title: Muscle rep3 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 23749_Sua7_D.Gross_Lab_25C_-_WT_BY4741

status: Public on Oct 27 2022

type: SRA

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

country: USA

institute: Cornell University

description: WT BY. XO

library_source: genomic

data_processing:
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
calculate coverage of read1 5' tag using ScriptManager bam-format-converter tools (RRID:SCR_021797)
calculate a scaling factor for each sample using (1-TF target and 2-RNAseq samples) NCIS in ScriptManager with blacklist and control BAM files from Rossi et al, 2020, (3-Nucleosome target) tally the coverage in a 25bp region around the NFR for 03_TFO and 04_UNB gene classes (defined by Rossi et al, 2020, STable 1)
scale coverage of each sample and convert it to BigWig format
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 1 across the genome
Library strategy: ChIP-exo

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: S. cerevisiae cultures were grown in 50 mL YPDA medium to an O.D600 of 0.6-0.8 at 25 ˚C.

extract_protocol:
50 mL cell pellets were resuspended in 750 uL FA lysis buffer (50 mM HEPES-KOH, pH7.5, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and complete protease inhibitor (Roche) along with 1 ml of 0.5 mm acid washed zirconia beads. Lysis was performed by bead beating for 4 cycles of 3 min on and 7 min off in a Mini-Beadbeater-96 machine (Biospec). Whole cell lysates were centrifuged at 14,000 rpm for 3 min at 4 ˚C. Cytoplasmic supernatants were discarded and nuclear pellets were resuspended in 200 uL FA lysis buffer supplemented with 0.1% SDS and 75 uL 0.1 mm zirconia beads. Nuclear samples were sonicated in a Bioruptor (Diagenode) for 4 cycles of 30 sec on and 30 sec off. Samples were centrifuged at 14,000 rpm for 10 min to collect sonicated chromatin fraction which was predominantly enriched with DNA fragments in a range of 100-500 bp in size (verified on agarose gels). Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: anti H3K120ub (Cell Signaling, 5546S), anti-H2B (Abcam, 1790), anti-IgG (Sigma, i5006), anti-TBP (Abcam, 61411), anti-PolII (Santa Cruz Biotechnology, 8WG16), anti-H3 (Abcam, 1791), anti-H3K9ac (Millipore Sigma, 07-352), anti-H3K14ac (Abcam, ab52946). Sera against Hsf1, Taf1 and SAGA subunits (Gcn5, Sgf73 and Spt3) were obtained from David Gross (Louisiana State University), Joe Reese (Pennsylvania State University) and Tony Weil (Vanderbilt School of Medicine) respectively. Chromatin obtained from 50 mL culture was used for a single ChIP experiment. Appropriate antibodies (3-5 ug per ChIP) were conjugated to protein A/G magnetic Sepharose resin (GE Healthcare Life Sciences) at 4 ˚C for 6-8 hr. Unconjugated antibody was removed, then chromatin sample were immunoprecipitated overnight (12-16 hr) at 4 ˚C. For TAP-tagged samples, 40 uL IgG-Dynabeads slurry was used per sample. Subsequent steps were performed as described previously (Rossi et al., 2018).
ChIP-exo libraries were gel purified and were sequenced in a paired-end mode with NextSeq 500 (Read_1 40 cycles, Read_2 36 cycles).

treatment_protocol: For inducing acute heat shock at 37 ˚C, 50 mL of YPDA at 55 ˚C was added to 50 mL cultures and quickly transferred to a shaker incubator (Badjatia et al., 2021)at 37 ˚C for 6 min.

tag: sampleID

tag: target

tag: antibody

tag: strain background

tag: genetic modification

value: WT

tag: temperature

tag: treatment chemicals


title: Muscle rep2 in EODR mice sacrified at ZT8

city: Changsha

first: Guolin

last: Li

state: Hunan

address: 177 Lushan Road

department: College of Life Sciences

country: China

institute: Hunan Normal University

description: every-other-day refeeding (EODR)

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Skeletal muscle

growth_protocol: Six-week-old male C57BL/6N mice were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd. Mice were housed in a temperature (25℃)-and light-controlled vivarium with free access to water and standard rodent chow food. All experiments were started with 8-week-old mice.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were randomly grouped to ad libitum (AL) group, acute fasting (AF) group, refeeding after acute fasting (AR) group, every-other-day fasting (EODF) group and every-other-day refeeding (EODR) group. All mice were single housed for 2 weeks prior to study initiation to allow for acclimation to the animal facility. The AL group mice were allowed unrestricted access to food. The mice of AF groups were allowed free access to food except the last day acute fasting for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively, before sacrificed. The mice of AR groups were allowed free access to food except the last two days followed an acute fasting for 24 h, and then refeeding for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively, before sacrificed. The mice of EODF and EODR groups were fed with 15 cycles of alternating 24 h periods of free access to food followed by 24-h fasting, then EODF mice were sacrificed after fasting for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively, while EODR mice were sacrificed after refeeding for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively. Considering the nocturnal eating characteristics of mice, all fasting and refeeding switches were started at Zeitgeber time 12.

tag: treatment

value: Mice refed for 20h after 24h fasted before sacrificed


title: Muscle rep5 in AF mice sacrified at ZT12

description: acute fasting (AF)

value: Mice fasted for 24h before sacrificed


title: 25314_Sgf73_Bethyl-Labs_37C_AR30_WT_BY4742

description: XO

value: Bethyl-Labs


title: 23451_H2B_ab1790_37C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: Muscle rep1 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 23450_H3_ab1791_37C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: 23448_H2BK123ub_5546S_25C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: Muscle rep3 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: 23447_H3K9ac_07-352_25C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: Muscle rep2 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: 23445_H3_ab1791_25C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: Muscle rep1 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: Muscle rep3 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)

value: Mice fasted for 20h before sacrificed


title: 23440_H3_ab1791_37C_-_sgf73D_BY4741

description: SGF73 gene is knocked out. XO


title: 23441_H2B_ab1790_37C_-_sgf73D_BY4741

description: SGF73 gene is knocked out. XO


title: Muscle rep4 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: 23438_H2BK123ub_5546S_25C_-_sgf73D_BY4741

description: SGF73 gene is knocked out. XO


title: 23442_H3K9ac_07-352_37C_-_sgf73D_BY4741

description: SGF73 gene is knocked out. XO


title: Muscle rep5 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: 23443_H2BK123ub_5546S_37C_-_sgf73D_BY4741

description: SGF73 gene is knocked out. XO


title: Muscle rep2 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: Muscle rep4 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: Muscle rep3 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: 23437_H3K9ac_07-352_25C_-_sgf73D_BY4741

description: SGF73 gene is knocked out. XO


title: Muscle rep5 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: 23452_H3K9ac_07-352_37C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: 23433_H2BK123ub_5546S_37C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: 23436_H2B_ab1790_25C_-_sgf73D_BY4741

description: SGF73 gene is knocked out. XO


title: Muscle rep2 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: Muscle rep1 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: 23432_H3K9ac_07-352_37C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: Muscle rep1 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: 23431_H2B_ab1790_37C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: Muscle rep4 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: 23446_H2B_ab1790_25C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: 23430_H3_ab1791_37C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: 23428_H2BK123ub_5546S_25C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: Muscle rep5 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: 23427_H3K9ac_07-352_25C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: Muscle rep4 in AL mice sacrified at ZT4

description: ad libitum (AL)

value: Mice fed ad libitum


title: Muscle rep3 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: 23426_H2B_ab1790_25C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: Muscle rep1 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: Muscle rep2 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: Muscle rep5 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)

value: Mice refed for 16h after 24h fasted before sacrificed


title: 23423_H2BK123ub_5546S_37C_-_WT_BY4741

description: WT. XO


title: 23422_H3K9ac_07-352_37C_-_WT_BY4741

description: WT. XO


title: Muscle rep3 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: Muscle rep4 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: 23421_H2B_ab1790_37C_-_WT_BY4741

description: WT. XO


title: Muscle rep1 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: 23418_H2BK123ub_5546S_25C_-_WT_BY4741

description: WT. XO


title: Muscle rep2 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: Muscle rep5 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: Muscle rep4 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: Muscle rep5 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: 23417_H3K9ac_07-352_25C_-_WT_BY4741

description: WT. XO


title: Muscle rep1 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: Muscle rep2 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: Muscle rep5 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)

value: Mice fasted for 16h before sacrificed


title: 21376_TBP_61411_37C_-_sgf73D_BY4741

description: XO 4.0

value: TBP


title: Muscle rep3 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: Muscle rep4 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: 21375_TBP_61411_25C_-_sgf73D_BY4741

description: XO 4.0


title: 23416_H2B_ab1790_25C_-_WT_BY4741

description: WT. XO


title: 21374_TBP_61411_37C_-_sgf29D_BY4741

description: XO 4.0


title: 21373_TBP_61411_25C_-_sgf29D_BY4741

description: XO 4.0


title: 23425_H3_ab1791_25C_-_gcn5D_BY4741

description: GCN5 gene is knocked out. XO


title: 21372_TBP_61411_37C_-_gcn5D_BY4741

description: XO 4.0


title: Muscle rep3 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: 21371_TBP_61411_25C_-_gcn5D_BY4741

description: XO 4.0


title: 23420_H3_ab1791_37C_-_WT_BY4741

description: WT. XO


title: 21370_TBP_61411_37C_-_spt20D_BY4741

description: XO 4.0


title: Muscle rep2 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: 21369_TBP_61411_25C_-_spt20D_BY4741

description: XO 4.0


title: Muscle rep4 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: 21360_Pol2_sc-56767_37C_-_gcn5D_BY4741

description: XO 4.0


title: 21358_Pol2_sc-56767_37C_-_spt20D_BY4741

description: XO 4.0


title: Muscle rep5 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: 21359_Pol2_sc-56767_25C_-_gcn5D_BY4741

description: XO 4.0


title: Muscle rep2 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: 21357_Pol2_sc-56767_25C_-_spt20D_BY4741

description: XO 4.0


title: Muscle rep3 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: Muscle rep1 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: 21354_Pol2_sc-56767_37C_-_WT_BY4741

description: XO 4.0


title: 20795_TBP_61411_37C_-_WT_BY4741

description: XO 4.0


title: Muscle rep4 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: Muscle rep1 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: Muscle rep3 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: Muscle rep5 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)

value: Mice refed for 12h after 24h fasted before sacrificed


title: Muscle rep5 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: 21353_Pol2_sc-56767_25C_-_WT_BY4741

description: XO 4.0


title: 20794_TBP_61411_25C_-_WT_BY4741

description: XO 4.0


title: 20783_TBP_61411_37C_-_sgf29D_BY4741

description: XO 4.0


title: 20793_TBP_61411_37C_-_sgf73D_BY4741

description: XO 4.0


title: Muscle rep3 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: Muscle rep1 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: Muscle rep4 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: 20782_TBP_61411_25C_-_sgf29D_BY4741

description: XO 4.0


title: Muscle rep2 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: Muscle rep2 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: 20792_TBP_61411_25C_-_sgf73D_BY4741

description: XO 4.0


title: 21367_TBP_61411_25C_-_ahc1D_BY4741

description: XO 4.0


title: 20326_Pol2_8WG16_37C_-_gcn5D_BY4741

description: XO 4.0


title: Muscle rep1 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: 20325_Pol2_8WG16_25C_-_gcn5D_BY4741

description: XO 4.0


title: Muscle rep5 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: Muscle rep4 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: 20324_Pol2_8WG16_37C_-_spt20D_BY4741

description: XO 4.0


title: 100nM TBT Day 14 Replicate 2

city: Irvine

first: Richard

middle: Cheng-An

last: Chang

address: 4311 Nature Science II

institute: University of California Irvine

data_processing:
RNA-Seq reads (fastq data) were aligned to the mouse genome reference sequence GRCm38/mm10 using the STAR aligner, and the resulting bam format aligned reads were subjected to QC analysis using fastQC (Babraham Institute) followed by extraction of uniquely mapped reads using samtools.
Uniquely mapped reads were assigned to the mm10 gene model and on-exon reads were counted using Bioconductor package “Rsubread.” The assigned read counts were normalized in the Bioconductor package “DESeq2” using the regularized log transformation. Differential expression was assessed in DESeq2 using the function DESeqDataSetFromMatrix with alpha = 0.01. Differentially expressed genes were defined by Benjamini-Hochberg corrected p-values (p-adj < 0.01) and fold change (absolute value of log2[fold change] > 0.2).
Supplementary files format and content: diff

source_name: Bone marrow mesenchymal stem cells

growth_protocol: Bone marrow-derived multipotent mesenchymal stromal cells from the long bones of C57BL/6 mice (MSCs) were purchased at passage 6 (OriCell, Cyagen Biosciences, Santa Clara, CA) and stored at passage 8 or 9 in liquid N2. Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% calf bovine serum (CBS), 10 mM HEPES, 1 mM sodium pyruvate, 100 IU/mL penicillin, and 100 ug/mL streptomycin.

extract_protocol:
Cells were lysed in TriPure (Roche, Basel, Switzerland) and total RNA isolated with MiniPrep columns (Zymo Research, Irvine, CA) Integrity of total RNA was evaluated using Tapestation high-sensitivity RNA screen tapes (Agilent Technologies, Santa Clara, CA). Range of the RNA integrity number (RIN) was 8.0 - 8.6.
Strand-specific, barcode-indexed RNA-seq deep sequencing libraries were synthesized from total RNA with ERCC spike-in controls (ThermoFisher Scientific, Waltham, MA) using Ovation RNA-Seq Systems 1-16 for Mouse (NuGen Technologies, San Carlos, CA).
Size distribution of the libraries were determined by Tapestation to be 200 – 800 bp, peaking at 300 bp. RNA-seq libraries were quantified using KAPA Illumina library quantification kit (KAPA Biosystems, Wilmington, MA), and up to 12 libraries were pooled in each run of the Illumina NextSeq500 deep sequencer (75 nt + 75 nt, paired-end) to generate fastq raw read sequence files.

treatment_protocol: MSCs were plated at 15,000 cells/cm2 in 12-well plates, and were allowed to attach and acclimate for 24 hours prior to 48 hours of chemical treatment with 0.1% DMSO, 10, 50, or 100 nM Tributyltin.

tag: strain

tag: cell type

value: Bone marrow mesenchymal stem cells

tag: time point

value: 100 nM TBT


title: 100nM TBT Day 14 Replicate 1


title: Muscle rep2 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: 20323_Pol2_8WG16_25C_-_spt20D_BY4741

description: XO 4.0


title: Muscle rep3 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: Muscle rep1 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: 100nM TBT Day 7 Replicate 4


title: Muscle rep5 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)

value: Mice fasted for 12h before sacrificed


title: 20322_Pol2_8WG16_37C_-_ahc1D_BY4741

description: XO 4.0


title: 100nM TBT Day 7 Replicate 3


title: 20590_Gcn5_i5006_37C_-_WT_BY4741

description: YEP


title: Muscle rep1 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: Muscle rep4 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: Muscle rep3 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: Muscle rep2 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: 20320_Pol2_8WG16_37C_-_WT_BY4741

description: XO 4.0


title: 100nM TBT Day 7 Replicate 1


title: Muscle rep4 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: 100nM TBT Day 7 Replicate 2


title: 20319_Pol2_8WG16_25C_-_WT_BY4741

description: XO 4.0


title: Muscle rep3 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: 20304_TBP_61411_25C_-_gcn5D_BY4741

description: XO 4.0


title: 20305_TBP_61411_37C_-_gcn5D_BY4741

description: XO 4.0


title: Muscle rep2 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: kit6-MCD

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

description:
LSECs from MCD mice infused with c-Kit+ LSECs
all.genes.expression_Kit_neg_vs_Kit_pos
all.genes.expression_Kit_neg_vs_Kit_pos

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values and counts for each Sample

source_name: liver

extract_protocol:
Total RNA was isolated from the cells using the Trizol (invitrogen). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies,USA) and then diluted to 10pM for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150bp) on HiSeq 3000.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: liver

value: LSECs

tag: genotype

value: Wild-type

tag: Sex

value: male

value: MCD-diet for 4w with c-Kit+ LSECs infusion


title: 100nM TBT Day 4 Replicate 3


title: 100nM TBT Day 4 Replicate 4


title: Muscle rep5 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: kit4-MCD


title: 20303_TBP_61411_37C_-_spt20D_BY4741

description: XO 4.0


title: kit3-MCD


title: 20302_TBP_61411_25C_-_spt20D_BY4741

description: XO 4.0


title: 100nM TBT Day 4 Replicate 1


title: kit1-MCD


title: Muscle rep4 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: Muscle rep5 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: 50nM TBT Day 14 Replicate 4

value: 50 nM TBT


title: 100nM TBT Day 4 Replicate 2


title: Muscle rep1 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: Muscle rep3 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: 20301_TBP_61411_37C_-_WT_BY4741

description: XO 4.0

value: WT


title: 50nM TBT Day 14 Replicate 3


title: 20300_TBP_61411_25C_-_WT_BY4741

description: XO 4.0


title: ct6-MCD

description:
LSECs from MCD mice infused with c-Kit- LSECs
all.genes.expression_Kit_neg_vs_Kit_pos
all.genes.expression_Kit_neg_vs_Kit_pos

value: MCD-diet for 4w with c-Kit- LSECs infusion


title: ct4-MCD


title: Muscle rep1 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: 50nM TBT Day 14 Replicate 2


title: Muscle rep2 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: 20298_TBP_61411_25C_-_ahc1D_BY4741

description: XO 4.0


title: 20299_TBP_61411_37C_-_ahc1D_BY4741

description: XO 4.0


title: ct2-MCD


title: 50nM TBT Day 7 Replicate 4


title: c-kit3

description:
c-Kit posituve LSECs
all.genes.expression.annot_Ctrl_vs_cKit
all.genes.expression.annot_Ctrl_vs_cKit


title: 20297_TBP_61411_25C_-_WT_BY4741

description: XO 4.0


title: 50nM TBT Day 7 Replicate 3


title: Muscle rep4 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)

value: Mice refed for 8h after 24h fasted before sacrificed


title: 20146_TBP_61411_37C_-_gcn5D_BY4741

description: XO 4.0


title: c-kit2


title: ct5-MCD


title: 50nM TBT Day 7 Replicate 2


title: c-kit1


title: 20145_TBP_61411_25C_-_gcn5D_BY4741

description: XO 4.0


title: Ctrl3

description:
c-Kit negative LSECs
all.genes.expression.annot_Ctrl_vs_cKit
all.genes.expression.annot_Ctrl_vs_cKit


title: 20143_TBP_61411_25C_-_spt20D_BY4741

description: XO 4.0


title: 20144_TBP_61411_37C_-_spt20D_BY4741

description: XO 4.0


title: 50nM TBT Day 7 Replicate 1


title: 50nM TBT Day 14 Replicate 1


title: Muscle rep5 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: 50nM TBT Day 4 Replicate 4


title: Ctrl1


title: Muscle rep3 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: Muscle rep5 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: Muscle rep1 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: 20142_TBP_61411_37C_-_WT_BY4741

description: XO 4.0


title: Ctrl2


title: 50nM TBT Day 4 Replicate 2


title: Muscle rep4 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: Kit-KO3

description:
LSECs from endothelial c-Kit-KO mice
all.genes.expression_Kit_CT_vs_Kit_KO
all.genes.expression_Kit_CT_vs_Kit_KO

value: Kit-KO

value: Tomaxifen induction


title: 20141_TBP_61411_25C_-_WT_BY4741

description: XO 4.0


title: Muscle rep3 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: 50nM TBT Day 4 Replicate 1


title: 20139_TBP_61411_25C_-_ahc1D_BY4741

description: XO 4.0


title: Muscle rep2 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: Muscle rep2 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: 5nM TBT Day 14 Replicate 4

value: 5 nM TBT


title: 5nM TBT Day 14 Replicate 3


title: 20138_TBP_61411_37C_-_WT_BY4741

description: XO 4.0

value: TBP


title: 20137_TBP_61411_25C_-_WT_BY4741

description: XO 4.0


title: 50nM TBT Day 4 Replicate 3


title: 5nM TBT Day 14 Replicate 2


title: Kit-CT3

description:
LSECs from control mice
all.genes.expression_Kit_CT_vs_Kit_KO
all.genes.expression_Kit_CT_vs_Kit_KO

value: Kit-CT


title: 5nM TBT Day 14 Replicate 1

value: Bone marrow mesenchymal stem cells


title: Kit-KO1


title: Kit-CT4


title: Muscle rep4 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)

value: Mice fasted for 8h before sacrificed


title: Muscle rep5 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: Kit-CT2


title: Muscle rep3 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: 20029_Gcn5_Weil-Lab_37C_-_WT_BY4741

description: YEP

value: Weil-Lab


title: 5nM TBT Day 7 Replicate 3


title: 19729_Pol2_8WG16_25C_AR30_Sua7-Dtag_CM005

description: D-tag on Sua7. XO 4.0


title: 5nM TBT Day 7 Replicate 4


title: Muscle rep1 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: YM3

city: Cincinnati

last: Lu

state: OH

address: 3333 BURNET AVENUE

department: Brain Tumor Center

institute: Cincinnati Children's Hospital Medical Center

description: Methyl-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence. Methyl-seq reads were aligned to mm10 using bwameth.
Methylation states of the CpG cytosines were called with MethylDackel
The program ‘metilene’ was applied to analyze the raw methylation ratios at all CpGs to identify differentially methylated regions (DMRs) with > 10 CpGs.
Assembly: mm10
Supplementary files format and content: bedgraph files for Methyl-seq
Library strategy: Methyl-seq

source_name: brain tumor tissue

growth_protocol: Mouse Neural Stem Cells (mNSC) were maintained in Neural Stem Cell (NSC) Basal Medium with NSC proliferation supplements, 10 ng/ml EGF, 20 ng/ml basic-FGF and 2 μg/ml Heparin (Stem Cell Technologies, Vancouver, Canada).

extract_protocol:
Genomic DNA was prepared using DNeasy Blood & Tissue Kit (Qiagen) as the manufatuer's guide.
SureSelect Methyl-Seq Target Enrichment System for human, mouse or rat (Agilent, Santa Clara, CA) was used to prepare the sequencing library as the manufacturer’s introductions.

value: brain

value: IUE with YAP-M


title: YM2

description: Methyl-seq


title: 20036_Spt7_Weil-Lab_37C_-_WT_BY4741

description: YEP


title: Muscle rep2 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: Kit-KO2

value: liver

value: LSECs


title: 5nM TBT Day 7 Replicate 2


title: Muscle rep1 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: 19726_Pol2_8WG16_25C_AR0_Taf1-Dtag_CM004

description: D-tag on Taf1. XO 4.0


title: 19727_Pol2_8WG16_25C_AR30_Taf1-Dtag_CM004

description: D-tag on Taf1. XO 4.0


title: 5nM TBT Day 7 Replicate 1


title: NSC3

description: Methyl-seq

source_name: neural progenitor cell

value: cell culture


title: Muscle rep5 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: 19725_Pol2_8WG16_25C_AR30_Spt20-Dtag_CM003

description: D-tag on Spt20. XO 4.0


title: Muscle rep4 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: NSC2

description: Methyl-seq


title: 5nM TBT Day 4 Replicate 4


title: NSC1

description: Methyl-seq


title: Muscle rep3 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: 19728_Pol2_8WG16_25C_AR0_Sua7-Dtag_CM005

description: D-tag on Sua7. XO 4.0


title: 19724_Pol2_8WG16_25C_AR0_Spt20-Dtag_CM003

description: D-tag on Spt20. XO 4.0


title: 19723_Pol2_8WG16_25C_AR30_Spt7-Dtag_CM002

description: D-tag on Spt7. XO 4.0


title: Muscle rep2 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: 5nM TBT Day 4 Replicate 2


title: Muscle rep1 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: YM1

description: Methyl-seq


title: 5nM TBT Day 4 Replicate 1


title: Muscle rep4 in AL mice sacrified at ZT16

description: ad libitum (AL)

value: Mice fed ad libitum


title: 19721_Pol2_8WG16_25C_AR30_Spt3-Dtag_CM001

description: D-tag on Spt3. XO 4.0


title: 19720_Pol2_8WG16_25C_AR0_Spt3-Dtag_CM001

description: D-tag on Spt3. XO 4.0


title: DMSO Day 14 Replicate 2

value: 0.1 percent DMSO


title: DMSO Day 14 Replicate 3


title: DMSO Day 14 Replicate 4


title: Output 3C

city: barcelona

first: benedetta

last: bolognesi

state: Barcelona

address: c comte borrell 232 5a-1a

country: Spain

institute: IBEC

description: PCR amplicon from plasmid library

data_processing:
Library strategy: DNA-Seq
FastQ files from paired-end sequencing of the Aß42 library before (‘input’) and after selection (‘output’) were processed using the DiMSum pipeline (https://github.com/lehner-lab/DiMSum)
Supplementary_files_format_and_content: aa_seq = amino acid sequence, ID= Mutation identifier, dataset= Mutation type (substitution, insertion, single deletion, truncation or deletion), mean_count= mean read count of the input replicates, nscore_c= Merged nucleation score centered to WT, nscore[1,2,3]_c= Nucleation score for [1,2,3] replicates, sigma= Merged error over nucleation score, fAD= Associated pathogenicity (non-fAD, dominant [fAD_d] or recessive [fAD_r])

source_name: yeast culture

growth_protocol: Yeast cells were transformed with the Aβ42 plasmid library in 3 biological replicas. A minimum of 100,000 yeast transformants were used for each replicate to ensure the coverage of the full library and reaching therefore a >30x coverage of each variant. Once the culture reached the exponential phase, cells were resuspended in 100mL protein inducing medium (-URA, 20% glucose, 100uM Cu2SO4) at OD600=0.05. Selection was performed in 5 technical replicas for each biological replica (biologial replicas 1-3, technical replicas A-D; see samples title). After 24h 5ml input pellets were collected and stored at -20C for later DNA extraction (input pellets). In parallel, 1 million cells/replicate were plated on -ADE-URA selection medium in 145cm2 plates. Plates were incubated at 30 C for 7 days inside an incubator. Finally colonies were scraped off the plates with PBS 1x, harvested by centrifugation and stored at -20C for later DNA extraction (output pellets).

extract_protocol:
The input and output pellets (3 biological x 5 technical replicas, 60 tubes in total) were thawed and resuspended in 2ml extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris pH 8, 1mM EDTA pH 8), and underwent two cycles of freezing and thawing in an ethanol-dry ice bath (10 min) and at 62C (10min).  Samples were then vortexed together with 1.5ml of phenol:chloroform:isoamyl 25:24:1 and 1.5g of glass beads (sigma). The aqueous phase was recovered by centrifugation and mixed again with 1.5ml phenol:chloroform:isoamyl 25:24:1. DNA precipitation was performed by adding 1:10V of 3M NaOAc and 2.2V of 100% cold ethanol to the aqueous phase and incubating the samples at -20C for 1h. After a centrifugation step, pellets were dried overnight at room temperature. Pellets were resuspended in 1ml resuspension buffer (10mM Tris pH 8, 1mM EDTA pH 8) and treated with 7.5ul RNase A (Thermo Scientific) for 30min at 37C. The DNA was finally purified using 75ul of silica beads (QIAEX II Gel Extraction Kit, Qiagen), washed and eluted in 375ul elution buffer.
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 50 million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Ilumina sequencing primers. PCR products from the first step were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. DNA concentration was then quantified by means of a Quant-iT™ PicoGreen® dsDNA Assay Kit (Promega). All replicates were pooled together in an equimolar ratio. Finally, the pooled sequencing library was run on a 2% agarose gel, purified and sent for 125 bp paired-end Illumina sequencing.
Other (DNA-seq of PCR amplicon)

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)


title: Output 3A

description: PCR amplicon from plasmid library


title: 18843_TBP_61411_25C_AR60_Spt20-Dtag_CM003

description: XO 4.0


title: Output 3B

description: PCR amplicon from plasmid library


title: 5nM TBT Day 4 Replicate 3


title: 18844_TBP_61411_25C_AR0_Taf1-Dtag_CM004

description: XO 4.0


title: Output 3E

description: PCR amplicon from plasmid library


title: 18842_TBP_61411_25C_AR30_Spt20-Dtag_CM003

description: XO 4.0


title: Output 2E

description: PCR amplicon from plasmid library


title: 19722_Pol2_8WG16_25C_AR0_Spt7-Dtag_CM002

description: D-tag on Spt7. XO 4.0


title: DMSO Day 7 Replicate 4


title: DMSO Day 7 Replicate 3


title: 18841_TBP_61411_25C_AR15_Spt20-Dtag_CM003

description: XO 4.0


title: Muscle rep2 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: Output 2D

description: PCR amplicon from plasmid library


title: DMSO Day 14 Replicate 1


title: Output 3D

description: PCR amplicon from plasmid library


title: Output 2C

description: PCR amplicon from plasmid library


title: 18840_TBP_61411_25C_AR7.5_Spt20-Dtag_CM003

description: XO 4.0


title: Muscle rep5 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)

value: Mice refed for 4h after 24h fasted before sacrificed


title: Output 2B

description: PCR amplicon from plasmid library


title: Muscle rep1 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: Muscle rep3 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: Muscle rep3 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: Muscle rep4 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: Output 2A

description: PCR amplicon from plasmid library


title: DMSO Day 4 Replicate 4


title: Muscle rep1 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: Muscle rep2 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: Output 1E

description: PCR amplicon from plasmid library


title: DMSO Day 4 Replicate 3


title: 18836_TBP_61411_25C_AR15_Spt7-Dtag_CM002

description: XO 4.0


title: Output 1D

description: PCR amplicon from plasmid library


title: 18838_TBP_61411_25C_AR60_Spt7-Dtag_CM002

description: XO 4.0


title: 18837_TBP_61411_25C_AR30_Spt7-Dtag_CM002

description: XO 4.0


title: Muscle rep5 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: Muscle rep4 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: Output 1C

description: PCR amplicon from plasmid library


title: 18835_TBP_61411_25C_AR7.5_Spt7-Dtag_CM002

description: XO 4.0


title: 18839_TBP_61411_25C_AR0_Spt20-Dtag_CM003

description: XO 4.0


title: DMSO Day 7 Replicate 2


title: Output 1B

description: PCR amplicon from plasmid library


title: 18834_TBP_61411_25C_AR0_Spt7-Dtag_CM002

description: XO 4.0


title: DMSO Day 4 Replicate 2


title: DMSO Day 7 Replicate 1


title: Muscle rep2 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: 18829_TBP_61411_25C_AR0_Spt3-Dtag_CM001

description: XO 4.0


title: Output 1A

description: PCR amplicon from plasmid library


title: DMSO Day 0 Replicate 4


title: DMSO Day 0 Replicate 3


title: Muscle rep3 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: Input 3E

description: PCR amplicon from plasmid library


title: DMSO Day 0 Replicate 2


title: 18828_TBP_61411_25C_AR60_WT_AB001

description: XO 4.0

value: WT


title: 18827_TBP_61411_25C_AR30_WT_AB001

description: XO 4.0


title: Muscle rep1 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: Input 3D

description: PCR amplicon from plasmid library


title: Muscle rep5 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)

value: Mice fasted for 4h before sacrificed


title: DMSO Day 0 Replicate 1


title: DMSO Day 4 Replicate 1


title: 18826_TBP_61411_25C_AR15_WT_AB001

description: XO 4.0


title: Input 3B

description: PCR amplicon from plasmid library


title: 18825_TBP_61411_25C_AR7.5_WT_AB001

description: XO 4.0


title: Muscle rep4 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: Input 3C

description: PCR amplicon from plasmid library


title: Input 3A

description: PCR amplicon from plasmid library


title: Input 2E

description: PCR amplicon from plasmid library


title: Sample 2_mCD45+, B16 tumor, Iso-ctrl

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger  software 5.0.0 by 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subcutaneous inoculated B16 tumor

extract_protocol:
Freshly collected mouse CD45+cells mice were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (PBS, 2% v/v FCS, 5mM EDTA). Live mouse CD45+cells were sorted using a FACS MELODY (Becton Dickinson) according to the presence or absence of Allophycocyanin signal. Mouse CD45+cells  were washed in PBS  and resuspended in PBS supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent. for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: mCD45+ cells

value: Subcutaneous inoculated B16 tumor

value: Vav-cre human LAIR1 transgenic and LAIR1-/- C57bl/6j mice

tag: age

value: 6-8 weeks old


title: Muscle rep3 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: 18824_TBP_61411_25C_AR0_WT_AB001

description: XO 4.0

value: TBP


title: 17605_Spt7_i5006_25C_-_WT_BY4741

description: ChIP-Exo


title: Sample 1_mCD45+, B16 tumor, anti-LAIR1

description: 10x Genomics


title: 16618_Sgf73_i5006_37C_-_WT_BY4741

description: ChIP-Exo


title: PDL1, scRNAseq

city: New Haven

first: Ana Luisa

last: Perdigoto

state: CT

address: 300 George Street

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0.
genome build: mm10
Supplementary files format and content: filtered_counts.h5ad is an AnnData object containing UMI counts for alpha, beta, and delta cells.

source_name: Pancreatic Islet

extract_protocol:
Single cell suspension in RT Master Mix was loaded on the Single Cell Chip and partition with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Upon dissolution of the Gel Beads in a GEM, the primers with the unique cell barcodes were released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produced barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture.
Full-length, barcoded cDNA was amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation and Size Selection are then used to optimize the cDNA amplicon size prior to library construction.
The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. Analysis steps such as demultiplexing, alignment, and gene counting, and visualization to generate expression data with single-cell resolution were performed.

treatment_protocol: Approximately 7-week-old NOD mice were treated with anti-PD-L1 (Bio X Cell, Clone 10F.9G2) or anti-CTLA4 (Bio X Cell, Clone 9D9) every three days for 2 doses. Two days after the second dose mice were sacrificed and islets were harvested and processed into single cells. Samples from N=3 mice treated with anti-PD-L1 were combined and samples from N=3 mice treated with anti-CTLA-4 were combined.

value: Pancreatic Islet

value: NOD

value: 7 weeks


title: Muscle rep5 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: Muscle rep1 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: Muscle rep2 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: Muscle rep4 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: 16616_Sgf73_i5006_37C_-_WT_BY4741

description: ChIP-Exo


title: Muscle rep3 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: FP.kcl_2h_2

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

description:
Riboseq.rsem.genes.expected_count.txt
Riboseq.rsem.genes.tpm.txt

data_processing:
library strategy: RIboSeq
RNA-Seq analysis: reads were filtered for rRNAs using STAR. The remaining reads were mapped to mm10 version of mouse genome using STAR. Expression levels were quantified using RSEM to produce transcript and gene level quantification TPM (Transcript Per Million) values.
Riboseq analysis: reads were filtered for rRNAs, tRNAs and snRNAs using STAR. The remaining reads were mapped to coding sequences of the mm10 mouse genome annotation using Bowtie. Expression levels were quantified using RSEM to produce transcript and gene level quantification TPM (Transcript Per Million) values.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with read count and TPM data for genes, produced by RSEM, as well as DoG genes, read-in genes and read-in estimations, produced by custom scripts

source_name: NIH3T3 cells

extract_protocol: Rna-Seq libraries were made using  NEB E7760 kit. Riboseq libraries were made as described in Sabath et al (https://doi.org/10.1073/pnas.2018138117).

value: Mouse embryonic fibroblasts NIH3T3

tag: stress type

value: Osmotic stress (KCl, 2h)

tag: replicate

tag: molecule type

value: Ribosome protected mRNA footprint


title: FP.kcl_7h_2

value: Osmotic stress (KCl, 7h)


title: FP.kcl_7h_1


title: Muscle rep2 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: FP.kcl_2h_1


title: Muscle rep1 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: Input 2D

description: PCR amplicon from plasmid library


title: Input 2B

description: PCR amplicon from plasmid library


title: Liver rep5 in AL mice sacrified at ZT12

description: ad libitum (AL)

source_name: Liver

value: Mice fed ad libitum


title: Input 2A

description: PCR amplicon from plasmid library

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)


title: Input 1E

description: PCR amplicon from plasmid library


title: FP.h2o2_FP.kcl_ctrl_2

value: Control for H2O2 and KCl


title: FP.h2o2_FP.kcl_ctrl_1


title: Input 1D

description: PCR amplicon from plasmid library


title: Input 1C

description: PCR amplicon from plasmid library


title: CTLA4, scRNAseq

description: 10x Genomics


title: Input 2C

description: PCR amplicon from plasmid library


title: 16617_Sgf73_i5006_25C_-_WT_BY4741

description: ChIP-Exo

tag: sampleID

tag: target

value: WT


title: Liver rep4 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: 24749_polyA-RNA_oligo-dT_37C_4,SU,treatment_sgf73D_BY4741

data_processing:
RNAseq reads were aligned using hisat2 with the following settings: hisat2 -I 10 -X 700 --very-sensitive --no-unal --no-mixed --no-discordant and then sorted with samtools
calculate coverage of read2 5' tag using ScriptManager bam-format-converter tools (RRID:SCR_021797)
calculate a scaling factor for each sample using NCIS in ScriptManager with blacklist and control BAM files from Rossi et al, 2020
scale coverage of each sample and convert it to BigWig format
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 2 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 2 across the genome

molecule: polyA RNA

extract_protocol:
Cells were labeled with 4-SU for 6 minutes. Nascent RNA was biotin labeled and purified streptavidin beads. PolyA enriched species were obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490S, Lot:10043249) and were used for library construction (NEBNext, #E7760S, Lot:10046628).. RS
RNA libraries were sequenced in a paired-end mode with NextSeq 500 (Read_1 40 cycles, Read_2 36 cycles).

tag: strain background


title: Input 1B

description: PCR amplicon from plasmid library


title: Liver rep3 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: FP.h2o2_7h_2

value: Oxidative stress (H2O2, 7h)


title: 24748_polyA-RNA_oligo-dT_25C_4,SU,treatment_sgf73D_BY4741

description: Cells were labeled with 4-SU for 6 minutes. Nascent RNA was biotin labeled and purified streptavidin beads. PolyA enriched species were obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490S, Lot:10043249) and were used for library construction (NEBNext, #E7760S, Lot:10046628).. RS

tag: genetic modification


title: Input 1A

description: PCR amplicon from plasmid library


title: FP.h2o2_7h_1


title: 16615_Sgf73_i5006_25C_-_WT_BY4741

description: ChIP-Exo

tag: antibody

tag: temperature


title: Liver rep2 in AL mice sacrified at ZT12

description: ad libitum (AL)

tag: treatment


title: 11952_Gcn5_i5006_25C_-_WT_BY4741

tag: treatment chemicals


title: 11953_Gcn5_i5006_37C_-_WT_BY4741


title: Liver rep1 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: 24747_polyA-RNA_oligo-dT_37C_4,SU,treatment_spt20D_BY4741


title: 24746_polyA-RNA_oligo-dT_25C_4,SU,treatment_spt20D_BY4741


title: FP.h2o2_2h_1

tag: cell type

value: Oxidative stress (H2O2, 2h)


title: Liver rep5 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)

value: Mice refed for 24h after 24h fasted before sacrificed


title: Liver rep4 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: 24744_polyA-RNA_oligo-dT_25C_4,SU,treatment_gcn5D_BY4741


title: 253T

city: Bogotá

first: Natalia

middle: Lizeth

last: Acosta Vega

state: Bogotá, D.C.

country: Colombia

institute: Instituto Nacional de Cancerología - Colombia

description: no processed data

data_processing:
Quality control using FASTQC
Aligned to human ribosomal RNA using STAR® v.2.5.2.
Unmapped reads to ribosomal RNA were used to map to human reference Homo_sapiens.GRCh38.78 (Ensembl).
Read counts and expression calculations were done using RSEM® v1.2.31.
Filtering for protein coding genes according to ENSEMBL.
Principal component analysis (PCA) excluded 2 outlier samples.
Genes with median counts of zero in all samples were filtered out.
Assembly: Homo_sapiens.GRCh38.78 (Ensembl)
Supplementary files format and content: Tab-delimited text file including raw counts for all samples.

organism: Homo sapiens

source_name: Prostate tumor - FFPE

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA FFPE kit® (Qiagen, Hilden, Germany) following the manufacturer’s recommendations. RNA quantity and quality were determined with Nanodrop 2000 Spectrophotometer® (ThermoFisher Scientific, Wilmington, USA) and the Agilent RNA 6000 Nano kit® (Agilent Technologies, Santa Clara, CA), respectively. All samples were suitable for library preparation.
For library preparation, 1 g of total RNA and the TruSeq Stranded Total RNA Library Prep kit® with Ribo-Zero Human/Mouse/Rat (Illumina, Inc., San Diego, CA, USA) were used. Fragmentation step was omitted in most of the samples due to sample quality, while in five samples it was done according to recommendations from Illumina®. Validation of libraries was performed in the Agilent 2100 Bioanalyzer® system and then normalization to 10 nM was done with the Qubit dsDNA HS Assay kit® (ThermoFisher Scientific, Wilmington, USA), before cluster generation. Sequencing was performed in 12-pooled samples at 1 x 75 bp with single-end strategy, with no sequencing results in six tumor samples.

treatment_protocol: Samples were obtained from FFPE (Formalin Fixed Paraffin Embedded) tissues from radical prostatectomies (RP). Patients did not have previous treatments.

value: Prostate tumor - FFPE

value: Radical prostatectomy

tag: previous treatment

value: No

tag: age at_diagnosis

tag: bmi

tag: erg status

value: Yes

tag: time to_bcr_(days)

tag: gleason grade_group_at_rp

tag: clinical stage_(ct)


title: KDM5C-KD2-Input

city: Wuhan

first: Qiong

last: Xiao

state: Hubei

address: street of luojia mountain

institute: College of Life Sciences, Wuhan University

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt version 1.18 , and masked for low-complexity or low-quality sequence
ChIP-seq reads were aligned to the hg19 genome assembly using  with bowtie2-align-s version 2.3.5.1
peaks were called using macs2 2.1.1.20160309 with the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using bedtools v2.25.0;each row represents the location of the peaks.

extract_protocol:
Cells were cross-linked with 1% formaldehyde,the cells were treated with digestion buffer and digested to 150-300 bp by Mnase.Supernatant was collected after extensive centrifugation and divided into three parts for IgG, H3K4me3 and H3K27ac immunoprecipitation incubated with protein G beads. The beads were washed with Wash Buffer I, Wash Buffer II, Wash Buffer III  and TE. DNA was eluted by ChIP elution buffer and extracted with DNA purification kit. The purified DNA was assayed  high throughput sequencing by Illumina Hiseq Xten platform.
ChIP-seq libraries were constructed with ChIP and input DNA using VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606). Briefly, 50 μL of DNA (8-10 ng) was end-repaired for dA tailing, followed by adaptor ligation. Each adaptor was marked with a barcode of 8 bp DNA. Adaptor-ligated DNA was purified by AMPure XP beads (1:1) and then amplified by PCR of 9 cycles with the primer matching with adaptor universal part. Amplified DNA was purified again using AMPure XP beads (1:1) in 35 μL EB elution buffer. For multiplexing, libraries with different barcode were mixed with equal molar quantities (30-50 million reads per library). Libraries were sequenced by Illumina Hiseq Xten platform with pair-end reads of 150 bp.

value: treated with KDM5C-sgRNA2 to knockdown KDM5C


title: 196T

description: no processed data

tag: tissue


title: 24743_polyA-RNA_oligo-dT_37C_4,SU,treatment_WT_BY4741

tag: sampleID


title: 192T

description: no processed data


title: 190T

description: no processed data


title: 181T

description: no processed data

value: RTU


title: 24745_polyA-RNA_oligo-dT_37C_4,SU,treatment_gcn5D_BY4741


title: TRIM11-KD2-Input

value: treated with TRIM11-sgRNA2 to knockdown TRIM11


title: Liver rep2 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: Liver rep3 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: KDM5C-KD1-Input

value: treated with KDM5C-sgRNA1 to knockdown KDM5C


title: 24742_polyA-RNA_oligo-dT_25C_4,SU,treatment_WT_BY4741


title: TRIM11-KD1-Input

value: treated with TRIM11-sgRNA1 to knockdown TRIM11


title: 170T

description: no processed data


title: Control-Input

value: treated with GFP-sgRNA as a control


title: 165T

description: no processed data


title: FP.h2o2_2h_2

value: Mouse embryonic fibroblasts NIH3T3

tag: stress type

tag: replicate

tag: molecule type

value: Ribosome protected mRNA footprint


title: Liver rep1 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: KDM5C-KD1-H3K27ac

tag: chip antibody

value: H3K27ac(Abcam Ab4729)


title: Liver rep5 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: Liver rep4 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: KDM5C-KD2-H3K27ac


title: 148T

description: no processed data


title: 163T

description: no processed data


title: Liver rep2 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: TRIM11-KD2-H3K27ac


title: Liver rep3 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: TRIM11-KD1-H3K27ac


title: T22

type: RNA

city: xi'an

first: Shanfeng

last: Jiang

state: shaanxi

address: No. 127, West Youyi Road, Beilin District

department: School of Life Sciences

institute: Northwestern Polytechnical University

hyb_protocol: RNA were hybridized by RNA probes that labeled by CY3.

scan_protocol: Hybridized RNA were scaned by Ribobio.

data_processing: The scanned images were analyzed with  GenePix Pro 7.2.29.002; Data matrix was normalized with with subtract background correction and quantile normalization method.

source_name: neonate

label_protocol: RNA probes were labeled by CY3. Labeling efficiency can be calculated by the concentration of CyDye and RNA measured by spectrophotometer. For good microarray result, the recommended labeling efficiency is 1.0~3.6.

extract_protocol: RNA were extracted by normal method. RNA quantity and purity were assessed using K5500 micro-spectrophotometer. A260/A280 ≥ 1.5 and A260/A230 ≥ 1 indicate acceptable RNA purity, and RIN value ≥ 7 by Agilent 2200 RNA assay indicates acceptable RNA integrity. Genomic DNA contamination was evaluated by gel electrophoresis.

value: vault of skull

tag: gender

value: male

tag: age

value: 1 week

tag: strain background

tag: genotype

value: shRNA targetting MACF2


title: T31

value: shRNA targetting MACF3


title: T32


title: T23


title: Liver rep5 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)

tag: treatment

value: Mice fasted for 24h before sacrificed


title: Liver rep1 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)

value: Mice refed for 24h after 24h fasted before sacrificed


title: 115T

description: no processed data

value: Prostate tumor - FFPE

value: Radical prostatectomy

tag: previous treatment

value: No

tag: age at_diagnosis

value: Yes


title: KDM5C-KD2-H3K4me3

value: treated with KDM5C-sgRNA2 to knockdown KDM5C


title: Liver rep4 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: 139T

description: no processed data

tag: bmi

tag: erg status


title: Control-H3K27ac


title: 123T

description: no processed data

tag: time to_bcr_(days)

tag: gleason grade_group_at_rp


title: KDM5C-KD1-H3K4me3

value: treated with KDM5C-sgRNA1 to knockdown KDM5C


title: T33

tag: tissue


title: Liver rep3 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: TRIM11-KD2-H3K4me3

value: treated with TRIM11-sgRNA2 to knockdown TRIM11


title: 173T

value: low

tag: clinical stage_(ct)


title: Muscle rep5 in AL mice sacrified at ZT16

description: ad libitum (AL)

value: Mice fed ad libitum


title: 147T

description: no processed data


title: Liver rep2 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: TRIM11-KD1-H3K4me3

value: treated with TRIM11-sgRNA1 to knockdown TRIM11


title: T13

value: vault of skull

value: shRNA targetting MACF1


title: T12

value: male

value: 1 week


title: T11


title: DKD2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of Fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19,mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
For cell RNA extraction, cells were scraped down and collected with centrifugation. Total RNA was extracted with RNA extraction kit (Aidlab). For tissue RNA extraction, 20 mg tissues were homogenized and collected with centrifugation. Total RNA was extracted with RNA extraction kit (CWBIO) according to the manufacturer’s manual.
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111)

value: breast cancer tumor

tag: cell line

value: treated with TRIM11-sgRNA2 and  KDM5C-sgRNA2 to knockdown TRIM11 and KDM5C


title: Liver rep4 in AF mice sacrified at ZT12

description: acute fasting (AF)

value: Mice fasted for 24h before sacrificed


title: Liver rep3 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 187T

value: Prostate tumor - FFPE


title: 168T

value: Radical prostatectomy


title: KDM5C-KD2


title: 151T

value: No

value: high


title: Control-H3K4me3

value: treated with GFP-sgRNA as a control


title: C33

value: scrambled shRNA


title: 137T

value: Yes


title: C32


title: Liver rep5 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: Liver rep1 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: C23


title: KDM5C-KD1

value: treated with KDM5C-sgRNA1 to knockdown KDM5C


title: C31


title: DKD1

value: treated with TRIM11-sgRNA1 and  KDM5C-sgRNA2 to knockdown TRIM11 and KDM5C


title: 131T


title: Liver rep2 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 134T

value: low


title: 171T


title: Liver rep1 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: TRIM11-KD2

value: treated with TRIM11-sgRNA2 to knockdown TRIM11


title: C13

value: vault of skull


title: C21

value: male


title: 125T


title: Liver rep5 in AL mice sacrified at ZT8

description: ad libitum (AL)

value: Mice fed ad libitum


title: C22

value: 1 week


title: C12


title: 122T


title: Liver rep4 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: TRIM11-KD1

value: breast cancer tumor

value: treated with TRIM11-sgRNA1 to knockdown TRIM11


title: 119T

value: Prostate tumor - FFPE


title: Control


title: Liver rep3 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: 106T

value: Radical prostatectomy


title: 113T

value: No


title: Liver rep2 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Liver rep1 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: 104T


title: mTCR CT 24-9-2

city: Perth

first: Caitlin

middle: M

last: Tilsed

address: QQ Block

country: Australia

institute: University of Western Australia

data_processing:
MIGEC and MIXCR pipelines were used to aggregate UMIs and align CDR3 sequences to the IMGT/V-QUEST reference genome80).
A unique CDR3 amino acid sequence is referred to as a TCRβ clone.

source_name: tumor

extract_protocol:
Frozen tumour dissociation with Trizol followed by chloroform extraction and purification using RNeasy MinElute
TCRβ libraries were prepared using an optimized protocol from R. Holt and colleagues (PMID: 19541912)

value: tumor

value: cyclophosphamide

tag: response

value: CR

tag: time point


title: mTCR CT 24-4-1

value: PR


title: Liver rep4 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)

value: Mice refed for 20h after 24h fasted before sacrificed


title: Liver rep5 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 102T

value: Yes


title: Liver rep3 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: WT virus, scRNAseq

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

description: 10x Genomics

data_processing:
Data were processed with a custom pipeline described at https://github.com/Russell-laboratory/NS1_interferon_variation
genome build/assembly: grch38, CanFam3.1, Influenza A virus (A/WSN/1933(H1N1))
Sample_supplementary_files_format_and_content: raw cell/gene tabulated files and matrix for canine cells and infected human cells.

organism:
Homo sapiens
Canis lupus familiaris
Influenza A virus (A/WSN/1933(H1N1))

source_name: canine MDCK-SIAT1 and infected A549 cells

extract_protocol:
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics) on methanol-fixed MDCK-SIAT1 and infected A549 cells.
Methanol fixed cells were used as input

tag: cell type

tag: agent

value: WT


title: 98T

value: high


title: mTCR CT 24-3-12


title: mTCR CT 24-16-6


title: NS1stop mutant, scRNAseq

description: 10x Genomics

value: canine MDCK-SIAT1 and infected A549 cells

value: NS1 4xstop


title: 95T


title: T21

value: vault of skull

tag: gender

value: male

tag: age

value: shRNA targetting MACF2


title: Liver rep2 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 90T


title: C11

value: 1 week

tag: strain background

tag: genotype

value: scrambled shRNA


title: mTCR CT 24-13-4

tag: treatment


title: Liver rep1 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 88T

value: Prostate tumor - FFPE

value: Radical prostatectomy

tag: previous treatment

tag: age at_diagnosis


title: Liver rep5 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: Liver rep4 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: 82T

value: No

tag: bmi

tag: erg status


title: mTCR CT 24-1-11

value: tumor

value: cyclophosphamide


title: mTCR CT 18-2-10

value: CR


title: 75T

value: low

tag: time to_bcr_(days)

tag: gleason grade_group_at_rp


title: Liver rep3 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)

value: Mice refed for 20h after 24h fasted before sacrificed


title: 74T

tag: tissue

value: Yes

tag: clinical stage_(ct)


title: Liver rep2 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: Liver rep1 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: mTCR CT 27-6-6

tag: cell line

tag: response


title: 72T

value: high


title: Liver rep5 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)

value: Mice fasted for 20h before sacrificed


title: mTCR CT 27-5-5

value: PR

tag: time point


title: mTCR CT 27-16-8


title: Liver rep4 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: 71T


title: 70T


title: mTCR CT 24-14-5


title: Liver rep3 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: mTCR CT 24-11-3


title: ASF1B ZF BS PCR

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: BS PCR data of ASF1B ZF

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
BS-seq reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Genome_build: tair10
Supplementary_files_format_and_content: bed, bigwig, wig
ATAC-seq analysis: ATAC-seq reads adaptors were removed with trim_galore. The reads were then mapped to Arabidopsis thaliana reference genome TAIR10 using Bowtie2 (-X 2000 -m 1)62. Reads of chloroplast and mitochondrial DNA were filtered and duplicate reads were removed using Samtools 63. ATAC-Seq open chromatin peaks of each replicate were called using MACS2 with parameters -p 0.01 --nomodel --shift -100 --extsize 200. Consensus set of chromatin peaks of each samples were merged by bedtools (v2.26.0) intersect with allowing 10 base pairs distance64. edgeR was used to define significantly changed peaks [Fold Change, (FC) > 2 and False Discovery Rate, (FDR) < 0.05]65. Chromosomal distributions of ATAC-seq were calculated by dividing Arabidopsis chromosomes into 100 Kb sized bins and count reads at each bin with bedtools. ATAC-seq peak distribution was annotated with ChIPseeker66. Arabidopsis protein coding genes were ranked and divided into 10 quantiles according to gene coding region length, and coding region of each gene was divided in proportion into 10 quantiles. Transcriptional factor footprints were analyzed by TOBIAS67 with 572 plant TF motifs downloaded from Jasper (http://jaspar.genereg.net/).
RNA-seq analysis: Cleaned short reads were aligned to reference genome tair10 by Bowtie2 (v2.1.0), and expression abundance was calculated by RSEM with default parameters68. Heatmaps were visualized with the R package pheatmap. To reduce false positive of differential expression, transcripts with less than 5 reads of all replicates in total were regarded as lowly expressed genes and have been removed in subsequent analysis. Differential expression analysis was conducted using edgeR. A threshold of p value < 0.05 and Fold Change > 2 were used to decide whether significant expression difference exists between samples.
ChIP-seq analysis: ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie (v1.1.2)70, allowing only uniquely mapping reads with 0 mismatches. Duplicated reads were removed by Samtools. ChIP-seq peaks were called by MACS2 (v2.1.1) and annotated with ChIPseeker71. Differential peaks were called by bdgdiff function in MACS2. ChIP-seq data metaplots were plotted by deeptools (v2.5.1)72. For Pol II 5’ occupancy analysis, Pol II occupancy was calculated based normalized reads count (RPKM) on a TSS +/- 200 bp region and a TSS +500 bp to TTS gene body region by bedtools.
Whole genome bisulfite sequencing (BS-seq) analysis: Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim adapters after filtering low quality reads. BS-seq reads were aligned to TAIR10 reference genome by Bismark (v0.18.2)73 with default settings. Reads with three or more consecutive CHH sites were considered as unconverted reads and filtered. DNA methylation levels were defined as #C/ (#C + #T). DMRs (Differentially Methylated Regions) were called by DMRcaller with p < 0.01 for where the differences in CG, CHG, and CHH methylation were at least 0.4, 0.2, and 0.1, respectively.
TSS-seq analysis: TSS-seq data were analyzed following previously published pipeline. TSS-seq reads were trimmed with Trim_galore and 5’ end UMI barcodes were trimmed using UMI-Tools. The reads were then aligned to TAIR10 genome assembly using STAR (v2.7.0e)76. Mapping files were filtered with MAPQ<10 and deduplicated using SAMtools (v1.9) before converted to stranded Bedgraph files using bedtools (v2.26.0). TSS peaks were identified with CAGEfightR (v0.99.0) and differential TSS peaks [Fold Change, (FC) >2 and p value<0.05] were called with DESeq2 (v1.28.1).
BS-PCR analysis: BS-PCR data were analyzed with a previously published pipeline. BS-PCR data were trimmed with primer sequences and mapped to TAIR10 reference genome with bsmap (v2.90) allowing 2 mismatches and 1 best hit (-v 2 -w 1).

organism: Arabidopsis thaliana

source_name: Arabidopsis floral tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants

extract_protocol:
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).
All Arabidopsis plants used in this study are in Columbia (Col-0) ecotype and were grown at 22°C in LD (16 hours light, 8 hours dark) conditions.
ATAC-seq: The nuclei collection process from inflorescence and meristem tissues is as described previously. Freshly isolated nuclei were used for ATAC-seq as described elsewhere. Inflorescence tissues were collected for extraction of nuclei as follows. About 5 g of inflorescence tissue was collected and immediately transferred into ice-cold grinding buffer (300 mM sucrose, 20 mM Tris pH 8, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, and 35% glycerol). The samples were ground with Omni International General Laboratory Homogenizer at 4°C and then filtered through a two-layer Miracloth and a 40-µm nylon mesh Cell Strainer (Fisher). Samples were spin filtered for 10 min at 3,000 g, the supernatant was discarded, and the pellet was resuspended with 25 ml of grinding buffer using a Dounce homogenizer. The wash step was performed twice in total, and nuclei were resuspended in 0.5 ml of freezing buffer (50 mM Tris pH 8, 5 mM MgCl2, 20% glycerol, and 5 mM β-mercaptoethanol). Nuclei were subjected to a transposition reaction with Tn5 (Illumina). For the transposition reaction, 25 µl of 2x DMF (66 mM Tris-acetate pH 7.8, 132 mM K-Acetate, 20 mM Mg-Acetate, and 32% DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37°C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo). Libraries were prepared with Phusion High-Fidelity DNA Polymerase (NEB) in a system containing 12.5 µl 2x Phusion, 1.25 µl 10 mM Ad1 primer, 1.25 µl 10 mM Ad2 primer, 4 µl ddH2O, and 6 µl purified transposed DNA fragments. The ATAC-seq libraries were sequenced on HiSeq 2500 platform (Illumina).
Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
RNA-seq library preparation: Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
ChIP-seq library preparation: 10 grams of inflorescence and meristem tissues were used for Flag, HA, Pol II, H3, and H3K36me2/3 ChIP-seq. ChIP were performed as described previously60 with anti-FLAG M2 (Sigma), anti-HA (Roche), anti-Pol II (Ab26721, Abcam), anti-H3 (Ab1791, Abcam), anti-H3K36me2 (Ab9049, Abcam), and anti-H3K36me3 (Ab9050, Abcam) antibodies. Anti-NRPB1 antibody was raised in rabbits and further affinity-purified by ABClonal (China) using the peptide HEGDKKDKTGKKDASKDDK. To evaluate Pol II occupancy at both 5' end and 3' end of gene body, we selected anti-RNA Pol II CTD repeat YSPTSPS antibody which can capture Pol II signal at both regions (Ser5P and Ser2P). Libraries were prepared with NuGen Ovation Ultra Low System V2 kit following the manufacturer instructions.
Whole genome bisulfite sequencing (BS-seq) library preparation: Leaf tissue was used as starting material for BS-seq libraries preparation. Genomic DNA was extracted and converted with bisulfite treatment with EpiTect Bisulfite Kit (Qiagen) following the manufacturer instructions.
TSS-seq library preparation: TSS-seq was performed on 14 day old seedlings grown on MS plate following previous protocol. Heat stress was conducted by treating plants with 2 hours of 37°C. Five micrograms of total RNA were treated with DNase and CIP (NEB) to remove DNA and all non-capped RNA. Then 5’ caps of capped RNA were removed with Cap-Clip (CellScript) and single-stranded rP5_RND adapter were ligated to 5’-ends with T4 RNA ligase 1 (NEB). Ligated RNAs were enriched and captured by oligo(dT) Dynabeads (Thermo Fisher Scientific). Enriched samples were fragmented for 5 mins at 80°C and first-strand cDNA was generated with SuperScript III (Invitrogen) and random primers. Second-strand cDNA was synthesized with Phusion High-Fidelity DNA Polymerase (NEB) and the BioNotI-P5-PET oligo, and captured by Dynabeads for end repairing with End Repair Enzyme Mix (NEB) and ligation with barcoded Illumina compatible adapter using T4 DNA Ligase (NEB). TSS-seq sequencing libraries were amplified and size selected for single-end sequencing with NovaSeq 6000 platform (Illumina).
BS-PCR and McrBC assay for FWA tandem repeat: For BS-PCR of FWA tandem repeat, genomic DNA was extracted from leaf tissue of ASF1B-ZF T2 with CTAB-based method and converted using the EZ DNA Methylation-Lighting kit (ZYMO research). Methylation level of FWA promoter region and several control regions have been amplified with primers described previously46. HiSeq 2500 (Illumina) sequencing libraries were made from purified PCR products using a Kapa Hyper DNA Library Prep kit. For McrBC of FWA tandem repeat, genomic DNA was extracted from leaf tissue with CTAB-based method, and treated with PureLink RNase (Invitrogen) and then with McrBC (NEB) for 4 hours at 37°C. FWA tandem repeat region was quantified by qPCR.
ATAC-seq; RNA-seq; ChIP-seq; WGBS; TSS-seq; BS-PCR;

value: floral tissue

tag: developmental stage

value: 5-6 weeks

tag: strain


title: mTCR CT 27-10-7


title: 69T


title: mTCR CT 23-20-4


title: 66T


title: fwa BS PCR

description: BS PCR data of fwa


title: Liver rep2 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: mTCR CT 18-1-9


title: mTCR CT 23-17-9


title: 73T


title: 64T


title: mTCR CT 21-2-2


title: Col-0 BS PCR

description: BS PCR data of Col-0


title: H31_H33_flag_control_rep-1

description: ChIP-seq data of flag control of H3.1 and H3.3 replicate 1

tag: antibody

value: anti-FLAG M2 (Sigma)


title: 63T


title: CT-23-5-5


title: Liver rep4 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: Liver rep3 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: asf1a1b_H3.3_Flag_ChIPseq_rep-1

description: ChIP-seq data of H3.3 flag in asf1a1b replicate 1

tag: target protein


title: 61T


title: CT-21-7-4


title: asf1a1b_H3.1_Flag_ChIPseq_rep-1

description: ChIP-seq data of H3.1 flag in asf1a1b replicate 1


title: Liver rep2 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: 59T


title: Col-0_H3.3_Flag_ChIPseq_rep-1

description: ChIP-seq data of H3.3 flag in Col-0 replicate 1


title: Liver rep1 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: Liver rep1 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: Col-0_H3.1_Flag_ChIPseq_rep-1

description: ChIP-seq data of H3.1 flag in Col-0 replicate 1


title: mTCR CT 19-23-11


title: fwa_input_rep-2

description: DNA input data of H3 in fwa replicate 2


title: Liver rep5 in AL mice sacrified at ZT4

description: ad libitum (AL)

value: Mice fed ad libitum


title: mTCR CT 19-21-10


title: 58T


title: 55T


title: Liver rep4 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: mTCR CT 19-11-7


title: Liver rep3 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: CT-23-12-8


title: 54T


title: ZF-ASF1B_input_rep-2

description: DNA input data of H3 in ASF1B ZF replicate 2


title: 53T


title: Liver rep5 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: 60T


title: Liver rep2 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: ZF-ASF1B_input_rep-1

description: DNA input data of H3 in ASF1B ZF replicate 1


title: Liver rep1 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: mTCR CT 18-13-6


title: fwa_H3_ChIPseq_rep-2

description: ChIP-seq data of H3 in fwa replicate 2

value: anti-H3 (Ab1791, Abcam)


title: fwa_input_rep-1

description: DNA input data of H3 in fwa replicate 1


title: 51T

value: Prostate tumor - FFPE


title: mTCR CT 17-19-2


title: 52T

value: Radical prostatectomy


title: Liver rep5 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)

value: Mice refed for 16h after 24h fasted before sacrificed


title: 50T

value: No


title: Liver rep4 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: mTCR CT 17-15-1

value: tumor

value: cyclophosphamide


title: fwa_H3_ChIPseq_rep-1

description: ChIP-seq data of H3 in fwa replicate 1


title: ZF-ASF1B_H3_ChIPseq_rep-2

description: ChIP-seq data of H3 in ASF1B ZF replicate 2


title: ZF-ASF1B_H3_ChIPseq_rep-1

description: ChIP-seq data of H3 in ASF1B ZF replicate 1


title: Liver rep3 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: mTCR CT 17-11-12


title: mTCR CT 18-16-3

value: CR


title: 46T


title: asf1a1b_DNA_input

description: DNA input data for asf1a1b H3 ChIP-seq


title: Liver rep2 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: mTCR CT 17-1-1


title: Liver rep1 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: LSECs isolated from bevacizumab-resistant HCT116 CRCLM xenografts #3 [1731-LSEC-RE3]

city: Guangzhou

first: Ming

last: Qi

email: 756410656@qq.com, qiming561@gmail.com

state: Guangdong

address: No.601 West Huangpu Avenue

institute: Jinan University

data_processing:
The index of the reference genome was built using Hisat2 (v2.0.5), and the paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
For the quantification of gene expression level, FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Analysis of differential expression was performed using the DESeq2 R package (1.16.1)
The differentially expressed mRNAs and genes were selected with statistical significance (P < 0.05) by R package-edgeR.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary LSECs

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

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Servicebio, Wuhan, China) at a ratio of 106 cells per mL of reagent according to the manufacturer’s instructions.
RNA-sequencing libraries were generated using ribosomal RNA depleted RNAs with the NEBNext Ultra II RNA Library Prep Kit (NEB) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the Bioanalyzer 2100 system (Agilent Technologies, CA).

value: primary LSECs

tag: cell type

value: liver sinusoidal endothelial cells

value: cultured for 24h


title: mTCR CT17-9-3

tag: treatment


title: 37T

tag: previous treatment

value: low

value: Yes


title: Liver rep5 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Liver rep4 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: 38T

tag: age at_diagnosis

value: high


title: 35T

tag: bmi


title: LSECs isolated from bevacizumab-resistant HCT116 CRCLM xenografts #2 [1731-LSEC-RE2]


title: Liver rep3 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: asf1a1b_Pol2_ChIPseq_rep-2

description: ChIP-seq data of asf1a1b Pol2 replicate 2

value: floral tissue

value: 5-6 weeks

value: anti-Pol II (Ab26721, Abcam)

value: Pol 2 (Ser5P and Ser2P)


title: 49T

value: Prostate tumor - FFPE

tag: erg status


title: LSECs isolated from bevacizumab-sensitive HCT116 CRCLM xenografts #3 [1731-LSEC-C3]


title: asf1a1b_Pol2_ChIPseq_rep-1

description: ChIP-seq data of asf1a1b Pol2 replicate 1


title: 33T

value: Radical prostatectomy

tag: time to_bcr_(days)


title: LSECs isolated from bevacizumab-sensitive HCT116 CRCLM xenografts #2 [1731-LSEC-C2]


title: 28T

tag: gleason grade_group_at_rp


title: Liver rep1 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)

value: Mice refed for 16h after 24h fasted before sacrificed


title: Liver rep2 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: Col_Pol2_ChIPseq_rep-1

description: ChIP-seq data of Col-0 Pol2 replicate 1

tag: tissue


title: LSECs isolated from bevacizumab-sensitive HCT116 CRCLM xenografts #1 [1731-LSEC-C1]


title: asf1a1b_H3K36me3_ChIPseq_rep-2

description: ChIP-seq data of asf1a1b H3K36me3 replicate 2

value: anti-H3K36me3 (Ab9050, Abcam)


title: Liver rep5 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)

value: Mice fasted for 16h before sacrificed


title: 8T

value: No

tag: clinical stage_(ct)


title: Col_DNA_input

description: DNA input data for Col-0 H3 ChIP-seq


title: 6T


title: Germacrone-treated DN6

city: Beijing

first: Shuang

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

data_processing:
Sequencing adapters removal performed with Trimmomatic (v0.32)
Reads in the size range of 18-50 nucleotides were selected and used for downstream analysis
Mapped against mature miRNAs in the mirBase (version 21) using BWA tool (command bwa aln; v0.7.5a)
MiRNAs expression counts were obtained with samtools (z1.2)
Differential expression analysis was performed using the edgeR (Bioconductor version 2.13). Counts were normalized and differential expression was inferred using the negative binomial distribution and a shrinkage estimator for the distribution variance of the counts.
Assembly: mirBase: r21 mature RNA
Supplementary files format and content: raw count of reads mapping to different miRNAs for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure Approximately 5 µg of total RNA were used to prepare small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
RNA libraries were prepared for sequencing using standard Illumina protocols；

value: kidney

value: Germacrone-treatment at a dosage of 10mg/kg/day


title: asf1a1b_H3K36me3_ChIPseq_rep-1

description: ChIP-seq data of asf1a1b H3K36me3 replicate 1


title: Col_H3K36me3_ChIPseq_rep-2

description: ChIP-seq data of Col-0 H3K36me3 replicate 2


title: Liver rep4 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: 45T


title: LSECs isolated from bevacizumab-resistant HCT116 CRCLM xenografts #1 [1731-LSEC-RE1]

tag: cell line

value: primary LSECs

value: liver sinusoidal endothelial cells


title: Germacrone-treated DN5


title: 5T

value: low


title: Col_Pol2_ChIPseq_rep-2

description: ChIP-seq data of Col-0 Pol2 replicate 2


title: Liver rep3 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: Germacrone-treated DN4


title: Liver rep2 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: Germacrone-treated DN3


title: Col_H3K36me3_ChIPseq_rep-1

description: ChIP-seq data of Col-0 H3K36me3 replicate 1


title: LX-2FAP #3

data_processing:
The index of the reference genome was built using Hisat2 (v2.0.5), and the paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
For the quantification of gene expression level, FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Analysis of differential expression was performed using the DESeq2 R package (1.16.1)
The differentially expressed mRNAs and genes were selected with statistical significance (P < 0.05) by R package-edgeR.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

value: hepatic stellate cells

value: cultured for 24h


title: asf1a1b_H3K36me2_ChIPseq_rep-2

description: ChIP-seq data of asf1a1b H3K36me2 replicate 2

value: floral tissue

value: anti-H3K36me2 (Ab9049, Abcam)


title: 3T

value: high


title: Germacrone-treated DN2


title: LX-2FAP #2


title: Liver rep1 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: LX-2FAP #1


title: Liver rep5 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: Germacrone-treated DN1


title: asf1a1b_H3K36me2_ChIPseq_rep-1

description: ChIP-seq data of asf1a1b H3K36me2 replicate 1

value: 5-6 weeks


title: Col_H3K36me2_ChIPseq_rep-2

description: ChIP-seq data of Col-0 H3K36me2 replicate 2


title: Liver rep4 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: DN6

value: The same volumes of 0.9percentsaline simultaneously.


title: LX-2Vector #3


title: asf1a1b_H3_ChIPseq_rep-2

description: ChIP-seq data of asf1a1b H3 replicate 2

value: anti-H3 (Ab1791, Abcam)


title: Liver rep3 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: DN5


title: Liver rep2 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: DN4


title: Liver rep1 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: DN3


title: asf1a1b_H3_ChIPseq_rep-1

description: ChIP-seq data of asf1a1b H3 replicate 1


title: HIF1A.HG.rep2

first: Xinyan

last: Yang

address: No.1023,South Shatai Road, Baiyun District

department: Developmental Biology

institute: Southern Medical University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Single-cell RNA-seq raw reads were processed to remove Template Switch Oligo (TSO) sequence and polyA tail sequence. And then the reads with adapter and low-quality bases were removed to obtain clean reads.
The clean reads were aligned to human genome (GRCh38, Gencode version) using Hisat2 (v 2.1.0) with default parameters, and uniquely mapped reads according to unique molecular identifiers (UMI) numbers were counted using HTSeq (v 0.11.3).
For all 960 sequenced single cells, we quantified the numbers of genes and transcripts in each cell. Cells with either fewer than 2,000 genes or fewer than 10,000 UMI detected were removed from downstream analysis. After filtering, we obtained 441 cells from DM donor 1 and 459 cells from DM donor 2.
For CUT&Tag, the adaptor sequence were removed using bbduk (v 38.18) and low-quality reads were trimmed by trimmomatic (v 0.39), with the length cut-off 35 bp. The clean reads were aligned to GRCm38 genome (Ensembl version) using bowtie2 (v 2.3.5.1) with the options (--very-sensitive --end-to-end). Then, low quality mapping reads were removed using samtools with the option (-q 35). The duplicated sequences were removed using picard (v 2.23.0) and biological replicates were merged. MACS2 (v 2.2.6) was used to call narrow peaks with the options (-g mm -f BAMPE -B --call-summits). Bigwig files were generated using genomeCoverageBed from bedtools (v 2.29.2) (scale factor = 20 million / <each sample’s total unique reads>) and bedGraphToBigWig (v 2.8).
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: text file, narrowPeak, bigwig

source_name: Mouse TM-4 cell

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs). CUT&Tag technology was used to study the binding site of HIF1A.
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene). For CUT&Tag, in order to study the distribution of HIF1α inTM4 cells, we used NovoNGS ® CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein, N259-YH01) to capture HIF1α-binding sites. The experimental process was performed according to the manufacturer’s instructions.

value: testis

tag: gender

value: male

tag: group

value: Hyperglycemia


title: Liver rep5 in AL mice sacrified at ZT0

institute: Hunan Normal University

description: ad libitum (AL)

value: Mice fed ad libitum


title: DN2

value: kidney


title: LX-2Vector #1


title: Liver rep4 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: Col_H3_ChIPseq_rep-2

description: ChIP-seq data of Col-0 H3 replicate 2

tag: developmental stage


title: Col_H3K36me2_ChIPseq_rep-1

description: ChIP-seq data of Col-0 H3K36me2 replicate 1

tag: strain


title: HIF1A.HG.rep1

tag: antibody


title: HIF1A.NC.rep2

value: Negetive Control


title: WT_Flag_ChIPseq_rep-2

description: ChIP-seq data of flag control replicate 2

value: anti-FLAG M2 (Sigma)

tag: target protein

value: control


title: HIF1A.NC.rep1


title: DN1


title: Liver rep2 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: Liver rep3 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: Con5


title: ASF1B_Flag_ChIPseq_rep-2

description: ChIP-seq data of ASF1B flag replicate 2


title: Con6


title: WT_Flag_ChIPseq_rep-1

description: ChIP-seq data of flag control replicate 1


title: S3C

first: Jiemei

last: Chen

address: Tianhe Road

department: Rehabilitation Medicine

institute: Sun Yat-Sen Unv

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt[2]) were aligned to reference genome using Hisat2 software(v2.0.4). The transcript abundances for each sample was estimated with StringTie (v1.2.3), and the Fragments Per Kilobase of gene model per Million mapped fragments (FPKM) value for gene level were calculated with R package Ballgown(v2.6.0).
The differentially expressed genes were filtered using R package Ballgown.
The novel genes were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown.
Genome_build: Rnor6
Supplementary_files_format_and_content: Gene expression files include Gene information and FPKM values for each Sample.
Supplementary_files_format_and_content: Novel gene expression files include Novel gene information and FPKM values for each Sample .

organism: Hippocampus

source_name: Rattus norvegicus

extract_protocol:
Total RNA was extracted from the hippocampi of 3 sham rats and 3 tMCAO rats at days 14 after the surgical intervention using TRIzol reagent, in accordance with the manufacturer’s  instructions.
RNA libraries were prepared for sequencing using standard lllumina protocols

treatment_protocol: tMCAO model protocol: After anesthetizing the rats, the left middle cerebral artery was occluded using a monofilament with a silica gel head end for 90 min then subsequently reperfused. Sham rats underwent the same protocol without occlusion of the middle cerebral artery.

tag: rat model

value: Sham

value: Sprague-Dawley rat


title: LX-2Vector #2

tag: cell type

value: hepatic stellate cells

tag: treatment

value: cultured for 24h


title: ASF1B_Flag_ChIPseq_rep-1

description: ChIP-seq data of ASF1B flag replicate 1

value: floral tissue


title: Con4

last: Li


title: Col_H3_ChIPseq_rep-1

description: ChIP-seq data of Col-0 H3 replicate 1


title: S2C


title: Liver rep5 in EODR mice sacrified at ZT0

first: Guolin

address: 177 Lushan Road

description: every-other-day refeeding (EODR)

value: Mice refed for 12h after 24h fasted before sacrificed


title: S1C


title: Con3


title: ASF1A_Flag_ChIPseq_rep-2

description: ChIP-seq data of ASF1A flag replicate 2

value: 5-6 weeks


title: Liver rep4 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)