title: IMFL_1

type: RNA

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Total RNA was extracted from flag leaf  shortly before heading. , non-transgenic, biological replicate 1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa

source_name: Total RNA was extracted from flag leaf  shortly before heading, non-transgenic, biological replicate 1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Rice seeds (Oryza sativa L. cv. Ilmi and OsMYB86-ov-23) were geminated on MS0 (Murashige and Skoog) medium, incubated in a growth chamber (28°C, 2 days in dark followed by 2 days in the light), and then transferred into soil and grown in a greenhouse (16-h-light/8-h-dark cycle).

extract_protocol: Total RNA was extracted from the transgenic and WT rice plants using TRI REAGENT® (Molecular Research Center, www.mrcgene.com)

treatment_protocol: Total RNA was extracted from flag leaves and panicles at 6 days before heading (DBH) of the transgenic (23 line) and WT plants and used for the microarray experiments

tag: cultivar

value: cv. Ilmi

value: wildtype

value: flag leaf


title: Abaxial petiole, WL, 160 minutes, rep 4

status: Public on Dec 20 2022

type: SRA

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

country: Netherlands

institute: Utrecht University

library_source: transcriptomic

data_processing:
perform quality control on FastQ files (using FastQC)
align reads of each sample in a run against reference genome (using STAR) and add read groups (using Picard)
perform quality control on generated BAM files (using Picard)
count reads in features (using HTSeq-count)
normalize read counts (using DESeq)
Assembly: TAIR10
Supplementary files format and content: output_readCounts_normalized.txt is a matrix (33602 rows and 204 columns) organised with 1 row per gene and 1 column per sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Leaf material

growth_protocol: 28-day old Arabidopsis, grown in light/dark 9 h/15 h, 20 °C, 70 % humidity, 130-150 µmol m-2 s-1 PAR, R/FR 2.0.

extract_protocol: BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction (Townsley et al., 2015 - Frontiers in Plant Science)

tag: tissue

value: Abaxial petiole

tag: replicate

value: rep 4

tag: ecotype

tag: treatment

value: WL, 160 minutes


title: Adaxial petiole, WL, 160 minutes, rep 4

value: Adaxial petiole


title: MYB86P_1

description: Total RNA was extracted from panicle of OsMYB14-ov-23 shortly before heading, transgenic, biological replicate 1

tag: genotype

value: panicle


title: MYB86P_2

description: Total RNA was extracted from panicle of OsMYB14-ov-23 shortly before heading, transgenic, biological replicate 2


title: IMP_1

description: Total RNA was extracted from  panicle samples shortly before heading. , non-transgenic, biological replicate 1

source_name: Total RNA was extracted from panicle samples shortly before heading, non-transgenic, biological replicate 1


title: Leaf tip, WL, 160 minutes, rep 4

value: Leaf tip


title: MYB86FL_1

description: Total RNA was extracted from flag leaf of OsMYB14-ov-23 shortly before heading, transgenic, biological replicate 1


title: Abaxial petiole, Frtip, 140 minutes, rep 4

value: Frtip, 140 minutes


title: Adrenal_ZT0_TRF_2_1

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

description: Library name: D13AD4

data_processing:
Basecalls were generated using CASAVA v1.8.
Data quality was assessed using FastQC v0.11.8.
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a.
Reads were annotated to genes using Homer v4.10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw.csv: Comma-separated text file includes the raw counts for each library (the sample resequencings are collapsed).

organism: Mus musculus

source_name: Adrenal

growth_protocol: 10-week-old C57BL/6J mice were purchased from the Jackson laboratory (#000664) and housed in 12 hr light:12 dark conditions for 2 weeks with normal chow diet.

extract_protocol:
RNA were extracted following the protocol from Allprep DNA/RNA Mini Kit (Qiagen) or using Trizol reagent, and RNA integrity number were measured through Agilent 2200 TapeStation system.
Libraries generated using Illumina TruSeq Stranded mRNA Sample Prep Kit, pooled and sequenced using an Illumina HiSeq 2500 or Novaseq 6000.

treatment_protocol: Mice were subjected to Ad-libitum feeding (ALF) or time-restricted feeding (TRF) of Western diet (45% fat, 17% sucrose, Research diets Inc. #12451) for 9 hr from ZT13-ZT22 for 7 weeks.

value: Adrenal

tag: strain

tag: feeding intervention

value: 9 hr time-restricted feeding

tag: time-point

value: wild type


title: Adrenal_ZT0_TRF_1_1

description: Library name: D13AD3


title: MYB86FL_2

description: Total RNA was extracted from flag leaf of OsMYB14-ov-23 shortly before heading, transgenic, biological replicate 2


title: Adrenal_ZT0_ALF_1_1

description: Library name: D13AD1

value: ad-libitum feeding


title: Adaxial petiole, Frtip, 140 minutes, rep 4


title: Leaf tip, Frtip, 140 minutes, rep 4


title: Arcuate_ZT22_TRF_2_1

description: Library name: C24ARC4

source_name: ARC

value: arcuate nucleus


title: Arcuate_ZT22_TRF_1_1

description: Library name: C24ARC3


title: Adaxial petiole, WL, 140 minutes, rep 4

value: WL, 140 minutes


title: Arcuate_ZT22_ALF_2_1

description: Library name: C24ARC2


title: Leaf tip, WL, 140 minutes, rep 4


title: Arcuate_ZT22_ALF_1_1

description: Library name: C24ARC1


title: Adaxial petiole, Frtip, 120 minutes, rep 4

value: Frtip, 120 minutes


title: Arcuate_ZT20_TRF_2_1

description: Library name: C23ARC4


title: Abaxial petiole, Frtip, 120 minutes, rep 4


title: Adrenal_ZT0_ALF_2_1

description: Library name: D13AD2


title: Arcuate_ZT20_TRF_1_1

description: Library name: C23ARC3


title: Arcuate_ZT20_ALF_2_1

description: Library name: C23ARC2


title: Leaf tip, Frtip, 120 minutes, rep 4


title: Abaxial petiole, WL, 120 minutes, rep 4

value: WL, 120 minutes


title: Arcuate_ZT18_TRF_2_1

description: Library name: C22ARC4


title: Arcuate_ZT18_TRF_1_1

description: Library name: C22ARC3


title: Adaxial petiole, WL, 120 minutes, rep 4


title: Arcuate_ZT20_ALF_1_1

description: Library name: C23ARC1


title: Adaxial petiole, Frtip, 100 minutes, rep 4

value: Frtip, 100 minutes


title: Leaf tip, WL, 120 minutes, rep 4


title: Adaxial petiole, WL, 100 minutes, rep 4

value: WL, 100 minutes


title: Arcuate_ZT18_ALF_2_1

description: Library name: C22ARC2


title: Abaxial petiole, Frtip, 100 minutes, rep 4

value: Abaxial petiole


title: Arcuate_ZT18_ALF_1_1

description: Library name: C22ARC1


title: Arcuate_ZT16_TRF_1_1

description: Library name: C21ARC3


title: Leaf tip, Frtip, 100 minutes, rep 4

value: rep 4


title: Abaxial petiole, WL, 140 minutes, rep 4


title: Arcuate_ZT16_ALF_2_1

description: Library name: C21ARC2


title: Abaxial petiole, Frtip, 80 minutes, rep 4

value: Frtip, 80 minutes


title: Adaxial petiole, Frtip, 80 minutes, rep 4

value: Adaxial petiole


title: Arcuate_ZT14_TRF_2_1

description: Library name: C20ARC4


title: Abaxial petiole, WL, 100 minutes, rep 4


title: Arcuate_ZT16_ALF_1_1

description: Library name: C21ARC1


title: Arcuate_ZT14_ALF_2_1

description: Library name: C20ARC2


title: Arcuate_ZT14_TRF_1_1

description: Library name: C20ARC3


title: Arcuate_ZT16_TRF_2_1

description: Library name: C21ARC4


title: Adaxial petiole, WL, 80 minutes, rep 4

value: WL, 80 minutes


title: Arcuate_ZT12_TRF_2_1

description: Library name: C19ARC4


title: Arcuate_ZT14_ALF_1_1

description: Library name: C20ARC1


title: Abaxial petiole, WL, 80 minutes, rep 4


title: Arcuate_ZT12_ALF_1_1

description: Library name: C19ARC2


title: Adaxial petiole, Frtip, 60 minutes, rep 4

value: Frtip, 60 minutes


title: Arcuate_ZT12_TRF_1_1

description: Library name: C19ARC3


title: Leaf tip, WL, 80 minutes, rep 4

value: Leaf tip


title: Arcuate_ZT10_TRF_1_1

description: Library name: C18ARC4


title: Abaxial petiole, Frtip, 60 minutes, rep 4


title: Arcuate_ZT10_ALF_2_1

description: Library name: C18ARC2


title: Leaf tip, WL, 100 minutes, rep 4


title: Arcuate_ZT10_ALF_1_1

description: Library name: C18ARC1


title: Arcuate_ZT8_TRF_2_1

description: Library name: C17ARC4


title: Adaxial petiole, WL, 60 minutes, rep 4

value: WL, 60 minutes


title: Leaf tip, WL, 60 minutes, rep 4


title: Leaf tip, Frtip, 40 minutes, rep 4

value: Frtip, 40 minutes


title: Arcuate_ZT8_ALF_2_1

description: Library name: C17ARC2

value: wild type


title: Arcuate_ZT8_TRF_1_1

description: Library name: C17ARC3

value: 9 hr time-restricted feeding


title: Leaf tip, Frtip, 80 minutes, rep 4


title: Adaxial petiole, Frtip, 300 minutes, rep 3

value: rep 3

value: Frtip, 300 minutes


title: Arcuate_ZT6_TRF_2_1

description: Library name: C16ARC4

value: arcuate nucleus


title: Leaf tip, Frtip, 300 minutes, rep 3


title: Arcuate_ZT6_TRF_1_1

description: Library name: C16ARC3


title: Arcuate_ZT6_ALF_2_1

description: Library name: C16ARC2

value: ad-libitum feeding


title: Arcuate_ZT4_TRF_1_1

description: Library name: C15ARC3


title: Abaxial petiole, WL, 300 minutes, rep 3

value: WL, 300 minutes


title: Leaf tip, WL, 300 minutes, rep 3


title: Abaxial petiole, Frtip, 180 minutes, rep 3

value: Frtip, 180 minutes


title: Arcuate_ZT4_ALF_1_1

description: Library name: C15ARC1


title: Adaxial petiole, Frtip, 180 minutes, rep 3


title: Abaxial petiole, WL, 60 minutes, rep 4

value: Abaxial petiole


title: Arcuate_ZT4_TRF_2_1

description: Library name: C15ARC4


title: Adaxial petiole, WL, 180 minutes, rep 3

value: WL, 180 minutes


title: Leaf tip, Frtip, 180 minutes, rep 3


title: Abaxial petiole, WL, 180 minutes, rep 3


title: Arcuate_ZT2_TRF_2_1

description: Library name: C14ARC4


title: Abaxial petiole, Frtip, 300 minutes, rep 3


title: Arcuate_ZT2_ALF_2_1

description: Library name: C14ARC2


title: Arcuate_ZT8_ALF_1_1

description: Library name: C17ARC1


title: Arcuate_ZT2_TRF_1_1

description: Library name: C14ARC3


title: Arcuate_ZT2_ALF_1_1

description: Library name: C14ARC1


title: Leaf tip, WL, 180 minutes, rep 3


title: Arcuate_ZT0_TRF_2_1

description: Library name: C13ARC4


title: Leaf tip, Frtip, 160 minutes, rep 3

value: Frtip, 160 minutes


title: Adaxial petiole, Frtip, 160 minutes, rep 3

value: Adaxial petiole


title: Adaxial petiole, WL, 300 minutes, rep 3


title: Abaxial petiole, Frtip, 160 minutes, rep 3


title: Adaxial petiole, WL, 160 minutes, rep 3

value: WL, 160 minutes


title: Arcuate_ZT6_ALF_1_1

description: Library name: C16ARC1


title: Arcuate_ZT0_ALF_2_1

description: Library name: C13ARC2


title: Leaf tip, WL, 160 minutes, rep 3


title: neutrophil granulocytes, murin, without [603-40]

city: Düsseldorf

first: Pascal

last: Bouvain

address: Universitätsstr. 1

department: molekulare Kardiologie

country: Germany

institute: Uniklinik Düsseldorf

description: 603_Murine_Expression Browser_All

data_processing:
Data analyses on fastq files were conducted with CLC Genomics Workbench (version 22.0.1, QIAGEN, Venlo. NL).
The reads of all probes were adapter trimmed (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2).
Mapping was done against the Mus musculus (mm39; GRCm39.105) (January 12, 2022) respectively the Homo sapiens (hg38; GRCh38.100) (June 05, 2020) genome sequence.
After grouping of samples (for biological replicates each) according to their respective experimental condition, the statistical differential expression was determined using the Differential Expression for RNA-Seq tool (version 2.6).
The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value < 0.05 was considered significant
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: neutrophil granulocytes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
The library preparation was performed according to the manufacturer's protocol using the Illumina® 'Stranded mRNA Prep, Ligation' Kit. Briefly, 25 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification.

treatment_protocol: Cells were treated either wich ConPFCs or mNPPfcs or left untreated.

tag: cell type

value: neutrophil granulocytes

value: without


title: Abaxial petiole, WL, 160 minutes, rep 3


title: Arcuate_ZT0_ALF_1_1

description: Library name: C13ARC1


title: Arcuate_ZT4_ALF_2_1

description: Library name: C15ARC2


title: BAT_ZT22_TRF_2_2

description: Library name: BAT_24H

source_name: BAT

value: Brown adipose tissue


title: BAT_ZT22_TRF_2_3

description: Library name: BAT_24H


title: Abaxial petiole, Frtip, 140 minutes, rep 3

value: Frtip, 140 minutes


title: BAT_ZT22_TRF_2_1

description: Library name: BAT_24H

value: wild type


title: Leaf tip, Frtip, 140 minutes, rep 3

value: Leaf tip


title: Adaxial petiole, WL, 140 minutes, rep 3

value: rep 3

value: WL, 140 minutes


title: Abaxial petiole, WL, 140 minutes, rep 3


title: BAT_ZT22_ALF_1_3

description: Library name: BAT_24C


title: BAT_ZT22_ALF_1_2

description: Library name: BAT_24C


title: Leaf tip, WL, 140 minutes, rep 3


title: BAT_ZT22_TRF_1_3

description: Library name: BAT_24B

value: 9 hr time-restricted feeding


title: Adaxial petiole, Frtip, 120 minutes, rep 3

value: Frtip, 120 minutes


title: Arcuate_ZT0_TRF_1_1

description: Library name: C13ARC3

value: arcuate nucleus


title: BAT_ZT22_TRF_1_2

description: Library name: BAT_24B


title: Leaf tip, Frtip, 120 minutes, rep 3


title: Abaxial petiole, Frtip, 120 minutes, rep 3


title: Adaxial petiole, WL, 120 minutes, rep 3

value: WL, 120 minutes


title: BAT_ZT22_TRF_1_1

description: Library name: BAT_24B


title: BAT_ZT20_TRF_2_3

description: Library name: BAT_23H


title: Abaxial petiole, WL, 120 minutes, rep 3

value: Abaxial petiole


title: BAT_ZT20_TRF_2_2

description: Library name: BAT_23H


title: Leaf tip, WL, 120 minutes, rep 3


title: BAT_ZT20_TRF_2_1

description: Library name: BAT_23H


title: Adaxial petiole, Frtip, 140 minutes, rep 3


title: Abaxial petiole, Frtip, 100 minutes, rep 3

value: Frtip, 100 minutes


title: BAT_ZT20_ALF_2_1

description: Library name: BAT_23G

value: ad-libitum feeding


title: Leaf tip, Frtip, 100 minutes, rep 3


title: Adaxial petiole, WL, 100 minutes, rep 3

value: Adaxial petiole

value: WL, 100 minutes


title: BAT_ZT22_ALF_2_1

description: Library name: BAT_24G


title: BAT_ZT20_ALF_1_1

description: Library name: BAT_23A


title: BAT_ZT20_TRF_1_1

description: Library name: BAT_23B


title: BAT_ZT22_ALF_1_1

description: Library name: BAT_24C


title: Abaxial petiole, WL, 100 minutes, rep 3


title: Leaf tip, Frtip, 60 minutes, rep 4

value: rep 4

value: Frtip, 60 minutes


title: BAT_ZT18_ALF_2_1

description: Library name: BAT_22E

value: Brown adipose tissue


title: BAT_ZT18_TRF_2_1

description: Library name: BAT_22H


title: Abaxial petiole, Frtip, 80 minutes, rep 3

value: Frtip, 80 minutes


title: BAT_ZT18_TRF_1_3

description: Library name: BAT_22B

value: wild type


title: Leaf tip, WL, 100 minutes, rep 3

value: Leaf tip


title: Adaxial petiole, Frtip, 80 minutes, rep 3

value: rep 3


title: BAT_ZT18_ALF_1_1

description: Library name: BAT_22C


title: BAT_ZT18_TRF_1_2

description: Library name: BAT_22B


title: Adaxial petiole, WL, 80 minutes, rep 3

value: WL, 80 minutes


title: BAT_ZT16_TRF_2_1

description: Library name: BAT_21F

value: 9 hr time-restricted feeding


title: BAT_ZT18_TRF_1_1

description: Library name: BAT_22B


title: Leaf tip, Frtip, 80 minutes, rep 3


title: Adaxial petiole, Frtip, 100 minutes, rep 3


title: Abaxial petiole, WL, 80 minutes, rep 3


title: BAT_ZT20_ALF_2_2

description: Library name: BAT_23G


title: Leaf tip, WL, 80 minutes, rep 3


title: Adaxial petiole, Frtip, 60 minutes, rep 3


title: BAT_ZT16_ALF_2_1

description: Library name: BAT_21E


title: BAT_ZT16_ALF_1_1

description: Library name: BAT_21C


title: BAT_ZT16_TRF_1_3

description: Library name: BAT_21B


title: Abaxial petiole, Frtip, 60 minutes, rep 3


title: Adaxial petiole, WL, 60 minutes, rep 3

value: WL, 60 minutes


title: Leaf tip, Frtip, 60 minutes, rep 3


title: Abaxial petiole, WL, 60 minutes, rep 3


title: BAT_ZT14_TRF_2_1

description: Library name: BAT_20H


title: BAT_ZT16_TRF_1_2

description: Library name: BAT_21B


title: BAT_ZT16_TRF_1_1

description: Library name: BAT_21B


title: BAT_ZT14_ALF_2_1

description: Library name: BAT_20E


title: Day2 Th17 cell (n=4)

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
Assembly: mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Supplementary files format and content: Text files include TPM values for each Sample

source_name: Spleen

growth_protocol: See "description".

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN) was used for library constraction according to the manufacturer's protocol.

treatment_protocol: Pharmacolgical drug was not treated in this assay

value: Spleen

value: Differentiated Th17 cells

value: WT

value: Two-day cultured Th17 cells generated from primary splenic Naïve CD4_T cells


title: Day2 Th2 cell (n=4)

value: Differentiated Th2 cells

value: Two-day cultured Th2 cells generated from primary splenic Naïve CD4_T cells


title: Day2 Th0 cell (n=4)

value: Differentiated Th0 cells

value: Two-day cultured Th0 cells generated from primary splenic Naïve CD4_T cells


title: Day0 Naïve CD4 T  cell (n=4)

value: Naive CD4 T Cells

value: Splenic Naïve CD4_T cells


title: Day2 Treg cell (n=4)

value: Differentiated Treg cells

value: Two-day cultured Treg cells generated from primary splenic Naïve CD4_T cells


title: Leaf tip, Frtip, 40 minutes, rep 3

value: Leaf tip

value: Frtip, 40 minutes


title: BAT_ZT14_TRF_1_2

description: Library name: BAT_20D

value: Brown adipose tissue

value: wild type


title: Day2 Th1 cell (n=4)

value: Differentiated Th1 cells

value: Two-day cultured Th1 cells generated from primary splenic Naïve CD4_T cells


title: Abaxial petiole, WL, 40 minutes, rep 3

value: Abaxial petiole

value: rep 3

value: WL, 40 minutes


title: Day2 Treg cell (n=3)

value: Spleen

value: WT


title: Day2 Th17 cell (n=3)

value: Differentiated Th17 cells

value: Two-day cultured Th17 cells generated from primary splenic Naïve CD4_T cells


title: BAT_ZT14_TRF_1_1

description: Library name: BAT_20D

value: 9 hr time-restricted feeding


title: Leaf tip, WL, 40 minutes, rep 3


title: Day2 Th2 cell (n=3)

value: Differentiated Th2 cells

value: Two-day cultured Th2 cells generated from primary splenic Naïve CD4_T cells


title: Day2 Th1 cell(n=3)


title: Day2 Th0 cell (n=3)

value: Differentiated Th0 cells

value: Two-day cultured Th0 cells generated from primary splenic Naïve CD4_T cells


title: BAT_ZT14_ALF_1_1

description: Library name: BAT_20A

value: ad-libitum feeding


title: Adaxial petiole, Frtip, 300 minutes, rep 2

value: Adaxial petiole

value: rep 2

value: Frtip, 300 minutes


title: BAT_ZT12_TRF_2_1

description: Library name: BAT_19H

value: Brown adipose tissue

value: wild type


title: Day0 Naïve CD4 T  cell (n=3)

value: Naive CD4 T Cells

value: Splenic Naïve CD4_T cells


title: Day2 Treg cell (n=2)

value: Spleen

value: Differentiated Treg cells

value: Two-day cultured Treg cells generated from primary splenic Naïve CD4_T cells


title: Leaf tip, WL, 60 minutes, rep 3

value: Leaf tip

value: rep 3

value: WL, 60 minutes


title: BAT_ZT12_ALF_2_3

description: Library name: BAT_19G


title: Day2 Th17 cell (n=2)

value: Differentiated Th17 cells

value: WT

value: Two-day cultured Th17 cells generated from primary splenic Naïve CD4_T cells


title: BAT_ZT14_TRF_1_3

description: Library name: BAT_20D

value: 9 hr time-restricted feeding


title: Adaxial petiole, WL, 40 minutes, rep 3

value: Adaxial petiole

value: WL, 40 minutes


title: Day2 Th1 cell (n=2)

value: Differentiated Th1 cells

value: Two-day cultured Th1 cells generated from primary splenic Naïve CD4_T cells


title: Leaf tip, Frtip, 300 minutes, rep 2

value: rep 2

value: Frtip, 300 minutes


title: BAT_ZT12_ALF_2_2

description: Library name: BAT_19G

value: Brown adipose tissue

value: ad-libitum feeding

value: wild type


title: Adaxial petiole, WL, 300 minutes, rep 2

value: WL, 300 minutes


title: Day0 Naïve CD4 T  cell (n=2)

value: Spleen

value: Naive CD4 T Cells

value: Splenic Naïve CD4_T cells


title: BAT_ZT12_ALF_2_1

description: Library name: BAT_19G


title: Day2 Th0 cell (n=2)

value: Differentiated Th0 cells

value: Two-day cultured Th0 cells generated from primary splenic Naïve CD4_T cells


title: Day2 Treg cell (n=1)

value: Differentiated Treg cells

value: WT

value: Two-day cultured Treg cells generated from primary splenic Naïve CD4_T cells


title: Abaxial petiole, WL, 300 minutes, rep 2

value: Abaxial petiole


title: Day2 Th17 cell (n=1)

value: Differentiated Th17 cells

value: Two-day cultured Th17 cells generated from primary splenic Naïve CD4_T cells


title: Day2 Th2 cell (n=1)

value: Differentiated Th2 cells

value: Two-day cultured Th2 cells generated from primary splenic Naïve CD4_T cells


title: Day2 Th1 cell (n=1)

value: Differentiated Th1 cells

value: Two-day cultured Th1 cells generated from primary splenic Naïve CD4_T cells


title: BAT_ZT12_TRF_1_3

description: Library name: BAT_19D

value: Brown adipose tissue

value: 9 hr time-restricted feeding

value: wild type


title: Day2 Th0 cell (n=1)

value: Spleen


title: BAT_ZT12_TRF_1_2

description: Library name: BAT_19D


title: Adaxial petiole, Frtip, 180 minutes, rep 2

value: Adaxial petiole

value: rep 2

value: Frtip, 180 minutes


title: BAT_ZT12_TRF_1_1

description: Library name: BAT_19D


title: Day0 Naïve CD4 T  cell (n=1)

value: Naive CD4 T Cells

value: Splenic Naïve CD4_T cells


title: Abaxial petiole, Frtip, 300 minutes, rep 2

value: Frtip, 300 minutes


title: Abaxial petiole, Frtip, 180 minutes, rep 2

value: Abaxial petiole


title: monocytes, human, Targeting PFCs [603-92]

description: 603_Human_Expression Browser_All

organism: Homo sapiens

source_name: monocytes

value: monocytes

value: Targeting PFCs


title: monocytes, human, Ctrl PFCs [603-91]

description: 603_Human_Expression Browser_All

value: Ctrl PFCs


title: Day2 Th2 cell (n=2)

value: Differentiated Th2 cells

value: WT

value: Two-day cultured Th2 cells generated from primary splenic Naïve CD4_T cells


title: BAT_ZT12_ALF_1_3

description: Library name: BAT_19C

value: Brown adipose tissue

value: ad-libitum feeding


title: monocytes, human, without [603-90]

description: 603_Human_Expression Browser_All

value: without


title: monocytes, human, Targeting PFCs [603-89]

description: 603_Human_Expression Browser_All


title: BAT_ZT12_ALF_1_2

description: Library name: BAT_19C

value: wild type


title: Leaf tip, Frtip, 180 minutes, rep 2

value: Leaf tip


title: BAT_ZT12_ALF_1_1

description: Library name: BAT_19C


title: Leaf tip, WL, 300 minutes, rep 2

value: rep 2

value: WL, 300 minutes


title: Abaxial petiole, WL, 180 minutes, rep 2

value: WL, 180 minutes


title: BAT_ZT10_TRF_2_3

description: Library name: BAT_18F

value: 9 hr time-restricted feeding


title: monocytes, human, without [603-87]

description: 603_Human_Expression Browser_All


title: neutrophil granulocytes, human, without [603-84]

description: 603_Human_Expression Browser_All

value: neutrophil granulocytes


title: monocytes, human, Ctrl PFCs [603-88]

description: 603_Human_Expression Browser_All


title: neutrophil granulocytes, human, Ctrl PFCs [603-85]

description: 603_Human_Expression Browser_All


title: Leaf tip, WL, 180 minutes, rep 2


title: neutrophil granulocytes, human, Targeting PFCs [603-86]

description: 603_Human_Expression Browser_All


title: Adaxial petiole, Frtip, 160 minutes, rep 2

value: Adaxial petiole

value: Frtip, 160 minutes


title: BAT_ZT10_TRF_2_1

description: Library name: BAT_18F


title: neutrophil granulocytes, human, Ctrl PFCs [603-82]

description: 603_Human_Expression Browser_All


title: neutrophil granulocytes, human, Targeting PFCs [603-83]

description: 603_Human_Expression Browser_All

value: Targeting PFCs


title: BAT_ZT10_ALF_2_1

description: Library name: BAT_18E


title: BAT_ZT10_TRF_1_3

description: Library name: BAT_18B


title: Leaf tip, Frtip, 160 minutes, rep 2


title: Adaxial petiole, WL, 180 minutes, rep 2


title: Adaxial petiole, WL, 160 minutes, rep 2

value: WL, 160 minutes


title: neutrophil granulocytes, human, Targeting PFCs [603-77]

description: 603_Human_Expression Browser_All


title: neutrophil granulocytes, human, without [603-81]

description: 603_Human_Expression Browser_All


title: neutrophil granulocytes, human, Targeting PFCs [603-80]

description: 603_Human_Expression Browser_All


title: neutrophil granulocytes, human, without [603-75]

description: 603_Human_Expression Browser_All


title: monocytes, human, Targeting PFCs [603-36]

description: 603_Human_Expression Browser_All

value: monocytes


title: neutrophil granulocytes, human, without [603-78]

description: 603_Human_Expression Browser_All


title: monocytes, human, Ctrl PFCs [603-35]

description: 603_Human_Expression Browser_All

value: Ctrl PFCs


title: BAT_ZT10_TRF_1_2

description: Library name: BAT_18B


title: BAT_ZT10_TRF_2_2

description: Library name: BAT_18F


title: monocytes, human, without [603-34]

description: 603_Human_Expression Browser_All


title: monocytes, human, Targeting PFCs [603-33]

description: 603_Human_Expression Browser_All


title: Leaf tip, WL, 160 minutes, rep 2


title: neutrophil granulocytes, human, Ctrl PFCs [603-79]

description: 603_Human_Expression Browser_All


title: Adaxial petiole, Frtip, 140 minutes, rep 2

value: Frtip, 140 minutes


title: BAT_ZT10_ALF_1_1

description: Library name: BAT_18A

value: Brown adipose tissue


title: monocytes, human, without [603-19]

description: 603_Human_Expression Browser_All


title: monocytes, human, Ctrl PFCs [603-20]

description: 603_Human_Expression Browser_All


title: Abaxial petiole, Frtip, 160 minutes, rep 2

value: Abaxial petiole


title: BAT_ZT8_TRF_2_3

description: Library name: BAT_17F


title: Abaxial petiole, Frtip, 140 minutes, rep 2


title: BAT_ZT8_TRF_2_2

description: Library name: BAT_17F


title: neutrophil granulocytes, human, Ctrl PFCs [603-76]

description: 603_Human_Expression Browser_All


title: Leaf tip, Frtip, 140 minutes, rep 2


title: Abaxial petiole, WL, 160 minutes, rep 2


title: BAT_ZT8_TRF_2_1

description: Library name: BAT_17F


title: BAT_ZT10_TRF_1_1

description: Library name: BAT_18B


title: BAT_ZT8_ALF_2_1

description: Library name: BAT_17E

value: ad-libitum feeding


title: Leaf tip, WL, 140 minutes, rep 2

value: WL, 140 minutes


title: Adaxial petiole, WL, 140 minutes, rep 2


title: BAT_ZT8_ALF_2_3

description: Library name: BAT_17E

value: wild type


title: BAT_ZT8_TRF_1_2

description: Library name: BAT_17B


title: ChIP-Seq H3K9ac KAT6A WH1mut

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

library_source: genomic

data_processing:
ChIP-Seq data were aligned to human genome hg19 or hg38 using Bowtie, allowing one mismatch.
SAM files were converted to bigwig files using SamTools, and deepTools/bamCoverage. Data were normalized to RPKM.
Assembly: hg19,hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: Human embryonic kidney–293 (HEK293) cells were cultured with DMEM/F-12 (Gibco, 31331-028), supplemented with 10% FBS and 1x penicillin/streptomycin.

extract_protocol:
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode).
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode).

treatment_protocol: HEK293 cells were transfected with and an empty vector or expression constructs for Flag-HA tagged KAT6A wt, KAT6A WH1 mutant or KAT6A HAT mutant.

tag: cell line

value: Human embryonic kidney

value: Flag-KAT6A WH1mut

tag: chip antibody

value: H3K9ac (Diagenode, C15410004)


title: BAT_ZT8_ALF_2_2

description: Library name: BAT_17E


title: Abaxial petiole, WL, 140 minutes, rep 2

value: rep 2


title: Abaxial petiole, Frtip, 120 minutes, rep 2

value: Frtip, 120 minutes


title: ChIP-Seq H3K9ac KAT6A wt


title: ChIP-Seq H3K9ac KAT6A HATmut

value: Flag-KAT6A HATmut


title: Leaf tip, Frtip, 120 minutes, rep 2

value: Leaf tip


title: BAT_ZT8_TRF_1_1

description: Library name: BAT_17B

value: 9 hr time-restricted feeding


title: ChIP-Seq Flag KAT6A HATmut

value: Flag (Sigma, F3165)


title: ChIP-Seq H3K9ac empty

value: empty


title: BAT_ZT8_ALF_1_3

description: Library name: BAT_17A


title: Adaxial petiole, Frtip, 120 minutes, rep 2

value: Adaxial petiole


title: Nontransgenic_ biological replicate 3

city: Nagoya

first: Koji

last: Yamanaka

address: Furo-cho, Chikusa-ku

department: Neuroscience and Pathobiology

institute: Research Institute of Environmental Medicine, Nagoya University

description: Lumbar spinal cord_Nontransgenic_rep3

hyb_protocol: Fifteen micrograms of biotinylated cRNA was hybridized with a Mouse Genome 430_2.0 Array according to the standard protocol available from Affymetrix.

scan_protocol: After hybridization, the arrays were washed and stained, and then scanned (GeneChip Scanner, Affymetrix). CEL files obtained using GCOS v1.2 (Affymetrix).

data_processing: All CEL files were normalized with the MAS5 algorithm with GeneSpring GX v14.9 software (Agilent Technologies, Santa Clara, CA)

label: biotin

source_name: Lumbar spinal cord, Nontransgenic

label_protocol: Two micrograms of total RNA was first reverse transcribed into cDNA, then the cDNA was converted to biotinylated cRNA.

extract_protocol: TRIzol (Life Technologies, Carlsbad, CA) followed by an RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of extracted RNA was verified by its purity (i.e., A260/290 ratio > 1.9) and integrity (RNA integrity number (RIN) > 7.3, measured with an Agilent 2100 bioanalyzer)

value: Nontransgenic

tag: age

value: 11 months

value: Lumbar spinal cord

tag: condition

value: healthy


title: SOD1G85R_ biological replicate 1

description: Lumbar spinal cord_SOD1G85R_rep1

source_name: Lumbar spinal cord, SOD1G85R

value: symptomatic stage


title: SOD1G85R_ biological replicate 3

description: Lumbar spinal cord_SOD1G85R_rep3


title: Nontransgenic_ biological replicate 2

description: Lumbar spinal cord_Nontransgenic_rep2


title: SOD1G85R_ biological replicate 2

description: Lumbar spinal cord_SOD1G85R_rep2


title: SOD1WT_ biological replicate 1

description: Lumbar spinal cord_SOD1WT_rep1

source_name: Lumbar spinal cord, SOD1WT

value: almost healthy


title: Nontransgenic_ biological replicate 1

description: Lumbar spinal cord_Nontransgenic_rep1


title: SOD1WT_ biological replicate 3

description: Lumbar spinal cord_SOD1WT_rep3


title: ChIP-Seq Flag KAT6A WH1mut

value: Human embryonic kidney


title: SOD1WT_ biological replicate 2

description: Lumbar spinal cord_SOD1WT_rep2


title: SOD1G37R_ biological replicate 2

description: Lumbar spinal cord_SOD1G37R_rep2

source_name: Lumbar spinal cord, SOD1G37R


title: SOD1G37R_ biological replicate 1

description: Lumbar spinal cord_SOD1G37R_rep1


title: Adaxial petiole, WL, 120 minutes, rep 2

value: WL, 120 minutes


title: SOD1G37R_ biological replicate 3

description: Lumbar spinal cord_SOD1G37R_rep3


title: BAT_ZT8_ALF_1_2

description: Library name: BAT_17A

value: Brown adipose tissue

value: ad-libitum feeding

value: wild type


title: Abaxial petiole, WL, 120 minutes, rep 2

value: Abaxial petiole

value: rep 2


title: BAT_ZT6_TRF_2_3

description: Library name: BAT_16H

value: 9 hr time-restricted feeding


title: ChIP-Seq Flag KAT6A wt

value: Flag-KAT6A wt

value: Flag (Sigma, F3165)


title: BAT_ZT8_ALF_1_1

description: Library name: BAT_17A


title: ChIP-Seq Flag empty

value: empty


title: Adaxial petiole, Frtip, 100 minutes, rep 2

value: Adaxial petiole

value: Frtip, 100 minutes


title: Leaf tip, WL, 120 minutes, rep 2

value: Leaf tip


title: Abaxial petiole, Frtip, 100 minutes, rep 2


title: BAT_ZT6_TRF_2_2

description: Library name: BAT_16H


title: BAT_ZT6_TRF_2_1

description: Library name: BAT_16H


title: Leaf tip, Frtip, 100 minutes, rep 2


title: NS_control2

city: 成都

first: Hanwen

last: Li

state: 四川

address: 四川省成都市武侯区人民南路四川大学华西校区

country: China

institute: 四川大学华西口腔医学院

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BMDM

growth_protocol: BMDMs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Cells were treated with ox-dsDNA90(5ug/10^6 cell) by liposome3000 or just empty vector liposome3000.
Cells were then fed with DMEM supplemented with 10% FBS  for 6 hours.

value: BMDM

value: macrophage

value: WT

value: liposome

tag: time


title: NS_control1

address: 四川省成都市武侯区人民南路四川大学华西校区


title: ox-dsDNA90_1

address: 四川省成都市武侯区人民南路四川大学华西校区


title: ox-dsDNA90_3

address: 四川省成都市武侯区人民南路四川大学华西校区


title: NS_control3

address: 四川省成都市武侯区人民南路四川大学华西校区


title: ox-dsDNA90_2

address: 四川省成都市武侯区人民南路四川大学华西校区


title: BAT_ZT6_ALF_2_1

description: Library name: BAT_16E


title: DN_3

address: 四川省成都市武侯区人民南路四川大学华西校区

treatment_protocol:
Cells were treated with AA-DNA(5ug/10^6 cell) by liposome3000 or just empty vector liposome3000.
Cells were then fed with DMEM supplemented with 10% FBS  for 6 hours.

value: liposome+AA-DNA


title: DN_2

address: 四川省成都市武侯区人民南路四川大学华西校区


title: DN_1

address: 四川省成都市武侯区人民南路四川大学华西校区


title: NS_3

address: 四川省成都市武侯区人民南路四川大学华西校区


title: BAT_ZT6_ALF_1_1

description: Library name: BAT_16C

value: Brown adipose tissue


title: Adaxial petiole, WL, 100 minutes, rep 2

value: WL, 100 minutes


title: Abaxial petiole, WL, 100 minutes, rep 2


title: NS_1

address: 四川省成都市武侯区人民南路四川大学华西校区


title: BAT_ZT6_TRF_1_1

description: Library name: BAT_16B

value: wild type


title: NS_2

address: 四川省成都市武侯区人民南路四川大学华西校区


title: Kidney medulla_ZT22_TRF_2_1

description: Library name: KIM24H

source_name: KIM

value: kidney medulla


title: Leaf tip, WL, 100 minutes, rep 2

value: rep 2


title: BAT_ZT4_TRF_2_1

description: Library name: BAT_15F

value: 9 hr time-restricted feeding


title: Kidney medulla_ZT22_ALF_1_2

description: Library name: KIM24C

value: ad-libitum feeding


title: Kidney medulla_ZT22_ALF_2_1

description: Library name: KIM24G


title: Adaxial petiole, Frtip, 80 minutes, rep 2

value: Frtip, 80 minutes


title: Kidney medulla_ZT22_ALF_1_3

description: Library name: KIM24C


title: BAT_ZT4_ALF_2_2

description: Library name: BAT_15E


title: Kidney medulla_ZT22_TRF_1_1

description: Library name: KIM24B


title: Abaxial petiole, Frtip, 80 minutes, rep 2

value: Abaxial petiole


title: Kidney medulla_ZT22_ALF_1_1

description: Library name: KIM24C


title: BAT_ZT4_ALF_2_1

description: Library name: BAT_15E


title: Kidney medulla_ZT20_TRF_2_1

description: Library name: KIM23H


title: BAT_ZT4_TRF_1_1

description: Library name: BAT_15D


title: BAT_ZT4_ALF_1_1

description: Library name: BAT_15A


title: Kidney medulla_ZT20_ALF_2_1

description: Library name: KIM23G


title: Kidney medulla_ZT18_TRF_2_2

description: Library name: KIM22H


title: Adaxial petiole, WL, 80 minutes, rep 2

value: Adaxial petiole

value: WL, 80 minutes


title: Leaf tip, Frtip, 80 minutes, rep 2

value: Leaf tip


title: Kidney medulla_ZT20_TRF_1_1

description: Library name: KIM23B


title: Abaxial petiole, WL, 80 minutes, rep 2


title: Kidney medulla_ZT20_ALF_1_1

description: Library name: KIM23A


title: Kidney medulla_ZT18_TRF_2_1

description: Library name: KIM22H


title: Kidney medulla_ZT18_ALF_2_1

description: Library name: KIM22E


title: Kidney medulla_ZT18_ALF_1_1

description: Library name: KIM22C


title: Adaxial petiole, Frtip, 60 minutes, rep 2

value: Frtip, 60 minutes


title: Leaf tip, WL, 80 minutes, rep 2


title: BAT_ZT2_ALF_2_1

description: Library name: BAT_14E


title: BAT_ZT2_TRF_1_2

description: Library name: BAT_14D


title: Abaxial petiole, Frtip, 60 minutes, rep 2


title: Kidney medulla_ZT16_TRF_2_1

description: Library name: KIM21F


title: BAT_ZT2_TRF_2_1

description: Library name: BAT_14H


title: Leaf tip, Frtip, 60 minutes, rep 2


title: Kidney medulla_ZT16_TRF_1_1

description: Library name: KIM21B


title: Kidney medulla_ZT14_TRF_2_1

description: Library name: KIM20H


title: BAT_ZT2_ALF_1_3

description: Library name: BAT_14A


title: Adaxial petiole, WL, 60 minutes, rep 2

value: WL, 60 minutes


title: Kidney medulla_ZT16_ALF_1_1

description: Library name: KIM21C


title: Kidney medulla_ZT14_ALF_2_1

description: Library name: KIM20E


title: BAT_ZT2_ALF_1_2

description: Library name: BAT_14A


title: Kidney medulla_ZT14_TRF_1_1

description: Library name: KIM20D


title: Leaf tip, WL, 60 minutes, rep 2


title: Kidney medulla_ZT14_ALF_1_1

description: Library name: KIM20A


title: Abaxial petiole, WL, 60 minutes, rep 2


title: BAT_ZT2_ALF_1_1

description: Library name: BAT_14A


title: BAT_ZT0_TRF_2_1

description: Library name: BAT_13H


title: Kidney medulla_ZT12_ALF_2_1

description: Library name: KIM19E


title: Kidney medulla_ZT12_TRF_1_1

description: Library name: KIM19D


title: Adaxial petiole, Frtip, 40 minutes, rep 2

value: Frtip, 40 minutes


title: Kidney medulla_ZT18_TRF_1_1

description: Library name: KIM22B


title: Kidney medulla_ZT18_ALF_1_2

description: Library name: KIM22C


title: Kidney medulla_ZT16_ALF_2_1

description: Library name: KIM21E


title: Kidney medulla_ZT12_ALF_1_1

description: Library name: KIM19C


title: BAT_ZT0_ALF_2_3

description: Library name: BAT_13G


title: Kidney medulla_ZT12_ALF_1_2

description: Library name: KIM19C


title: Abaxial petiole, Frtip, 40 minutes, rep 2


title: BAT_ZT2_TRF_1_1

description: Library name: BAT_14D


title: Leaf tip, Frtip, 40 minutes, rep 2


title: Kidney medulla_ZT10_ALF_2_1

description: Library name: KIM18E


title: Kidney medulla_ZT10_TRF_1_1

description: Library name: KIM18B


title: Kidney medulla_ZT10_ALF_1_1

description: Library name: KIM18A


title: BAT_ZT0_ALF_2_1

description: Library name: BAT_13G


title: Adaxial petiole, WL, 40 minutes, rep 2

value: WL, 40 minutes


title: Kidney medulla_ZT8_TRF_2_1

description: Library name: KIM17F


title: BAT_ZT0_TRF_1_1

description: Library name: BAT_13B


title: Kidney medulla_ZT8_ALF_2_2

description: Library name: KIM17E


title: Kidney medulla_ZT8_ALF_2_1

description: Library name: KIM17E


title: Kidney medulla_ZT12_TRF_2_1

description: Library name: KIM19H


title: BAT_ZT0_ALF_1_3

description: Library name: BAT_13A


title: Kidney medulla_ZT8_TRF_1_1

description: Library name: KIM17B


title: Adaxial petiole, Frtip, 300 minutes, rep 1

value: rep 1

value: Frtip, 300 minutes


title: Kidney medulla_ZT8_ALF_1_2

description: Library name: KIM17A


title: Abaxial petiole, Frtip, 300 minutes, rep 1


title: Leaf tip, WL, 40 minutes, rep 2


title: Kidney medulla_ZT8_ALF_1_1

description: Library name: KIM17A


title: BAT_ZT0_ALF_1_2

description: Library name: BAT_13A

value: Brown adipose tissue


title: Kidney medulla_ZT10_TRF_2_1

description: Library name: KIM18F

value: wild type


title: BAT_ZT0_ALF_2_2

description: Library name: BAT_13G


title: BAT_ZT0_ALF_1_1

description: Library name: BAT_13A


title: Kidney medulla_ZT6_ALF_2_1

description: Library name: KIM16E

value: kidney medulla


title: Hypothalamus_ZT22_TRF_2_1

description: Library name: B24HYPO4

source_name: Hypothalamus

value: Hypothalamus


title: Kidney medulla_ZT6_ALF_1_1

description: Library name: KIM16C


title: Kidney medulla_ZT6_TRF_1_2

description: Library name: KIM16B

value: 9 hr time-restricted feeding


title: Adaxial petiole, WL, 300 minutes, rep 1

value: WL, 300 minutes


title: Leaf tip, Frtip, 300 minutes, rep 1


title: Kidney medulla_ZT6_TRF_2_1

description: Library name: KIM16H


title: Kidney medulla_ZT6_ALF_1_2

description: Library name: KIM16C

value: ad-libitum feeding


title: Kidney medulla_ZT6_TRF_1_1

description: Library name: KIM16B


title: Kidney medulla_ZT4_TRF_2_1

description: Library name: KIM15F


title: Abaxial petiole, WL, 300 minutes, rep 1

value: Abaxial petiole


title: Hypothalamus_ZT22_TRF_1_1

description: Library name: B24HYPO3


title: Leaf tip, WL, 300 minutes, rep 1


title: Kidney medulla_ZT4_ALF_2_1

description: Library name: KIM15E


title: Hypothalamus_ZT22_ALF_2_2

description: Library name: B24HYPO2


title: Adaxial petiole, Frtip, 180 minutes, rep 1

value: Adaxial petiole

value: Frtip, 180 minutes


title: Kidney medulla_ZT4_ALF_1_1

description: Library name: KIM15A


title: Kidney medulla_ZT2_TRF_2_2

description: Library name: KIM14H


title: Abaxial petiole, Frtip, 180 minutes, rep 1


title: Kidney medulla_ZT2_TRF_1_2

description: Library name: KIM14D


title: Kidney medulla_ZT2_ALF_2_1

description: Library name: KIM14E


title: Hypothalamus_ZT22_ALF_1_2

description: Library name: B24HYPO1


title: Kidney medulla_ZT2_TRF_1_1

description: Library name: KIM14D


title: Hypothalamus_ZT22_ALF_1_1

description: Library name: B24HYPO1


title: Adaxial petiole, WL, 180 minutes, rep 1

value: WL, 180 minutes


title: Kidney medulla_ZT2_TRF_2_1

description: Library name: KIM14H


title: Hypothalamus_ZT22_TRF_1_2

description: Library name: B24HYPO3


title: Kidney medulla_ZT2_ALF_1_1

description: Library name: KIM14A


title: Abaxial petiole, WL, 180 minutes, rep 1


title: Leaf tip, Frtip, 180 minutes, rep 1

value: Leaf tip


title: Kidney medulla_ZT0_TRF_2_1

description: Library name: KIM13H


title: Kidney medulla_ZT0_ALF_2_1

description: Library name: KIM13G


title: Kidney medulla_ZT0_TRF_2_2

description: Library name: KIM13H


title: Kidney medulla_ZT4_TRF_1_1

description: Library name: KIM15D


title: Hypothalamus_ZT20_TRF_2_1

description: Library name: B23HYPO4


title: Leaf tip, WL, 180 minutes, rep 1


title: Kidney medulla_ZT0_ALF_1_1

description: Library name: KIM13A


title: Adaxial petiole, Frtip, 160 minutes, rep 1

value: Frtip, 160 minutes


title: Kidney cortex_ZT22_TRF_2_2

description: Library name: KIC24H

source_name: KIC

value: kidney cortex


title: Hypothalamus_ZT20_TRF_1_1

description: Library name: B23HYPO3


title: Kidney medulla_ZT4_ALF_1_2

description: Library name: KIM15A


title: Hypothalamus_ZT22_ALF_2_1

description: Library name: B24HYPO2


title: Hypothalamus_ZT20_ALF_2_2

description: Library name: B23HYPO2


title: Kidney cortex_ZT22_TRF_2_1

description: Library name: KIC24H


title: Abaxial petiole, Frtip, 160 minutes, rep 1


title: Kidney cortex_ZT22_ALF_2_1

description: Library name: KIC24G


title: Kidney cortex_ZT22_ALF_1_2

description: Library name: KIC24C


title: Kidney cortex_ZT22_TRF_1_1

description: Library name: KIC24B


title: Adaxial petiole, WL, 160 minutes, rep 1

value: WL, 160 minutes


title: Kidney cortex_ZT20_TRF_2_2

description: Library name: KIC23H


title: Hypothalamus_ZT20_ALF_1_1

description: Library name: B23HYPO1


title: Hypothalamus_ZT18_TRF_2_2

description: Library name: B22HYPO4


title: Kidney cortex_ZT20_TRF_1_1

description: Library name: KIC23B


title: Kidney medulla_ZT0_TRF_1_1

description: Library name: KIM13B


title: Hypothalamus_ZT20_TRF_1_2

description: Library name: B23HYPO3


title: Kidney cortex_ZT20_ALF_1_1

description: Library name: KIC23A


title: Hypothalamus_ZT20_ALF_1_2

description: Library name: B23HYPO1


title: Kidney cortex_ZT18_TRF_2_1

description: Library name: KIC22H


title: Leaf tip, WL, 160 minutes, rep 1

value: rep 1


title: Hypothalamus_ZT18_TRF_2_1

description: Library name: B22HYPO4


title: Kidney cortex_ZT20_TRF_2_1

description: Library name: KIC23H


title: Kidney cortex_ZT18_ALF_1_1

description: Library name: KIC22C


title: Abaxial petiole, WL, 160 minutes, rep 1


title: Kidney cortex_ZT20_ALF_2_1

description: Library name: KIC23G


title: Hypothalamus_ZT18_TRF_1_2

description: Library name: B22HYPO3


title: Kidney cortex_ZT18_TRF_1_1

description: Library name: KIC22B


title: Abaxial petiole, Frtip, 140 minutes, rep 1

value: Frtip, 140 minutes


title: Hypothalamus_ZT18_TRF_1_1

description: Library name: B22HYPO3


title: Leaf tip, Frtip, 160 minutes, rep 1


title: Kidney cortex_ZT16_TRF_2_1

description: Library name: KIC21F


title: Hypothalamus_ZT20_ALF_2_1

description: Library name: B23HYPO2


title: Kidney cortex_ZT22_ALF_1_1

description: Library name: KIC24C


title: Kidney cortex_ZT16_ALF_2_1

description: Library name: KIC21E


title: Adaxial petiole, WL, 140 minutes, rep 1

value: WL, 140 minutes


title: Kidney cortex_ZT16_ALF_1_1

description: Library name: KIC21C

value: wild type


title: Kidney cortex_ZT16_TRF_1_1

description: Library name: KIC21B


title: Hypothalamus_ZT18_ALF_2_1

description: Library name: B22HYPO2


title: Abaxial petiole, WL, 140 minutes, rep 1


title: Kidney cortex_ZT14_TRF_2_2

description: Library name: KIC20H


title: Adaxial petiole, Frtip, 140 minutes, rep 1


title: Kidney cortex_ZT14_TRF_2_1

description: Library name: KIC20H


title: Kidney cortex_ZT14_ALF_2_1

description: Library name: KIC20E


title: Hypothalamus_ZT18_ALF_1_2

description: Library name: B22HYPO1


title: Leaf tip, WL, 140 minutes, rep 1


title: Kidney cortex_ZT18_ALF_2_1

description: Library name: KIC22E


title: Hypothalamus_ZT18_ALF_1_1

description: Library name: B22HYPO1


title: Adaxial petiole, Frtip, 120 minutes, rep 1

value: Frtip, 120 minutes


title: Kidney cortex_ZT14_ALF_1_1

description: Library name: KIC20A


title: Kidney cortex_ZT12_TRF_2_1

description: Library name: KIC19H


title: Abaxial petiole, Frtip, 120 minutes, rep 1


title: Kidney cortex_ZT14_ALF_1_2

description: Library name: KIC20A


title: Kidney cortex_ZT12_ALF_2_2

description: Library name: KIC19E


title: Hypothalamus_ZT16_TRF_2_2

description: Library name: B21HYPO4

value: Hypothalamus


title: Hypothalamus_ZT16_TRF_2_1

description: Library name: B21HYPO4

value: 9 hr time-restricted feeding


title: Kidney cortex_ZT12_ALF_2_1

description: Library name: KIC19E


title: Leaf tip, Frtip, 120 minutes, rep 1


title: Kidney cortex_ZT12_TRF_1_1

description: Library name: KIC19D


title: Hypothalamus_ZT16_TRF_1_2

description: Library name: B21HYPO3


title: Kidney cortex_ZT12_ALF_1_1

description: Library name: KIC19C


title: Leaf tip, Frtip, 140 minutes, rep 1


title: Adaxial petiole, WL, 120 minutes, rep 1

value: WL, 120 minutes


title: Kidney cortex_ZT10_TRF_2_1

description: Library name: KIC18F


title: Kidney cortex_ZT10_ALF_2_1

description: Library name: KIC18E

value: ad-libitum feeding


title: Hypothalamus_ZT16_TRF_1_1

description: Library name: B21HYPO3


title: Abaxial petiole, WL, 120 minutes, rep 1

value: Abaxial petiole


title: Kidney cortex_ZT14_TRF_1_1

description: Library name: KIC20D


title: Kidney cortex_ZT10_TRF_1_1

description: Library name: KIC18B


title: Hypothalamus_ZT16_ALF_2_2

description: Library name: B21HYPO2


title: Leaf tip, WL, 120 minutes, rep 1


title: Kidney cortex_ZT10_ALF_1_2

description: Library name: KIC18A


title: Kidney cortex_ZT10_ALF_1_1

description: Library name: KIC18A


title: Hypothalamus_ZT16_ALF_2_1

description: Library name: B21HYPO2


title: Kidney cortex_ZT8_TRF_2_1

description: Library name: KIC17F


title: Kidney cortex_ZT8_TRF_2_2

description: Library name: KIC17F


title: Adaxial petiole, Frtip, 100 minutes, rep 1

value: Adaxial petiole

value: Frtip, 100 minutes


title: Hypothalamus_ZT16_ALF_1_2

description: Library name: B21HYPO1


title: Kidney cortex_ZT8_ALF_1_1

description: Library name: KIC17A


title: Hypothalamus_ZT16_ALF_1_1

description: Library name: B21HYPO1


title: Abaxial petiole, Frtip, 100 minutes, rep 1


title: Kidney cortex_ZT8_ALF_2_1

description: Library name: KIC17E


title: Kidney cortex_ZT8_TRF_1_1

description: Library name: KIC17B


title: Hypothalamus_ZT14_TRF_2_2

description: Library name: B20HYPO4


title: Kidney cortex_ZT6_ALF_1_1

description: Library name: KIC16C


title: Kidney cortex_ZT6_TRF_2_1

description: Library name: KIC16H


title: Hypothalamus_ZT14_TRF_2_1

description: Library name: B20HYPO4


title: Adaxial petiole, WL, 100 minutes, rep 1

value: WL, 100 minutes


title: Kidney cortex_ZT6_ALF_2_1

description: Library name: KIC16E


title: Abaxial petiole, WL, 100 minutes, rep 1


title: Hypothalamus_ZT14_TRF_1_2

description: Library name: B20HYPO3


title: Kidney cortex_ZT4_TRF_2_1

description: Library name: KIC15F


title: Kidney cortex_ZT6_TRF_1_1

description: Library name: KIC16B


title: Leaf tip, WL, 100 minutes, rep 1

value: Leaf tip


title: Kidney cortex_ZT4_ALF_2_1

description: Library name: KIC15E


title: Kidney cortex_ZT4_TRF_1_1

description: Library name: KIC15D


title: Adaxial petiole, Frtip, 80 minutes, rep 1

value: Frtip, 80 minutes


title: Kidney cortex_ZT4_ALF_1_2

description: Library name: KIC15A

value: kidney cortex


title: Hypothalamus_ZT14_ALF_2_2

description: Library name: B20HYPO2


title: Kidney cortex_ZT4_ALF_1_1

description: Library name: KIC15A


title: Kidney cortex_ZT2_TRF_2_2

description: Library name: KIC14H


title: Leaf tip, Frtip, 100 minutes, rep 1


title: Abaxial petiole, Frtip, 80 minutes, rep 1


title: Hypothalamus_ZT14_ALF_2_1

description: Library name: B20HYPO2


title: Kidney cortex_ZT2_ALF_2_1

description: Library name: KIC14E


title: Leaf tip, Frtip, 80 minutes, rep 1


title: Hypothalamus_ZT14_ALF_1_2

description: Library name: B20HYPO1


title: Kidney cortex_ZT6_TRF_1_2

description: Library name: KIC16B


title: Hypothalamus_ZT14_ALF_1_1

description: Library name: B20HYPO1


title: Kidney cortex_ZT0_TRF_2_1

description: Library name: KIC13H


title: Abaxial petiole, WL, 80 minutes, rep 1

value: WL, 80 minutes


title: Kidney cortex_ZT0_ALF_2_2

description: Library name: KIC13G


title: Hypothalamus_ZT12_TRF_2_2

description: Library name: B19HYPO4


title: Kidney cortex_ZT0_ALF_2_1

description: Library name: KIC13G


title: Kidney cortex_ZT0_TRF_1_1

description: Library name: KIC13B


title: Hypothalamus_ZT12_TRF_2_1

description: Library name: B19HYPO4


title: Hypothalamus_ZT14_TRF_1_1

description: Library name: B20HYPO3


title: Kidney cortex_ZT0_ALF_1_2

description: Library name: KIC13A


title: Kidney cortex_ZT0_ALF_1_1

description: Library name: KIC13A


title: Adaxial petiole, Frtip, 60 minutes, rep 1

value: rep 1

value: Frtip, 60 minutes


title: Ileum_ZT22_TRF_2_1

description: Library name: Ile_24H

source_name: Ileum

value: Ileum


title: Hypothalamus_ZT12_TRF_1_2

description: Library name: B19HYPO3

value: wild type


title: Kidney cortex_ZT2_TRF_2_1

description: Library name: KIC14H


title: Ileum_ZT22_ALF_2_2

description: Library name: Ile_24G


title: Abaxial petiole, Frtip, 60 minutes, rep 1

source_name: Leaf material


title: Kidney cortex_ZT2_TRF_1_1

description: Library name: KIC14D


title: Ileum_ZT22_ALF_1_1

description: Library name: Ile_24C


title: Adaxial petiole, WL, 80 minutes, rep 1


title: Hypothalamus_ZT12_TRF_1_1

description: Library name: B19HYPO3


title: Leaf tip, Frtip, 60 minutes, rep 1


title: Ileum_ZT20_TRF_2_1

description: Library name: Ile_23H


title: Kidney cortex_ZT2_ALF_1_1

description: Library name: KIC14A


title: Ileum_ZT22_TRF_1_1

description: Library name: Ile_24B


title: Ileum_ZT20_ALF_2_1

description: Library name: Ile_23G


title: Ileum_ZT20_TRF_1_3

description: Library name: Ile_23B


title: Hypothalamus_ZT12_ALF_2_1

description: Library name: B19HYPO2


title: Abaxial petiole, WL, 60 minutes, rep 1

value: WL, 60 minutes


title: Ileum_ZT20_ALF_1_2

description: Library name: Ile_23A


title: Leaf tip, WL, 80 minutes, rep 1


title: Leaf tip, WL, 60 minutes, rep 1


title: Hypothalamus_ZT12_ALF_1_2

description: Library name: B19HYPO1

value: Hypothalamus


title: Ileum_ZT18_ALF_2_2

description: Library name: Ile_22E


title: Hypothalamus_ZT12_ALF_1_1

description: Library name: B19HYPO1


title: Ileum_ZT18_ALF_1_2

description: Library name: Ile_22C


title: Leaf tip, Frtip, 40 minutes, rep 1

value: Frtip, 40 minutes


title: Ileum_ZT16_TRF_2_2

description: Library name: Ile_21F

value: 9 hr time-restricted feeding


title: Leaf tip, WL, 40 minutes, rep 1

value: WL, 40 minutes


title: Ileum_ZT18_TRF_1_3

description: Library name: Ile_22B


title: Hypothalamus_ZT10_TRF_1_2

description: Library name: B18HYPO3


title: Hypothalamus_ZT12_ALF_2_2

description: Library name: B19HYPO2

value: ad-libitum feeding


title: Adaxial petiole, WL, 60 minutes, rep 1

value: Adaxial petiole


title: Ileum_ZT16_TRF_1_3

description: Library name: Ile_21B


title: Hypothalamus_ZT10_TRF_2_1

description: Library name: B18HYPO4


title: Hypothalamus_ZT10_TRF_1_1

description: Library name: B18HYPO3


title: Ileum_ZT14_TRF_2_1

description: Library name: Ile_20H


title: HEK293T_DNMT1_KO_IgG

city: Guangzhou

first: Lijun

last: Xiang

state: Guangdong

address: No.55, West of Zhongshan Avenue

department: Guangzhou Key Laboratory of Insect Development Regulation and Application Research

institute: South China Normal University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT&Tag reads were trimmed from 3' end until the final base had a quality score > 20, using TrimGalore-0.6.7, discarding reads left with < 20 bp
CUT&Tag reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.4.5.
The aligned reads were removed with Picard MarkDuplicates, and the deduplicated BAM files were normalized to the total aligned reads (reads per million, BPM) with the bamCoverage command from deepTools 3.3.0
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=1E-5
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

source_name: HEK293T, IgG, Sigma-Aldrich

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
CUT&Tag was performed essentially as described by Kaiwei Liang et al. 2021, with minor modifications according the Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China).One hundred thousand HepG2 cells were used for the CUT&Tag experiment, and cell counting was performed by using a Cellometer Mini (Nexcelom Bioscience, Boston, MA, USA). pA-Tn5 transposase was used to cut the genome and add a special adaptor sequence to build a library.
Libraries were prepared according to Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China)

value: Human embryonic kidney


title: Ileum_ZT16_ALF_2_1

description: Library name: Ile_21E


title: Ileum_ZT14_ALF_2_1

description: Library name: Ile_20E


title: HEK293T_WT_IgG

value: WT


title: Hypothalamus_ZT10_ALF_1_2

description: Library name: B18HYPO1


title: Ileum_ZT14_TRF_1_2

description: Library name: Ile_20D


title: HEK293T_DNMT1_KO_BG4

source_name: HEK293T, BG4, Sigma-Aldrich


title: Ileum_ZT14_ALF_1_1

description: Library name: Ile_20A


title: Ileum_ZT16_ALF_1_1

description: Library name: Ile_21C


title: Ileum_ZT18_TRF_2_2

description: Library name: Ile_22H


title: Ileum_ZT12_ALF_2_1

description: Library name: Ile_19G


title: Hypothalamus_ZT8_TRF_2_2

description: Library name: B17HYPO4


title: Hypothalamus_ZT10_ALF_1_1

description: Library name: B18HYPO1


title: HEK293T_WT_BG4


title: Ileum_ZT12_TRF_2_1

description: Library name: Ile_19H


title: Ileum_ZT12_TRF_1_2

description: Library name: Ile_19D


title: HEK293T,DNMT1_KO,rep3

data_processing:
RNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using TrimGalore-0.6.7, discarding reads left with < 20 bp.
Trimmed sequence reads were mapped to hg38 using hisat2 with default setting.
The BAM files were normalized to the total aligned reads (Counts Per Million mapped reads, CPM) with the bamCoverage command from deepTools 3.3.0
Assembly: hg38
Supplementary files format and content: bigwig

molecule: polyA RNA

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.


title: Hypothalamus_ZT8_TRF_2_1

description: Library name: B17HYPO4


title: Ileum_ZT12_ALF_1_1

description: Library name: Ile_19C


title: HEK293T,DNMT1_KO,rep2


title: Ileum_ZT10_TRF_2_2

description: Library name: Ile_18F


title: Ileum_ZT10_TRF_1_1

description: Library name: Ile_18B


title: Ileum_ZT10_ALF_2_2

description: Library name: Ile_18E


title: Hypothalamus_ZT8_TRF_1_2

description: Library name: B17HYPO3


title: Ileum_ZT10_ALF_1_2

description: Library name: Ile_18A


title: Hypothalamus_ZT8_TRF_1_1

description: Library name: B17HYPO3


title: HEK293T,DNMT1_KO,rep1


title: Ileum_ZT8_TRF_2_2

description: Library name: Ile_17F


title: Ileum_ZT8_TRF_1_2

description: Library name: Ile_17B


title: HEK293T,WT,rep3


title: HEK293T,WT,rep2


title: Hypothalamus_ZT8_ALF_2_2

description: Library name: B17HYPO2


title: Ileum_ZT8_ALF_2_2

description: Library name: Ile_17E


title: Ileum_ZT8_ALF_1_2

description: Library name: Ile_17A


title: Ileum_ZT6_TRF_2_1

description: Library name: Ile_16H


title: HEK293T,WT,rep1


title: Hypothalamus_ZT8_ALF_2_1

description: Library name: B17HYPO2


title: Ileum_ZT6_ALF_2_3

description: Library name: Ile_16E


title: Ileum_ZT6_TRF_1_1

description: Library name: Ile_16B


title: Hypothalamus_ZT8_ALF_1_2

description: Library name: B17HYPO1


title: Hypothalamus_ZT8_ALF_1_1

description: Library name: B17HYPO1


title: Ileum_ZT4_TRF_2_2

description: Library name: Ile_15F


title: Ileum_ZT4_ALF_2_2

description: Library name: Ile_15E


title: Ileum_ZT4_TRF_1_2

description: Library name: Ile_15D


title: Hypothalamus_ZT6_TRF_2_2

description: Library name: B16HYPO4


title: Ileum_ZT4_ALF_1_2

description: Library name: Ile_15A


title: Hypothalamus_ZT6_TRF_2_1

description: Library name: B16HYPO4


title: Ileum_ZT2_TRF_2_1

description: Library name: Ile_14H


title: Biliary atresia liver sample P0414

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Biliary atresia liver sample

data_processing:
The RNA-seq reads were aligned to the human genome (GRCh37/hg19) using TopHat (version 2.1.0)
Transcript quantifications were performed by Cufflinks v2.2.1
Transcript abundances were normalized in reads per kilobase of exon per million mapped reads (RPKM)
Assembly: GrCh37/hg19
Supplementary files format and content: Tab-delimited files with RPKM

source_name: Liver

extract_protocol:
Total RNA was isolated from liver biopsies using the miRNeasy Kit (QIAGEN). RNA purity was assessed using the Agilent 2100 Bioanalyzer. Total RNA was converted to cDNA using High-Capacity cDNA Reverse Transcrition Kit (ABI).
The cDNA was then used for Illumina sequencing library preparation by TruSeq Stranded mRNA Library Prep Kit. DNA fragments were further end repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls and adapters were ligated for single end or paired end sequencing on Illumina HiSeq 2500.

value: Liver

tag: disease state

value: Biliary Atresia


title: Hypothalamus_ZT6_TRF_1_2

description: Library name: B16HYPO3


title: Ileum_ZT2_ALF_2_2

description: Library name: Ile_14E


title: Intrahepatic cholestasis liver sample Cint7

description: Intrahepatic cholestasis liver sample

value: Intrahepatic Cholestasis


title: Hypothalamus_ZT6_TRF_1_1

description: Library name: B16HYPO3


title: Biliary atresia liver sample Cint6

description: Biliary atresia liver sample


title: Hypothalamus_ZT6_ALF_1_2

description: Library name: B16HYPO1


title: Ileum_ZT2_TRF_1_1

description: Library name: Ile_14D


title: Intrahepatic cholestasis liver sample Cint5

description: Intrahepatic cholestasis liver sample


title: Intrahepatic cholestasis liver sample B97

description: Intrahepatic cholestasis liver sample


title: Ileum_ZT2_ALF_1_1

description: Library name: Ile_14A


title: Hypothalamus_ZT6_ALF_1_1

description: Library name: B16HYPO1


title: Ileum_ZT6_ALF_1_2

description: Library name: Ile_16C


title: Ileum_ZT0_TRF_2_2

description: Library name: Ile_13H


title: Intrahepatic cholestasis liver sample B88

description: Intrahepatic cholestasis liver sample


title: Hypothalamus_ZT4_TRF_2_1

description: Library name: B15HYPO4


title: Donor 2 TCL1A, mRNA-derived cDNA

city: Palo Alto

first: Jayakrishnan (Jk)

last: Gopakumar

state: CA

address: 240 Pasteur Dr Rm 4600

institute: Stanford

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz.gz, features.tsv.gz.gz, matrix.mtx.gz.gz
Library strategy: 10X CITE-Seq

source_name: Hematopoietic Cells

growth_protocol: CD34+ cells were thawed and cultured in HSPC Expansion media (StemSpanII + 10% CD34+ Expansion Supplement + 0.1% Penicillin/Streptomycin) for 48 hours before lentiviral transduction. 72 hours after lentivirus addition, Lineage- CD34+ CD38- CD45RA- GFP+ were sorted and plated.

extract_protocol:
Seven days after sort, 10X 3'v3.1 with Feature Barcoding was performed. 60,000-120,000 cells were harvested and resuspended in 50 uL of PBS + 1% BSA. Cells were then blocked with 5 uL of TruStain FX for 10 minutes. Next, cells were stained with 0.5 uL of each TotalSeq-B antibody (CD34, CD38, CD45RA, CD90, CD49f, CD35, CD11a, CD59, CD117) for 30 minutes. Following 4 washes with PBS + 1% BSA, 10,000 cells were loaded onto a Chromium Next GEM Chip G
GEM generation & barcoding, post GEM–RT cleanup & cDNA amplification, 3’ gene expression library construction, and cell surface protein library construction were performed as described in CG000317_ChromiumNextGEMSingleCell3'v3.1_CellSurfaceProtein_RevC (https://support.10xgenomics.com/single-cell-gene-expression/index/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v31-chemistry-dual-index-with-feature-barcoding-technology-for-cell-surface-protein). Gene expression and cell surface protein libraries were pooled together at a ratio of 4:1 and sequenced on an Illumina NovaSeq.

value: Hematopoietic Cells

value: In vitro cultured CD34+

value: Donor 2 (T/T) TCL1A-eGFP

tag: library type

value: mRNA

tag: antibodies/tags


title: Donor 2 control, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
ADT processed data included in Cell Ranger output files located on cDNA samples.

library_source: other

molecule: protein

tag: tissue

value: Donor 2 (T/T) control-eGFP

value: ADT

value: TotalSeq-B antibody (CD34, CD38, CD45RA, CD90, CD49f, CD35, CD11a, CD59, CD117)


title: Ileum_ZT0_ALF_2_2

description: Library name: Ile_13G

value: Ileum

value: wild type


title: Ileum_ZT0_TRF_1_2

description: Library name: Ile_13B

value: 9 hr time-restricted feeding


title: Donor 2 control, mRNA-derived cDNA


title: Ileum_ZT0_ALF_1_2

description: Library name: Ile_13A

value: ad-libitum feeding


title: Intrahepatic cholestasis liver sample B87

description: Intrahepatic cholestasis liver sample


title: Hypothalamus_ZT4_ALF_2_2

description: Library name: B15HYPO2

value: Hypothalamus


title: Donor 2 TCL1A, ADT-derived cDNA


title: Intrahepatic cholestasis liver sample B74

description: Intrahepatic cholestasis liver sample


title: Hypothalamus_ZT4_ALF_2_1

description: Library name: B15HYPO2


title: Intrahepatic cholestasis liver sample B68

description: Intrahepatic cholestasis liver sample


title: Hypothalamus_ZT4_TRF_1_1

description: Library name: B15HYPO3


title: 5i8d2: BFRTV8d miRNAseq

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

data_processing:
Illumina seqencing reads were cleaned and adapter-removed for quality control and tested the results using FastQC(version0.10.1).
High-quality reads were mapped to the refer genome to obtain SAM files using Bowtie(v1.1.2)
Known miRNA and Novel miRNA were identified by miRDeep2(v2.0.0.5) software,also obtained the read count of each sample and the Reads Per Million(RPM) was then calculated for downstream analysis.
Differential expression analysis was performed using DESeq2 (v1.16.1) with read count,target genes detection and function enrichment were performed.
Genome_build: CaprahircusARS1
Supplementary_files_format_and_content: count and RPM values for each Sample

organism: Capra hircus

source_name: Induced mammary epithelial cell

extract_protocol:
Extract total RNA from each sample,then total RNA was separated by 15% agarose gels to extract the small RNA (18-30 nt).
After ethanol precipitation and small RNA sample enrichment by centrifugation, the libraries were prepared according to the method and process of the Small RNA Sample Preparation Kit (Illumina, RS-200-0048).The main contents are as follows: First,connecting the 3' adaptor and 5' adaptor to the separated small RNA.Then RT-PCR.Finally,recycling strips of 145-160bp (22-30nt RNA).

treatment_protocol: GEFs were seeded at a density of 5×104 cells per well of a 4-well plate or 5×105 cells per 60 mm dish and cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with fibroblast culture medium. The next day, the fibroblast medium was replaced by BFRTV induction medium. The culture was continued for 8 days, and the induction medium was refreshed every 2 days. On day 8, those induced cells with primary colonies were named BFRTV-8d cells/CiMECs-P0 and were further passaged at a ratio of 1:3 every 3-4 days; the cells were cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with goat MEC culture medium changed every 2 days. The culture plates or dishes were precoated with Matrigel® Matrix (Corning, 356230).

value: Induced mammary epithelial cell

tag: induction time


title: Donor 1 TCL1A, mRNA-derived cDNA

value: Donor 1 (G/G) TCL1A-eGFP


title: Donor 1 control, ADT-derived cDNA

value: Donor 1 (G/G) control-eGFP


title: Hypothalamus_ZT4_TRF_1_2

description: Library name: B15HYPO3


title: Hypothalamus_ZT4_ALF_1_2

description: Library name: B15HYPO1


title: Intrahepatic cholestasis liver sample B67

description: Intrahepatic cholestasis liver sample

value: Liver


title: Intrahepatic cholestasis liver sample B62

description: Intrahepatic cholestasis liver sample

value: Intrahepatic Cholestasis


title: CK2: BFRTV0d miRNAseq

source_name: Ear fibroblasts

value: Ear fibroblasts


title: Donor 1 control, mRNA-derived cDNA

value: Hematopoietic Cells

value: In vitro cultured CD34+


title: CK1: BFRTV0d miRNAseq


title: Intrahepatic cholestasis liver sample B61

description: Intrahepatic cholestasis liver sample


title: Hypothalamus_ZT2_TRF_2_1

description: Library name: B14HYPO4


title: Hypothalamus_ZT4_ALF_1_1

description: Library name: B15HYPO1


title: Biliary atresia liver sample B83

description: Biliary atresia liver sample

value: Biliary Atresia


title: Hypothalamus_ZT18_ALF_2_2

description: Library name: B22HYPO2


title: Biliary atresia liver sample 2-0707

description: Biliary atresia liver sample


title: Donor 1 TCL1A, ADT-derived cDNA


title: Hypothalamus_ZT2_TRF_1_2

description: Library name: B14HYPO3


title: Hypothalamus_ZT2_TRF_1_1

description: Library name: B14HYPO3


title: Biliary atresia liver sample B9

description: Biliary atresia liver sample


title: W3110_WT_osm__2

city: La Jolla

first: Cameron

last: Lamoureux

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

description:
minicoli_log_tpm.csv
minicoli_counts.csv

data_processing:
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: minicoli_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: minicoli_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

organism: Escherichia coli

source_name: bacterial cell

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

value: bacterial cell

value: wild type - osmotic stress

tag: Stage

value: mid-log phase culture


title: Biliary atresia liver sample B47

description: Biliary atresia liver sample


title: W3110_WT_glc__2

tag: treatment

value: wild type - glucose


title: W3110_WT_glc__1


title: 5i8d1: BFRTV8d miRNAseq


title: Biliary atresia liver sample B153

description: Biliary atresia liver sample


title: Omicron_101_2nd

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

source_name: PBMCs

growth_protocol: Blood samples were collected from the COVID-19 patients infected by Omicron varient.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: gender

value: Female

tag: group (by covid-19 vaccination, prior infection)

value: No vaccination, No prior infection

tag: omicron sublineage

tag: days after positive pcr results

tag: geographical location

value: Austria

value: PBMC


title: Hypothalamus_ZT2_ALF_2_1

description: Library name: B14HYPO2

value: Hypothalamus

tag: strain

tag: feeding intervention

value: ad-libitum feeding

tag: time-point

tag: genotype

value: wild type


title: Biliary atresia liver sample B151

description: Biliary atresia liver sample

value: Liver


title: Hypothalamus_ZT2_ALF_1_2

description: Library name: B14HYPO1


title: W3110_urid__2

tag: cell type

value: wild type - uridine


title: Omicron_99_2nd

value: Male

tag: age

tag: disease state


title: Omicron_103_2nd

value: No vaccination, Prior infection


title: Omicron_100_2nd


title: Hypothalamus_ZT2_ALF_1_1

description: Library name: B14HYPO1


title: Omicron_96_2nd


title: W3110_sorb__2

value: wild type - sorbitol


title: Omicron_94_2nd


title: Hypothalamus_ZT0_TRF_2_1

description: Library name: B13HYPO4

value: 9 hr time-restricted feeding


title: W3110_WT_osm__1

value: bacterial cell


title: W3110_sorb__1


title: Hypothalamus_ZT0_TRF_1_2

description: Library name: B13HYPO3


title: Omicron_91_2nd


title: W3110_pyr__2

value: wild type - pyruvate


title: Hypothalamus_ZT2_ALF_2_2

description: Library name: B14HYPO2


title: NC_2

city: Shenzhen

first: Xiaojun

last: Xu

address: No. 3025, Shennan Middle Road

department: Department of Orthopedics

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: macrophage

value: macrophage


title: NC_3


title: NC_1


title: M1G_3

value: LPS+IFN-γ


title: W3110_pyr__1

value: mid-log phase culture


title: M1G_2


title: W3110_ph5__2

value: wild type - pH 5


title: Hypothalamus_ZT0_ALF_2_2

description: Library name: B13HYPO2


title: Hypothalamus_ZT0_ALF_2_1

description: Library name: B13HYPO2


title: Omicron_84_2nd

value: Female

value: Austria


title: W3110_urid__1


title: M1G_1


title: Omicron_89_2nd

value: No vaccination, No prior infection

value: PBMC


title: W3110_ph5__1


title: Hypothalamus_ZT0_ALF_1_2

description: Library name: B13HYPO1

value: Hypothalamus

value: ad-libitum feeding

value: wild type


title: M1_3

value: LPS+IFN-γ+Garcinol


title: Omicron_75_2nd

value: No vaccination, Prior infection


title: M1_2


title: M1_1


title: W3110_osm__1

value: wild type - osmotic stress


title: Omicron_74_2nd


title: Omicron_73_2nd


title: Hypothalamus_ZT0_TRF_1_1

description: Library name: B13HYPO3

value: 9 hr time-restricted feeding


title: SCN_ZT22_TRF_2_1

description: Library name: A24SCN4

source_name: SCN

value: suprachiasmatic nucleus


title: W3110_N_starve__2

value: bacterial cell

value: wild type - nitrogen starvation


title: Omicron_72_2nd

value: Male


title: SCN_ZT22_TRF_1_2

description: Library name: A24SCN3


title: patient 7 mtDNA cerebellum [8B]

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

country: United Kingdom

institute: University of Exeter

data_processing:
Sequencing, basecalling and demultiplexing using Illumina HiSeq Control Software and CASAVA 1.8.2
Raw reads trimmed using TrimGalore
Trimmed reads aligned to human reference genome GrCh38 through Bismark v0.23.1 using Bowtie 2
Mapped reads de-duplicated and methylation called using Bismark v0.23.1
Genome_build: GrCh38
Supplementary_files_format_and_content: Percentage methylation and read coverage for each position in each sample stored in excel spreadsheet chrM_methylation.xlsx

source_name: cerebellum

extract_protocol:
Mitochondria were isolated from frozen, post-mortem brain. MtDNA was further enriched through the use of a custom library designed to amplify the mitochondrial genome
Libraries were prepared according to Illumina's instructions for Whole-Genome Bisulfite Sequencing

tag: patient id

tag: patient sex

tag: patient age (years)

value: cerebellum


title: SCN_ZT22_TRF_2_2

description: Library name: A24SCN4

tag: tissue


title: patient 6 mtDNA cerebellum [7B]


title: Omicron_85_2nd


title: W3110_N_starve__1

tag: treatment

tag: Stage

value: mid-log phase culture


title: W3110_LB__2

value: wild type - LB


title: SCN_ZT22_TRF_1_1

description: Library name: A24SCN3


title: Omicron_67_2nd

tag: gender

value: Female

tag: group (by covid-19 vaccination, prior infection)

value: Austria


title: patient 5 mtDNA cerebellum [6B]


title: W3110_LB__1


title: patient 4 mtDNA cerebellum [5B]


title: W3110_osm__2


title: Hypothalamus_ZT0_ALF_1_1

description: Library name: B13HYPO1


title: SCN_ZT22_ALF_2_2

description: Library name: A24SCN2


title: W3110_Fe_starve__2

value: wild type - iron starvation


title: patient 3 mtDNA cerebellum [3B]


title: SCN_ZT22_ALF_2_1

description: Library name: A24SCN2


title: SCN_ZT22_ALF_1_2

description: Library name: A24SCN1


title: Omicron_66_2nd

value: No vaccination, No prior infection

tag: omicron sublineage

tag: days after positive pcr results

value: PBMC


title: Omicron_55_2nd

tag: geographical location


title: patient 2 mtDNA cerebellum [2B]


title: Omicron_54_2nd


title: SCN_ZT22_ALF_1_1

description: Library name: A24SCN1

tag: strain

tag: feeding intervention

value: ad-libitum feeding

value: wild type


title: Omicron_53_2nd


title: patient 1 mtDNA cerebellum [1B]


title: Omicron_70_2nd

value: No vaccination, Prior infection


title: SCN_ZT20_TRF_2_2

description: Library name: A23SCN4

tag: time-point

tag: genotype


title: patient 7 mtDNA superior temporal gyrus [8A]

source_name: superior temporal gyrus

value: superior temporal gyrus


title: Omicron_51_2nd

tag: age

tag: cell type


title: SCN_ZT20_TRF_2_1

description: Library name: A23SCN4

value: 9 hr time-restricted feeding


title: patient 6 mtDNA superior temporal gyrus [7A]

tag: patient id


title: W3110_glc__2

value: wild type - glucose


title: W3110_glc__1

value: bacterial cell


title: Omicron_43_2nd

tag: disease state


title: patient 5 mtDNA superior temporal gyrus [6A]

tag: patient sex

tag: patient age (years)


title: SCN_ZT20_TRF_1_2

description: Library name: A23SCN3

tag: tissue

value: suprachiasmatic nucleus


title: Omicron_42_2nd

value: Male


title: SCN_ZT20_TRF_1_1

description: Library name: A23SCN3


title: patient 4 mtDNA superior temporal gyrus [5A]


title: W3110_fruc__2

tag: treatment

value: wild type - fructose

tag: Stage


title: W3110_Fe_starve__1

value: mid-log phase culture


title: Omicron_38_2nd

tag: gender

tag: group (by covid-19 vaccination, prior infection)


title: SCN_ZT20_ALF_1_2

description: Library name: A23SCN1


title: Omicron_37_2nd

tag: omicron sublineage

tag: days after positive pcr results


title: patient 3 mtDNA superior temporal gyrus [3A]


title: W3110_glyc__1

tag: strain

value: wild type - glycerol


title: patient 2 mtDNA superior temporal gyrus [2A]

value: Female


title: W3110_glyc__2


title: Omicron_35_2nd

tag: geographical location

value: Austria


title: W3110_cyt__1

value: wild type - cytidine


title: patient 1 mtDNA superior temporal gyrus [1A]


title: W3110_cyt__2


title: SCN_ZT20_ALF_1_1

description: Library name: A23SCN1

tag: feeding intervention

tag: time-point


title: minE_urid__2

value: reduced strain - uridine


title: SCN_ZT18_TRF_2_1

description: Library name: A22SCN4

tag: genotype


title: Omicron_34_2nd

tag: age

value: No vaccination, No prior infection

tag: cell type

value: PBMC


title: Arabidopsis root cells - sc_114

city: Durham

first: Philip

middle: N.

last: Benfey

state: North Carolina

address: 130 Science Drive

department: Biology

institute: Duke University

library_source: transcriptomic single cell

data_processing:
Processed by COPILOT (https://github.com/ohlerlab/COPILOT)
Assembly: TAIR10
Supplementary files format and content: Seurat object

source_name: Arabidopsis root cells - Benfey Lab

growth_protocol: Arabidopsis accession Columbia-0 (Col-0) was used as wild type. The following lines were previously described: bri1  GABI_134E10 (Jaillais et al., 2011); bri1-116brl1brl3 triple mutant (bri1-T) (Irani et al., 2012); pGL2:BRI1-GFP/bri1-T (Vragović et al., 2015); gtl1-1 (WiscDsLox413-416C9), df1-1 (SALK_106258), and gtl1-1 df1-1 (Shibata et al., 2018); JKD-Ypet recombineering line (Moreno-Risueno et al., 2015). Seeds were sterilized using 50% (v/v) bleach with 0.05% Tween-20 for 10-15 minutes, plated on 1/2 Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media, and stratified 2-4 days at 4°C in the dark. Plates were kept vertically in a Percival growth chamber set to 22°C, 16 hours light/8 hours dark and grown for 7 days. Chemical treatments were conducted by cooling the growth media to approximately 60°C after autoclaving and adding DMSO (a mock solvent), 1μM Brassinazole (BRZ, SML1406,  Sigma) or 100nM Brassinolide (BL, 21594, Cayman Chemical).

extract_protocol:
For each sample, ~0.5cm root tips were harvested from 1000-3000 roots and placed into a 35mm petri dish containing a 70 μm cell strainer and 4.5mL enzyme solution (1.5% [w/v] cellulase [ONOZUKA R-10, GoldBio], 0.1% Pectolyase [Sigma P3026], 0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol). The digestion was incubated on an 85 rpm shaker at 25°C for one hour with additional stirring every 15-20 minutes. The resulting cell solution was filtered twice through 40 μm cell strainers and centrifuged for 5 minutes at 500g in a swinging bucket rotor. The pellet was washed with 2mL washing solution (0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol), centrifuged again at 500g for 3 minutes, and the pellet resuspended in washing solution at a concentration of ~2000 cells/uL. We loaded 16,000 cells, with the aim to capture 10,000 cells per sample with the 10X Genomics Chromium 3` Gene expression v3 or v3.1 kits.
Cell barcoding and library construction were performed following the manufacturer’s instructions. cDNA and final library quality were verified using a Bioanalyzer High Sensitivity DNA Chip (Agilent) and sequenced on an Illumina NovaSeq 6000 instrument to produce 100bp paired-end reads.

treatment_protocol: For BL scRNA-seq, we first grew plants on 1 μM BRZ to deplete endogenous BRs, then transferred plants to either a fresh BRZ plate or 100nM BL. We monitored the efficacy of these treatments using a constitutively expressed 35S:BES1-GFP line. In agreement with previous reports (Gampala et al., 2007; Ryu et al., 2007; Yin et al., 2002), BES1-GFP was predominantly present in the cytoplasm under low BR conditions resulting from BRZ treatment but accumulated in the nucleus following BL treatment (Figures S1A and S1B). We performed two separate BL scRNA-seq treatment experiments. The first consisted of a BRZ and 2 hour BL treatment. The second experiment included two additional replicates of BRZ and BL 2 hours along with the other time points in our time course (BL 0.5, 1, 4, and 8 hour treatments). Each of the BL treatments was staggered so that all samples were collected simultaneously.WT, bri1-T, and pGL2:BRI1-GFP/bri1-T were similarly profiled in a side-by-side scRNA-seq experiment under control conditions with two replicates per genotype. Lastly, scRNA-seq was performed on WT, gtl1, df1, and gtl1 df1 in duplicate under control conditions.

tag: name

value: WT BRZ without CaCl2

value: WT

tag: full genotype

value: WT Col-0

value: BRZ

tag: concentration

tag: timepoint

tag: time trt

tag: rep

tag: date

tag: seq run

tag: 10x chemistry

tag: number of_cells

tag: number of_genes_detected

tag: median umi_counts_per_cell


title: minE_urid__1

tag: strain

tag: treatment

tag: Stage


title: Omicron_33_2nd

tag: gender

tag: age

tag: group (by covid-19 vaccination, prior infection)

tag: omicron sublineage

tag: days after positive pcr results

tag: disease state

tag: geographical location


title: W3110_fruc__1

tag: cell type


title: Arabidopsis root cells - sc_112

tag: name

value: WT BRZ + CaCl2

tag: genotype

tag: full genotype

tag: concentration

tag: timepoint

tag: time trt

tag: rep

tag: date


title: minE_sorb__2

tag: strain

value: bacterial cell

tag: treatment

value: reduced strain - sorbitol

tag: Stage


title: minE_sorb__1


title: Omicron_31_2nd

tag: gender

value: Male

tag: age

tag: group (by covid-19 vaccination, prior infection)


title: SCN_ZT18_TRF_1_1

description: Library name: A22SCN3

tag: tissue

value: suprachiasmatic nucleus

tag: feeding intervention

value: 9 hr time-restricted feeding

tag: time-point

value: wild type


title: SCN_ZT18_ALF_2_2

description: Library name: A22SCN2

value: ad-libitum feeding


title: SCN_ZT20_ALF_2_1

description: Library name: A23SCN2


title: Omicron_32_2nd

value: No vaccination, Prior infection

tag: omicron sublineage

tag: days after positive pcr results

tag: disease state

tag: geographical location

value: Austria

tag: cell type


title: Omicron_30_2nd

value: Female


title: Arabidopsis root cells - sc_111

tag: name

value: WT DMSO control + CaCl2

tag: genotype

tag: full genotype

tag: concentration

tag: timepoint

tag: time trt

tag: seq run

tag: 10x chemistry

tag: number of_cells

tag: number of_genes_detected

tag: median umi_counts_per_cell


title: SCN_ZT18_ALF_2_1

description: Library name: A22SCN2

tag: tissue

tag: strain

tag: feeding intervention

tag: time-point


title: minE-pyr__2

tag: treatment

value: reduced strain - pyruvate

tag: Stage

value: mid-log phase culture


title: Omicron_29_2nd

tag: gender

tag: age

tag: group (by covid-19 vaccination, prior infection)

value: No vaccination, No prior infection

tag: omicron sublineage

tag: days after positive pcr results

tag: disease state

tag: geographical location

tag: cell type

value: PBMC


title: minE-pyr__1


title: SCN_ZT18_ALF_1_2

description: Library name: A22SCN1

tag: genotype


title: Omicron_28_2nd


title: minE_ph5__2

value: reduced strain - pH 5


title: SCN_ZT18_ALF_1_1

description: Library name: A22SCN1


title: Omicron_27_2nd


title: SCN_ZT18_TRF_1_2

description: Library name: A22SCN3


title: minE_ph5__1


title: Arabidopsis root cells - sc_113

tag: name

value: WT DMSO control without CaCl2

value: WT

tag: full genotype

value: WT Col-0

value: DMSO

tag: concentration

tag: timepoint

tag: time trt

tag: rep

tag: date

tag: seq run

tag: 10x chemistry

tag: number of_cells

tag: number of_genes_detected


title: SCN_ZT16_TRF_2_2

description: Library name: A21SCN4

tag: tissue

value: suprachiasmatic nucleus

tag: strain

tag: feeding intervention

tag: time-point


title: Omicron_26_2nd

tag: gender

tag: age

tag: group (by covid-19 vaccination, prior infection)

tag: omicron sublineage

tag: days after positive pcr results

tag: disease state

tag: geographical location

tag: cell type


title: SCN_ZT16_TRF_2_1

description: Library name: A21SCN4

value: 9 hr time-restricted feeding

tag: genotype


title: sc_DR_3

city: Berlin

first: Anika

last: Neuschulz

address: Hannoversche Strasse 28

institute: Max-Delbrück-Center for Molecular Medicine

data_processing:
Reads were demultiplexed using bcl2fastq v2.19.
Data was mapped using cellranger v6.1.1
MD tags were added using samtools v1.14
mutation calling and quality filtering (illumina Q20) using custom code (see https://github.com/anikaneuschulz/MTglob_pipeline)
Identification of UMIs with at least 2 labelling events and calculation of labelled / total readounts per gene
Assembly: dr11.95
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: whole larvae

extract_protocol:
10 dechorionated larvae were anaesthetized by placing them in 2 ml centrifuge tubes on ice for 5 minutes. We then washed them twice using ice cold HBSS (Life Technologies GmbH #14175095) and removed the supernatant afterwards. For dissociation the larvae were resuspended in 500 µl TryplE Mix (1xTrypleE (Life Technologies GmbH #A1217701) in HBSS, 1mM EDTA pH 8 (Molekula #900493), 10 mM 4sU) and incubated at 37°C for 30 min. When all visible tissue had disappeared, we inactivated the enzymes by adding 15 µl 10% BSA  (Sigma-Aldrich; #A4503) to the suspension and spun down at 1000 g for 5 minutes (4 °C). Finally, the cells were washed once in ice cold HBSS (no 4sU added). Then, we fixed sample 1 in Methanol immediately, while the other two were submitted to FACS sorting with the gates set to include everything apart from very small debris and extremes in size and granularity. The samples were stored on ice for ~15 minutes during FACS setup. Sorting lasted 10 minutes per sample with no 4sU present in the FACS buffer (HBSS w/ 1% BSA). 10mm 4sU was added to the FACS buffer in the cooled receiving tube. Both samples were spun down and washed immediately after their sort before we resuspended the cells in ice cold HBSS (no 4sU added). Sample 2 was fixed in methanol directly afterwards, while sample 3 was left to incubate on ice for another 30 minutes in order to simulate waiting times when preparing multiple samples. Eventually sample 3 was also fixed using methanol.
The cells were fixed at -20°C for at least 30 minutes. For IAA treatment the samples were brought back to RT and IAA dissolved in 20% HBSS / 80% MeOH (Th. Geyer #1437.2511) was added to a final concentration of 10 mM IAA. After converting for 16 hours, the cells were spun down at 1000 g and 4°C for 10 min, the supernatant was removed and quencing buffer added (DBPS, Gibco #14190144, 0.1% BSA, 1 U/µl RNaseOUT, Life Technologies #10777019, 100 mM DTT, Carl Roth #6908.1). We incubated the sample at RT for 5 min on order to quench the remaining IAA. Afterwards the cells were spun down again and resuspended in a small amount of resuspension buffer (DPBS containing 0.01% BSA, 0.5 U/ µl RNaseOUT and 1 mM DTT) and loaded onto the chromium controller using a Chromium Single Cell 3’ v3.1 kit (10x Genomics #1000121). After successful encapsulation we proceeded with library preparation according to the manufacturer's instructions.

treatment_protocol: 30 min 4sU during dissociation, FACSed, 30 min on ice, MeOH fixed afterwards

value: whole larvae


title: sc_DR_2

treatment_protocol: 30 min 4sU during dissociation, FACSed, MeOH fixed afterwards


title: SCN_ZT16_TRF_1_2

description: Library name: A21SCN3

data_processing:
Basecalls were generated using CASAVA v1.8.
Data quality was assessed using FastQC v0.11.8.
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a.
Reads were annotated to genes using Homer v4.10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw.csv: Comma-separated text file includes the raw counts for each library (the sample resequencings are collapsed).

value: wild type


title: Omicron_25_2nd

value: Male


title: Omicron_24_2nd

value: Austria


title: sc_DR_1

treatment_protocol: 30 min 4sU during dissociation, MeOH fixed afterwards


title: SCN_ZT16_TRF_1_1

description: Library name: A21SCN3


title: WT-PEPD-mix_GEX-v3.1 804110_GX10

city: Oxford

first: Katherine

last: Bull

address: Wellcome Centre for Human Genetics

institute: University of Oxford

description:
WT-PEPD-mix_GEX-v3.1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.1) and aligning to the mm10-1.2.0 genome build.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Spleen

extract_protocol:
All mice are on a C57BL/6 background. For the scRNAseq analysis of chimeric T cells, magnetically isolated T cell populations from 4 WT:WT and 4 WT: Pepd-/- BM chimeric mice were hashtagged by samples for multiplexing using Biolegend TotalSeq-B hashing antibodies by protocol (B0301 #155831, B0302 #155833, B0303 #155835, B0304 #155837, B0305 #155839, B0306 #155841, B0307 #155843, B0308 #155845). Pooled hashtagged CD45.2+ T cells were isolated by FACS, then labelled with  TotalSeq-A antibodies by protocol (anti-CD4 #100569, anti-CD8a #100773, anti-CD279 (PD-1) #109123, anti-CD44 #103063, anti-CD62L #104451, anti-CD25 #102055, anti-CD127 (IL7R), #135045, anti-ICOS #313555, anti-CD69 #104546, anti-CD27 #124235, anti-CD5 #100637, anti-KLRG1 #138431, anti-CD95 #152614,, then sequenced as above.  After washing, cells were loaded into the chromium controller (10X-Genomics) chip and sequenced as described.
Cells were loaded into the chromium controller (10×-Genomics) chip following the standard protocol for the chromium single cell 3’ kit. (Multi-omic single cell analysis resolves novel stromal cell populations in healthy and diseased human tendon., Kendel et al. Scientific Reports., 2020)
Total-Seq-A ADT and Total-Seq-B Hashtag-seq as previously described following biolegend protocols (Multi-omic single cell analysis resolves novel stromal cell populations in healthy and diseased human tendon., Kendel et al. Scientific Reports., 2020)
3' GEX, Total-Seq-A ADT, Total-Seq-B HTO

value: Spleen

value: T cells

tag: library type

value: mRNA

tag: antibodies/tags


title: WT-PEPD-mix_HTO-TSB 804110_GX80

description:
WT-PEPD-mix_HTO-TSB
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: HTO


title: WT-PEPD-mix_CITE-TSA 804110_AF21

description:
WT-PEPD-mix_CITE-TSA
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)+Q32

source_name: spleen

value: spleen

value: ADT


title: minE_osm__1

value: bacterial cell

tag: treatment

value: reduced strain - osmotic stress

tag: Stage

value: mid-log phase culture


title: minE_osm__2


title: Omicron_17_2nd

value: No vaccination, No prior infection

value: PBMC


title: minE_N_starve__2

value: reduced strain - nitrogen starvation


title: minE_N_starve__1


title: WT-PEPD-mix_HTO-TSB 794105_GX80

tag: tissue


title: SCN_ZT16_ALF_2_2

city: San Diego

first: April

last: Williams

institute: Salk Institute for Biological Studies

description: Library name: A21SCN2

extract_protocol:
RNA were extracted following the protocol from Allprep DNA/RNA Mini Kit (Qiagen) or using Trizol reagent, and RNA integrity number were measured through Agilent 2200 TapeStation system.
Libraries generated using Illumina TruSeq Stranded mRNA Sample Prep Kit, pooled and sequenced using an Illumina HiSeq 2500 or Novaseq 6000.

value: suprachiasmatic nucleus

tag: strain

value: ad-libitum feeding


title: WT-PEPD-mix_CITE-TSA 794105_AF21

description:
WT-PEPD-mix_CITE-TSA
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)


title: minE_LB__2

value: reduced strain - LB


title: WT-PEPD-mix_GEX-v3.1 794105_GX10


title: SCN_ZT16_ALF_2_1

description: Library name: A21SCN2

tag: feeding intervention

value: wild type


title: SCN_ZT16_ALF_1_1

description: Library name: A21SCN1

tag: time-point


title: minE_LB__1


title: Omicron_106_1st

tag: gender

value: Male

value: day 5

value: Austria


title: minE_Fe_starve__2

value: reduced strain - iron starvation


title: Omicron_107_1st

value: Female

tag: age

value: day 3