Placenta, 11F, RNA-seq


title: Sars-CoV-2 Placenta, 15F, RNA-seq


title: Control Placenta, 9M, RNA-seq

description:
Maternal_Normalised_counts.txt
Maternal_Raw_counts.txt

value: Maternal Placental Compartment


title: periventricular zone, low workload, ZT05, rep2

description:
PVZ_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: IB115 cells, 2Gy exposition, biol rep 1

city: Gradignan

first: Hervé

last: Seznec

address: 19 Chemin du Solarium

country: France

description: PCR-cDNA barcoding kit on R9.4.1 flowcell

data_processing:
guppy v6.1.4 was used to perform high-accuracy base-calling and demultiplexing of the fast5 files
Alignment was performed using minimap2 on the hg38 human transcriptome and read count was extracted using a custom Python script
Supplementary files format and content: comma-separated text file including raw counts for each sample

molecule: polyA RNA

source_name: Sarcoma

growth_protocol: Sarcoma cells were harvested with trypsin-EDTA (0.05%, v/v, Thermo Fischer Scientific, Illkirch, France, cat. no 25300062) right away irradiation, and 2000 cells were seeded in a 12-well cell culture plate (CellstarTM, Grenier Bio-one, Dutscher Sas, Bernolsheim, France, cat. no 665180).

extract_protocol:
Total RNA was extracted from cells after NPs exposure and/or irradiation using the RNeasy mini kit (Qiagen SAS, Courtaboeuf, France cat. no 74104) according to the manufacturer’s instructions.
Whole-transcriptome cDNA libraries were first constructed from extracted mRNA using a PCR-cDNA barcoding kit (Oxford Nanopore Technologies, Oxford, UK, cat. no SQK-PCB109).

value: Sarcoma

tag: cell line

tag: cell type

value: Cell line derived from patient sarcoma

value: 2Gy exposition


title: IB115 cells, 2Gy-TNs exposition, biol rep 1

tag: tissue

value: 2Gy-TNs exposition


title: IB115 cells, 2Gy-TNs exposition, biol rep 2


title: periventricular zone, low workload, ZT05, rep1

description:
PVZ_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: strain

value: male


title: IB115 cells, 2Gy exposition, biol rep 2


title: Control Placenta, 8M, RNA-seq

tag: time


title: periventricular zone, low workload, ZT01, rep2

description:
PVZ_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: Sex

tag: treatment

value: low workload


title: NRCMs, 3Cl-HBA, rep2

city: Nantong

first: Mengkang

last: Fan

state: Jiangsu

address: Xisi Road No.20

institute: Affiliated Hospital of Nantong University

data_processing:
Agilent Bioanalyzer 2100 system
The libraries were sequenced on an Illumina HiSeq X Ten platform
ESeq2 was used to analyse RNA-seq data.
Assembly: Ensembl

organism: Rattus norvegicus

source_name: Neonatal rat cardiomyocytes (NRCMs)

growth_protocol: Neonatal rat cardiomyocytes (NRCMs) were separated from 1-day-old Sprague–Dawley rats. Briefly, neonatal Sprague–Dawley rats were euthanized. Their hearts were excised and digested with PBS containing 0.08% collagenase type II. Cardiomyocytes were cultured in Dulbecco’s modified Eagle’s medium with 10% foetal bovine serum

extract_protocol:
RNA was extracted using the KAPA RiboErase RNA-Seq kit (Roche, Basel, Switzerland)
The libraries were sequenced on an Illumina HiSeq X Ten platform. DESeq2 was used to analyse RNA-seq data.

treatment_protocol: 3Cl-HBA (40 μM for 48 h) for HBA1, HBA2,HBA3  and DMSO for C1,C2,C3.

value: Neonatal rat cardiomyocytes (NRCMs)

value: WT


title: Control Placenta, 7M, RNA-seq


title: Normal.DER-1

value: Normal


title: IB115 cells, 1Gy-TNs exposition, biol rep 2

value: 1Gy-TNs exposition


title: Normal.DER-2


title: NRCMs, 3Cl-HBA, rep1


title: Control Placenta, 5M, RNA-seq

value: Placenta


title: IB115 cells, 1Gy-TNs exposition, biol rep 1


title: Sars-CoV-2 Placenta, 4M, RNA-seq


title: NRCMs, DMSO, rep2

value: DMSO


title: NRCMs, DMSO, rep3


title: paraventricular nucleus thalamus, high workload, ZT21, rep1

description:
PVT_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: paraventricular nucleus thalamus

value: paraventricular nucleus thalamus

value: high workload

tag: zeitgeber time


title: Control Placenta, 3M, RNA-seq

value: Control

value: immediately after term delivery


title: IB115 cells, 1Gy exposition, biol rep 1

value: 1Gy exposition


title: NRCMs, DMSO, rep1


title: Control Placenta, 2M, RNA-seq

value: Maternal Placental Compartment


title: paraventricular nucleus thalamus, high workload, ZT17, rep2

description:
PVT_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: NRCMs, 3Cl-HBA, rep3


title: paraventricular nucleus thalamus, high workload, ZT17, rep1

description:
PVT_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: periventricular zone, low workload, ZT01, rep1

description:
PVZ_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: periventricular zone


title: Sars-CoV-2 Placenta, 1M, RNA-seq


title: IB115 cells, Control, biol rep 2

value: Sarcoma

value: Cell line derived from patient sarcoma


title: IB115 cells, TNs exposition, biol rep 1

value: TNs exposition


title: Sars-CoV-2 Placenta, 17M, RNA-seq


title: paraventricular nucleus thalamus, high workload, ZT13, rep1

description:
PVT_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: IB115 cells, Control, biol rep 1


title: Sars-CoV-2 Placenta, 16M, RNA-seq


title: siRNLTR12-int_biological_replicate2

city: Cambridge

first: Tanay

last: Ghosh

address: Granta Park

department: Cambridge Institute of Science

country: United Kingdom

institute: AltosLabs

data_processing:
Data were pre-processed through sortMeRNA, trimmomatics.
Rat transcriptome (Rnor_6.0.cdna+Rnor_6.0.ncrna) index was build and quantification was performed using Salmon (Quasi mode).
Differential expression was analysed using DEseq2 package. Criteria for differential expression: adjusted P value (Wald test followed by Benjamini-Hochberg FDR)<0.05 and |fold change|>2.
Assembly: Rat transcriptome (Rnor_6.0.cdna+Rnor_6.0.ncrna)
Supplementary files format and content: tab-delimited text file includes differentialy expressed genes, log fold changes, adjusted pvalues
Supplementary files format and content: tab-delimited text file includes normalised values

source_name: Brain

extract_protocol:
Total RNA was isolated using mirVana RNA isolation kit (Ambion). Subsequently, DNAase treatment and purification was performed and RNA quality was verified in a bioanalyzer before used for RNAseq library preparation. RIN values were: 9-10.
Qiaseq Fast Select – rRNA HMR (Cat. No. / ID: 334385) was used for ribodepletion and paired end directional library was prepared using NEB NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L), and run on Novaseq SP.

treatment_protocol: OPC were isolated from P7 rats. Approx. 40,000 cells were plated per well of a 12 well plate. Subsequently transfection (control siRNA/siRNLTR12-int) was performed (Transfection reagent: Lipofectamine RNAiMAX, ThermoFisher scientific) and cells were kept at differentiating media for 4-5 days. Media was changed to differentiating media at the time of transfection.

value: Brain

value: Oligodendrocytes progenitor cells undergoing differentiation

value: WT

value: siRNA against RNLTR12-int


title: siRNLTR12-int_biological_replicate1


title: paraventricular nucleus thalamus, high workload, ZT21, rep2

description:
PVT_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: paraventricular nucleus thalamus, high workload, ZT09, rep2

description:
PVT_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Sars-CoV-2 Placenta, 14M, RNA-seq

value: Placenta


title: paraventricular nucleus thalamus, high workload, ZT09, rep1

description:
PVT_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: paraventricular nucleus thalamus


title: IB106 cells, 2Gy-TNs exposition, biol rep 3

value: 2Gy-TNs exposition


title: Sars-CoV-2 Placenta, 13M, RNA-seq


title: control_siRNA_biological_replicate2

value: control siRNA


title: IB115 cells, 1Gy exposition, biol rep 2


title: control_siRNA_biological_replicate4


title: control_siRNA_biological_replicate3


title: IB115 cells, TNs exposition, biol rep 2


title: Control Placenta, 12M, RNA-seq

value: Control

value: immediately after term delivery


title: siRNLTR12-int_biological_replicate3


title: paraventricular nucleus thalamus, high workload, ZT05, rep2

description:
PVT_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: high workload


title: IB106 cells, 2Gy-TNs exposition, biol rep 1


title: paraventricular nucleus thalamus, high workload, ZT05, rep1

description:
PVT_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: IB106 cells, 2Gy-TNs exposition, biol rep 2


title: paraventricular nucleus thalamus, high workload, ZT13, rep2

description:
PVT_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: paraventricular nucleus thalamus, high workload, ZT01, rep2

description:
PVT_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: control_siRNA_biological_replicate1


title: IB106 cells, 2Gy exposition, biol rep 3

value: 2Gy exposition


title: Control Placenta, 11M, RNA-seq

description:
Maternal_Normalised_counts.txt
Maternal_Raw_counts.txt

value: Maternal Placental Compartment


title: HPAD, IL-17A+TNFa

city: San Diego

first: Kellen

last: Cavagnero

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

description:
IL-17A & TNFa
KC73.csv

data_processing:
Alignment to reference genome using STAR
Raw counts table generated using FeatureCounts
Assembly: mm10 for mouse; hg38 for human
Supplementary files format and content: CSV files with raw counts values for each sample

source_name: HPAD

extract_protocol:
ThermoFisher PureLink RNA Kit
Illumina stranded mRNA or Illumina total RNA prep (ribodepletion)

value: HPAD

value: Fibroblast

value: Wild type

tag: in vitro or in vivo

value: in vitro

tag: protocol

value: Illumina stranded mRNA


title: paraventricular nucleus thalamus, low workload, ZT21, rep2

description:
PVT_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male

value: low workload


title: paraventricular nucleus thalamus, high workload, ZT01, rep1

description:
PVT_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d7_SSEA4_rep1_deeper_sequencing

first: Felix

department: Bioinformatics

institute: Altos Labs

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters)
Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3, parameters --bowtie2)
Assembly: NCBIM37
Supplementary files format and content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Reprogramming fibroblast

extract_protocol:
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).
Post-bisulfite adaptor tagging (PBAT)

value: Reprogramming fibroblast

tag: donor age

tag: days of_reprogramming


title: HPAD, TNFa

description:
TNFa
KC73.csv

tag: genotype

value: TNFa


title: IB106 cells, 2Gy exposition, biol rep 1

description: PCR-cDNA barcoding kit on R9.4.1 flowcell

value: Sarcoma

value: Cell line derived from patient sarcoma


title: BS_seq, O2_d7_SSEA4_rep1_deeper_sequencing


title: HPAD, IL-17A

description:
IL-17A
KC73.csv


title: BS_seq, O1_d7_SSEA4_rep1_deeper_sequencing


title: BS_seq, Y2_d15_SSEA4_rep1_deeper_sequencing


title: paraventricular nucleus thalamus, low workload, ZT21, rep1

description:
PVT_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: paraventricular nucleus thalamus


title: paraventricular nucleus thalamus, low workload, ZT17, rep2

description:
PVT_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: HPAD, Vehicle

description:
Vehicle
KC73.csv

value: Vehicle


title: BS_seq, Y2_Fib_rep1_deeper_sequencing

source_name: Fibroblast


title: IB106 cells, 1Gy-TNs exposition, biol rep 2

value: 1Gy-TNs exposition


title: IB106 cells, 2Gy exposition, biol rep 2


title: IB106 cells, 1Gy-TNs exposition, biol rep 3


title: paraventricular nucleus thalamus, low workload, ZT17, rep1

description:
PVT_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: paraventricular nucleus thalamus, low workload, ZT13, rep2

description:
PVT_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: IB106 cells, 1Gy exposition, biol rep 3

value: 1Gy exposition


title: BS_seq, O1_d15_SSEA4_rep1_deeper_sequencing


title: BS_seq, O2_d15_SSEA4_rep1_deeper_sequencing


title: IB106 cells, 1Gy-TNs exposition, biol rep 1


title: paraventricular nucleus thalamus, low workload, ZT13, rep1

description:
PVT_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d54_SSEA4_rep1_deeper_sequencing

source_name: iPSC

value: iPSC


title: IB106 cells, 1Gy exposition, biol rep 1


title: GSC827 cells, LMP400+Olaparib treated, Biological replicate 2

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

institute: National Cancer Institute

data_processing:
The samples have 33 to 50 million pass filter reads with more than 94% of bases above the quality score of Q30
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human_hg38) and the annotated transcripts using STAR
gene expression quantification analysis was performed for all samples using STAR/RSEM tools
Assembly: Human hg38
Supplementary files format and content: tab-delimited text file includes raw count values for each sample

extract_protocol:
Cells were harvested and RNA was extracted using PureLink RNA Mini Kit (#12183018A, Thermo Fisher Scientific) following manufacturer’s instructions, including on-column DNase treatment to remove contaminating DNA (#12185010, PureLink DNase Set, Invitrogen)
TruSeq Stranded mRNA Library Prep

value: glioma stem-like cells


title: GSC827 cells, LMP400 treated, Biological replicate 2


title: IB106 cells, TNs exposition, biol rep 3

value: TNs exposition


title: BS_seq, O1_d54_SSEA4_rep1_deeper_sequencing


title: GSC827 cells, LMP400 treated, Biological replicate 1


title: BS_seq, O2_d54_SSEA4_rep1_deeper_sequencing


title: paraventricular nucleus thalamus, low workload, ZT05, rep2

description:
PVT_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O2_d9_SSEA4_rep1_deeper_sequencing


title: GSC827 cells, Control, Biological replicate 2

value: Control


title: paraventricular nucleus thalamus, low workload, ZT05, rep1

description:
PVT_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: GSC827 cells, Olaparib treated, Biological replicate 1

value: Olaparib


title: IB106 cells, TNs exposition, biol rep 1


title: BS_seq, O2_d11_SSEA4_rep1_deeper_sequencing


title: IB106 cells, 1Gy exposition, biol rep 2


title: paraventricular nucleus thalamus, low workload, ZT01, rep2

description:
PVT_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: GSC827 cells, Control, Biological replicate 1


title: BS_seq, O2_Fib_rep1_deeper_sequencing

value: Fibroblast


title: paraventricular nucleus thalamus, low workload, ZT01, rep1

description:
PVT_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: IB106 cells, Control, biol rep 2


title: GSC827 cells, LMP400+Olaparib treated, Biological replicate 1


title: BS_seq, Y2_d11_SSEA4_rep1_deeper_sequencing


title: IB106 cells, Control, biol rep 1


title: paraventricular nuclei, high workload, ZT21, rep1

description:
PVN_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: paraventricular nuclei

value: paraventricular nuclei

value: high workload


title: Reference9

city: Ludwigshafen

first: Astrid

last: Wachter

address: Knollstrasse

country: Germany

institute: AbbVie Deutschland GmbH & Co. KG

data_processing:
fastQC, multiQC
STAR alignment
FeatureCounts
retaining only genes expressed at >=1 CPMs in at least 4 samples
Assembly: GRCh38 (gencode v31)
Supplementary files format and content: raw counts, filtered

source_name: brain tissue, superior temporal gyrus

extract_protocol: We performed laser capture microdissection of Ab plaques, the 50mm halo around them, tangles with the 50mm halo around them, and areas distant (>50mm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing.

tag: pathology

value: technical control sample

tag: sample type

value: reference

tag: apoe status


title: paraventricular nuclei, high workload, ZT21, rep2

description:
PVN_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O1_Fib_rep1_deeper_sequencing


title: BS_seq, O1_d11_SSEA4_rep1_deeper_sequencing

value: Reprogramming fibroblast


title: paraventricular nucleus thalamus, low workload, ZT09, rep2

description:
PVT_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: paraventricular nucleus thalamus

value: low workload


title: paraventricular nucleus thalamus, low workload, ZT09, rep1

description:
PVT_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Reference8


title: Reference7


title: IB106 cells, Control, biol rep 3

value: Sarcoma

value: Cell line derived from patient sarcoma


title: BS_seq, N3_d11_CD13_rep2

source_name: Failing to reprogram fibroblast

value: Failing to reprogram fibroblast


title: IB106 cells, TNs exposition, biol rep 2


title: Reference6


title: GSC827 cells, Olaparib treated, Biological replicate 2


title: paraventricular nuclei, high workload, ZT17, rep1

description:
PVN_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: BS_seq, O2_d11_SSEA4_rep2


title: paraventricular nuclei, high workload, ZT13, rep2

description:
PVN_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d13_SSEA4_rep1


title: Reference5


title: paraventricular nuclei, high workload, ZT13, rep1

description:
PVN_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Reference4


title: BS_seq, Y2_d15_CD13_rep1


title: paraventricular nuclei, high workload, ZT09, rep2

description:
PVN_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O1_d13_SSEA4_rep1


title: paraventricular nuclei, high workload, ZT09, rep1

description:
PVN_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Reference3


title: Reference2


title: Reference10


title: paraventricular nuclei, high workload, ZT05, rep1

description:
PVN_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d15_SSEA4_rep1


title: paraventricular nuclei, high workload, ZT05, rep2

description:
PVN_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d11_SSEA4_rep2


title: BS_seq, O2_d13_SSEA4_rep1


title: Reference1


title: paraventricular nuclei, high workload, ZT17, rep2

description:
PVN_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: paraventricular nuclei, high workload, ZT01, rep2

description:
PVN_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CTRL6

value: CTRL

value: GM

value: F


title: BS_seq, Y1_d13_SSEA4_rep1


title: paraventricular nuclei, low workload, ZT21, rep2

description:
PVN_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: paraventricular nuclei, high workload, ZT01, rep1

description:
PVN_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N2_d11_CD13_rep2


title: BS_seq, O1_d13_CD13_rep1


title: CTRL5

value: M


title: AD10_plaque

value: AD


title: BS_seq, O2_d13_CD13_rep1


title: paraventricular nuclei, low workload, ZT17, rep2

description:
PVN_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: AD10_tangle


title: BS_seq, N2_d13_CD13_rep1


title: AD10_close


title: BS_seq, N2_d13_SSEA4_rep1


title: BS_seq, Y2_d13_CD13_rep1


title: paraventricular nuclei, low workload, ZT17, rep1

description:
PVN_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: paraventricular nuclei


title: paraventricular nuclei, low workload, ZT13, rep2

description:
PVN_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CTRL2


title: BS_seq, N2_d15_SSEA4_rep1


title: CTRL3


title: paraventricular nuclei, low workload, ZT09, rep1

description:
PVN_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_d13_CD13_rep1


title: CTRL7


title: paraventricular nuclei, low workload, ZT09, rep2

description:
PVN_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: paraventricular nuclei, low workload, ZT21, rep1

description:
PVN_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: paraventricular nuclei, low workload, ZT05, rep2

description:
PVN_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CTRL1


title: paraventricular nuclei, low workload, ZT05, rep1

description:
PVN_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD2_plaque


title: AD2_tangle


title: BS_seq, Y2_d13_SSEA4_rep1


title: paraventricular nuclei, low workload, ZT01, rep2

description:
PVN_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d13_CD13_rep1


title: paraventricular nuclei, low workload, ZT01, rep1

description:
PVN_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD2_far


title: BS_seq, N3_d15_CD13_rep1


title: AD2_close


title: AD10_far


title: paraventricular nuclei, low workload, ZT13, rep1

description:
PVN_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT21, rep2

description:
PRC_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: prefrontal cortex

value: prefrontal cortex

value: high workload


title: BS_seq, O2_d11_CD13_rep2


title: BS_seq, O1_d15_SSEA4_rep1


title: AD1_tangle


title: BS_seq, N2_d15_CD13_rep1


title: AD8_plaque


title: AD8_tangle


title: BS_seq, N3_d15_SSEA4_rep1


title: prefrontal cortex, high workload, ZT17, rep2

description:
PRC_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT17, rep1

description:
PRC_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT13, rep2

description:
PRC_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD8_far


title: BS_seq, Y1_d15_SSEA4_rep1


title: BS_seq, O2_d15_CD13_rep1


title: prefrontal cortex, high workload, ZT13, rep1

description:
PRC_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD8_close


title: BS_seq, N2_d11_SSEA4_rep2


title: BS_seq, Y1_d15_CD13_rep1


title: prefrontal cortex, high workload, ZT09, rep2

description:
PRC_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD1_far


title: AD1_plaque


title: BS_seq, O2_d15_SSEA4_rep1


title: prefrontal cortex, high workload, ZT01, rep2

description:
PRC_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT05, rep1

description:
PRC_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD7_tangle


title: AD7_plaque


title: prefrontal cortex, low workload, ZT21, rep2

description:
PRC_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD1_close


title: BS_seq, Y2_d7_CD13_rep1


title: prefrontal cortex, low workload, ZT21, rep1

description:
PRC_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD4_tangle


title: BS_seq, N3_d9_SSEA4_rep1


title: CTRL8


title: prefrontal cortex, low workload, ZT17, rep2

description:
PRC_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT05, rep2

description:
PRC_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT09, rep1

description:
PRC_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD6_tangle


title: BS_seq, O1_d9_CD13_rep1


title: prefrontal cortex, low workload, ZT17, rep1

description:
PRC_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT01, rep1

description:
PRC_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O1_d15_CD13_rep1


title: AD7_close


title: AD6_plaque


title: BS_seq, Y1_d9_CD13_rep1


title: prefrontal cortex, low workload, ZT13, rep2

description:
PRC_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, high workload, ZT21, rep1

description:
PRC_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_d11_CD13_rep2


title: AD7_far


title: BS_seq, O2_d9_SSEA4_rep1


title: BS_seq, O1_d9_SSEA4_rep1


title: AD6_far


title: prefrontal cortex, low workload, ZT13, rep1

description:
PRC_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d9_CD13_rep1


title: prefrontal cortex, low workload, ZT09, rep2

description:
PRC_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, low workload, ZT01, rep2

description:
PRC_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O1_d11_SSEA4_rep2


title: BS_seq, O1_d11_CD13_rep2


title: AD5_plaque


title: BS_seq, N2_d9_SSEA4_rep1


title: AD4_plaque


title: prefrontal cortex, low workload, ZT05, rep2

description:
PRC_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, low workload, ZT05, rep1

description:
PRC_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: preoptic area, high workload, ZT21, rep2

description:
POA_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: preoptic area

value: preoptic area


title: AD4_close


title: prefrontal cortex, low workload, ZT09, rep1

description:
PRC_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: prefrontal cortex, low workload, ZT01, rep1

description:
PRC_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d7_SSEA4_rep1

value: Reprogramming fibroblast


title: AD4_far


title: BS_seq, O2_d9_CD13_rep1


title: AD3_tangle


title: AD5_far


title: AD5_close


title: BS_seq, N2_d9_CD13_rep1


title: BS_seq, Y1_d9_SSEA4_rep1


title: AD5_tangle


title: BS_seq, N2_d7_SSEA4_rep1


title: BS_seq, Y2_d9_SSEA4_rep1


title: preoptic area, high workload, ZT21, rep1

description:
POA_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d11_CD13_rep2


title: AD6_close


title: preoptic area, high workload, ZT17, rep2

description:
POA_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: preoptic area, high workload, ZT17, rep1

description:
POA_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD3_plaque


title: BS_seq, Y2_d11_SSEA4_rep2


title: BS_seq, Y2_d9_CD13_rep1


title: AD3_close


title: BS_seq, N3_d7_CD13_rep1


title: AD9_tangle


title: BS_seq, Y1_d11_SSEA4_rep2


title: preoptic area, high workload, ZT13, rep2

description:
POA_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d7_SSEA4_rep1


title: BS_seq, O1_d7_SSEA4_rep1


title: preoptic area, high workload, ZT05, rep2

description:
POA_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: preoptic area, high workload, ZT09, rep2

description:
POA_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_d7_SSEA4_rep1


title: preoptic area, high workload, ZT09, rep1

description:
POA_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N2_d7_CD13_rep1


title: preoptic area, high workload, ZT13, rep1

description:
POA_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O2_d7_CD13_rep1


title: AD9_plaque


title: preoptic area, high workload, ZT05, rep1

description:
POA_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: preoptic area, high workload, ZT01, rep1

description:
POA_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Febrile [13F]

city: Nairobi

first: Kelvin

middle: Muteru

last: Kimenyi

department: Biochemistry

country: Kenya

institute: University of Nairobi

data_processing:
sequence reads were accessed for quality
Sequence reads were mapped to the reference Plasmodium falciparum (3D7 strain) from PlasmoDB, release 55, using Kallisto (default settings)
Genes with less that 2 counts per million in 10 or less samples were dropped
TMM Normalization was done
Assembly: 3D7 strain, PlasmoDB, release 55
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes normalized counts for each sample

organism: Plasmodium falciparum 3D7

source_name: host peripheral blood mononuclear cells (PBMCs)

extract_protocol:
using the ISOLATE II RNA Mini Kit (Bioline)
libraries for RNA-seq were prepared using the NEBNextTM Ultra II FS DNA library preparation kit (New England Biolabs) following manufacturers protocol

tag: infection status

value: Febrile


title: preoptic area, high workload, ZT01, rep2

description:
POA_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AD9_far


title: AD9_close


title: Febrile [12F]

value: host peripheral blood mononuclear cells (PBMCs)


title: preoptic area, low workload, ZT21, rep2

description:
POA_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: AD3_far


title: preoptic area, low workload, ZT21, rep1

description:
POA_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CTRL4


title: BS_seq, O2_d7_SSEA4_rep1


title: BS_seq, N3_d34_SSEA4_rep1


title: BS_seq, O1_d7_CD13_rep1


title: Febrile [9F]


title: preoptic area, low workload, ZT17, rep2

description:
POA_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d11_CD13_rep1


title: preoptic area, low workload, ZT13, rep2

description:
POA_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Asymptomatic [12A]

value: Asymptomatic


title: Asymptomatic [9A]


title: BS_seq, O2_d21_CD13_rep2

value: Failing to reprogram fibroblast


title: Asymptomatic [11A]


title: preoptic area, low workload, ZT13, rep1

description:
POA_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: preoptic area, low workload, ZT17, rep1

description:
POA_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Asymptomatic [7A]


title: Asymptomatic [4A]


title: preoptic area, low workload, ZT09, rep1

description:
POA_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: preoptic area, low workload, ZT09, rep2

description:
POA_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: preoptic area, low workload, ZT05, rep2

description:
POA_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d21_CD13_rep1


title: BS_seq, N3_d21_SSEA4_rep1


title: BS_seq, N3_Fib_rep1

value: Fibroblast


title: BS_seq, Y1_d7_CD13_rep1


title: Febrile [7F]


title: preoptic area, low workload, ZT05, rep1

description:
POA_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O1_d29_CD13_rep1


title: Asymptomatic [13A]


title: Febrile [5F]


title: preoptic area, low workload, ZT01, rep2

description:
POA_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Febrile [4F]


title: BS_seq, N2_d40_SSEA4_rep1


title: olfactory bulb, high workload, ZT21, rep2

description:
OLB_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: olfactory bulb

value: olfactory bulb


title: Febrile [15F]


title: Febrile [11F]


title: BS_seq, O2_d21_SSEA4_rep1


title: BS_seq, O2_d11_CD13_rep1


title: olfactory bulb, high workload, ZT17, rep2

description:
OLB_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: olfactory bulb, high workload, ZT17, rep1

description:
OLB_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O2_d11_SSEA4_rep1


title: olfactory bulb, high workload, ZT21, rep1

description:
OLB_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Febrile [8F]


title: Febrile [10F]


title: preoptic area, low workload, ZT01, rep1

description:
POA_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: olfactory bulb, high workload, ZT13, rep1

description:
OLB_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_d21_SSEA4_rep1


title: BS_seq, N3_d11_CD13_rep1


title: Febrile [14F]


title: BS_seq, Y2_d29_CD13_rep1


title: Febrile [6F]


title: Febrile [3F]


title: BS_seq, Y1_d11_CD13_rep1


title: BS_seq, Y2_d29_SSEA4_rep1


title: olfactory bulb, high workload, ZT09, rep1

description:
OLB_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_d34_SSEA4_rep1


title: Febrile [2F]


title: Febrile [1F]


title: olfactory bulb, high workload, ZT05, rep2

description:
OLB_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Asymptomatic [5A]


title: Febrile [16F]


title: BS_seq, O2_Fib_rep1


title: olfactory bulb, high workload, ZT13, rep2

description:
OLB_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: olfactory bulb, high workload, ZT05, rep1

description:
OLB_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O2_d29_CD13_rep1


title: Asymptomatic [15A]


title: BS_seq, O1_d34_SSEA4_rep1


title: olfactory bulb, high workload, ZT01, rep1

description:
OLB_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_d40_SSEA4_rep1


title: olfactory bulb, low workload, ZT21, rep2

description:
OLB_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N2_d29_CD13_rep1


title: Asymptomatic [10A]


title: Asymptomatic [16A]


title: BS_seq, Y2_d21_SSEA4_rep1


title: olfactory bulb, high workload, ZT09, rep2

description:
OLB_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d21_CD13_rep1


title: olfactory bulb, low workload, ZT21, rep1

description:
OLB_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Asymptomatic [14A]


title: BS_seq, N2_d21_SSEA4_rep1


title: olfactory bulb, low workload, ZT17, rep2

description:
OLB_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Asymptomatic [6A]


title: BS_seq, N2_d29_SSEA4_rep1


title: olfactory bulb, low workload, ZT17, rep1

description:
OLB_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Asymptomatic [3A]


title: olfactory bulb, low workload, ZT13, rep1

description:
OLB_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d40_SSEA4_rep1


title: BS_seq, O2_d34_SSEA4_rep1


title: olfactory bulb, low workload, ZT09, rep2

description:
OLB_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Asymptomatic [2A]


title: olfactory bulb, low workload, ZT09, rep1

description:
OLB_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: olfactory bulb, high workload, ZT01, rep2

description:
OLB_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Dental epithelium cells, DKO_P5_3

city: Bethesda

first: Bing

last: He

state: MD

address: 30 Convent Dr MSC 4370

institute: NIDCR/NIH

data_processing:
RNA-seq raw reads were mapped to mm10, followed RNA-seq raw reads were mapped to mm10, followed by data analysis using Partek Genomics Suite.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Dental epithelium cells, DKO, P5

growth_protocol: No cell growth involved. Total RNA was prepared from mouse molar epithelium tissues.

extract_protocol:
Mouse embryonic tooth tissues were homogenized using a Mixer Homogenizer, followed by RNA extraction using Trizol reagent.
For RNA-seq libraries preparation, 1µg of total RNA (RIN>7) was used for rRNA depletion by using NEB rRNA Depletion Kit (E6310).  Next, the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina(E7770S) and NEBNext NEBNext® Multiplex Oligos for Illumina® (E7335) were used for library construction.

treatment_protocol: Mouse tooth germs were treated with 1U/ML Dispase to separate the dental epithelium cells and mesenchyme.

value: molar epithelium

value: dental epithelium cells

value: DKO (Hmgn1-/-; Hmgn2-/-)

tag: developmental stage


title: olfactory bulb, low workload, ZT05, rep2

description:
OLB_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: Asymptomatic [1A]


title: Asymptomatic [8A]


title: BS_seq, Y2_d40_SSEA4_rep1

tag: cell type


title: BS_seq, O1_d40_SSEA4_rep1


title: Dental epithelium cells, DKO_P5_1

tag: tissue


title: olfactory bulb, low workload, ZT05, rep1

description:
OLB_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: strain


title: BS_seq, O1_d21_SSEA4_rep1


title: Dental epithelium cells, DKO_P5_2


title: olfactory bulb, low workload, ZT01, rep1

description:
OLB_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: olfactory bulb, low workload, ZT01, rep2

description:
OLB_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O2_d29_SSEA4_rep1


title: Dental epithelium cells, WT_P5_3

source_name: Dental epithelium cells, WT, P5

value: WT


title: BS_seq, Y2_d34_SSEA4_rep1


title: liver, high workload, ZT21, rep2

description:
LIV_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: liver

value: liver


title: BS_seq, N3_d11_SSEA4_rep1


title: Dental epithelium cells, WT_P5_2


title: Dental epithelium cells, WT_P5_1


title: liver, high workload, ZT17, rep2

description:
LIV_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: high workload


title: liver, high workload, ZT21, rep1

description:
LIV_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d11_SSEA4_rep1


title: BS_seq, N2_d11_SSEA4_rep1


title: BS_seq, N2_d34_SSEA4_rep1


title: Dental epithelium cells, DKO_P0_3

source_name: Dental epithelium cells, DKO, P0


title: liver, high workload, ZT17, rep1

description:
LIV_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Dental epithelium cells, DKO_P0_2


title: Dental epithelium cells, WT_P0_1

source_name: Dental epithelium cells, WT, P0


title: BS_seq, N2_Fib_rep1


title: Dental epithelium cells, DKO_P0_1


title: BS_seq, Y1_d11_SSEA4_rep1


title: BS_seq, O2_d40_SSEA4_rep1


title: liver, high workload, ZT05, rep2

description:
LIV_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver, high workload, ZT13, rep3

description:
LIV_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver, high workload, ZT13, rep2

description:
LIV_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Dental epithelium cells, DKO_E17_1

source_name: Dental epithelium cells, DKO, E17


title: Dental epithelium cells, WT_P0_2


title: liver, high workload, ZT01, rep2

description:
LIV_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N2_d11_CD13_rep1


title: Dental epithelium cells, WT_E17_2

source_name: Dental epithelium cells, WT, E17


title: liver, high workload, ZT09, rep2

description:
LIV_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O1_d29_SSEA4_rep1

source_name: Reprogramming fibroblast


title: liver, high workload, ZT09, rep1

description:
LIV_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver, high workload, ZT13, rep1

description:
LIV_H_ZT13_X14
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Dental epithelium cells, WT_P0_3


title: BS_seq, O1_d11_SSEA4_rep1


title: Dental epithelium cells, WT_E17_3


title: BS_seq, O1_d11_CD13_rep1


title: liver, high workload, ZT01, rep1

description:
LIV_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Dental epithelium cells, DKO_E17_3


title: BS_seq, O1_Fib_rep1

source_name: Fibroblast


title: liver, low workload, ZT21, rep2

description:
LIV_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver, high workload, ZT05, rep1

description:
LIV_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, O2_d21_CD13_rep1


title: Dental epithelium cells, DKO_E17_2


title: BS_seq, N3_d47_SSEA4_rep1


title: BS_seq, N2_d21_CD13_rep1


title: Dental epithelium cells, WT_E17_1


title: liver, low workload, ZT21, rep1

description:
LIV_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_d47_SSEA4_rep1


title: BS_seq, Y1_d21_CD13_rep1


title: BS_seq, O1_d54_SSEA4_rep1

source_name: iPSC

value: iPSC


title: liver, low workload, ZT17, rep2

description:
LIV_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_Fib_rep1


title: liver, low workload, ZT09, rep1

description:
LIV_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N2_d54_SSEA4_rep1


title: liver, low workload, ZT13, rep2

description:
LIV_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y2_d54_SSEA4_rep1


title: BS_seq, N3_d54_SSEA4_rep1


title: liver, low workload, ZT17, rep1

description:
LIV_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver, low workload, ZT13, rep1

description:
LIV_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: liver, low workload, ZT09, rep2

description:
LIV_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ZZMQ_N

city: beijing

first: Chen

last: Tan

state: BEIJING

address: BEIJING DONGJIAOMIN NO 1

institute: Capital Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: larynx and hypopharynx

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: individual

value: Patient ZZMQ

tag: disease state

value: laryngo-hypopharyngeal carcinoma

value: larynx and hypopharynx

tag: tissue type

value: Normal

tag: response to induction chemotherapy

value: response

tag: gender


title: ZZMQ_T

value: Tumor


title: YCJQ_N

value: Patient YCJQ

value: non-response


title: liver, low workload, ZT05, rep2

first: Laura

description:
LIV_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
TES_L_ZT21_X27 was removed from the analysis because it was an extreme outlier
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 300ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

value: CBA/CaJ

tag: Sex

tag: treatment

value: low workload

tag: zeitgeber time


title: WJYQ_N

value: Patient WJYQ


title: BS_seq, Y1_d54_SSEA4_rep1

tag: donor age

tag: days of_reprogramming


title: ZLKQ_N

value: Patient ZLKQ


title: WJYQ_T

value: male


title: BS_seq, O2_d54_SSEA4_rep1


title: lateral hypothalamus rostral, high workload, ZT17, rep2

description:
LHr_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: lateral hypothalamus rostral

value: lateral hypothalamus rostral


title: Mapt-EGFP+_biological rep 3

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

hyb_protocol: Target cRNA generated from each sample was processed as per manufacturer's recommendation using an Affymetrix GeneChip 3000 System. Spike controls were added to 15 µg fragmented cRNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin.

scan_protocol: The sample was scanned on an Affymetrix GeneChip 3000 system.

data_processing: After initial checks for chip quality, probe-level data were pre-processed by robust multiple-array analysis (RMA), quantile normalization using perfect match probe only, and median polish for probe level signal summarization using R packages.

label: biotin/streptavidin-phycoerythrin

source_name: cells sorted from mouse colon

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from approximately 50 ng of total RNA.

extract_protocol: Total RNA was isolated from Mapt-EGFP+ colonic neurons and Mapt-EGFP- myenteric cells using RNA-Bee (AMSBIO, Cambridge, MA, USA) and purified with RNeasy Mini Kit (Qiagen, Germantown, MD, USA).

treatment_protocol: Mice underwent surgical laparotomy under pentobarbital (50mg/kg) anesthesia. The celiac ganglion of each mouse was injected with 3-5 μL of 25 mg/mL Alexa Fluor 647-labeled cholera toxin subunit B (CTB-AF647; Thermo Fisher Scientific, Waltham, MA, USA) with the intention of labeling the cell soma of intestinofugal neurons in the myenteric plexus of the colon. The animals were killed 3-4 days after surgery.

tag: sample type

value: FACS-purified cells

value: Mapt-EGFP+ colonic neurons


title: Mapt-EGFP-_biological rep 3

value: Mapt-EGFP- myenteric cells


title: Mapt-EGFP-_biological rep 1


title: Mapt-EGFP+_biological rep 1


title: Mapt-EGFP+_biological rep 2


title: Mapt-EGFP-_biological rep 2


title: ZLKQ_T


title: liver, low workload, ZT05, rep1

city: La Jolla

last: van Rosmalen

institute: Salk Institute for Biological Studies

description:
LIV_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: liver


title: BS_seq, N3_d29_SSEA4_rep1

value: Reprogramming fibroblast


title: lateral hypothalamus rostral, high workload, ZT17, rep1

description:
LHr_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: high workload


title: BS_seq, O2_d47_SSEA4_rep1


title: liver, low workload, ZT01, rep1

description:
LIV_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: lateral hypothalamus rostral, high workload, ZT21, rep1

description:
LHr_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N2_d47_SSEA4_rep1


title: lateral hypothalamus rostral, high workload, ZT21, rep2

description:
LHr_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: lateral hypothalamus rostral, high workload, ZT13, rep1

description:
LHr_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, N3_d29_CD13_rep1

source_name: Failing to reprogram fibroblast

value: Failing to reprogram fibroblast


title: WHFQ_N

value: Patient WHFQ

value: laryngo-hypopharyngeal carcinoma

value: larynx and hypopharynx

value: Normal


title: WJCQ_T

value: Patient WJCQ

value: Tumor

value: non-response


title: lateral hypothalamus rostral, high workload, ZT13, rep2

description:
LHr_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: BS_seq, Y2_d47_SSEA4_rep1


title: WHFQ_T

value: male


title: WJCQ_N


title: BS_seq, O1_d47_SSEA4_rep1


title: WGYQ_N

value: Patient WGYQ


title: lateral hypothalamus rostral, high workload, ZT09, rep1

description:
LHr_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: lateral hypothalamus rostral


title: WGMQ_N

value: Patient WGMQ


title: lateral hypothalamus rostral, high workload, ZT05, rep2

description:
LHr_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: lateral hypothalamus rostral, high workload, ZT09, rep2

description:
LHr_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: BS_seq, Y1_Fib_rep1

value: Fibroblast


title: lateral hypothalamus rostral, high workload, ZT05, rep1

description:
LHr_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: WFLQ_T

value: Patient WFLQ

value: response

value: female


title: WFLQ_N


title: lateral hypothalamus rostral, high workload, ZT01, rep2

description:
LHr_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: high workload


title: MYZQ_N

value: Patient MYZQ


title: lateral hypothalamus rostral, high workload, ZT01, rep1

description:
LHr_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: RIP_INPUT

first: Jiaxing

last: Zhang

state: China

address: 58 Zhongshan 2nd Road

institute: First Affiliated Hospital of Sun Yat-sen University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads containing more than10%of unknown nucleotides(N); 3) Removing low quality reads containing more than50%of low quality(Q-value≤20) bases.
Short reads alignment tool Bowtie2(2.2.8) was used for mapping reads to ribosome RNA(rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2(version2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is22) Disables the coverage based search for junctions3) The distance between mate-pair reads is50bp4) The standard deviation for the distribution on inner distance between mate-pair reads is80bp After aligned with reference genome, unmapped reads(or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well.
The reconstruction of transcripts was carried out with software StringTie, which allows to identify splice variants. During the last step of assembly, all of the reassembles fragments were aligned with reference genes and then similar fragments were removed
To indentify regions of IP enrichment over background, we used the RIPSeeker algorithm, which is a de novo method for detecting peaks(indicating protein–RNA interactions) based on hidden Markov models(HMM). eFDR<0.05and IP count>10were used to select peaks. Then, the information of genomic location, fold enrichment and significant level of peaks were all displayed. According to the genomic location information and gene annotation information of peak, peak related genes can be confirmed. Besides, the distribution of peak on different function regions, such as protein_coding, pseudogene and antisense, was performed.
Assembly: hg19
Supplementary files format and content: txt file for raw count

extract_protocol:
Total RNA from tumor tissues or cell lines was extracted with TRIzol (Invitrogen). Total RNA was reverse transcribed using 4× Reverse Transcription Master Mix (EZBioscience, USA) according to the manufacturer’s instructions.
After total RNA was extracted, rRNAs were removed to retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP(dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG(Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM4000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
The libraries were sequenced by Illumina (Illumina, USA) with paired-end.

tag: cell line

value: renal cell carcinoma

tag: antibody

value: input


title: RIP_IP


title: MYZQ_T

value: laryngo-hypopharyngeal carcinoma

value: larynx and hypopharynx


title: S7_D7_30h, replicate 1, scRNAseq

city: London

first: Tiago

last: Rito

address: 1 Midland Rd

institute: The Francis Crick Institute

description: 10x Genomics Chromium Single-Cell 3′ mRNA V3.1

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the Homo sapiens GRCh38-3.0.0 reference genome using CellRanger (v4.0.0, 10X Genomics) and the analyses were performed using Scanpy67 (v1.7.0). Cells were filtered for a minimum of 200 genes, mitochondrial UMIs between 1-20%, total counts between 10,000-50,000 and doublet cells were filtered using Scrublet68 with a threshold of 0.2. Counts were normalized to a target sum of 10000 excluding highly expressed genes (3%). “Highly variable genes” were called using Scanpy’s function with default parameters.
Assembly: Homo sapiens GRCh38-3.0.0
Supplementary files format and content: mtx

source_name: differentiated hESCs

extract_protocol:
16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%.
The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs.

value: differentiated hESCs

tag: day

tag: hour


title: S5_D7_18h, replicate 1, scRNAseq

tag: cell type


title: lateral hypothalamus rostral, low workload, ZT21, rep1

address: 10010 N Torrey Pines Rd

description:
LHr_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: tissue

tag: strain

value: low workload


title: S6_D7_24h, replicate 1, scRNAseq


title: S4_D5_24h, replicate 1, scRNAseq


title: HQCQ_N

tag: individual

value: Patient HQCQ

tag: disease state

value: Normal

value: non-response


title: lateral hypothalamus rostral, low workload, ZT17, rep2

description:
LHr_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: lateral hypothalamus rostral

value: CBA/CaJ

value: male


title: S3_D5_18h, replicate 1, scRNAseq


title: lateral hypothalamus rostral, low workload, ZT17, rep1

description:
LHr_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S2_D3_24h, replicate 1, scRNAseq


title: CDMQ_N

value: Patient CDMQ

tag: tissue type

tag: response to induction chemotherapy


title: lateral hypothalamus rostral, low workload, ZT13, rep2

description:
LHr_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: Sex