title: Jurkat cells, shATG4B 3

city: suzhou

first: Wenjuan

last: Ma

state: Jiang su

address: 199 Ren'ai Rd

department: Hematology Center Cyrus Tang medical institute

institute: Soochow University

data_processing:
Sample QC. Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
mRNA Isolation. A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
mRNA Fragmentation, cDNA Synthesis
End Repair, Add A and Adaptor Ligation
The PCR reaction system and program are configured and set up to amplify the product.Library QC
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: core_table_gene.xls.gz includes raw counts for each sample

source_name: Peripheral Blood

growth_protocol: jurkat cells were cultured in 1640 medium in a 37° incubator containing 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini kit(tian gen).500ng of total RNA was used for the consyruction of sequencing libraries
RNA libaary for RNA-seq were prepared use DNBSEQ platform

treatment_protocol: Scrambled and shATG4B sequence were delivered with lentiviral vectors into Jurkat cells.

value: Peripheral Blood

value: Jurkat

value: T-ALL leukemia  cell


title: CYCGFP, D10, ZT4, GFP, CUT&RUN, Rep 2

status: Public on Dec 31 2025

type: SRA

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

country: USA

institute: Purdue University

library_source: genomic

data_processing:
Read trimming with Trimmomatic version 0.39
Alignment with Bowtie2 version 2.5.1, dovetail mates considered concordant
Indexing, generation of BAM files using Samtools version 1.8
CPM-normalized bigWigs generated with deepTools version 3.5.4
Assembly: BDGP6.46
Supplementary files format and content: bigWig files, CPM-normalized

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: outer photoreceptors

growth_protocol: Flies were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 200 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated ZTs (ZT4, ZT12, ZT16).

extract_protocol:
Photoreceptor nuclei were immunoenriched using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn). For CUT&RUN, 1 ug of either anti-GFP antibody (Abcam ab6556), or IgG (EpiCypher CUTANA IgG Negative Control Antibody) was used.  MNase digestion was performed for 5 min using 1 ug of antibody.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. Modifications to the library preperation were made to preserve short DNA fragments generated in TF CUT&RUN (dx.doi.org/10.17504/protocols.io.bagaibse).
CUT&RUN

tag: tissue

value: outer photoreceptors

tag: age

tag: time (zt)

tag: antibody

value: GFP

tag: Sex

value: M

tag: genotype

value: w; PBac{y[+mDint2] w[+mC]=cyc-GFP.FPTB}VK00037/+; P{w[+mC]=[UAS-GFP-Msp3 00KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]/+


title: 4mWT_gills [replicate_3]

city: Tokyo

first: Jiancheng

last: Liang

state: Bunkyo

department: Graduate school of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
Raw reads with low-quality bases and adapters were removed using BBTools (parameters: minlen=50 qtrim=rl trimq=20 ref=adapters.fa ktrim=r k=25 mink=11 hdist=1 tbo tpe). STAR for genome mapping and alignment to the Danio rerio GRCz11 reference genome (Ensembl.Danio.rerio.GRCz11.112), (parameters: STAR –genomeDir --runThreadN 16  --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --readFilesCommand gunzip -c). RSEM for quantifying the expression (parameters: rsem-calculate-expression --alignments --paired-end -p 30 --append-names --estimate-rspd). DESeq2 for differential expression analysis.
Assembly: Ensembl.Danio.rerio.GRCz11.112
Supplementary files format and content: tab-delimited text file includes expected counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

molecule: total RNA

organism: Danio rerio

source_name: Gills

extract_protocol:
Zebrafish were euthanized using Tricaine, dissected, and gathered the corresponding organs kept in NucleoProtect RNA (TAKARA) solution. Total RNA was extract using NucleoSpin RNA Clean-up Kit (TAKARA) following the manufacturer's protocols and verified the RNA quality and concentration using TapeStation RNA ScreenTape (Agilent).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following the manufacture’s protocols.

value: Gills

tag: time

value: 4 month

value: WT


title: Ad-GFP-2

city: Xi'an

first: XIAN

last: GUO

address: Xinyi Road

country: China

institute: Air Force Medical University

description: Library name: Ad-GFP-2

data_processing:
The reads were aligned to the human genome hg19 for all the samples. RNA-seq: differential gene expression analysis was performed using DESeq2 package in R .
Assembly: hg19
Supplementary files format and content: xslx files include FPKM values for each Sample

organism: Homo sapiens

source_name: human aortic smooth muscle cell

extract_protocol:
Refer to the instruction manual of Trizol (Invitrogen, CA, USA) to extract total RNA.RNA contamination was assessed by 1.5% agarose gel.
The mRNA was purified from the total RNA using poly‐T oligo‐attached magnetic beads. Sequencing libraries were generated from the purified mRNA using the V AHTS Universal V6 RNA-seq Library Kit for MGI (V azyme, Nanjing, China) following the manufacturer's recommendations with unique index codes.

tag: cell type

value: human aortic smooth muscle cell

value: Ad-GFP


title: Jurkat cells, shATG4B 2

tag: cell line


title: CYCGFP, D10, ZT4, IgG, CUT&RUN, Rep 2

value: IgG


title: 4mWT_skin [replicate_2]

source_name: Skin

value: Skin


title: 4mWT_muscle [replicate_2]

source_name: Muscle

value: Muscle


title: Jurkat cells, shATG4B 1


title: CYCGFP, D10, ZT4, IgG, CUT&RUN, Rep 1


title: CYCGFP, D10, ZT4, GFP, CUT&RUN, Rep 1


title: 4mWT_gills [replicate_2]


title: Jurkat cells, Scramble 1


title: 4mWT_intestine [replicate_2]

source_name: Intestine

value: Intestine


title: UKMD286_5293 deletion mutant biol rep 2

city: Bangi

first: Sylvia

last: Chieng

state: Selangor

address: Faculty of Science & Technology

department: Department of Biological Sciences & Biotechnology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description: Library name: 2276.R2

data_processing:
NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina)
Quality of raw sequencing reads were assessed by FastQC v0.11.8. Preprocessing of the data were performed using Trimmomatic v0.38.
Assembly: GCF_902141795.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Burkholderia pseudomallei

source_name: bacterial cell

growth_protocol: Wild-type and mutant B. pseudomallei were grown in LB broth overnight at 37C, 250rpm.

extract_protocol:
Overnight culture was pelleted and resuspended in TRI Reagent and BCP. Mixtures were vortexed and incubated for 15 min. Aqueous phase was collected and RNA were precipitated using isopropyl alcohol, followed by washing with 75% ethanol. RNA pellet were obtained and resuspended in nuclease free water. The RNA samples were further purified with Pure-NA Biospin Total RNA Extraction Kit (Research Instruments) with on-column DNAseI treatment.
A 1μg total RNA was used for following library preparation. The rRNA was depleted from total RNA using rRNA removal Kit. The ribosomal depleted RNA was then fragmented and reverse-transcribed. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase with random primers and Actinomycin D. The second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix (include dACG-TP/dUTP). The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends.

value: bacterial cell

value: mutant


title: Jurkat cells, Scramble 3

value: Peripheral Blood

value: Jurkat


title: THP1 cells_empty vector+Ada_rep1

city: Guiyang

first: Dan

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

description:
Library name: Samples 13
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-EV-Ada-1

data_processing:
Sequence was trimmed using Fastp v0.20 to remove adaptor and low quality reads
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Assembly: GRCh_38
Supplementary files format and content: AllSamples_Genes_ReadsCount.txt: Tab-delimited text file contains counts for each sample.

source_name: Homo sapiens

growth_protocol: 1640,10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was isolated and purified from cultured cells using TRIzol reagent following the manufacturer's procedure.
cDNA

treatment_protocol: The S100A9 knockdown in U937 cells and S100A9 overexpression in THP-1 cells were achieved using lentiviral vectors. Lentivirus was transduced into U937 and THP-1 cells according to the manufacturer's instructions. After transduction, cells were selected with puromycin (2 μg/mL) starting 48 hours post-transfection for at least 24 hours. Transfected THP-1 cells, both control and S100A9-overexpressing, were then treated with Adavivint (1 μM) for 36 hours. All cells were cultured in RPMI 1640 medium under controlled conditions.

value: Homo sapiens

value: Acute myeloid leukemia


title: 4mWT_brain [replicate_3]

source_name: Brain

value: Brain


title: UKMD286_5293 deletion mutant biol rep 3

description: Library name: 2276.R3


title: 4mWT_eyes [replicate_3]

source_name: Eyes

value: Eyes


title: CLKGFP, D50, ZT16, IgG, CUT&RUN, Rep 2

value: outer photoreceptors

value: M


title: Ad-GFP-1

description: Library name: Ad-GFP-1


title: CLKGFP, D50, ZT16, GFP, CUT&RUN, Rep 3

value: GFP


title: 4mWT_eyes [replicate_2]

value: 4 month

value: WT


title: THP1 cells_OES100A9+Ada_rep3

description:
Library name: Samples 18
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-OE-Ada-3

value: S100A9 overexpression


title: CLKGFP, D50, ZT16, IgG, CUT&RUN, Rep 3

value: IgG


title: THP1 cells_OES100A9+Ada_rep2

description:
Library name: Samples 17
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-OE-Ada-2


title: Jurkat cells, Scramble 2

value: T-ALL leukemia  cell


title: 4mWT_heart [replicate_2]

source_name: Heart

value: Heart


title: UKMD286_5293 deletion mutant biol rep 1

description: Library name: 2276.R1

value: bacterial cell


title: THP1 cells_OES100A9+Ada_rep1

description:
Library name: Samples 16
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-OE-Ada-1


title: CLKGFP, D50, ZT16, GFP, CUT&RUN, Rep 1


title: THP1 cells_empty vector+Ada_rep2

description:
Library name: Samples 14
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-EV-Ada-2


title: CLKGFP, D50, ZT16, GFP, CUT&RUN, Rep 2


title: Wild-type B. pseudomallei UKM D286 biol rep 3

description: Library name: D286.R3

value: wild-type


title: THP1 cells_OES100A9_rep3

description:
Library name: Samples 12
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-OE-3


title: CLKGFP, D50, ZT16, IgG, CUT&RUN, Rep 1


title: THP1 cells_OES100A9_rep2

description:
Library name: Samples 11
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-OE-2


title: 4mWT_heart [replicate_1]


title: CLKGFP, D50, ZT12, GFP, CUT&RUN, Rep 3


title: CLKGFP, D50, ZT12, IgG, CUT&RUN, Rep 3


title: 3-day_MSB_AtfA_ChIP-seq_rep2

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

description: Library name: 3-day_MSB_AtfA_ChIP-seq_rep2

data_processing:
ChIP-seq experiments were performed in two replicates per culture condition. After quality control of the sequenced data, reads were aligned to the appropriate Aspergillus nidulans reference genome (https://mycocosm.jgi.doe.gov/Aspnid1/Aspnid1.home.html) with Bowtie2 (ChIP-seq) softwares.
The Picard toolkit (Broad Institute, GitHub repository. https://broadinstitute.github.io/picard/) removes PCR duplicates from BAM files created by SAMtools package.
RPKM normalization is performed by deeptools. In ChIP-seq analysis MACS2 determines peaks in bedGraph files with the default parameters.
The obtained binding sites (BED files) were used for further analyses. Using bedtools, the corresponding sequences were extracted from the A. nidulans reference genome.
Assembly: Aspergillus nidulans reference genome (https://mycocosm.jgi.doe.gov/Aspnid1/Aspnid1.home.html)
Supplementary files format and content: bw, bed

organism: Aspergillus nidulans

source_name: conidia

growth_protocol: atfA::3XFLAG (pyrG89; pyroA4; ΔatfA::AfupyrG+; atfA-3XFLAG::pyroA+; veA+) strain for ChIP analysis was constructed with the complementation of ΔatfA (pyrG89; pyroA4; ΔatfA::AfupyrG+; veA+) with pHS13 vector carrying atfA::3XFLAG sequence with atfA’s native promoter as well as trpC terminator of A. nidulans.

extract_protocol:
2 d and 3 d old untreated and 3d old 0.04 mM MSB-treated conidia were crosslinked with freshly prepared 1% formaldehyde at room temperature for 30 min. Following that, 1/20 volume of 2.5 M glycine solution was added to stop the cross-linking reaction. Conidia were then collected by centrifugation (5000 g, 5 min, 4 oC) and washed with ice-cold PBS three times. About 1.5 ml FA lysis buffer {50 mM HEPES-KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS, 1 protease inhibitor cocktail tablet (Roche) per 50 ml} was added before use. Glass beads were added into cross-linked cell lysates, which were broken by a mini-bead beater (MagNa Lyser instrument, Roche, Switzerland) for three cycles (1 min homogenization followed by 1.5 min resting on ice). Subsequently the samples were sonicated for eight cycles (60 s on, 60 s off) with a sonifier level 5 of output control in a Diagenode Bioruptor (Diagenode, USA). All steps were carried out at 4 oC. The sonicated cell lysates were cleared of cellular debris by centrifugation at 13 000 rpm for 10 mins at 4 oC. The supernatant was collected and subjected to chromatin IP with mouse monoclonal Anti-Flag M2 antibody (Merck, USA) using MAGnify™ Chromatin Immunoprecipitation System (Invitrogen, USA) following the manufacturer’s protocol.
ChIP-Seq libraries were prepared with Ovation Ultralow Library Systems V2 (Tecan, Switzerland) according to the manufacturer’s instructions. Briefly, 10 ng of immunoprecipitated DNA was used for library generation. Repairing end step was followed by indexed adaptor ligation and enrichment of adaptor ligated fragments by 10 PCR cycles. Fragment size distribution of the libraries was check on BioAnalyzer 2100 (Agilent Technologies, USA) using DNA High Sensitivity chip. Single read 75 bp sequencing reads were generated by NextSeq 500 sequencer (Illumina, USA). Library preparations and sequencing were performed by the Genomic Medicine and Bioinformatics Core Facility of the University of Debrecen.

treatment_protocol: For sample preparation, 2 d and 3 d old untreated and 3d old 0.04 mM MSB-treated conidia (~2x109 conidia) from surface cultures grown on NMM agar plate from the strain atfA::3XFLAG.

value: conidia

value: 3-day-old spore

tag: treatment

value: MSB


title: THP1 cells_OES100A9_rep1

description:
Library name: Samples 10
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-OE-1

value: Homo sapiens

value: Acute myeloid leukemia


title: THP1 cells_empty vector_rep2

description:
Library name: Samples 8
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-EV-2


title: 3-day_MSB_AtfA_ChIP-seq_rep1

description: Library name: 3-day_MSB_AtfA_ChIP-seq_rep1


title: THP1 cells_empty vector_rep1

description:
Library name: Samples 7
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-EV-1


title: Wild-type B. pseudomallei UKM D286 biol rep 2

description: Library name: D286.R2


title: 3-day_untr_AtfA_ChIP-seq_rep2

description: Library name: 3-day_untr_AtfA_ChIP-seq_rep2

value: untr


title: CLKGFP, D50, ZT12, IgG, CUT&RUN, Rep 2

value: outer photoreceptors


title: CLKGFP, D50, ZT12, GFP, CUT&RUN, Rep 2

value: M


title: 4mWT_muscle [replicate_1]

value: Muscle


title: 4mWT_eyes [replicate_1]

value: Eyes

value: 4 month


title: 4mWT_intestine [replicate_1]

value: Intestine

value: WT


title: CLKGFP, D50, ZT12, GFP, CUT&RUN, Rep 1

value: GFP


title: 4mWT_brain [replicate_2]

value: Brain


title: THP1 cells_empty vector_rep3

description:
Library name: Samples 9
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-EV-3


title: 4mWT_brain [replicate_1]


title: 3-day_untr_AtfA_ChIP-seq_rep1

description: Library name: 3-day_untr_AtfA_ChIP-seq_rep1


title: U937 cells_shS100A9_rep3

description:
Library name: Samples 6
Column name in AllSamples_Genes_ReadsCount.xls: U-A9-si-3

value: S100A9 knockdown


title: CLKGFP, D50, ZT12, IgG, CUT&RUN, Rep 1

value: IgG


title: U937 cells_shS100A9_rep2

description:
Library name: Samples 5
Column name in AllSamples_Genes_ReadsCount.xls: U-A9-si-2


title: 2-day_untr_AtfA_ChIP-seq_rep2

description: Library name: 2-day_untr_AtfA_ChIP-seq_rep2

value: conidia

value: 2-day-old spore


title: Wild-type B. pseudomallei UKM D286 biol rep 1

description: Library name: D286.R1

value: bacterial cell

value: wild-type


title: 4mATF3OE_skin [replicate_4]

value: Skin

value: ATF3 overexpression


title: 4mATF3OE_muscle [replicate_4]


title: CLKGFP, D50, ZT4, GFP, CUT&RUN, Rep 3

value: outer photoreceptors


title: 2-day_untr_AtfA_ChIP-seq_rep1

description: Library name: 2-day_untr_AtfA_ChIP-seq_rep1

value: untr


title: U937 cells_empty vector_rep3

description:
Library name: Samples 3
Column name in AllSamples_Genes_ReadsCount.xls: U-A9-EV-3

value: Homo sapiens

value: Acute myeloid leukemia


title: 4mATF3OE_heart [replicate_4]

value: Heart

value: 4 month


title: 4mATF3OE_intestine [replicate_4]

value: Intestine


title: CLKGFP, D50, ZT4, IgG, CUT&RUN, Rep 3

value: M


title: CLKGFP, D50, ZT4, GFP, CUT&RUN, Rep 2

value: GFP


title: CLKGFP, D50, ZT4, IgG, CUT&RUN, Rep 2


title: U937 cells_empty vector_rep2

description:
Library name: Samples 2
Column name in AllSamples_Genes_ReadsCount.xls: U-A9-EV-2

value: WT


title: HFD liver (Refeeding period, Day7)_2

city: Hong Kong

first: Man Yuen

last: LEE

address: Hunghom

department: Department of Applied Biology and Chemical Technology

country: Hong Kong

institute: The Hong Kong Polytechnic University

description: Library name: RF2

data_processing:
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
HISAT were used to align the clean reads to the reference genome and Bowtie2 to align the clean reads to the reference genes.
Assembly: Reference Genome Version: GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample (gene_count.txt)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample (gene_fpkm.txt)

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA were extracted by service provider BGI and the quality were verified by Agilent2100 with Equalbit RNA BR Assay Kit. All samples with RIN between 6.6-8.5.
Non-strand specific Poly A tail enrichment library construction. mRNA-Seq Library based on BGI DNBSEQ sequencing technology.

value: Liver

value: HFD (Refeeding period, Day7)


title: HFD liver (Refeeding period, Day7)_3

description: Library name: RF3


title: 4mATF3OE_gills [replicate_4]

value: Gills


title: HFD liver (Calorie restriction period, Day 3)_4

description: Library name: IF4

value: HFD (Calorie restriction period, Day 3)


title: VICs, shVAPB-3

city: Jinan

first: Xiaolin

last: Liu

address: 6699 Qingdao Road,Jinan, Shandong Province CHINA

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description: Library name: sample 6

data_processing:
CLC genomics workbench v11.0.1
Assembly: 36
Supplementary files format and content: xls files include FPKM valves for each sample

source_name: aortic valve

extract_protocol:
RNA was extracted from cells using the FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme, China). 1µg of total RNA was used for the construction of squencing libraries.
After the total RNA samples were tested to be qualified, the MGIEasy RNA  library preparation kit was used for library construction.  Magnetic beads  with oligo (DT) were used for enrichment and purification;  Fragment  buffer was added to the purified mRNA to make its fragment into a short  fragment;  the fragment mRNA was used as a template for reverse  transcription into double stranded cDNA with six base random primers,  and then the product was purified.  The purified double stranded cDNA was  subjected to end repair, addition of dA tail, linker connection and PCR  amplification.  After the amplified product was qualified, it was denatured  and single stranded cyclized, and the cyclized product was inspected

value: aortic valve

value: VICs

value: valve interstitial cells

value: VAPB knockdown

value: Osteogenic differentiation


title: CLKGFP, D50, ZT4, IgG, CUT&RUN, Rep 1

value: outer photoreceptors

value: IgG


title: 4mATF3OE_eyes [replicate_4]

value: Eyes

value: ATF3 overexpression


title: HFD liver (Calorie restriction period, Day 3)_3

description: Library name: IF3


title: 4mATF3OE_brain [replicate_4]

value: Brain

value: 4 month


title: VICs, shVAPB-2

description: Library name: sample 5


title: 4mATF3OE_skin [replicate_3]

value: Skin


title: HFD liver (Calorie restriction period, Day 3)_2

description: Library name: IF2


title: U937 cells_shS100A9_rep1

description:
Library name: Samples 4
Column name in AllSamples_Genes_ReadsCount.xls: U-A9-si-1

value: Homo sapiens

value: Acute myeloid leukemia

value: S100A9 knockdown


title: VICs, shVAPB-1

description: Library name: sample 4


title: CLKGFP, D10, ZT16, IgG, CUT&RUN, Rep 3

value: M


title: 4mATF3OE_muscle [replicate_3]

value: Muscle


title: U937 cells_empty vector_rep1

description:
Library name: Samples 1
Column name in AllSamples_Genes_ReadsCount.xls: U-A9-EV-1

value: WT


title: CLKGFP, D50, ZT4, GFP, CUT&RUN, Rep 1

value: GFP


title: HFD liver (Refeeding period, Day7)_1

description: Library name: RF1

value: Liver

value: HFD (Refeeding period, Day7)


title: HFD liver (control Ad lib feeding)_4

description: Library name: HFD4

value: HFD (control Ad lib feeding)


title: VICs, NC-3

description: Library name: sample 3

value: aortic valve

value: VICs

value: valve interstitial cells

value: Osteogenic differentiation


title: VICs, NC-2

description: Library name: sample 2


title: CLKGFP, D10, ZT16, IgG, CUT&RUN, Rep 2

value: outer photoreceptors

value: IgG


title: HFD liver (control Ad lib feeding)_3

description: Library name: HFD3


title: 4mATF3OE_intestine [replicate_3]

value: Intestine

value: 4 month

value: ATF3 overexpression


title: 4mATF3OE_gills [replicate_3]

value: Gills


title: CLKGFP, D10, ZT16, GFP, CUT&RUN, Rep 1

value: M


title: HFD liver (control Ad lib feeding)_2

description: Library name: HFD2


title: 4mATF3OE_heart [replicate_3]

value: Heart


title: CLKGFP, D10, ZT16, GFP, CUT&RUN, Rep 3


title: THP1 cells_empty vector+Ada_rep3

description:
Library name: Samples 15
Column name in AllSamples_Genes_ReadsCount.xls: T-A9-EV-Ada-3

value: Homo sapiens

value: Acute myeloid leukemia

value: WT


title: 4mATF3OE_eyes [replicate_3]

value: Eyes


title: Soat1KOPD1treat_S1_L001-oligo

city: Shanghai

first: guangchuan

last: Wang

state: Shanghai

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

library_source: transcriptomic single cell

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software). Briefly, all samples were performed sample de-multiplexing, barcode processing, and single-cell 3' unique molecular identifier (UMI) counting with default parameters. Processed reads were then aligned to GRCh38 genome reference using STAR (2.7.2b). Valid cells were automatically identified based on the UMI number distribution of each cell by using the “barcodeRanks” function of the DropletUtils tool to remove background beads and the beads that had UMI counts less than the threshold value. Finally, we used PISA to calculate the gene expression of cells and create a gene  cell matrix for  each library.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
The fresh tumor samples were cut into approximately 1mm3 pieces and washed with 4ml cold PBS solution 3 times. Then the samples were minced into small pieces, and enzymatically digested using the MACS Tumor Dissociation Kit (Miltenyi Biotec) for 30 min with agitation, according to the manufacturer’s instructions. The dissociated cells were subsequently passed through a 70-μm and 40-µm cell-strainer (Miltenyi Biotec) and centrifuged at 300g for 10 min. After removing the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Tiangen Biotech #RT122-1) and incubated at 4 ° C for 10 min to lyse red blood cells. The cell pellets were re-suspended in washing buffer (0.04% bovine serum albumin [BSA] in Dulbecco ’ s phosphate-buffered saline [DPBS]) after washing two times with washing buffer. The final cell concentration was adjusted to 1,000 cells/μL (viability≥80%) in all samples by using Countess™ 3 Automated Cell Counter (Life)
DNBelab C Series High-throughput Single-Cell RNA Library (940-000519-00) was utilized for scRNA-seq library preparation. In brief, Briefly, the cells were diluted to a concentration of 1,000 cells/mL and loaded into the cell reservoir of the microfluidic chip. Barcoded beads and droplet-generation oil were successively added to the beads and oil reservoirs. Encapsulated droplets were generated and collected using a DNBelab C4 /DNBelabTaiM4 system. Beads that captured the mRNA were recovered for reverse transcription (RT). Following polymerase chain reaction (PCR) amplification by polymerase chain reaction, complementary DNA (cDNA) was purified and quan-tified using a Qubit dsDNA kit (Thermo Fisher Scientific). Libraries of 3’-end transcripts were subsequently constructed through cDNA fragmentation, size selection, end repair and A-tailing, adapter ligation, PCR for indexing libraries, and cyclisation of sequencing libraries, according to the manufacturer ’ s instructions. Sequencing libraries were purified and quantified using the Qubit ssDNA kit (Thermo Fisher Scientific) and Qsep100 (Bioptic).

value: tumor

value: Liver cancer cell

value: Soat1 knockdown aPD1 treat

value: Intraperitoneal injection of PD1 antibody


title: HFD liver (Calorie restriction period, Day 3)_1

description: Library name: IF1

value: Liver

value: HFD (Calorie restriction period, Day 3)


title: Soat1KOPD1treat_S1_L001-cDNA


title: 4mATF3OE_skin [replicate_2]

value: Skin


title: CLKGFP, D10, ZT12, IgG, CUT&RUN, Rep 3

value: outer photoreceptors

value: IgG


title: Soat1KOnotreat_S1_L001-oligo

value: Soat1 knockdown

value: Intraperitoneal injection of PBS


title: CLKGFP, D10, ZT16, GFP, CUT&RUN, Rep 2

value: GFP

value: M


title: VICs, NC-1

description: Library name: sample 1

value: aortic valve

value: VICs

value: valve interstitial cells

value: Osteogenic differentiation


title: 4mATF3OE_brain [replicate_3]

value: Brain

value: 4 month

value: ATF3 overexpression


title: CLKGFP, D10, ZT12, IgG, CUT&RUN, Rep 2


title: 4mATF3OE_muscle [replicate_2]

value: Muscle


title: CLKGFP, D10, ZT12, GFP, CUT&RUN, Rep 2


title: Soat1KOnotreat_S1_L001-cDNA

value: tumor

value: Liver cancer cell


title: 4mATF3OE_heart [replicate_2]

value: Heart


title: CLKGFP, D10, ZT12, GFP, CUT&RUN, Rep 1

value: outer photoreceptors


title: controlPD1treat_S1_L001-cDNA

value: WT aPD1 treat

value: Intraperitoneal injection of PD1 antibody


title: CLKGFP, D10, ZT12, GFP, CUT&RUN, Rep 3


title: CLKGFP, D10, ZT12, IgG, CUT&RUN, Rep 1

value: IgG


title: Human primary coronary artery smooth muscle cells, Osteogenic medium YM201636_donor 3

type: RNA

city: Dresden

first: Claudia

last: Goettsch

state: SA

address: Fetsherstr. 74

country: Germany

institute: TU Dresden Faculty of Medicine Carl Gustav Carus

description: Gene expression data from OM-calcified human coronary artery smooth muscle cells treated with YM201636 for 7 days.

hyb_protocol: Affymetrix GeneChip Hybridization, Wash & Stain Kit , according to the manufacturer's protocol;

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 controlled by GeneChip Command Console (AGCC) version 4.0 to produce CEL intensity files.

data_processing: The raw data were analyzed by using the Transcriptome Analysis Console software (TAC4.0, ThermoFisher Scientific, USA) with default parameters for gene level expression analysis based on the annotation Hg38 clariom_D_Human.r1.na36.hg38.a1.transcript.csv. SST-RMA was applied for normalization and summarization.

label: biotin

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: Human coronary artery smooth muscle cells from three independent donors were cultured in the presence of control media (DMEM, 10% FBS, 1% penicillin-streptomycin).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Calcification was induced for 7 days with osteogenic medium (OM) consisting of control media supplemented with 10 nM dexamethasone, 10 mM β-glycerol phosphate and 100 µM l-ascorbate phosphate. Cells were treated with Apilimod, YM201636 or DMSO control drung this time.

value: OM YM


title: 4mATF3OE_gills [replicate_2]

value: Gills


title: CLKGFP, D10, ZT16, IgG, CUT&RUN, Rep 1

value: M


title: Human primary coronary artery smooth muscle cells, Osteogenic medium YM201636_donor 2

source_name: Human coronary artery smooth muscle cells


title: CLKGFP, D10, ZT4, GFP, CUT&RUN, Rep 3

value: GFP


title: Human primary coronary artery smooth muscle cells, Osteogenic medium YM201636_donor 1


title: 4mATF3OE_eyes [replicate_2]

value: Eyes


title: Human primary coronary artery smooth muscle cells, Osteogenic medium Apilimod_donor 1

description: Gene expression data from OM-calcified human coronary artery smooth muscle cells treated with Apilimod for 7 days.

value: OM Apilimod


title: Human primary coronary artery smooth muscle cells, Osteogenic medium Apilimod_donor 3


title: controlPD1treat_S1_L001-oligo


title: CLKGFP, D10, ZT4, IgG, CUT&RUN, Rep 3


title: 4mATF3OE_brain [replicate_2]

value: Brain


title: RNA-seq of macaque lung at 21 dpi, sample C953, omicron infection

city: Cheong-ju

first: Dong-yeon

last: Kim

address: Yeongudangi-ro

country: South Korea

institute: KRIBB

description: Library name: C953_lung_21dpi

data_processing:
Cell Ranger pipeline (v6.0.2) from 10× Genomics. Gene expression matrices were generated and analyzed in R with the Seurat package (v4.3.0).
Assembly: Raw sequencing data (FASTQ) were aligned to the *Macaca fascicularis* reference genome (Ensembl release 106) using the Cell Ranger pipeline (v6.0.2, 10x Genomics).
Supplementary files format and content: Processed data include filtered gene expression matrices generated by the Cell Ranger pipeline (filtered_feature_bc_matrix), which contain UMI-based counts of gene expression per cell. These matrices were further analyzed using the Seurat package (v4.3.0) in R (v4.0.3). Quality control filtering was applied to remove cells with <500 or >5000 detected genes, UMI counts <500, or >25% mitochondrial reads. Data were normalized using the SCTransform function, and batch effects were removed via Seurat’s integration workflow. Dimensionality reduction was performed using PCA, clustering using the shared nearest-neighbor method, and visualization using UMAP. Differential expression and marker gene analysis were conducted using FindAllMarkers and FindMarkers. Processed data are provided in CSV and/or RDS format containing normalized gene expression values, metadata, and clustering results.

organism: Macaca fascicularis

source_name: lung

extract_protocol:
Lung tissues were dissociated using a tumor dissociation kit (Miltenyi Biotech, Bergisch Gladbach, Germany) and incubated with enzyme mixtures in RPMI for 30 min. Subsequently, the lung and LNs were homogenized using a gentleMACS™ Dissociator (Miltenyi Biotech, Bergisch Gladbach, Germany) for subsequent analysis.
Raw sequencing data were aligned to the Macaca fascicularis reference genome using the Cell Ranger pipeline (v6.0.2) from 10× Genomics. Gene expression matrices were generated and analyzed in R with the Seurat package (v4.3.0). Cells were filtered based on gene count, unique molecular identifier levels, and mitochondrial content. Data were normalized using SCTransform, and batch effects were corrected by integrating the samples

value: lung

tag: infection

value: 21 dpi, omicron infection


title: 4mATF3OE_muscle [replicate_1]

value: Muscle

value: 4 month

value: ATF3 overexpression


title: Human primary coronary artery smooth muscle cells, Osteogenic medium_donor 3

description: Gene expression data from OM-calcified human coronary artery smooth muscle cells treated with DMSO for 7 days.

value: OM DMSO


title: 4mATF3OE_skin [replicate_1]

value: Skin


title: Human primary coronary artery smooth muscle cells, Osteogenic medium Apilimod_donor 2


title: CLKGFP, D10, ZT4, IgG, CUT&RUN, Rep 2

source_name: outer photoreceptors

value: outer photoreceptors


title: RNA-seq of macaque lung at 21 dpi, sample C401, omicron infection

description: Library name: C401_lung_21dpi


title: CLKGFP, D10, ZT4, GFP, CUT&RUN, Rep 2


title: CLKGFP, D10, ZT4, GFP, CUT&RUN, Rep 1


title: 4mATF3OE_intestine [replicate_1]

value: Intestine


title: controlnotreat_S1_L001-cDNA

value: tumor

value: Liver cancer cell

value: WT

value: Intraperitoneal injection of PBS


title: 4mATF3OE_intestine [replicate_2]


title: RNA-seq of macaque lung at control, sample C910

description: Library name: C910_lung_ctrl

value: control


title: CLKGFP, D10, ZT4, IgG, CUT&RUN, Rep 1

value: IgG

value: M


title: 4mATF3OE_heart [replicate_1]

value: Heart


title: RNA-seq of macaque lung at control, sample C726

description: Library name: C726_lung_ctrl

value: lung


title: Human primary coronary artery smooth muscle cells, Osteogenic medium_donor 1


title: RNA-seq of macaque lung at 21 dpi, sample C302, omicron infection

description: Library name: C302_lung_21dpi

value: 21 dpi, omicron infection


title: Human primary coronary artery smooth muscle cells, Osteogenic medium_donor 2


title: iphenethiol treated for 24h, biological rep 2

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Biotinylated cRNA was hybridized using the Hybridization, Wash, and Stain Kit (Affymetrix, Cleveland, OH, USA).

scan_protocol: GeneChips were scanned with a GeneChip Scanner 3000 7G (Affymetrix, Cleveland, OH, USA).

data_processing: Data collection was performed using Affymetrix GeneChip Command Console Software (AGCC) (Affymetrix, Cleveland, OH, USA).

organism: Arabidopsis thaliana

source_name: 7-day old Arabidopsis seedlings

label_protocol: Biotinylated complementary RNA (cRNA) was synthesized from 100 ng of total RNA using the GeneChip 3’ IVT Express Kit (Affymetrix, Cleveland, OH, USA).

growth_protocol: Seedlings were grown in 50 mL vials containing 5 mL of 1/2 MS liquid medium in the light at 22°C for 7 days.

extract_protocol: Total RNA was extracted using the Total RNA Extraction Kit (Plant; RBC Biosciences, New Taipei, Taiwan).

treatment_protocol: Seedlings were treated with ACC for 3 or 24 hours, or iphenethiol for 24 hours.

value: seedling

value: 7-day old

value: iphenethiol

tag: time point

value: 24 hours


title: iphenethiol treated for 24h, biological rep 1


title: 4mATF3OE_gills [replicate_1]

source_name: Gills

value: Gills

value: 4 month

value: ATF3 overexpression


title: controlnotreat_S1_L001-oligo

value: tumor


title: ACC treated for 24h, biological rep 3

value: ACC


title: Stressed calf 10

city: Fort Collins

first: Grace

middle: Marie

last: Jakes

state: CO

address: 2500 Flintridge Pl

department: Microbiology, Immunology, Pathology

institute: Colorado State University

description:
Library name: BovLav253180
Column name in counts.txt: BovLav253180

data_processing:
Raw data were filtered using Fastp (version 0.23.2) by removing reads containing adapters and for Phred scores >30
Filtered reads were aligned with STAR (v. 2.7.10b, ARS-UCD1.3 genome assembly).
Aligned reads were annotated and counted using FeatureCounts (version 2.0.1)
Normalization and differential gene expression was analyzed using DESeq2
Assembly: ARS-UCD1.3
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: Bronchoalveolar Lavage Fluid

extract_protocol:
Total RNA was extracted from filtered, washed, and pelleted bronchoalveolar lavage cells using the Qiagen Rneasy Mini Kit. RNA quality was evaluated using an Agilent 2100 bioanalyzer to verify minimum RNA integrity levels.
Total RNA was poly-A enriched using magnetic beads (Novogene Corp.), and libraries were prepared using Novogene Corporation protocols

value: Bronchoalveolar Lavage Fluid

tag: experimental group

value: Stressed


title: Stressed calf 11

description:
Library name: BovLav255204
Column name in counts.txt: BovLav255204


title: iphenethiol treated for 24h, biological rep 3


title: RNA-seq of macaque lung at control, sample C539

description: Library name: C539_lung_ctrl

value: control


title: RNA-seq of macaque medLN at 21 dpi, sample C953, omicron infection

description: Library name: C953_medLN_21dpi

source_name: mediastinal lymph node

value: mediastinal lymph node


title: 4mATF3OE_eyes [replicate_1]

value: Eyes


title: Stressed calf 8

description:
Library name: BovLav58778
Column name in counts.txt: BovLav58778


title: 4mATF3OE_brain [replicate_1]

value: Brain


title: Stressed calf 9

description:
Library name: BovLav101614
Column name in counts.txt: BovLav101614


title: 4mATF3KO_skin [replicate_4]

source_name: Skin

value: Skin

value: ATF3 knockout


title: ACC treated for 24h, biological rep 1

value: seedling


title: 4mATF3KO_muscle [replicate_4]

source_name: Muscle

value: Muscle


title: Acclimated calf 7

description:
Library name: BovLav742132
Column name in counts.txt: BovLav742132

value: Acclimated


title: RNA-seq of macaque medLN at control, sample C910

description: Library name: C910_medLN_ctrl


title: Stressed calf 12

description:
Library name: BovLav587932
Column name in counts.txt: BovLav587932


title: RNA-seq of macaque medLN at 21 dpi, sample C302, omicron infection

description: Library name: C302_medLN_21dpi

value: 21 dpi, omicron infection


title: ACC treated for 3h, biological rep 2

value: 7-day old

value: 3 hours


title: ACC treated for 3h, biological rep 3


title: ACC treated for 24h, biological rep 2

value: 24 hours


title: RNA-seq of macaque medLN at control, sample C726

description: Library name: C726_medLN_ctrl


title: 4mATF3KO_intestine [replicate_4]

source_name: Intestine

value: Intestine

value: 4 month


title: ACC treated for 3h, biological rep 1

value: ACC


title: RNA-seq of macaque medLN at 21 dpi, sample C401, omicron infection

description: Library name: C401_medLN_21dpi


title: Acclimated calf 6

description:
Library name: BovLav466718
Column name in counts.txt: BovLav466718

value: Bronchoalveolar Lavage Fluid


title: RNA-seq of macaque medLN at control, sample C539

description: Library name: C539_medLN_ctrl

value: control


title: 4mATF3KO_heart [replicate_4]

value: Heart


title: Acclimated calf 5

description:
Library name: BovLav465113
Column name in counts.txt: BovLav465113


title: 4mATF3KO_gills [replicate_4]

value: Gills


title: mock treated for 24h, biological rep 3

value: mock


title: Acclimated calf 4

description:
Library name: BovLav463021
Column name in counts.txt: BovLav463021


title: 4mATF3KO_eyes [replicate_4]

value: Eyes


title: 1.65nM Monkey4-brain

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description: Testing the accuracy of the quantitative standard curve

data_processing:
Raw data (read1) were pre-processed using the FASTX Toolkit (v0.0.14). The first 70 bp of each read were retained, and low-quality sequences were filtered out (-q 20, -p 90). After quality filtering, adapter sequences were trimmed, requiring a minimum 10-nucleotide match at the 3' end. Reads without detected adapter or shorter than 32 bp were discarded. Only reads with "CGA" at positions 4-6 were retained, corresponding to the 5' random adapter. UMI extraction was performed with UMI_tools (v0.5.1) using the following parameters: extract --extract-method regex --bc-pattern="^(?P<umi_1>.{3})(?P<cell_1>.{3})(?P<umi_2>.{4})([A,T,C,G]{5,100})(?P<umi_3>.{4})$". Processed reads were aligned to the target genome using Bowtie (v1.2.1.1) with parameters --best -v 0. Duplicate reads were removed with UMI_tools using the following parameters: dedup --edit-distance-threshold 1 --soft-clip-threshold 0 --method adjacency. Unaligned reads were mapped to the spike-in reference sequences using Bowtie with parameters --best -v 1 --norc and de-duplicated in the same manner. Remaining unmapped reads were aligned to the isomiR reference library with the same parameters and de-duplicated. Molecules aligned to the genome were merged with isomiR molecules for downstream analysis. Molecules were annotated based on the following priority: mature miRNA > isomiR > tRNA > rRNA > snoRNA > snRNA > scRNA > scaRNA > YRNA > lncRNA > mRNA > piRNA > novel miRNA. Mature miRNA, isomiR, piRNA, and novel miRNA were annotated based on exact sequence and length matches, while other small RNA categories were aligned to known sequences using Bowtie with parameters -k=100 -v=0 -norc. Reads that aligned to the genome but lacked known annotations were classified as "others". The expression of molecules in each library was normalized using the standard curve generated from the external spike-ins.
Assembly: human:hg38;  mouse:mm10; crab-eating monkey:macFas5
Supplementary files format and content: tab-delimited text files include absolute quantification of miRNA expression for each Sample

source_name: brain

extract_protocol:
1 ml of Trizol reagent (Invitrogen) was added to lyse the cells completely. Subsequently, 200 µl of trichloromethane was added and mixed thoroughly. The solution was then centrifuged at 12,000 rpm for 15 min at 4°C. The upper aqueous phase (450 µl) was transferred into a new 1.5 ml EP tube, followed by the addition of 900 µl of absolute ethanol. The solution was mixed by inversion, left to stand at -30°C for 30 min, and then centrifuged again at 12,000 rpm for 15 min at 4°C, until a distinct precipitate formed at the bottom of the tube. After removing the supernatant, the pellet was washed twice with 80% ethanol, air-dried for 2-3 min at room temperature, and dissolved in DEPC-treated water. RNA concentration was measured using a Nanodrop spectrophotometer, and the sample was diluted to a concentration of 100 ng/µl.
100 ng RNA with 0.05 µl of 20 nM EM or RM spike-in control oligos was ligated to a 0.55 µM 3' randomized adapter using 25 U/µl T4 RNA ligase 2 truncated KQ (NEB) in 0.83X T4 RNA ligase reaction buffer (NEB), supplemented with 20% PEG 8000 (NEB) at 25°C overnight. The ligated RNA was then annealed with 1.28 µM RTP. To remove the 3’ adapter-RTP byproduct, 3.33 U/µl 5’ deadenylase (NEB) and 0.2 U/µl lambda exonuclease (NEB) were added, followed by incubation at 30°C for 1 h and 37°C for 2 h, respectively. Subsequently, the product was ligated to a 5’ randomized adapter using 0.4 U/µl of T4 RNA ligase 1 (NEB) in 0.74X T4 RNA ligase reaction buffer, supplemented with 0.7 mM ATP and 17.3% PEG 8000 (NEB) at 25°C for 1 h. Reverse transcription was carried out using 5 U/µl of ProtoScriptII reverse transcriptase (NEB) in 1X ProtoScriptII RT reaction buffer (NEB), containing 0.5 mM dNTPs (Promega) and 10 mM DTT (NEB), at 50°C for 1 h. The resulting cDNA was then amplified using 0.02 U/µl of KOD-Plus-Neo (TOYOBO) in 1X PCR Buffer for KOD-Plus-Neo (TOYOBO), along with 0.5 µM primers, 1.5 mM MgSO4 (TOYOBO), and 0.2 mM dNTPs (TOYOBO). After PCR amplification, the cDNA was gel-purified on a 6% polyacrylamide gel to remove adapter dimers and sequenced using the Illumina NovaSeq platform.

value: brain

tag: libtype

value: qMap-seq


title: Monkey-thymus-3

description: 18 tissues sample from monkeys

source_name: thymus

value: thymus


title: Monkey-thymus-3-1

description: 18 tissues sample from monkeys


title: 4mATF3KO_brain [replicate_4]

source_name: Brain

value: Brain

value: ATF3 knockout


title: 4mATF3KO_skin [replicate_3]

value: Skin


title: Stressed calf 7

description:
Library name: BovLav442765
Column name in counts.txt: BovLav442765

value: Stressed


title: Monkey-thymus-2

description: 18 tissues sample from monkeys


title: I5

city: Cleveland

first: Cody

last: Rutledge

state: OH

address: 2103 Cornell Road

department: Medicine

institute: CWRU

data_processing:
per Novogene
Supplementary files format and content: fpkm

source_name: Heart

extract_protocol: per Novogene

treatment_protocol: see manuscript

value: no intervention


title: 4mATF3KO_muscle [replicate_3]

value: Muscle


title: Monkey-thymus-1

description: 18 tissues sample from monkeys


title: I4


title: Acclimated calf 1

description:
Library name: BovLav420826
Column name in counts.txt: BovLav420826

value: Acclimated


title: mock treated for 24h, biological rep 2

value: seedling

value: 7-day old

value: 24 hours


title: 4mATF3KO_intestine [replicate_3]

value: Intestine

value: 4 month


title: Monkey-stomach-3-1

description: 18 tissues sample from monkeys

source_name: stomach

value: stomach


title: Stressed calf 6

description:
Library name: BovLav107720
Column name in counts.txt: BovLav107720

value: Bronchoalveolar Lavage Fluid


title: I2

value: Heart


title: Monkey-stomach-3

description: 18 tissues sample from monkeys

value: qMap-seq


title: 4mATF3KO_heart [replicate_3]


title: I3


title: Stressed calf 5

description:
Library name: BovLav106915
Column name in counts.txt: BovLav106915


title: 4mATF3KO_gills [replicate_3]

value: Gills


title: I1


title: mock treated for 24h, biological rep 1

value: mock


title: Acclimated calf 3

description:
Library name: BovLav461618
Column name in counts.txt: BovLav461618


title: mock treated for 3h, biological rep 2

value: 3 hours


title: Monkey-stomach-2

description: 18 tissues sample from monkeys


title: 4mATF3KO_eyes [replicate_3]

source_name: Eyes

value: Eyes

value: ATF3 knockout


title: Stressed calf 4

description:
Library name: BovLav105226
Column name in counts.txt: BovLav105226

value: Stressed


title: Monkey-spleen-4

description: 18 tissues sample from monkeys

source_name: spleen

value: spleen


title: mock treated for 3h, biological rep 1

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: Acclimated calf 2

description:
Library name: BovLav429617
Column name in counts.txt: BovLav429617

value: Acclimated


title: H4

value: cardiac arresr 7d


title: 4mATF3KO_brain [replicate_3]

value: Brain


title: Monkey-spleen-3

description: 18 tissues sample from monkeys


title: H3


title: Stressed calf 2

description:
Library name: BovLav12745
Column name in counts.txt: BovLav12745


title: Stressed calf 3

description:
Library name: BovLav13014
Column name in counts.txt: BovLav13014


title: mock treated for 3h, biological rep 3

value: seedling

value: 7-day old


title: Monkey-spleen-2

description: 18 tissues sample from monkeys


title: H2


title: 4mATF3KO_muscle [replicate_2]

value: Muscle

value: 4 month


title: Monkey-spleen-1

description: 18 tissues sample from monkeys


title: H1


title: 4mATF3KO_intestine [replicate_2]

value: Intestine


title: Monkey-skin-4

description: 18 tissues sample from monkeys

source_name: skin

value: skin


title: PBMC, BCG vaccinated, challenged, week 17, rep 3

city: Edinburgh

first: Elisabeth

middle: Margaretha Diana Louise

last: van der Heijden

state: Midlothian

address: Easter Bush Campus

department: Division of Immunology

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

description: Library name: Sample 12

data_processing:
FastQC (v 0.11.9) (default parameters)
TrimGalore (v 0.6.4) (parameters: --quality 30 --illumina --length 17 --max_length 28 –fastqc)
bowtie (default parameters)
miRDeep2 mapper module (parameters: -e -h -j -k AGATCGGAAGAGCACACGTCT -l 17 -m)
miRDeep2 mirdeep module (parameters: -t Cow)
miRDeep2 quantifier module (default parameters)
Assembly: bosTau9 (ARS-UCD1.2) and miRbase v22
Supplementary files format and content: Comma-separated values file with raw counts of Bos taurus miRNAs for each sample

source_name: PBMC

growth_protocol: PBMC were isolated and cryopreserved in FCS with 10% DMSO

extract_protocol:
Total RNA extraction, QC using Agilent 2100 bioanalyzer. Average yield of 456 ng/µL RNA/sample; average RNA integrity number (RIN) of 8.1.
Double-stranded cDNA library constructed using NEB Next® Multiplex Small RNA Library Prep Set for Illumina (Set 1).
50bp single-end Novaseq Illumina sequencing

treatment_protocol: PBMC originated from animals either vaccinated with live M. bovis BCG (Danish SSI 1331; 0.5 mL 4.6 x 10^6) or unvaccinated; pre- or post-challenge with M. bovis (AF2122/97; 10^4 CFU).

value: PBMC

value: vaccinated/challenged (protected)


title: 4mATF3KO_heart [replicate_2]

value: Heart


title: PBMC, BCG vaccinated, challenged, week 17, rep 2

description: Library name: Sample 11


title: G3

value: sham 7d


title: G4


title: 4mATF3KO_gills [replicate_2]

value: Gills


title: PBMC, unvaccinated, challenged, week 17, rep 3

description: Library name: Sample 9

value: unvaccinated/challenged (unprotected)


title: 4mATF3KO_eyes [replicate_2]

value: Eyes

value: ATF3 knockout


title: G1


title: PBMC, BCG vaccinated, challenged, week 17, rep 1

description: Library name: Sample 10


title: 4mATF3KO_skin [replicate_2]

value: Skin


title: Monkey-skin-1

description: 18 tissues sample from monkeys

value: qMap-seq


title: G2


title: Monkey-rectum-4

description: 18 tissues sample from monkeys

source_name: rectum

value: rectum


title: 4mATF3KO_brain [replicate_2]

value: Brain


title: F4

value: cardiac arresr 3d


title: Stressed calf 1

description:
Library name: BovLav12132
Column name in counts.txt: BovLav12132

value: Bronchoalveolar Lavage Fluid

value: Stressed


title: Monkey-skin-2

description: 18 tissues sample from monkeys


title: F3


title: PBMC, BCG vaccinated, uninfected, week 8, rep 3

description: Library name: Sample 6

value: vaccinated/unchallenged (vaccinated)


title: 4mATF3KO_skin [replicate_1]

value: 4 month


title: PBMC, unvaccinated, challenged, week 17, rep 1

description: Library name: Sample 7

value: PBMC


title: Monkey-rectum-2

description: 18 tissues sample from monkeys


title: Monkey-rectum-1

description: 18 tissues sample from monkeys


title: 4mATF3KO_muscle [replicate_1]

value: Muscle


title: Monkey-skin-3

description: 18 tissues sample from monkeys

value: skin


title: PBMC, BCG vaccinated, uninfected, week 8, rep 2

description: Library name: Sample 5


title: 4mATF3KO_intestine [replicate_1]

value: Intestine


title: Monkey-pancreas-4

description: 18 tissues sample from monkeys

source_name: pancreas

value: pancreas


title: F1

value: Heart


title: PBMC, BCG vaccinated, uninfected, week 8, rep 1

description: Library name: Sample 4


title: 4mATF3KO_heart [replicate_1]


title: PBMC, unvaccinated, challenged, week 17, rep 2

description: Library name: Sample 8

value: unvaccinated/challenged (unprotected)


title: PBMC, unvaccinated, uninfected, week 8, rep 3

description: Library name: Sample 3

value: unvaccinated/unchallenged (control)


title: E4

value: sham 3 d


title: Monkey-pancreas-3

description: 18 tissues sample from monkeys

value: qMap-seq


title: E3


title: Monkey-pancreas-2

description: 18 tissues sample from monkeys


title: PBMC, unvaccinated, uninfected, week 8, rep 2

description: Library name: Sample 2


title: Monkey-pancreas-1

description: 18 tissues sample from monkeys


title: 4mATF3KO_gills [replicate_1]

source_name: Gills

value: Gills

value: ATF3 knockout


title: 4mATF3KO_brain [replicate_1]

value: Brain


title: PBMC, unvaccinated, uninfected, week 8, rep 1

description: Library name: Sample 1


title: Monkey-muscle-4

description: 18 tissues sample from monkeys

source_name: muscle

value: muscle


title: E1


title: D25 bovine embryo, replicate 2, scRNA seq

city: Storrs

first: Yue

last: Su

address: 1390 Storrs Road

institute: University of Connecticut

data_processing:
The raw data was aligned with the bovine reference genome and analyzed with the cell ranger pipeline (10x Genomics) to map gene expression results to each individual cell with the help of barcodes from the gel beads. We used R software v4.1.2 (https://www.r-project.org/) and Seurat v4.3.0 package (15) to read gene expression matrix from the .h5 file and performed further analysis. To ensure the accuracy and robustness of our results, we used DoubletFinder (16) to integrate multiple copies and remove potential doublets. Cells with less than 200 genes or more than 4,000 genes, and more than 5% mitochondrial gene expressed, as well as all genes not expressed in at least five cells, were filtered out.
Assembly: bosTau9
Supplementary files format and content: processedRNAcount.csv

source_name: D25 bovine embryo

extract_protocol:
Day 25 flushed bovine chimeric embryos were cut into small pieces and treated with 2 mg/ml papain (Worthington Biochemical, LS003119), 1 mg/ml DNase I (Roche, 10104159001) and 0.5x Glutamax in 2 ml Hibernate A without calcium (BrainBits, HACA500) at 37°C for 40 min. After digestion, 2 ml DPBS with 2% FBS was added to neutralize the enzyme. The embryos were singularized by pipetting 15 to 20 times. The dissociated cell suspension was passed through a 70 μm strainer and centrifuged at 300g for 5 min at 4°C. The cell pellet was resuspended in 1 ml cold RPMI medium with 2% FBS and subjected to cell sorting. After sorting, the cell pellet was resuspended in DPBS with 2% FBS at 800 cells/μL. The concentrated cells were then loaded for 10x single cell RNA sequencing.
Prepared cells were processed for single cell transcriptome analysis using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, Pleasanton, CA, USA).  Cells were diluted to the appropriate concentration per manufacturer recommendations prior to ensure proper loading.  GEM reverse transcription, cDNA amplification and library generation followed manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA).

value: D25 bovine embryo


title: Monkey-muscle-3

description: 18 tissues sample from monkeys


title: 2mWT_skin [replicate_4]

source_name: Skin

value: Skin

value: 2 month

value: WT


title: D4

value: cardiac arresr 1d


title: D25 bovine embryo, replicate 1, scRNA seq


title: F2

value: cardiac arresr 3d


title: 2mWT_muscle [replicate_4]

source_name: Muscle

value: Muscle


title: Monkey-muscle-2

description: 18 tissues sample from monkeys


title: D3


title: 2mWT_intestine [replicate_4]

source_name: Intestine

value: Intestine


title: Mammary, Low Lys, 3

city: GUELPH

first: Boning

last: Li

state: ON

address: 50 Stone Road East

department: Animal Biosciences

country: Canada

institute: University of Guelph

data_processing:
RNA was sequenced on an Illumina NovaSeq 6000, producing 150 base pair paired-end reads with a minimum sequencing depth of 150 million reads. Reads were cleaned with ‘fastp’ (Chen et al., 2018). The LM2 sample did not pass quality checks and were excluded from downstream analysis. Originally there was a C3 sample, but this was not succesfully sequenced and is not included in this Accession. Approximately 90% of the average 155 million reads per sample were aligned to the bovine reference genome (ARS-UCD1.2; NCBI: GCA_002263795.2) using ‘STAR’ aligner (Dobin et al., 2013). Genes were counted using ‘featureCounts’ (Liao et al., 2014) referenced to the Ensembl (Yates et al., 2019) 100 annotation file (Bos_taurus.ARS-CD1.2.dna.toplevel.fa.gz).
Assembly: ARS-UCD1.2; GCA_002263795.2
Supplementary files format and content: counts_matrix.txt - a matrix with first column as Ensembl ID and subsequent columns as raw counts (output from featureCounts)

source_name: Mammary gland

growth_protocol: Primary bovine mammary epithelial cell was collected from lactating Holstein cows post-slaughter. The tissue was cleaned, minced, and digested with collagenase Type III and DNase I at 37°C for 4 hours. After filtration and centrifugation, the enriched epithelial organoids were either cryopreserved or seeded in collagen-coated dishes with a specialized medium. The culture medium consisted of a 1:1 mixture of DMEM/F12 and MCDB170, supplemented with 10% (vol/vol) fetal bovine serum, 0.1% (wt/vol) albumax II, 7.5 μg/mL bovine insulin, 0.3 μg/mL hydrocortisone, 5 ng/mL recombinant human epidermal growth factor, 2.5 μg/mL bovine apo-transferrin, 5 μM isoproterenol, 5 pM 3,3′,5-triiodo-l-thyronine, 0.5 pM β-estradiol, 0.1 nM oxytocin, and 1× antibiotics/antimycotics. Medium was refreshed every 3 days during the first week and, once most organoids had attached to the dish, replaced every 2 days in an incubator at 37°C with a 5% CO2 humidified atmosphere until primary mammary epithelial cells were further passaged.

extract_protocol:
Total RNA was extracted from the cells using the Invitrogen PureLink RNA Mini Kit according to the manufacturer’s instructions.
Quality check of total RNA and library preparation were performed at the Advanced Analysis Centre (University of Guelph, Guelph ON) using TruSeq stranded mRNA sample preparation kit (Illumina, San Diego, USA) following the manufacturer’s protocol.

treatment_protocol: Treatments were base medium with 1) 80 μM L-Lys, 20 μM L-Met, and 40 μM L-His (CTL), 2) 20 μM L-Lys, 20 μM L-Met, and 40 μM L-His (LK), 3) 80 μM L-Lys, 5 μM L-Met, and 40 μM L-His (LM), and 4) 80 μM L-Lys, 20 μM L-Met, and 10 μM L-His (LH). All amino acids except lysine, methionine and histidine were added at their normal physiological concentrations of (in µM) 180 L-alanine, 80 L-arginine, 50 L-Asparagine, 10 L-Aspartic acid, 12 L-Cysteine; 60 L-Glutamic acid, 170 L-Glutamine, 200 L-Glycine, 120 L-Isoleucine, 180 L-Leucine, 50 L-Phenylalanine, 70 L-Proline, 70 L-Serine, 110 L-Threonine, 30 L-Tryptophan, 50 L-Tyrosine, and 240 L-Valine.

value: Mammary gland

value: Primary epithelial cell

value: Low Lys


title: D2

value: Heart


title: Mammary, Low Lys, 2


title: Monkey-muscle-1

description: 18 tissues sample from monkeys

value: qMap-seq


title: 2mWT_heart [replicate_4]

first: Jiancheng

data_processing:
Raw reads with low-quality bases and adapters were removed using BBTools (parameters: minlen=50 qtrim=rl trimq=20 ref=adapters.fa ktrim=r k=25 mink=11 hdist=1 tbo tpe). STAR for genome mapping and alignment to the Danio rerio GRCz11 reference genome (Ensembl.Danio.rerio.GRCz11.112), (parameters: STAR –genomeDir --runThreadN 16  --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --readFilesCommand gunzip -c). RSEM for quantifying the expression (parameters: rsem-calculate-expression --alignments --paired-end -p 30 --append-names --estimate-rspd). DESeq2 for differential expression analysis.
Assembly: Ensembl.Danio.rerio.GRCz11.112
Supplementary files format and content: tab-delimited text file includes expected counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

extract_protocol:
Zebrafish were euthanized using Tricaine, dissected, and gathered the corresponding organs kept in NucleoProtect RNA (TAKARA) solution. Total RNA was extract using NucleoSpin RNA Clean-up Kit (TAKARA) following the manufacturer's protocols and verified the RNA quality and concentration using TapeStation RNA ScreenTape (Agilent).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following the manufacture’s protocols.


title: E2

value: sham 3 d


title: Monkey-lung-4

description: 18 tissues sample from monkeys

source_name: lung

value: lung


title: D1


title: Mammary, Low Lys, 1


title: Monkey-lung-3

description: 18 tissues sample from monkeys


title: Mammary, Low Met, 3

value: Low Met


title: 2mWT_gills [replicate_4]

value: Gills


title: Monkey-lung-2

description: 18 tissues sample from monkeys


title: 4mATF3KO_eyes [replicate_1]

value: Eyes

value: 4 month

value: ATF3 knockout


title: 2mWT_eyes [replicate_4]

value: 2 month

value: WT


title: C3

value: sham 1d


title: C4


title: Mammary, Low Met, 2


title: Monkey-lung-1

description: 18 tissues sample from monkeys


title: Mammary, Low Met, 1


title: 2mWT_skin [replicate_3]

value: Skin


title: C1


title: 2mWT_brain [replicate_4]

source_name: Brain

value: Brain


title: Monkey-liver-4

description: 18 tissues sample from monkeys

source_name: liver

value: liver


title: Mammary, Low His, 3

value: Mammary gland

value: Primary epithelial cell

value: Low His


title: C2

source_name: Heart

value: Heart


title: 2mWT_muscle [replicate_3]

value: Muscle


title: B4

value: cardiac arresr 0.5d


title: Mammary, Low His, 2


title: Monkey-liver-2

description: 18 tissues sample from monkeys

value: qMap-seq


title: 2mWT_intestine [replicate_3]

value: Intestine


title: B3


title: Monkey-liver-1

description: 18 tissues sample from monkeys


title: Monkey-liver-3

description: 18 tissues sample from monkeys


title: Mammary, control, 2

value: Control


title: 2mWT_heart [replicate_3]


title: 2mWT_gills [replicate_3]

value: Gills


title: Mammary, control, 1


title: Monkey-leukocyte-4

description: 18 tissues sample from monkeys

source_name: leukocyte

value: leukocyte


title: B2


title: 2mWT_eyes [replicate_3]

source_name: Eyes

value: Eyes

value: 2 month


title: B1


title: Treg_depleted_P9_4

city: London

first: Niwa

last: Ali

address: King’s College London, 28th Floor, Tower Wing  Guy’s Hospital, Great Maze Pond

institute: King's College London

description: Library name: Whole skin scRNA_8

library_source: other

data_processing:
A standard pipeline was used in which raw fastq files were demultiplexed, quality-checked, and aligned to the appropriate reference genome, followed by UMI correction and digital gene expression quantification to generate an expression matrix using CellRanger.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: csv file contains FPKM values.

molecule: other

extract_protocol:
Where applicable, RNA was extracted using miRvana miRNeasy kit as per manufacturer's protocol.
10x single cell RNA-seq library was constructed by the Blizard Institute as per manufacturer's protocol. R

value: DT

tag: batch


title: Monkey-leukocyte-2

description: 18 tissues sample from monkeys


title: A3

value: sham 0.5 d


title: A4


title: 2mWT_skin [replicate_2]

city: Tokyo

last: Liang

institute: The University of Tokyo

value: Skin

value: WT


title: A2


title: 2mWT_brain [replicate_3]

value: Brain


title: Monkey-leukocyte-1

description: 18 tissues sample from monkeys


title: Treg_depleted_P9_3

description: Library name: Whole skin scRNA_7


title: Treg_depleted_P9_2

description: Library name: Whole skin scRNA_6


title: 2mWT_muscle [replicate_2]


title: Mammary, Low His, 1

value: Mammary gland

value: Primary epithelial cell


title: 2mWT_intestine [replicate_2]


title: Treg_sufficient_P9_4

description: Library name: Whole skin scRNA_4

value: PBS


title: Monkey-kidney-3

description: 18 tissues sample from monkeys

source_name: kidney

value: kidney


title: Treg_depleted_P9_1

description: Library name: Whole skin scRNA_5


title: Vibrio cholerae A1552 single cell rna seq, second run

city: Sydney

first: M. Mozammel

last: Hoque

state: NSW

address: 15 Broadway, Ultimo

department: Australian Institute for Microbiology & Infection (AIMI)

country: Australia

institute: University of Technology Sydney

description:
Library name: Vibrio cholerae A1552 scrna, run second
Vibrio cholerae A1552 single cell rna seq in Tetrahymena

data_processing:
Single-cell gene expression matrices were obtained by mapping the cDNA reads (Read 1) to the reference genome of V. cholerae O1 El Tor strain N16961 using STAR aligner (v2.7.10b)
The matrices obtained from two runs were combined using seurat pipleine and cells specific to the conditions tested in this study were analysed.
Assembly: Vibrio cholerae O1 El Tor strain N16961 (RefSeq accession numbers NC_002505 and NC_002506 for chromosome I and II respectively)
Supplementary files format and content: barcodes, features, and matrix

organism: Vibrio cholerae

growth_protocol: Tetrahymena pyriformis were infected with V. cholerae A1552 WT strains for 5 hrs at room temperature, 60 rpm

extract_protocol:
Intracellular Vibrio cholerae bacteria recovered from Tetrahymena pyriformis and from EFVs were fixed in 4% formaldehyde at 4 degc overnight and then the MicroSPLiT protocol was perfromed to individalluy tage the mRNA of the bacteria
Single cell RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Single cell RNA-Seq, The sequencing library were sequenced twice (first and second run) to obtain suffcient cell sumbers across conditions.

value: ElTor

value: Wild type


title: 2mWT_heart [replicate_2]

value: Heart


title: Monkey-kidney-2

description: 18 tissues sample from monkeys

value: qMap-seq


title: 2mWT_gills [replicate_2]

value: Gills


title: Monkey-kidney-1

description: 18 tissues sample from monkeys


title: Vibrio cholerae A1552 single cell rna seq, first run

description:
Library name: Vibrio cholerae A1552 scrna, run first
Vibrio cholerae A1552 single cell rna seq in Tetrahymena


title: 2mWT_eyes [replicate_2]


title: Treg_sufficient_P9_3

description: Library name: Whole skin scRNA_3


title: Monkey-heart-3

description: 18 tissues sample from monkeys

source_name: heart

value: heart


title: Monkey-heart-4

description: 18 tissues sample from monkeys


title: 2mWT_brain [replicate_2]


title: Treg_sufficient_P9_1

description: Library name: Whole skin scRNA_1


title: Treg_sufficient_P9_2

description: Library name: Whole skin scRNA_2


title: Monkey-kidney-4

description: 18 tissues sample from monkeys


title: 2mWT_skin [replicate_1]


title: MD-WD_Placenta_8_M

city: Manchester

first: Hannah

middle: L

last: Morgan

address: Oxford Road

institute: University of Manchester

description: Library name: MH8

data_processing:
Raw reads were trimmed of Illumina adapters and low quality (Q<20) nucleotides using TrimGalore (v 0.6.7). Reads shorter than 15 bp were discarded.
Trimmed reads were aligned to Mus musculus reference genome GRCm39 using HISAT2 (v 2.2.1)
StringTie (v 2.2.1) was used to assemble genes and calculate gene abundance
DESeq2 was used to perform differential expression
Assembly: GRCm39
Supplementary files format and content: tab-deliminated txt file with normalised counts for each samples

source_name: Placenta

extract_protocol:
Total RNA was isolated from one quarter of snap-frozen (liquid nitrogen) placenta at late gestation using the miRNeasy mini kit (Qiagen, UK), following tissue disruption in Qiazol (Qiagen, UK) in accordance with the manufacturer’s instructions. RNA was treated with QIAseq FastSelect -rRNA HMR, to prevent any rRNA present from being converted into the sequencing library
Stranded RNA-seq libraries were prepared from 500 ng of total RNA per sample, using the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (NEB; E7760) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Pairs) (NEBNext; E6440). Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (ThermoFisher Scientific; Q32854). Library fragment-length distributions were analysed using the Agilent 4200 TapeStation and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent; 5067-5584 and 5067-5585). Libraries were pooled in equimolar amounts and final library quantification was performed using the KAPA Library Quantification Kit for Illumina (Roche; KK4824). The library pool was sequenced on the Illlumina NextSeq500 over three NextSeq500 High Output 150 cycle kits (Illumina; 20024907), to generate over 40 million pairs of 75-bp paired-end reads per sample.

value: Placenta

value: Male

tag: strain

value: Western Diet  + methyl donors


title: 2mWT_muscle [replicate_1]

value: Muscle

value: 2 month


title: MD-WD_Placenta_7_M

description: Library name: MH7


title: Monkey-heart-2

description: 18 tissues sample from monkeys


title: E2-4_etoh

city: Fujian

first: Rongmei

last: Lu

address: East Street No.134，Gulou District，Fuzhou

institute: Fujian Provincial Hospital

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.   a: The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min  b: Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA)  c: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: GT1-7 cells

label_protocol: After quality control, the miRCURY™ Hy3™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a: 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C.   b: The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C  c: Terminated by incubation for 15 min at 65°C.

growth_protocol: GT1-7 cells, gift from Ruijin Hospital, Shanghai Jiaotong University School of Medicine, were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Hyclone) with 10% fetal bovine serum (FBS, Gibco). GT1-7 cells were maintained in an incubator at 37℃ supplied with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: 0.04g DEX (Sigma-Aldrich) was dissolved in 10mL absolute ethanol to make a 107nM stock solution. Analysis of miRNA expression profiling after treated with 50nM DEX or etoh for 24h.

value: GT1-7 cells

value: etoh


title: E2-4_50nM DEX

value: 50nM DEX


title: A1

value: sham 0.5 d


title: E. coli hfq mutant - P1vir infection time 20 min - rep. 2

city: Gdańsk

first: Grzegorz

middle: M.

last: Cech

state: Pomorskie

address: Wita Stwosza 59

department: Department of Bacterial Molecular Genetics, Department of Bacterial Molecular Genetics, University of Gdańsk

country: Poland

institute: Faculty of Biology, University of Gdańsk

data_processing:
Reads quality control was performed with Trimmomatic software (Bolger et al., 2014).
Read sequences were filtrated out with an average quality score of 20 required on a sliding window of 5 bases. Reads with length less than 50 bp were rejected. E. coli rRNA sequences were filtrated out and reads were mapped to genome using Bowtie 2 software (Langmead and Salzberg, 2012).
Estimation of PCR duplicates within the mapped reads was performed using Picard tools (http://broadinstitute.github.io/picard/).
PCR duplicates were not removed from analysis. The featureCounts software from Subread package was used to count paired-end reads uniquely mapped to individual genes (Liao et al., 2013).
Differential gene expression analysis was performed using DESeq2 software (Love et al., 2014) and was compared to analyses performed in edgeR i DESeq software packages.
Assembly: Escherichia coli K12 MG1655 (NC_000913)
Assembly: P1 phage (NC_005856)
Supplementary files format and content: See README file

organism: Escherichia coli

growth_protocol: Bacterial wild type and dksA strains were cultured in LB broth containing 10 mM CaCl2 at 37°C with shaking to OD600 = 0.2

extract_protocol:
NGS Library Preparation, Bacterial Ribosome Reduction and Rapid Run flow cell with Paired End 50bp reads were done at The University of Alabama at Birmingham, Heflin Centre for Human Genetics - Genomics Core Facility (USA)
Library prepared with TruSeq Stranded Total RNA Sample Prep Kit (Illumina).

treatment_protocol: Bacteriophage P1vir was added to the final MOI = 10. Samples of 500 µl were withdrawn after 0, 10, and 20 min of the P1vir infection (plus  0 min. , no phage added), mixed with the RNAprotect® Bacteria Reagent (Qiagen). RNA was extracted using RNeasy® Mini Kit (Qiagen), and RNase-Free DNase Set (Qiagen). RNA elution was performed with 50 µl of RNase-free water. The purity and integrity of the RNA was assessed using the Bioanalyzer 2100 (Agilent Technologies, USA) and Agilent RNA 6000 Nano Kit. RNA samples were stored at -80°C prior to RNA sequencing

tag: strain type

value: MG1655 ∆hfq

tag: strain id

value: infected with P1vir phage

tag: condtions

value: 20 min after phage added

tag: replicates

value: experiment 2


title: Monkey-leukocyte-3

description: 18 tissues sample from monkeys

tag: tissue

value: leukocyte


title: E2-3_etoh


title: E. coli hfq mutant - P1vir infection time 20 min - rep. 1

value: experiment 1


title: Monkey-heart-1

description: 18 tissues sample from monkeys

value: qMap-seq


title: E2-3_50nM DEX


title: 2mWT_intestine [replicate_1]

value: Intestine

value: WT


title: Monkey-erythrocyte-4

description: 18 tissues sample from monkeys

source_name: erythrocyte

value: erythrocyte


title: MD-WD_Placenta_5_M

description: Library name: MH5

value: Placenta

tag: Sex

value: Male

value: Western Diet  + methyl donors


title: Monkey-erythrocyte-3

description: 18 tissues sample from monkeys


title: E. coli hfq mutant - P1vir infection time 10 min - rep. 2

value: 10 min after phage added


title: MD-WD_Placenta_4_F

description: Library name: MH4

value: Female


title: MD-WD_Placenta_3_M

description: Library name: MH3


title: Monkey-erythrocyte-2

description: 18 tissues sample from monkeys


title: 2mWT_eyes [replicate_1]

value: Eyes

value: 2 month

tag: genotype


title: 2mWT_brain [replicate_1]

value: Brain

tag: time


title: MD-WD_Placenta_2_F

description: Library name: MH2


title: E. coli hfq mutant - P1vir infection time 10 min - rep. 1

value: MG1655 ∆hfq

value: infected with P1vir phage


title: E. coli hfq mutant - P1vir infection time 0 min - rep. 2

value: 0 min after phage added

value: experiment 2


title: E. coli hfq mutant - P1vir infection time 0 min - rep. 1

value: experiment 1


title: 2mATF3OE_skin [replicate_4]

value: Skin

value: ATF3 overexpression


title: MD-WD_Placenta_6_F

description: Library name: MH6


title: Monkey-colon-3

description: 18 tissues sample from monkeys

source_name: colon

value: colon

value: qMap-seq


title: Monkey-colon-4

description: 18 tissues sample from monkeys


title: WD_Placenta_8_F

description: Library name: H8

value: Placenta

value: Western Diet


title: Monkey-colon-2

description: 18 tissues sample from monkeys


title: E. coli hfq mutant - no P1vir added, time 0 min - rep. 2

value: untreated

value: 0 min - no phage added


title: E. coli hfq mutant - no P1vir added, time 0 min - rep. 1


title: 2mATF3OE_intestine [replicate_4]

value: Intestine


title: WD_Placenta_7_F

description: Library name: H7

value: Female


title: 2mWT_heart [replicate_1]

value: Heart

value: 2 month

value: WT


title: WD_Placenta_6_F

description: Library name: H6


title: 2mATF3OE_heart [replicate_4]


title: 2mWT_gills [replicate_1]

source_name: Gills

value: Gills


title: Monkey-breast-4

description: 18 tissues sample from monkeys

source_name: breast

value: breast


title: wild type E. coli - P1vir infection time 20 min - rep. 1

value: MG1655 wild type

value: infected with P1vir phage

value: 20 min after phage added


title: Monkey-erythrocyte-1

description: 18 tissues sample from monkeys

value: erythrocyte


title: MD-WD_Placenta_1_F

description: Library name: MH1

value: Western Diet  + methyl donors


title: Monkey-breast-3

description: 18 tissues sample from monkeys

value: qMap-seq


title: 2mATF3OE_gills [replicate_4]

value: ATF3 overexpression


title: 2mATF3OE_eyes [replicate_4]

value: Eyes


title: wild type E. coli - P1vir infection time 10 min - rep. 1

value: 10 min after phage added

value: experiment 1


title: wild type E. coli - P1vir infection time 10 min - rep. 2

value: experiment 2


title: WD_Placenta_4_M

description: Library name: H4

value: Placenta

value: Male

value: Western Diet


title: 2mATF3OE_brain [replicate_4]

value: Brain

value: 2 month


title: WD_Placenta_2_M

description: Library name: H2


title: Monkey-breast-2

description: 18 tissues sample from monkeys

value: breast


title: wild type E. coli - P1vir infection time 0 min - rep. 2

value: MG1655 wild type

value: 0 min after phage added


title: 2mATF3OE_skin [replicate_3]

source_name: Skin

value: Skin


title: WD_Placenta_3_M

description: Library name: H3


title: wild type E. coli - P1vir infection time 0 min - rep. 1

value: infected with P1vir phage


title: 2mATF3OE_muscle [replicate_4]

source_name: Muscle

value: Muscle


title: Monkey-colon-1

description: 18 tissues sample from monkeys

value: colon

value: qMap-seq


title: wild type E. coli - P1vir infection time 20 min - rep. 2

value: 20 min after phage added


title: Monkey-breast-1

description: 18 tissues sample from monkeys


title: wild type E. coli - no P1vir added, time 0 min - rep. 2

value: untreated

value: 0 min - no phage added


title: 2mATF3OE_muscle [replicate_3]

value: ATF3 overexpression


title: WD_Placenta_1_F

description: Library name: H1

value: Placenta

value: Female


title: 2mATF3OE_intestine [replicate_3]

source_name: Intestine

value: Intestine


title: MD-LPD_Placenta_8_F

description: Library name: M8

value: Low protein diet + methyl donors


title: WD_Placenta_5_M

description: Library name: H5

value: Male

value: Western Diet


title: 2mATF3OE_heart [replicate_3]

value: Heart

value: 2 month


title: MD-LPD_Placenta_7_M

description: Library name: M7


title: Monkey-brain-4

description: 18 tissues sample from monkeys

source_name: brain

value: brain


title: wild type E. coli - no P1vir added, time 0 min - rep. 1

value: MG1655 wild type

value: experiment 1


title: Monkey-breast-2-1

description: 18 tissues sample from monkeys

value: breast


title: MD-LPD_Placenta_6_M

description: Library name: M6


title: WT_DSS_6

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

description: Library name: WT_DSS_6

data_processing:
MAP-RSeq(43) is an integrated RNA-seq bioinformatics pipeline developed at the Mayo Clinic for comprehensive analysis of raw RNA sequencing paired-end reads. MAP-RSeq employs STAR(44), a splice-aware, accurate and fast aligner for aligning reads to the reference mouse genome (build mm10). Gene and exon expression quantification is performed using Subread package to obtain raw and normalized (CPM – counts per million reads mapped) reads. Comprehensive quality control modules from the RSeQC(45) package are run on aligned reads to assess the quality of the sequenced libraries. Volcano plots and PCA visualization were generated using R package ggplot2, and heatmaps were generated using R packages pheatmap and gplots.
Assembly: mm10
Supplementary files format and content: tsv format containg raw gene counts and FPKM normalized expression values

source_name: Colon

growth_protocol: The colon was harvested from mice upon sacrifice and intestinal epithelial cells were isolated via the The Cell Press Star Protocol “Isolation and analyses of lamina propria lymphocytes from mouse intestines”.

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
RNA-seq was performed using Eukaryotic Transcriptome Library Construction Protocol, an RNase H method for library prep, and libraries were sequenced on HiSeqXten by 150bp paired end.

value: Colon

tag: cell type

value: Intestinal epithelial cells

value: Treg WTcre

value: 2% DSS


title: 2mATF3OE_gills [replicate_3]

value: Gills

value: ATF3 overexpression


title: MD-LPD_Placenta_5_M

description: Library name: M5

value: Placenta


title: Monkey-brain-2

description: 18 tissues sample from monkeys

tag: cell line

value: qMap-seq


title: Monkey-brain-3

description: 18 tissues sample from monkeys


title: 2mATF3OE_eyes [replicate_3]

value: Eyes


title: Monkey-brain-4-1

description: 18 tissues sample from monkeys


title: Monkey-brain-1

description: 18 tissues sample from monkeys


title: WT_DSS_4

description: Library name: WT_DSS_4

tag: treatment


title: 2mATF3OE_brain [replicate_3]

source_name: Brain

value: Brain


title: MD-LPD_Placenta_4_M

description: Library name: M4

value: Male

value: Low protein diet + methyl donors


title: KO_DSS_12

description: Library name: KO_DSS_12

value: Treg IL-6RaKO


title: MD-LPD_Placenta_3_F

description: Library name: M3

value: Female


title: Monkey-blood-4

description: 18 tissues sample from monkeys

source_name: blood

value: blood


title: 2mATF3OE_skin [replicate_2]

value: Skin

value: 2 month


title: Monkey-blood-3

description: 18 tissues sample from monkeys


title: KO_DSS_11

description: Library name: KO_DSS_11

value: Colon


title: MD-LPD_Placenta_2_F

description: Library name: M2


title: 2mATF3OE_muscle [replicate_2]

value: Muscle


title: KO_DSS_10

description: Library name: KO_DSS_10

value: Intestinal epithelial cells


title: MD-LPD_Placenta_1_F

description: Library name: M1


title: 2mATF3OE_intestine [replicate_2]

value: Intestine


title: WT_H20_3

description: Library name: WT_H20_3

value: Treg WTcre


title: LPD_Placenta_8_F

description: Library name: L8

value: Low protein diet


title: Monkey-blood-1

description: 18 tissues sample from monkeys


title: Monkey-adipose-4

description: 18 tissues sample from monkeys

source_name: adipose

value: adipose


title: WT_DSS_5

description: Library name: WT_DSS_5

value: 2% DSS


title: WT_H20_2

description: Library name: WT_H20_2


title: 2mATF3OE_gills [replicate_2]

value: Gills

value: ATF3 overexpression


title: WT_H20_1

description: Library name: WT_H20_1


title: Monkey-adipose-3

description: 18 tissues sample from monkeys

value: qMap-seq


title: LPD_Placenta_7_M

description: Library name: L7

value: Placenta

value: Male


title: LPD_Placenta_6_M

description: Library name: L6


title: Monkey-adipose-2

description: 18 tissues sample from monkeys


title: 2mATF3OE_eyes [replicate_2]

source_name: Eyes

value: Eyes


title: LPD_Placenta_4_M

description: Library name: L5


title: KO_H20_8

description: Library name: KO_H20_8

value: Treg IL-6RaKO


title: 2mATF3OE_brain [replicate_2]

value: Brain


title: Monkey-adipose-1

description: 18 tissues sample from monkeys


title: LPD_Placenta_5_F

description: Library name: L4

value: Female


title: Monkey-blood-2

description: 18 tissues sample from monkeys

value: blood


title: 2mATF3OE_skin [replicate_1]

value: Skin

value: 2 month


title: bpcV-3

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

description: Library name: bpcV-S294

data_processing:
Paired-end sequencing was performed. Reads were aligned to the Arabidopsis TAIR10 annotation of the A. thaliana transcriptome with bowtie2 (Langmead & Salzberg, 2012)
Gene expression levels were estimated by RSEM (B. Li & Dewey, 2011)and differential analyses of gene expression were executed with edgeR (Robinson et al., 2010)
The Genewise Negative Binomial Generalized (glmQLFTest) was applied to test for statistically significant differences. P-values were corrected using the Benjamini Hochberg procedure for the control of the False Discovery Rate and only genes showing a p-value <= 0.01 following the FDR adjustment were considered as differentially expressed (DEGs).
Assembly: TAIR10
Supplementary files format and content: *.genes.results: reads counts per genes as estimated by RSEM
Supplementary files format and content: risultati_finali_RNAseq_BPC.csv: differential gene expression analysis results. Only genes with at least 10 reads in at least one sample were considered. For every gene cpm in all the six samples are reported along with the logFC, p-value and FDR

source_name: inflorescences apexes with flowers up to stage 12

growth_protocol: Plants  grown in a controlled environment at 20–22 °C under long day conditions (16 h light/8 h dark)

extract_protocol:
RNA was extracted from the samples using the NucleoSpin RNA Plant kit from Macherey Nagel
Sequencing libraries were prepared by BioDiversa with poly-A enrichment

treatment_protocol: No treatment

value: bpcV


title: LPD_Placenta_3_F

description: Library name: L3


title: MERVL GFP negative

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

description:
Library name: sample2
MERVL GFP negative

data_processing:
Overall sequence quality was examined using FastQC (v0.11.2) and adaptor sequences were clipped using Trim Galore (v0.6.4). The reads were mapped to the mouse genome (mm10) and a count matrix was generated using STAR (v2.7.6a)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mESC

extract_protocol:
Cell RNA were extracted and purified by Total RNA Extraction Kit (LS1040, Promega).
RNA-seq libraries were constructed according to the standard protocol of NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, 7530L).

value: mESC

value: MERVL GFP negative


title: 2mATF3OE_muscle [replicate_1]

value: Muscle


title: 2mATF3OE_heart [replicate_2]

source_name: Heart

value: Heart


title: bpcV-2

description: Library name: bpcV-S293

value: inflorescences apexes with flowers up to stage 12


title: LPD_Placenta_2_M

description: Library name: L2

source_name: Placenta

value: Low protein diet


title: 2mATF3OE_intestine [replicate_1]

value: Intestine

value: ATF3 overexpression


title: MERVL GFP positive

description:
Library name: sample1
MERVL GFP positive

value: MERVL GFP positive


title: LPD_Placenta_1_F

description: Library name: L1

value: Placenta


title: Lin-c-Kit+ cell, Copper deficiency, 5weeks, rep3

city: Hangzhou

first: Liyun

last: Chen

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Illumina Casava 1.7 software used for basecalling
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
RNA was havested using Trizol reagent,1.3ug of total RNA was used for the constructon of  sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

value: bone marrow

value: Lin-c-Kit+ cell

value: hematopoietic cell

tag: phenotype

value: Copper deficiency


title: Lin-c-Kit+ cell, Copper deficiency, 5weeks, rep2


title: WT-3

description: Library name: WT3-S291

value: wild type


title: CD_Placenta_8_M

description: Library name: N8

value: Male

value: Control diet


title: 2mATF3OE_gills [replicate_1]

value: Gills

value: 2 month


title: 2mATF3OE_heart [replicate_1]


title: KO_H20_7

description: Library name: KO_H20_7

value: Colon

value: Intestinal epithelial cells

value: Treg IL-6RaKO


title: WT-2

description: Library name: WT2-S290

value: inflorescences apexes with flowers up to stage 12


title: CD_Placenta_7_F

description: Library name: N7

value: Female


title: WT-1

description: Library name: WT1-S289


title: CD_Placenta_6_F

description: Library name: N6


title: Lin-c-Kit+ cell, WT control, 5weeks, rep3

value: control


title: Lin-c-Kit+ cell, WT control, 5weeks, rep2


title: 2mATF3OE_brain [replicate_1]

value: Brain

value: ATF3 overexpression


title: 2mATF3OE_eyes [replicate_1]

value: Eyes


title: HG3

city: XI an

first: Wei

last: Liu

address: Weiyang street

institute: Shaanxi University of Science & Technology

data_processing:
Illumina Casava2.19 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low quality sequence
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell
Assembly: mm9
Supplementary files format and content: Excel file includes readcount value for each sample

organism: Candida albicans

source_name: yeast cell

growth_protocol: grow in RPMI for 6 h at 35 °C

extract_protocol:
Candida albicans were collected,flash frozen on dry ice, and RNA was harvested using Trizol reagent Illumina TruSeq RNA Sample Prep kit(Cat#FC-122-10)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: treated with HG for 6 h

value: yeast cell

value: HG


title: HG2


title: Lin-c-Kit+ cell, WT control, 5weeks, rep1

value: bone marrow

value: Lin-c-Kit+ cell

value: hematopoietic cell


title: CD_Placenta_5_F

description: Library name: N5

value: Placenta

value: Control diet


title: 2mATF3KO_muscle [replicate_4]

value: Muscle

value: 2 month

value: ATF3 knockout


title: 2mATF3KO_skin [replicate_4]

value: Skin


title: bpcV-1

description: Library name: bpcV-S292

value: inflorescences apexes with flowers up to stage 12

value: bpcV


title: CD_Placenta_4_M

description: Library name: N4

value: Male


title: HG1


title: CD_Placenta_3_M

description: Library name: N3


title: 2mATF3KO_intestine [replicate_4]

value: Intestine


title: RNA shNC rep2

city: Seoul

first: Sunghan

last: Lee

state: South Korea

address: Building 203 Room 526, 1, Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

description: RNA-seq

data_processing:
Sequencing reads were first mapped to the combined human-SARS-CoV-2 genome using STAR with options accommodating non-canonical viral junctions. Only uniquely mapped reads were used for gene-level quantification with featureCounts. Normalized gene counts were calculated using the R/Bioconductor package DESeq2.
Assembly: STAR index were built using concatenated genome of human genome (GRCh38.primary_assembly) and SARS-CoV-2 genome (NC_045512.2).
Supplementary files format and content: Comma-delimited csv files include the DESeq2-normalized counts of RNA-seq samples.

extract_protocol:
RNAs were isolated using Direct-zol RNA miniprep kit (Zymo Research).
The library was constructed following the manufacturer’s instructions using the MGIEasy RNA Directional Library Prep Set (MGI tech).

value: human lung cancer cell line

value: shNC


title: CD_Placenta_2_F

description: Library name: N2

value: Female


title: Lin-Sca1+c-Kit+ cell, Slc31a1 knockout, 5weeks, rep3

data_processing:
Illumina Casava 1.7 software used for basecalling
Assembly: mm9
Supplementary files format and content: tab-delimited txt file includes FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: Slc31a1 knockout


title: RNA shNC rep1

description: RNA-seq


title: 2mATF3KO_heart [replicate_4]

value: Heart


title: Lin-Sca1+c-Kit+ cell, Slc31a1 knockout, 5weeks, rep2

value: bone marrow


title: CD_Placenta_1_M

description: Library name: N1


title: 2mATF3KO_gills [replicate_4]

source_name: Gills

value: Gills


title: PTBP1-immunoprecipitated RNAseq Primar culture Sertoli cell_3

city: Minato

first: Manabu

last: Ozawa

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

description:
Library name: Sertoli_cell_PTBP1-IP_3
SC_RIP_2_1

data_processing:
For RNAseq of FACSed Sertoli cells,Paired-end reads (2 × 36 bases) were obtained by sequencing on NextSeq 500 (Illumina) at Tsukuba i-Laboratory LLP (Tsukuba, Japan). Raw sequencing data files were processed in FASTQ format and imported into CLC Genomics Workbench (CLC GW, Version 10.1.1, Qiagen). Sequences were mapped to the mouse genome (mm10) and quantified using the 49,585 annotated genes provided in CLC GW. Total count values were used for pairwise comparison using the Empirical Analysis of DGE tool in CLC GW. For PTBP1-immunoprecipitated RNAseq,The fastq files were generated using bcl2fastq-2.20. Adapter sequences and low-quality bases were trimmed from the raw reads using cutadapt(59) ver v1.18. The trimmed reads that mapped to mouse rRNA and tRNA using Bowtie2 (version 2.3.5.1) were filtered out. The remaining reads were then aligned to the mouse reference genome (mm10) using STAR(60) ver 2.6.0c with the GENCODE (gencode.vM23) gtf file. Uniquely mapped reads were counted and summarized at the gene level (protein coding) using htseq-count(61) v0.11.2 with the GENCODE gtf file. The immunoprecipitated RNAs (genes) were identified as differentially expressed genes (DEGs) relative to the input as the control by calculating fold changes and false discovery rates (FDR) using DESeq2(62) v1.30.0.
Assembly: mm10
Supplementary files format and content: .txt formatted CPM values or .xlsx formatted FPKM values

source_name: Testis

extract_protocol:
NucleoSpin RNA plus (TaKaRa).
For RNAseq of FACSed Sertoli cells, Poly-A RNA was isolated from 100 ng of total purified RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490), and converted into a sequencing library using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7420). For PTBP1-immunoprecipitated RNAseq, RNA-seq libraries from total RNA were generated using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB).

value: Testis

value: WT


title: Lin-c-Kit+ cell, Copper deficiency, 5weeks, rep1

value: Lin-c-Kit+ cell

value: hematopoietic cell

value: Copper deficiency


title: RNA shGIGYF2 rep2

description: RNA-seq


title: Lin-Sca1+c-Kit+ cell, Slc31a1 knockout, 5weeks, rep1


title: RNA shGIGYF2 rep1

description: RNA-seq


title: Lin-Sca1+c-Kit+ cell, WT, 5weeks, rep1


title: PTBP1-immunoprecipitated RNAseq Primar culture Sertoli cell_2

description:
Library name: Sertoli_cell_PTBP1-IP_2
SC_RIP_1_2


title: 2mATF3KO_brain [replicate_4]

value: Brain

value: 2 month

value: ATF3 knockout