title: KO_2

description:
0203_3
3_S3


title: 06H133 [re-analysis]

status: Public on Apr 23 2025

type: SRA

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: reanalysis of GSM1634297

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters for samples sequenced using stranded libraries.
Strand orientation is reverse for stranded samples, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

molecule: total RNA

organism: Homo sapiens

source_name: Heparinised blood

extract_protocol:
TruSeq RNA Sample Preparation  (Illumina)
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Sequencing libraries were prepared from total RNA using a poly-A selection and either the TruSeq unstranded RNA Sample Preparation (Illumina), TruSeq Stranded RNA Sample Preparation (Illumina) or the KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

tag: tissue

value: Heparinised blood

tag: cell type

value: acute myeloid leukemia

tag: strand orientation

value: unstranded


title: 04H078 [re-analysis]

description: reanalysis of GSM1634284

source_name: Bone marrow

value: Bone marrow


title: 04H140 [re-analysis]

description: reanalysis of GSM1634286


title: 05H143 [re-analysis]

description: reanalysis of GSM1634292


title: 04H025 [re-analysis]

description: reanalysis of GSM1634283


title: WT_2

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
0203_4
4_S4

data_processing:
FASTQ-file generation and demultiplexing was performed using bcl2fastq 4.0.3
Alignment to genome and gene counts were generated with the nfcore-rnaseq pipeline v. 3.11.2 using the STAR->Salmon workflow
Assembly: GRCm38
Supplementary files format and content: Tab-seperated file containing the raw gene counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample

molecule: polyA RNA

organism: Mus musculus

source_name: Skeletal muscle

extract_protocol:
Total RNA was isolated from QUAD with Trizol and RNeasy kit (Qiagen), and its quality was verified with 2100 Bioanalyzer Instrument (Agilent).
ssRNA-seq; Libraries were prepared using the Universal Plus mRNA-seq protocol (Tecan) as recommended by the manufacturer. Libraries were quantified with NuQuant using the Qubit fluorometer (Thermo Fisher Scientific), quality checked using a TapeStation instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina).

value: Skeletal muscle

tag: genotype

value: WT

tag: rin


title: KO_1

description:
0203_1
1_S1

value: KO


title: 17H176

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters
Strand orientation is reverse, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

source_name: Blood

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Stranded sequencing libraries were prepared from total RNA using the NEBNext PolyA mRNA Magnetic Isolation Module.

value: Blood

value: Acute myeloid leukemia


title: 03H052 [re-analysis]

description: reanalysis of GSM1634282


title: 05H030 [re-analysis]

description: reanalysis of GSM1634289


title: 03H033 [re-analysis]

description: reanalysis of GSM1634281


title: AUS2098

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

country: USA

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
STAR was used to align reads to the mm39 genome build
Reads were quantified to mm39 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Assembly: mm39
Supplementary files format and content: Text file including CPM for each sample (in columns) and gene (in rows)

source_name: Lung

extract_protocol:
RNEasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: Sex

value: Male

tag: treatment

value: vehicle


title: 17H082


title: AUS2097


title: AUS2096


title: 12H180 [re-analysis]

description: reanalysis of GSM1521623


title: 17H064


title: 12H098 [re-analysis]

description: reanalysis of GSM1521621


title: 03H016 [re-analysis]

description: reanalysis of GSM1634280


title: 02H009 [re-analysis]

description: reanalysis of GSM1634279


title: 12H045 [re-analysis]

description: reanalysis of GSM1521620


title: 12H183 [re-analysis]

description: reanalysis of GSM1521624


title: 17H167


title: 12H166 [re-analysis]

description: reanalysis of GSM1521622


title: WT_1

description:
0203_2
2_S2


title: AUS2092


title: 17H073


title: AUS2091


title: 11H107 [re-analysis]

description: reanalysis of GSM1521619


title: 10H119 [re-analysis]

description: reanalysis of GSM1521618


title: 17H045


title: 10H030 [re-analysis]

description: reanalysis of GSM1521617


title: AUS2090


title: 09H040 [re-analysis]

description: reanalysis of GSM1521616


title: 17H036


title: 08H042 [re-analysis]

description: reanalysis of GSM1521614


title: 17H033


title: 08H072 [re-analysis]

description: reanalysis of GSM1521615


title: 08H034 [re-analysis]

description: reanalysis of GSM1521613


title: AUS2085

value: Female


title: 06H035 [re-analysis]

description: reanalysis of GSM1521611


title: AUS2082


title: AUS2086


title: 05H184 [re-analysis]

description: reanalysis of GSM1521610


title: AUS2084


title: 17H059


title: 05H042 [re-analysis]

description: reanalysis of GSM1521608


title: AUS2080


title: 05H118 [re-analysis]

description: reanalysis of GSM1521609


title: 16H148


title: 17H013


title: 03H083 [re-analysis]

description: reanalysis of GSM1521607


title: 03H065 [re-analysis]

description: reanalysis of GSM1521606


title: AUS2079


title: 13H140 [re-analysis]

description: reanalysis of GSM1521604


title: 13H058 [re-analysis]

description: reanalysis of GSM1521605


title: 13H066 [re-analysis]

description: reanalysis of GSM1521603


title: 11H179 [re-analysis]

description: reanalysis of GSM1521602


title: 16H142


title: ARV3828


title: 17H027


title: 11H022 [re-analysis]

description: reanalysis of GSM1521601


title: 16H139


title: ARV3827


title: 07H137 [re-analysis]

description: reanalysis of GSM1521612


title: 17H023


title: 10H008 [re-analysis]

description: reanalysis of GSM1521600


title: 08H099 [re-analysis]

description: reanalysis of GSM1521599


title: 16H132


title: ARV3826


title: ARD3823


title: 06H115 [re-analysis]

description: reanalysis of GSM1521598


title: ARD3822


title: 16H115


title: 05H113 [re-analysis]

description: reanalysis of GSM1521595


title: 16H119


title: 05H136 [re-analysis]

description: reanalysis of GSM1521596


title: ARD3821


title: STING KO MEF DMXAA treated 10h, 2

city: Dallas

last: Yan

state: TX

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

description: Library name: MEFSKOD2

data_processing:
Data is processed with Astrocyte RNASeq Analysis Workflow on UTSW BioHPC
Assembly: GRCh38, GRCm38
Supplementary files format and content: txt files include FPKM for the samples

source_name: MEF

extract_protocol:
The total RNA was first extracted using TRI Reagent, followed by a clean up with RNeasy plus mini. All steps were done according to manufacturer's protocol
For cerebrum samples, the RNA library was prepared non-stranded with polyA enrichment. For cell line samples, the RNA library was prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's instructions

tag: cell line

value: MEF

value: Fibroblasts

value: Sting-/-

value: DMXAA


title: STING KO MEF Vehicle treated 10h, 2

description: Library name: MEFSKOV2

value: DMSO


title: 16H108


title: 04H030 [re-analysis]

description: reanalysis of GSM1521594

value: acute myeloid leukemia


title: STING KO MEF DMXAA treated 10h, 1

description: Library name: MEFSKOD1


title: 03H095 [re-analysis]

description: reanalysis of GSM1521593

value: unstranded


title: STING KO MEF Vehicle treated 10h, 1

description: Library name: MEFSKOV1


title: 12H148 [re-analysis]

description: reanalysis of GSM1521592

value: Bone marrow


title: 16H107


title: 16H112


title: ARC3817

value: normoxic


title: MEF DMXAA treated 10h, 2

description: Library name: MEFWTD2

value: WT


title: ARC3816


title: ARC3815


title: 16H106


title: 11H205 [re-analysis]

description: reanalysis of GSM1521591


title: 06H020 [re-analysis]

description: reanalysis of GSM1521597


title: ACE9432


title: 10H107 [re-analysis]

description: reanalysis of GSM1521590

value: Heparinised blood


title: MEF Vehicle treated 10h, 2

description: Library name: MEFWTV2


title: MEF Vehicle treated 10h, 1

description: Library name: MEFWTV1


title: 16H099


title: ACE259

value: Mas KO


title: 10H063 [re-analysis]

description: reanalysis of GSM1521589


title: 16H100

value: Blood

value: Acute myeloid leukemia


title: 10H046 [re-analysis]

description: reanalysis of GSM1521588


title: ACE169

value: Lung

value: Male


title: 16H098


title: 07H038 [re-analysis]

description: reanalysis of GSM1521587


title: 16H093


title: ACE168


title: 16H044


title: 04H063 [re-analysis]

description: reanalysis of GSM1521585


title: 04H050 [re-analysis]

description: reanalysis of GSM1521584


title: 05H179 [re-analysis]

description: reanalysis of GSM1521586


title: ACE71


title: 16H089


title: 16H018


title: 12H165 [re-analysis]

description: reanalysis of GSM1521583


title: MEF DMXAA treated 10h, 1

description: Library name: MEFWTD1


title: 16H105


title: GFI1KO, scRNA

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

description: 10X single-cell multiome

library_source: transcriptomic single cell

data_processing:
RNA and ATAC raw reads from WT and GFI1ΔCD8 T cell samples were processed with CellRanger-arc v2.0.2 to map RNA transcripts and ATAC peaks to mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Tab separated matrix files for scRNA and bigwig files fro scATAC data

molecule: nuclear RNA

source_name: spleen

extract_protocol:
Cells were pelleted for 5 mins at 300 × g followed by nuclei isolation by incubating cells with chilled cell lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% tween-20, 0.1% IGEPAL CA-630, 0.01% digitonin, 1mM dithiothreitol, 1 U/μL RNase inhibitor and 1% BSA) for 3 min. Nuclei were washed twice in 1 ml of wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1 mM dithiothreitol and 1 U/µL RNase inhibitor and 1% BSA) by centrifuging at 500 × g for 5 min. After centrifugation, cells were resuspended in chilled Nuclei Buffer (1× Nuclei Buffer, 1 mM dithiothreitol and 1 U/µL RNase inhibitor).
Nuclei were incubated in transposition mix according to the Chromium Next GEM Single Cell Multiome ATAC + GEX user guide (protocol CG000338 Rev F). Following transposition, GEMs were generated using 10x Chip J. Sample cleanup and amplification PCR were performed as per the user guide.

treatment_protocol: P14 CD8+ T cells were FAC-sorted from mice at day 7 after LCMVc13 infection. CD8+ T cells were pooled from 3-5 mice and ~1×105 cells were used for nuclei isolation.

tag: strain

value: spleen

value: CD8+ T cells

tag: library type

value: 10x single cell ATAC + GEX


title: 12H044 [re-analysis]

description: reanalysis of GSM1521582


title: D160_p18_96h_4Gy

type: RNA

city: Heidelberg

first: Johannes

last: Betge

address: Im Neuenheimer Feld 580

department: Signaling and Functional Genomics

country: Germany

institute: German Cancer Research Center (DKFZ)

description: D160, radiated, replicate 4

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays according to user manual GeneChip® 3' IVT PLUS Reagent Kit, P/N 703210

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731)

data_processing: Data were normalized using the 'affy' R/Bioconductor package. Normalization steps include background correction using the 'rma' method and quantile normalization.

label: biotin

source_name: patient derived cancer organoids

label_protocol: The Affymetrix Gene Chip 3´IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100ng total RNA, Label: Biotin

growth_protocol: Organoids were cultured in ENA media

extract_protocol: Qiagen RNeasy Extraction Kit

treatment_protocol: Organoids were radiated with 4 Gy or left untreated. Some organoid samples had additionally been treated with DMSO.

value: colorectal cancer


title: D160_p17_96h_4Gy

description: D160, radiated, replicate 3


title: D160_p17_96h_0Gy

description: D160, unradiated, replicate 3


title: WT, scRNA

description: 10X single-cell multiome


title: 16H013


title: 16H011


title: ACE70


title: D160_p18_96h_0Gy

description: D160, unradiated, replicate 4


title: MCMV infection, WT, D7, ATAC, rep3

library_source: genomic

data_processing:
Read quality was assessed and low quality reads trimmed with fastp.
Trimmed reads were mapped to the mouse genome (mm10) using bowtie2, with standard parameters.
Picard was used to remove PCR duplicates. The deduplicated reads were then filtered to remove mitochondrial chromosome, Y chromosome, improperly paired and non-mapping reads using samtool flags.
Peak summits were called using macs2 using parameter --nomodel, --keep-dup all and --call-summits.
Identification of differentially accessible regions (at least a 1-fold-change and false discovery rate less than 0.05) was performed using DiffBind package.
Assembly: mm10
Supplementary files format and content: bigwig files for each sample

molecule: genomic DNA

extract_protocol:
Nuclei were washed and resuspended in 50 μL 1× TDE1 buffer (Illumina) containing 2.5 μL TDE1 transposase (Illumina). The transposase reaction was conducted at 37 °C for 30 min, with mild shaking.
Library amplification and barcoding were performed with NEBNext Ultra II Q5 Master Mix (New England Biolabs) using IDT dual index primer set (Integrated DNA Technologies). PCR was conducted for 10–11 cycles. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and library size distribution was assessed using the TapeStation High Sensitivity DNA Kit (Agilent).

treatment_protocol: 50,000 sorted P14 CD8+ T cells were lysed to extract nuclei using cell lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% tween-20, 0.1% IGEPAL CA-630, 0.01% digitonin and 1% bovine serum albumin).

value: C57BL/6 mice


title: 16H008


title: GFI1KO, scATAC

description: 10X single-cell multiome

library_source: genomic single cell


title: MCMV infection, WT, D7, ATAC, rep2


title: 11H104 [re-analysis]

description: reanalysis of GSM1521580


title: 09H066 [re-analysis]

description: reanalysis of GSM1521579


title: 15H138


title: 09H016 [re-analysis]

description: reanalysis of GSM1521578

source_name: Leukapheresis

value: Leukapheresis


title: MCMV infection, WT, D7, ATAC, rep1


title: 08H081 [re-analysis]

description: reanalysis of GSM1521577

value: acute myeloid leukemia


title: 16H015


title: D080_p21_96h_0Gy

description: D080, unradiated, replicate 4


title: 15H135


title: D080_p22_96h_4Gy

description: D080, radiated, replicate 5


title: MCMV infection,GFI1-KO, D7, ATAC, rep3


title: 12H042 [re-analysis]

description: reanalysis of GSM1521581

value: unstranded


title: D080_p20_96h_0Gy

description: D080, unradiated, replicate 3


title: D080_p20_96h_4Gy

description: D080, radiated, replicate 3


title: 15H122

value: Bone marrow


title: MCMV infection,GFI1-KO, D7, ATAC, rep2


title: 07H144 [re-analysis]

description: reanalysis of GSM1521576


title: D007_p19_96h_4Gy

description: D007, radiated, replicate 5


title: MCMV infection,GFI1-KO, D7, ATAC, rep1


title: D080_p21_96h_4Gy

description: D080, radiated, replicate 4


title: 06H151 [re-analysis]

description: reanalysis of GSM1521575


title: 04H091 [re-analysis]

description: reanalysis of GSM1521574


title: LCMVc13 infection, WT, D7, ATAC, rep3


title: 15H106


title: D007_p19_96h_0Gy

description: D007, unradiated, replicate 5


title: 15H103


title: LCMVc13 infection, WT, D7, ATAC, rep2


title: 15H090


title: LCMVc13 infection, WT, D7, ATAC, rep1


title: 03H112 [re-analysis]

description: reanalysis of GSM1521572


title: D007_p17_96h_4Gy

description: D007, radiated, replicate 3


title: D007_p18_96h_0Gy

description: D007, unradiated, replicate 4


title: 15H083


title: LCMVc13 infection,GFI1-KO, D7, ATAC, rep3


title: 15H085


title: 15H119


title: 03H109 [re-analysis]

description: reanalysis of GSM1521571


title: LCMVc13 infection,GFI1-KO, D7, ATAC, rep2


title: D007_p17_96h_0Gy

description: D007, unradiated, replicate 3


title: 15H082


title: D007_p18_96h_4Gy

description: D007, radiated, replicate 4


title: 04H061 [re-analysis]

description: reanalysis of GSM1521573


title: LCMVc13 infection,GFI1-KO, D7, ATAC, rep1


title: Naïve CD8 T cells, GFI1-KO, ATAC, rep3


title: 10H022 [re-analysis]

description: reanalysis of GSM1521569


title: 10H055 [re-analysis]

description: reanalysis of GSM1521570


title: D160T01_p28_DMSO_4Gy_2

description: D160, radiated, replicate 1


title: 15H071


title: 15H068


title: 10H127 [re-analysis]

description: reanalysis of GSM1521567


title: D160T01_p29_DMSO_0Gy_2

description: D160, unradiated, replicate 2


title: Naïve CD8 T cells, GFI1-KO, ATAC, rep2


title: 04H080 [re-analysis]

description: reanalysis of GSM1521568


title: Naïve CD8 T cells, GFI1-KO, ATAC, rep1


title: D160T01_p28_DMSO_0Gy_2

description: D160, unradiated, replicate 1


title: 10H058 [re-analysis]

description: reanalysis of GSM1521566


title: 15H063


title: 15H062


title: D080T01_p14_DMSO_4Gy_2

description: D080, radiated, replicate 2


title: Naïve CD8 T cells, WT, ATAC, rep3


title: D160T01_p29_DMSO_4Gy_2

description: D160, radiated, replicate 2


title: 09H098 [re-analysis]

description: reanalysis of GSM1521565


title: 15H059


title: 09H032 [re-analysis]

description: reanalysis of GSM1521564


title: Naïve CD8 T cells, WT, ATAC, rep2


title: 09H010 [re-analysis]

description: reanalysis of GSM1521563


title: Naïve CD8 T cells, WT, ATAC, rep1


title: 15H049


title: D080T01_p14_DMSO_0Gy_2

description: D080, unradiated, replicate 2


title: D080T01_p13_DMSO_4Gy_1

description: D080, radiated, replicate 1


title: LCMVc13 infection, GFI1-Lo T cells, D7, rep2

data_processing:
Read quality was assessed and low quality reads trimmed with fastp.
Reads were mapped to the mouse genome (mm10) using STAR v2.7.10
After mapping, reads were quantified with featureCounts v2.0.1
Assembly: mm10
Supplementary files format and content: Read counts following mapping to mm10 using featurecount

extract_protocol:
RNA was extracted from CD8+ T cell isolated using RNeasy Plus Micro kit (Qiagen)
Libraries were prepared with TruSeq Stranded Total RNA kit (Illumina). LCMVc31-D21 samples were processed with NEBNext Single Cell/low Input Library prep kit (New England Biolabs).


title: D007T01_p34_DMSO_4Gy_1

description: D007, radiated, replicate 2


title: 15H036


title: 08H021 [re-analysis]

description: reanalysis of GSM1521561


title: 15H023


title: 07H045 [re-analysis]

description: reanalysis of GSM1521560


title: Haemorrhoid_3

city: Kunming

first: Heng

last: Zhang

state: Yunnan

address: No. 2628 Xiangyuan Street, Chenggong District, Kunming, Yunnan Province, China

country: China

institute: Kunming Municipal Hospital of Traditional Chinese Medicine

description: Library name: Simple 6

data_processing:
Data analysis of miRNAs using ACGT101-miR (v4.2).
Assembly: GRCh38
Supplementary files format and content: The Excel sheet contains the expression profiles of all miRNAs and their detailed information (Pre-miRNA Index, miRNA_Index, miR_name, miR_seq, len, genomeID, strand, start, end, pre-miRNA_seq, #mir/MIR, mirIDs ,, rep_mirID, rep_mirSeq, rep_miRID, rep_miRSeq, type, Sequence in miRbase, group, SS, hairpinLen, CG%, dG, C_1(raw), C_2(raw), C_3(raw), H_1(raw), H_2(raw), H_3(raw), C_1(norm), C_2(norm), C_3(norm), H_1(norm), H_2(norm), H_3(norm), Expression level)

source_name: Haemorrhoid

extract_protocol:
RNA from total samples was isolated and purified using TRIzol (Invitrogen, CA, USA) according to the operating protocol provided by the vendor
Prepare sRNA sequencing libraries for miRNA-Seq using the TruSeq Small RNA Sample Preparation Kit.

value: Haemorrhoid


title: Haemorrhoid_2

description: Library name: Simple 5


title: 15H013


title: D080T01_p13_DMSO_0Gy_1

description: D080, unradiated, replicate 1


title: 07H041 [re-analysis]

description: reanalysis of GSM1521559


title: 15H044


title: D007T01_p33_DMSO_4Gy_1

description: D007, radiated, replicate 1


title: D007T01_p33_DMSO_0Gy_1

description: D007, unradiated, replicate 1


title: LCMVc13 infection, GFI1-Lo T cells, D7, rep3


title: 08H139 [re-analysis]

description: reanalysis of GSM1521562


title: LCMVc13 infection, GFI1-HI T cells, D7, rep2


title: Haemorrhoid_1

description: Library name: Simple 4


title: 07H003 [re-analysis]

description: reanalysis of GSM1521558


title: 14H171


title: 06H117 [re-analysis]

description: reanalysis of GSM1521557


title: 14H172


title: D007T01_p34_DMSO_0Gy_1

description: D007, unradiated, replicate 2


title: Control_3

description: Library name: Simple 3

source_name: normal control tissue

value: normal control tissue


title: LCMVc13 infection, GFI1-HI T cells, D7, rep1


title: LCMVc13 infection, GFI1-Lo T cells, D7, rep1


title: 14H155


title: LCMVc13 infection, GFI1-HI T cells, D7, rep3


title: LCMVArm infection, GFI1-Low T cells, D7, rep3


title: Control_2

description: Library name: Simple 2


title: 06H066 [re-analysis]

description: reanalysis of GSM1521556


title: 05H128 [re-analysis]

description: reanalysis of GSM1521555

value: Heparinised blood


title: Control_1

description: Library name: Simple 1


title: LCMVArm infection, GFI1-Low T cells, D7, rep2


title: 14H145


title: 05H066 [re-analysis]

description: reanalysis of GSM1521554


title: BGC823 cells, Galangin, Day 0

city: Changchun

first: Dongxu

last: Wang

state: Jilin

address: Xi'an Road #5333

department: Laboratory Animal Center, College of Animal Science

institute: Jilin University

description: Library name: Galangin_823

data_processing:
DNBSEQ
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).  Total RNA was used for the construction of sequencing libraries RNA
Libraries for RNA-seq were prepared using DNBSEQ UMI Small RNA following manufacturer's protocols

value: Gastric cancer cell line

value: WT

value: Treated with galangin

tag: batch

value: Day 0


title: 14H143

value: Blood

value: Acute myeloid leukemia


title: LCMVArm infection, GFI1-Low T cells, D7, rep1

value: spleen

value: CD8+ T cells


title: LCMVArm infection, GFI1-HI T cells, D7, rep3


title: 14H126


title: 05H025 [re-analysis]

description: reanalysis of GSM1521553


title: 04H121 [re-analysis]

description: reanalysis of GSM1521552


title: 14H124


title: LCMVArm infection, GFI1-HI T cells, D7, rep2


title: LCMVArm infection, GFI1-HI T cells, D7, rep1


title: CD14+_H3K27ac_PA_R1_ChIP

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

data_processing:
Reads were aligned on the hg19 human genome version with Novoalign (V3.02.07). H3K27ac ChIP-seq peaks were called using MACS2 (version2.1.1.20160309, q-value <0.05). Peaks present in both the replicates were selected using csaw package in R and included in the analysis. H3K27ac peaks present in promoters of coding genes and ENCODE blacklisted regions were excluded. Differential analyses of enhancers were carried out using the edgeR package in R software. Super enhancer analysis was performed using the ROSE algorithm
Assembly: hg19
Supplementary files format and content: tdf (tiled data file) coverage file generated by igvtools which is the binary read count density file for faster display in IGV

growth_protocol: Human CD14+ monocytes were obtained from commercial sources (All Cells. Alameda, CA) and cultured in RPMI medium with 10% FBS, penicillin (100 U/mL), streptomycin (100 μg/mL), 2 mmol/L glutamine, 5.5 mmol/L glucose.

extract_protocol:
Human CD14+ monocytes treated with PA (200 µM) or vehicle BSA for 24 hours. After treatment, cells were fixed using 4% formaldehyde for 10 minutes and glycine (125 mM) was added, followed by incubation for 5 minutes at room temperature. Then cells were washed twice with PBS containing protease inhibitor (Roche, cat#04693132001). Cells were lysed, and sonicated for 10 cycles (30 sec on 30 sec off cycle) using Bioruptor Pico sonicator (Diagenode).
Sequencing library preparation and reactions were conducted at City of Hope’s Integrative Genomics Core. Briefly, 10 ng of immunoprecipitated DNA was end-repaired (Epicenture), and a single adenosine was added using Klenow exo- (New England Biolabs (NEB)) and ligated to Illumina adaptor oligonucleotides (Illumina).

value: CD14+ Monocytes

value: PA


title: 03H067 [re-analysis]

description: reanalysis of GSM1521550


title: MCMV infection, WT, D7, rep3

value: C57BL/6 mice


title: 14H109


title: CD14+_PA_Input_R2

treatment_protocol: Human CD14+ monocytes treated with PA (200 µM) or vehicle BSA for 24 hours.


title: 14H093


title: 02H032 [re-analysis]

description: reanalysis of GSM1521549

value: acute myeloid leukemia


title: CD14+_PA_Input_R1


title: MCMV infection, WT, D7, rep1


title: 14H089


title: MCMV infection, WT, D7, rep2


title: BGC823 cells, Control, Day 0

description: Library name: control


title: CD14+_H3K27ac_BSA_R2_ChIP

value: BSA


title: 01H001 [re-analysis]

description: reanalysis of GSM1521548

value: unstranded


title: CD14+_H3K27ac_BSA_R1_ChIP


title: 14H049

value: Bone marrow


title: MCMV infection,GFI1-KO, D7, rep3


title: MCMV infection,GFI1-KO, D7, rep2


title: 08H129 [re-analysis]

description: reanalysis of GSM1521546


title: CD14+_H3K27ac_PA_R2_ChIP


title: CD14+_BSA_Input_R2


title: 04H041 [re-analysis]

description: reanalysis of GSM1521551


title: 14H028


title: MCMV infection,GFI1-KO, D7, rep1


title: CD14+_BSA_Input_R1


title: 08H085 [re-analysis]

description: reanalysis of GSM1521545


title: 14H026


title: 06H152 [re-analysis]

description: reanalysis of GSM1521544


title: LCMVc13 infection,WT, D21, rep3


title: SCC25 cells, DMSO 3

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

institute: Southern Medical University

data_processing:
Hisat2 v2.0.5
Clean reads were generated by removing low quality reads and then aligned to the Human Genome Assembly GRCh38/hg38 using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads mapped to each gene, and then the FPKM (Fragments Per Kilobase of sequence per Millions base pairs) of each gene were calculated based on the length of the gene and reads count mapped to the gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was first purified using TRIzol Reagent t and then assessed by 1% agarose gel electrophoresis and the Bioanalyzer 2100 system.
Sequencing libraries were constructed using the NEBNext UltraTM RNA Library Prep Kit for Illumina.

value: Oral squamous cell

value: DMSO

tag: time


title: 14H003


title: 02H017 [re-analysis]

description: reanalysis of GSM1521543


title: SCC25 cells, DMSO 2


title: WT, scATAC

description: 10X single-cell multiome

value: 10x single cell ATAC + GEX


title: 12H057 [re-analysis]

description: reanalysis of GSM1521547


title: LCMVc13 infection,WT, D21, rep1


title: SCC25 cells, DMSO 1

value: WT


title: 12H030 [re-analysis]

description: reanalysis of GSM1273641

value: Heparinised blood


title: 13H173


title: D080_p22_96h_0Gy

description: D080, unradiated, replicate 5

value: colorectal cancer


title: 11H170 [re-analysis]

description: reanalysis of GSM1273640


title: SCC25 cells, ACGs 3

value: ACGs


title: 13H166

value: Acute myeloid leukemia


title: LCMVc13 infection,GFI1-KO, D21, rep2

value: spleen


title: 11H151 [re-analysis]

description: reanalysis of GSM1273639


title: LCMVc13 infection,GFI1-KO, D21, rep1

value: CD8+ T cells


title: 11H129 [re-analysis]

description: reanalysis of GSM1273638


title: SCC25 cells, ACGs 1


title: 13H132


title: LCMVc13 infection, WT, D7, rep3


title: 11H019 [re-analysis]

description: reanalysis of GSM1273637


title: SCC15 cells, DMSO 3


title: LCMVc13 infection,WT, D21, rep2


title: 13H118

value: Blood


title: 11H008 [re-analysis]

description: reanalysis of GSM1273636


title: LCMVc13 infection, WT, D7, rep2


title: SCC15 cells, DMSO 2


title: 10H161 [re-analysis]

description: reanalysis of GSM1273635


title: 13H182


title: LCMVc13 infection,GFI1-KO, D21, rep3


title: LCMVc13 infection, WT, D7, rep1


title: SCC15 cells, DMSO 1


title: SCC25 cells, ACGs 2


title: 10H113 [re-analysis]

description: reanalysis of GSM1273634


title: 13H084


title: 13H064


title: 13H170


title: 10H109 [re-analysis]

description: reanalysis of GSM1273633


title: 13H012


title: LCMVc13 infection,GFI1-KO, D7, rep2


title: 10H038 [re-analysis]

description: reanalysis of GSM1273632


title: 13H060


title: LCMVc13 infection,GFI1-KO, D7, rep1


title: SCC15 cells, ACGs 1


title: 12H141


title: Neo_iCM, MGT+shScd1 replicate 2, Day7

city: wuhan

first: yu

middle: zhang

last: yi

state: hubei

address: donghu street

department: wuhan

institute: wuhan university

data_processing:
Raw sequencing data was initially filtered by Trimmomatic (version 0.36), with the discarding of low-quality reads and the trimming of reads contaminated with adaptor sequences.
Clean reads were mapped to the reference genome of mouse (mm10) using STRA software (version 2.5.3a) with default parameters.
The counting of reads mapped to the exon regions of each gene was carried out by featureCounts (Subread-1.5.1; Bioconductor).
Resulting BAM files were sorted and indexed using SAMtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: heart

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, cat. NO15596026). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina) with PE150 model.

value: heart

value: Primary cell

value: cardiac fibroblast

tag: age


title: 10H031 [re-analysis]

description: reanalysis of GSM1273631

value: acute myeloid leukemia


title: platelet, non_PSL, rep3

city: Beijing

first: Jun

last: Xiao

address: 30 Fucheng Road

institute: Air Force Medical Center, Air Force Medical University

description:
non_PSL_3
Readcount.txt

data_processing:
Basecalls were performed using illumina Casava v1.8 for sequencing output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using illumina Casava
Assembly: hg18
Supplementary files format and content: Readcount.txt

source_name: platelet

extract_protocol:
(1) Agarose gel electrophoresis analysis of RNA degradation and whether there is pollution;(2) Nanodrop detection of RNA purity (OD260/280 ratio);(3) Qubit for precise quantification of RNA concentration;(4) Agilent 2100 Accurate Detection of RNA Integrity
After passing the sample detection, a library was constructed using the Small RNA Sample Pre Kit. The special structures at the 3 'and 5' ends of Small RNA were utilized (with complete phosphate groups at the 5 'end and hydroxyl groups at the 3' end), and total RNA was used as the starting sample. Two ends of Small RNA were directly connected with connectors, and then reverse transcribed into cDNA. Subsequently, after PCR amplification, the target DNA fragment was separated by PAGE gel electrophoresis, and the cDNA library was obtained by gel cutting and recycling.

value: male

value: platelet

tag: group

value: nonPSL


title: 12H132

value: Bone marrow


title: Neo_iCM, MGT+shScd1 replicate 1, Day7


title: 09H054 [re-analysis]

description: reanalysis of GSM1273630

value: unstranded


title: 12H119


title: platelet, non_PSL, rep2

description:
non_PSL_2
Readcount.txt


title: Neo_iCM, MGT+shNT replicate 2, Day7

value: WT

value: MGT+shNT


title: 09H046 [re-analysis]

description: reanalysis of GSM1273629

value: Heparinised blood


title: LCMVc13 infection,GFI1-KO, D7, rep3

value: C57BL/6 mice


title: 12H086

value: Acute myeloid leukemia


title: SCC15 cells, ACGs 3

value: Oral squamous cell

value: ACGs


title: platelet, non_PSL, rep1

description:
non_PSL_1
Readcount.txt


title: Neo_iCM, MGT+shNT replicate 1, Day7


title: platelet, PSL, rep3

description:
PSL_3
Readcount.txt

value: PSL


title: SCC15 cells, ACGs 2


title: macrophage, TNF-a , rep4

city: Westmead

first: Jianwei

last: Chen

state: NSW

address: 176 Hawkesbury Rd

department: CTRR

institute: The Westmead Institute for Medical

data_processing:
Short-read sequencing was performed on the Novaseq X platform (Illumina) with 150bp pair-end reads. Library sequencing quality was determined using FastQC (Babraham Bioinformatics: www.bioinformatics.babraham.ac.uk/).
Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore (Babraham Bioinformatics). STAR was used to align reads to mouse genome mm10 using ENSEMBL gene annotations as a guide.
Read counts data corresponding to ENSEMBL gene annotations were generated the STAR flag --quantMode GeneCounts. Multiqc was used to verify quality metrics. All analyses were performed in the R Statistical Environment with tidyverse.
Briefly, counts data were background corrected and normalized for library size using edgeR. DGE was determined using the QLFtest (BH MTC p <0.05).
Gene lists were functionally annotated with Gene Ontology (GO), REACTOME and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (adjusted p value <0.05) using the cluster Profiler package
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes matrix table for each Sample
Supplementary files format and content: Excel file includes logFC, pValue, FDR, ect for each Sample

growth_protocol: Bone marrow macrophages were maintained in  DMEM supplemented with 10% Fetal bovine serum (FBS), 1X penicillin and streptomycin, 2mM glutamine, 1XNon-Essential Amino Acid (NEAA), and 10ng/ml macrophage colony-stimulating factor (M-CSF) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was isolated from mouse macrophages using Ambion 463 RiboPure RNA Purification Kit (AM1924, Thermo Fisher).
Poly-A selected mRNA libraries were generated using the Illumina stranded mRNA Prep Kit (20040534, Illumina) and validated with the Agilent Tapestation 4200 and qPCR before sequencing.

treatment_protocol: S29-32 are samples  stimulatedbyTNF-a

value: macrophage

value: TNF-a


title: 08H118 [re-analysis]

description: reanalysis of GSM1273626


title: 09H031 [re-analysis]

description: reanalysis of GSM1273628


title: 11H220

value: Blood


title: 12H053


title: 09H018 [re-analysis]

description: reanalysis of GSM1273627

value: acute myeloid leukemia


title: 11H230


title: platelet, PSL, rep2

description:
PSL_2
Readcount.txt

value: male


title: macrophage, TNF-a , rep3


title: 11H195


title: macrophage, TNF-a , rep1


title: platelet, PSL, rep1

description:
PSL_1
Readcount.txt

value: platelet


title: 08H112 [re-analysis]

description: reanalysis of GSM1273625


title: 11H182


title: 08H012 [re-analysis]

description: reanalysis of GSM1273623


title: Pnoc_LepR_WT_Pulldown_4

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

description:
Library name: Pnoc_LepR_WT_Pulldown_4
LepR Wildtype Pulldown

data_processing:
Preprocessing and Quality Control: RNA sequencing data was analyzed using the nf-core/rnaseq pipeline (v3.12.0), which included quality control of raw reads to assess sequencing quality and remove low-quality bases or adapter sequences.
Gene-Level Quanitification: Gene-level quantification was conducted using Salmon (v1.10.1), where reads were pseudoaligned to the GRCm38 reference genome to estimate transcript abundances.
Differential Gene Expression Analysis: Differential expression analysis was performed using DESeq2 (v1.38.3) in R. Raw counts were normalized, and statistical models were applied to identify differentially expressed genes across experimental conditions: Control-IP vs Control-Input, LeprKO-IP vs LeprKO-Input, and LeprKO-IP vs Control-IP.
Enrichment Analysis: Genes were classified as enriched in Pnoc neurons if they met specific criteria: adjusted p-value (padj) ≤ 0.01 and fold change (fc) ≥ 1.5. Enrichment was assessed under two conditions: Control-IP vs Control-Input and LeprKO-IP vs LeprKO-Input.
Filtering for Differentially Expressed Genes: Differentially expressed genes from the LeprKO-IP vs Control-IP comparison (padj ≤ 0.01) were filtered to retain only those enriched in Pnoc neurons based on the enrichment criteria.
Assembly: GRCm38
Supplementary files format and content: deseq2_results.csv: DESeq2 results
Supplementary files format and content: salmon.merged.gene_counts_scaled.tsv: Salmon Scaled Counts
Supplementary files format and content: salmon.merged.gene_tpm.tsv: Salmon Gene TPMs
Supplementary files format and content: salmon.merged.gene_counts.tsv: Salmon Gene Counts
Library strategy: Ribo-Seq

source_name: Brain, Hypothalamus

growth_protocol: Animals were kept on a C57Bl/6N background and housed in groups up to five animals per cage. Mice were kept on a 12-hour light/dark cycle in individually ventilated cages (IVCs) at 22°C–24°C. Animals had ad libitum access to water and food. All mice were fed a chow-diet (Ssniff V1554, 59484 Söest, Germany) containing 57% of calories from carbohydrates, 34% calories from protein and 9% calories from fat.

extract_protocol:
Immediately after sacrifice, hypothalamic samples from random fed mice (10–12-week-old) dissected out using a stainless-steel brain matrix (World precision instruments) and directly snap frozen in liquid nitrogen. Protein A Dynabeads (375 μl per IP, Invitrogen) were washed 3x in 0.15M KCl IP wash buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 150 mM KCl, 1% NP40, 0.5 mM DTT and 100 μg/ml cycloheximide). Beads were subsequently resuspended in 275 μl 0.15M KCl IP wash buffer and loaded with 50 μg of 19C8 and 50 μg of 19F7 (Cat# Htz-GFP-19F7 and Htz-GFP-19C8, Memorial Sloan Kettering Monoclonal Antibody Facility) and rotated over night at 4°C. Pooled hypothalamic tissue (4 pooled animals per sample; 4 samples per group) was homogenized in lysis buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 150 mM KCl, 0.5 mM DTT, 40 U/ml RNasin, 100 μg/ml cycloheximide, protease and phosphatase inhibitor cocktails [1 tablet of cOmplete mini EDTA-free protease inhibitor cocktail/7 mL and 2 tablets of PhosSTOP/10 ml]) 2x at 250 rpm, and 9x at 750 rpm on a rotating glass/teflon potter homogenizer (Potter S, Braun) at 4°C. Homogenates were transferred to microcentrifuge tubes (Nonstick, RNase-free microfuge tubes, 1.5 ml, Ambion, Invitrogen) and centrifuged at 2,000xg for 10 min at 4°C. Working on ice, the supernatant was transferred to a new tube, and 1/9 sample volume 10% NP-40 (final concentration: 1%) and 1/9 sample volume 300 mM DHPC (final concentration: 30 mM) was added. Solution was then incubated on ice for 2 min and before centrifuging at 17,000xg, 10 min at 4°C. The supernatant was moved to a new tube, and a 25 μl aliquot was removed, transferred to a new tube, flash frozen in liquid nitrogen and stored at 80°C for purification as input RNA. For immunoprecipitation (IP) 200 μl of antibody-bound magnetic beads were added to the remaining supernatant (800-1000 μl supernatant) and incubated at 4°C, 1h rotating. The magnetic beads were collected and resuspended in 1000 μl of 0.35 M KCl IP wash buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 350 mM KCl, 1% NP40, 0.5 mM DTT, 100 μg/ml cycloheximide). Beads were washed 3x more in 1000 μl of 0.35 M KCl IP wash buffer, and then collected. The RNA was eluted by addition of buffer RLT (350 μL) to the beads, allowed to incubate at RT for 5 minutes and RNA was purified subsequently using the RNeasy Micro Kit (QIAGEN). RNA integrity was assessed using an Agilent 2100 bioanalyzer.
Sequencing libraries were generated using the Illumina Nextera XT DNA sample preparation kit (San Diego, CA, USA), with 1 ng cDNA input.

treatment_protocol: Mice were kept on normal chow diet until tissue collection at 12 weeks of age, random fed (morning)

value: Brain, Hypothalamus

value: Control (Lepr-flox)

value: Random fed, chow diet


title: Pnoc_LepR_WT_Pulldown_1

description:
Library name: Pnoc_LepR_WT_Pulldown_1
LepR Wildtype Pulldown


title: Pnoc_LepR_WT_Pulldown_3

description:
Library name: Pnoc_LepR_WT_Pulldown_3
LepR Wildtype Pulldown


title: Pnoc_LepR_WT_Pulldown_2

description:
Library name: Pnoc_LepR_WT_Pulldown_2
LepR Wildtype Pulldown


title: ARDS model lung D6 (hashtag library)

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

country: Japan

institute: Institute of Science Tokyo

description: hashtag index A961: WT Day 6 hashtag index A962: IL-4 KO Day 6

data_processing:
Adapter trimming of sequencing data was performed by using Cutadapt 3.4. Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.15.0. Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.8. Associated cDNA reads were mapped to reference RNA (build GRCm38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 2 -D 20 -R 3 -N 0 -L 8 -i S,1,0.75 –norc –seed 656565 –reorder. Then, cell barcode information of each read were added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted by using mawk. Resulted count data was converted to genes x cells matrix file and inflection threshold of the knee-plot was detected by using DropletUtils package in R version 4.2.2 Patched (2022-11-10 r83330). In addition, we further estimate background beads by using emptyDrops formula in DropletUtils package.
Assembly: GRCm38 release-101
Supplementary files format and content: tab-separated values file

extract_protocol:
On day 6, the left lungs were first perfused with EDTA-containing PBS through the right ventricle, and lung tissues were dissociated by lung dissociation kit and gentleMACS Octo Dissociator (Miltenyi Biotec) according to the 37C_m_LDK_1 protocol. Lung single-cell suspensions were subjected to density separation with 25% and 65% Percoll PLUS (Cytiva), and isolated cells were incubated with biotinylated anti-mouse CD45 and H2-K antibodies followed by incubation with TotalSeq PE streptavidin (BioLegend).
Labeled cells (approximately 10,000 cells per sample) were trapped and reverse-transcribed using BD Rhapsody (BD Biosciences) according to the manufacturer’s instructions, followed by the preparation of cDNA and hashtag libraries by TAS-Seq method (Shichino et al. Commun Biol 2022). The sequencing analysis were performed a Novaseq 6000 sequencer

treatment_protocol: Seven-to-eleven-week-old male mice were intratracheally treated with LPS (20 mg/kg body weight; Escherichia coli O111:B4 strain purchased from MilliporeSigma) by using intratracheal sprayer under anesthesia with ketamine and xylazine.

value: Lung

value: Lung cells

value: Mixed (C57BL/6 WT and IL-4-KO)

value: Male mice were intratracheally treated with LPS (20 mg/kg body weight; Escherichia coli O111:B4 strain purchased from MilliporeSigma)


title: 11H089

value: Bone marrow

value: Acute myeloid leukemia


title: Usp28_WT_3

city: hangzhou

first: hangqi

last: luo

state: zhejiang

address: 浙江省杭州市浙江大学华家池校区

institute: zhejiang university

data_processing:
To get high quality clean reads, reads were further filtered by fastp(version 0.18.0)
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl release104
Supplementary files format and content: tab-delimited text file include raw counts and fpkm values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis
RNA libraries for RNA-seq were prepared by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: liver

value: Usp28 wildtype


title: 07H099 [re-analysis]

description: reanalysis of GSM1273622

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters for samples sequenced using stranded libraries.
Strand orientation is reverse for stranded samples, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

extract_protocol:
TruSeq RNA Sample Preparation  (Illumina)
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Sequencing libraries were prepared from total RNA using a poly-A selection and either the TruSeq unstranded RNA Sample Preparation (Illumina), TruSeq Stranded RNA Sample Preparation (Illumina) or the KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: Heparinised blood

value: unstranded


title: ARDS model lung D6 (cDNA library)


title: macrophage, TNF-a , rep2

value: macrophage

value: TNF-a


title: 08H048 [re-analysis]

description: reanalysis of GSM1273624

value: acute myeloid leukemia


title: 10H075

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters
Strand orientation is reverse, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Stranded sequencing libraries were prepared from total RNA using the NEBNext PolyA mRNA Magnetic Isolation Module.


title: 06H135 [re-analysis]

description: reanalysis of GSM1273619


title: 10H138

value: Blood


title: Usp28_KO_3

address: 浙江省杭州市浙江大学华家池校区

value: Usp28 knockout


title: 06H088 [re-analysis]

description: reanalysis of GSM1273618


title: 07H069 [re-analysis]

description: reanalysis of GSM1273621


title: Pnoc_LepR_WT_Input_4

description:
Library name: Pnoc_LepR_WT_Input_4
LepR Wildtype Input

data_processing:
Preprocessing and Quality Control: RNA sequencing data was analyzed using the nf-core/rnaseq pipeline (v3.12.0), which included quality control of raw reads to assess sequencing quality and remove low-quality bases or adapter sequences.
Gene-Level Quanitification: Gene-level quantification was conducted using Salmon (v1.10.1), where reads were pseudoaligned to the GRCm38 reference genome to estimate transcript abundances.
Differential Gene Expression Analysis: Differential expression analysis was performed using DESeq2 (v1.38.3) in R. Raw counts were normalized, and statistical models were applied to identify differentially expressed genes across experimental conditions: Control-IP vs Control-Input, LeprKO-IP vs LeprKO-Input, and LeprKO-IP vs Control-IP.
Enrichment Analysis: Genes were classified as enriched in Pnoc neurons if they met specific criteria: adjusted p-value (padj) ≤ 0.01 and fold change (fc) ≥ 1.5. Enrichment was assessed under two conditions: Control-IP vs Control-Input and LeprKO-IP vs LeprKO-Input.
Filtering for Differentially Expressed Genes: Differentially expressed genes from the LeprKO-IP vs Control-IP comparison (padj ≤ 0.01) were filtered to retain only those enriched in Pnoc neurons based on the enrichment criteria.
Assembly: GRCm38
Supplementary files format and content: deseq2_results.csv: DESeq2 results
Supplementary files format and content: salmon.merged.gene_counts_scaled.tsv: Salmon Scaled Counts
Supplementary files format and content: salmon.merged.gene_tpm.tsv: Salmon Gene TPMs
Supplementary files format and content: salmon.merged.gene_counts.tsv: Salmon Gene Counts

value: Brain, Hypothalamus

value: Control (Lepr-flox)


title: Pnoc_LepR_WT_Input_1

description:
Library name: Pnoc_LepR_WT_Input_1
LepR Wildtype Input

value: Random fed, chow diet


title: 10H120


title: 06H045 [re-analysis]

description: reanalysis of GSM1273617


title: Usp28_KO_2

address: 浙江省杭州市浙江大学华家池校区


title: Usp28_WT_2

address: 浙江省杭州市浙江大学华家池校区


title: 09H117


title: Usp28_WT_1

address: 浙江省杭州市浙江大学华家池校区


title: 07H042 [re-analysis]

description: reanalysis of GSM1273620


title: Usp28_KO_1

address: 浙江省杭州市浙江大学华家池校区


title: Pnoc_LepR_WT_Input_2

description:
Library name: Pnoc_LepR_WT_Input_2
LepR Wildtype Input


title: 14H151


title: Pnoc_LepR_KO_Pulldown_7

description:
Library name: Pnoc_LepR_KO_Pulldown_7
LepR Knockout Pulldown

value: Pnoc Lepr deletion


title: 09H036


title: Pnoc_LepR_KO_Pulldown_6

description:
Library name: Pnoc_LepR_KO_Pulldown_6
LepR Knockout Pulldown


title: 10H045


title: 02H060 [re-analysis]

description: reanalysis of GSM1273615


title: D7GO_control_RNA_rep3

city: Shanghai

first: Yu

address: 138 Yi Xue Yuan Road

institute: Fudan university

data_processing:
All RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat2 2.1.1. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2 (Trapnell et al., 2012).
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Oocyte

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
Smart-seq2 libraries of oocytes and early embryos were prepared as previously reported (Picelli et al., 2017).

value: Oocyte

value: wild-type

tag: developmental stage

value: Growing oocyte D7


title: 08H046

city: Montreal

institute: Institute for Research in Immunology and Cancer

value: Bone marrow

value: Acute myeloid leukemia


title: Pnoc_LepR_KO_Pulldown_8

description:
Library name: Pnoc_LepR_KO_Pulldown_8
LepR Knockout Pulldown


title: 10H002


title: 05H094 [re-analysis]

description: reanalysis of GSM1273616


title: Pnoc_LepR_KO_Pulldown_5

description:
Library name: Pnoc_LepR_KO_Pulldown_5
LepR Knockout Pulldown


title: Pnoc_LepR_WT_Input_3

description:
Library name: Pnoc_LepR_WT_Input_3
LepR Wildtype Input


title: 11H160 [re-analysis]

description: reanalysis of GSM1203347

source_name: blood

value: blood


title: 07H138


title: D7GO_control_RNA_rep2


title: Pnoc_LepR_KO_Input_8

description:
Library name: Pnoc_LepR_KO_Input_8
LepR Knockout Input


title: 11H142 [re-analysis]

description: reanalysis of GSM1203346


title: D7GO_control_RNA_rep1


title: 11H126 [re-analysis]

description: reanalysis of GSM1203345

source_name: bone marrow

value: bone marrow


title: 07H091


title: Pnoc_LepR_KO_Input_7

description:
Library name: Pnoc_LepR_KO_Input_7
LepR Knockout Input


title: 11H095 [re-analysis]

description: reanalysis of GSM1203344

value: unstranded


title: D14GO_control_RNA_rep2

value: Growing oocyte D14


title: 07H059

source_name: Bone marrow


title: Pnoc_LepR_KO_Input_6

description:
Library name: Pnoc_LepR_KO_Input_6
LepR Knockout Input


title: Pnoc_LepR_KO_Input_5

description:
Library name: Pnoc_LepR_KO_Input_5
LepR Knockout Input


title: D14GO_control_RNA_rep1


title: 07H006


title: 11H072 [re-analysis]

description: reanalysis of GSM1203342


title: 06H090


title: FGO_H2A.ZmKO_RNA_rep2

value: Full grown oocyte


title: FGO_H2A.ZmKO_RNA_rep1


title: 11H058 [re-analysis]

description: reanalysis of GSM1203341

value: acute myeloid leukemia


title: OC_P8SC_DTR_rep6

city: Los Angeles

first: Ksenia

last: Gnedeva

state: CA

address: 1501 San Pablo Street

institute: USC

data_processing:
Reads were mapped to the mouse reference genome (Gencode Mm10v11) using STAR. Read counts were quantified by RSEM.
Assembly: mm10
Supplementary files format and content: Gene expression matrix txt file in .genes.results format

source_name: organ Of Corti

extract_protocol:
Organs of Corti from p1 LfngeGFP were dissected from p1 LfingGFP mice and cultured in the presence of 3 um DMSO or 3 uM TDI-000536 LKI for five days. The explants were then dissociated into a single cell suspension and eGFP-positive supporting cells were purified via fluorescence-activated cell sorting (FACs). Alternatively, supporting cells were purified from primary organs of Corti dissected from p8 LfngCreERT2/Rosa26LSL-tdTomato/Pou4f3+/+ or LfngCreERT2/Rosa26LSL-tdTomato /Pou4f3DTR/+  mice treated with tamoxifen to label supporting cells at p2 and diphtheria toxin to ablate hair cells at p4.
Cells were FAC-sorted directly into 300 uL of lysis buffer and RNA was immediately extracted from using the Quick-RNA MicroPrep Kit (Zymo Research R1050). After passing quality controls, RNA was used for library preparation using with QIAseq FX Single Cell RNA Library Kit and sequenced using HiSeq 4000.

value: organ Of Corti

value: supporting cells


title: 06H061

first: Guy

last: Sauvageau

address: 2950, Chemin de Polytechnique


title: FGO_control_RNA_rep2


title: 11H083 [re-analysis]

description: reanalysis of GSM1203343


title: OC_P8SC_DTR_rep5


title: 06H054


title: 07H083

source_name: Blood

value: Blood


title: FGO_control_RNA_rep1


title: 11H021 [re-analysis]

description: reanalysis of GSM1203339


title: OC_P8SC_DTR_rep3


title: FGO_H2A.ZmKO_H3K27ac_rep1

data_processing:
Basecalls performed using CASAVA version 1.8. Sequencing reads were trimmed with cutadapt v1.18 and then mapped to the mm9 genome by Bowtie2 (version 2.2.2) with the parameter: –t –q –N 1 –L 25 (Langmead and Salzberg, 2012)., replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
STAR ChIP-seq was performed following the previously described protocol(Zhang et al., 2016). Briefly, samples were directly lysed and fragmented by MNase at 37°C for 5 minutes, before being incubated with the primary antibody (H2A.Z, abcam, 4174;H3K36me3, Active Motif, 61021; H3K4me3(Zhang et al., 2016); H3K27me3, Diagenode, C15410069; H3K27ac, Active Motif, 39133) overnight with rotation at 4°C. The next day, 100 μg protein A dynabeads (Life Technologies) were added to each sample and incubated for 2-3 h with rotation at 4 °C. The beads were washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 27 μl ddH2O and 1 μl 10× Ex-Taq buffer (TaKaRa). 1 μl proteinase K (Roche, 10910000) was added to each sample and incubated at 55 °C for 90 min to elute DNA from beads. After incubation at 80°C for 40min to inactivate the proteinase K, individual sample was subjected to TELP library preparation without DNA purification

tag: chip antibody

value: H3K27ac (Active Motif, 39133)


title: D14GO_control_RNA_rep3


title: OC_P8SC_DTR_rep2


title: 14H051


title: 06H030


title: FGO_control_H3K27ac_rep1


title: OC_P8SC_DTR_rep1


title: OC_P8SC_DTR_rep7


title: 05H192


title: 10H166 [re-analysis]

description: reanalysis of GSM1203336


title: FGO_H2A.ZmKO_H3K4me3_rep2

value: H3K4me3 (Millipore, 05-748R-S)


title: OC_P8SC_Ctr_rep6


title: 05H160


title: 10H115 [re-analysis]

description: reanalysis of GSM1203335


title: 11H046 [re-analysis]

description: reanalysis of GSM1203340


title: 05H155


title: OC_P8SC_Ctr_rep5


title: 06H051


title: 10H101 [re-analysis]

description: reanalysis of GSM1203334


title: 05H108


title: 11H009 [re-analysis]

description: reanalysis of GSM1203338


title: FGO_control_H3K4me3_rep1

value: H3K4me3 (Millipore, 05-745R-S)


title: 10H095 [re-analysis]

description: reanalysis of GSM1203333


title: FGO_control_H3K4me3_rep2

value: Oocyte

value: H3K4me3 (Millipore, 05-746R-S)


title: 05H095


title: OC_P8SC_Ctr_rep1


title: OC_P8SC_Ctr_rep2


title: mESC_H2A.ZKO_H2A.Zac_rep2

source_name: Embryonic stem cell

value: Embryonic stem cell


title: 11H006 [re-analysis]

description: reanalysis of GSM1203337


title: mESC_H2A.ZKO_H2A.Zac_rep1


title: OC_P1SC_LKI_P1_5d_rep2

value: Lfng-eGFP

value: 5d LKI


title: 10H089 [re-analysis]

description: reanalysis of GSM1203331

value: blood


title: OC_P1SC_LKI_P1_5d_rep1


title: OC_P1SC_LKI_P1_5d_rep3


title: mESC_control_H2A.Zac_rep2

value: wild-type


title: 05H056

value: Bone marrow

value: Acute myeloid leukemia


title: FGO_H2A.ZmKO_H3K4me3_rep1

value: H3K4me3 (Millipore, 05-747R-S)

value: Full grown oocyte


title: 10H072 [re-analysis]

description: reanalysis of GSM1203330

value: bone marrow

value: acute myeloid leukemia

value: unstranded


title: OC_P1SC_DMSO_P1_5d_rep5

value: organ Of Corti

value: supporting cells

value: 5d DMSO


title: 05H046

value: Blood


title: mESC_control_H2A.Zac_rep1


title: 05H039


title: 10H068 [re-analysis]

description: reanalysis of GSM1203329


title: mESC_H2A.ZKO_H2A.Z_rep2


title: 05H033


title: 10H056 [re-analysis]

description: reanalysis of GSM1203328


title: OC_P1SC_DMSO_P1_5d_rep4


title: mESC_H2A.ZKO_H2A.Z_rep1


title: 05H073


title: 4h_P5

city: Daejeon

first: Chae Won

last: Kim

address: 291, Daehak-ro, Yuseong-gu  E7 Rm 5101

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling using Real Time Analysis software.
The base calls binary converted into FASTQ utilizing package bcl2fastq
Adapters are trimmed away from the reads using fastp
trimmed reads were mapped using HISAT2
Stringtie were utilized to assemble and merge transcripts
Assembly: Mm10
Supplementary files format and content: gft files obtained after stringtie processing

source_name: GL261 cell line

extract_protocol:
Total RNA was extracted using RNeasy Mini plus kit (Qiagen)
TruSeq Stranded Total RNA LT Sample Prep Kit (Gold)

treatment_protocol: In our experimental design, RNA was extracted from GL261 cells at 4 hours post-treatment with 1 uM of sodium chloride or propionate

value: GL261 cell line

value: sodium propionate


title: 04H107


title: 09H115 [re-analysis]

description: reanalysis of GSM1203326


title: mESC_control_H2A.Z_rep2

value: Embryonic stem cell


title: 10H052 [re-analysis]

description: reanalysis of GSM1203327


title: 10H092 [re-analysis]

description: reanalysis of GSM1203332


title: 4h_P4


title: 09H113 [re-analysis]

description: reanalysis of GSM1203325


title: mESC_control_H2A.Z_rep1


title: 4h_P1


title: 04H100


title: 04H094


title: 4h_C3

value: sodium chloride


title: 04H084


title: 09H111 [re-analysis]

description: reanalysis of GSM1203324

value: blood


title: FGO_H2A.ZmKO_H2A.Zac_rep2

value: Oocyte


title: 4h_C2


title: FGO_H2A.ZmKO_H2A.Zac_rep1


title: 04H021

value: Bone marrow


title: 09H083 [re-analysis]

description: reanalysis of GSM1203323


title: 09H043 [re-analysis]

description: reanalysis of GSM1203322


title: FGO_control_H2A.Zac_rep2

value: wild-type


title: FGO_H2A.ZmKO_H2A.Z_rep2


title: 07H135 [re-analysis]

description: reanalysis of GSM1203320


title: BMDM_WT3_mix

city: Cleveland

first: Tatiana

middle: V

last: Byzova

state: OH

address: 9500 Euclid Avenue

department: Neurosciences

institute: Lerner Research Institute, CCF

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include  RPKM values for each sample

source_name: bone marrow-derived macrophages

growth_protocol: BMDM cells were isolated from C57/BL6 mice bone marrow and incubated for 7 days with L929-conditioned media.

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (ThermoFisher Scientific) according to the manufacturer’s instructions.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA Hyper prep polyA selected kit with 201-300 bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input. Final library quality and quantity was analyzed by Agilent Technologies 4200 station and Qubit 3.0 (Thermo Fisher Scientific Inc, Waltham, MA) Fluorometer.
150 bp paired-end reads were sequenced on Illumina Hiseq4000 (Illumnia Inc., San Diego, CA).

treatment_protocol: Cells were incubated with or without 50μg/ml oxLDL at 37°C for 24 hours

value: bone marrow-derived macrophages

value: C57BL/6, WT

value: no treatment


title: 07H062 [re-analysis]

description: reanalysis of GSM1203319

value: acute myeloid leukemia


title: 4h_C1


title: BMDM_WT2_mix


title: 03H049

value: Acute myeloid leukemia


title: 04H011


title: FGO_control_H2A.Zac_rep1

value: Full grown oocyte


title: BMDM_WT3_mix_oxLDL

value: oxLDL


title: 03H097


title: BMDM_WT1_mix


title: 06H144 [re-analysis]

description: reanalysis of GSM1203318

value: unstranded


title: FGO_H2A.ZmKO_H2A.Z_rep1


title: 02H080

value: Blood


title: 07H160 [re-analysis]

description: reanalysis of GSM1203321


title: 06H028 [re-analysis]

description: reanalysis of GSM1203317

value: bone marrow


title: MK cultured with MSC rep4

city: New York

first: Avital

last: Mendelson

state: NY

address: 310 E67 Street

department: LFKRI

institute: NYBC

data_processing:
Raw counts for each transcript were quantified with kallisto using mouse reference genome mm10. Raw count data was normalized to transcript per million (TPM). Differential gene expression analysis was performed with Deseq2. Gene set enrichment analysis was performed with clusterProfiler.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts for each sample

extract_protocol:
Takara Nucleospin RNA isolation kit
Low input SMART-seq HT

value: megakaryocyte

value: Cultured with MSCs


title: MK cultured with MSC rep3


title: 18H208


title: 19H045


title: 03H092


title: FGO_control_H2A.Z_rep1


title: 05H181 [re-analysis]

description: reanalysis of GSM1203316


title: BMDM_WT2_mix_oxLDL


title: 03H004


title: WT1

growth_protocol: BMDM cells were isolated from C57/BL6 and C57BL/6-Kindlin3-integrin mutant mice bone marrow and incubated for 7 days with L929-conditioned media.


title: BMDM_WT1_mix_oxLDL


title: 18H207


title: 05H149 [re-analysis]

description: reanalysis of GSM1203314


title: 05H163 [re-analysis]

description: reanalysis of GSM1203315


title: MK cultured with MSC rep2


title: FGO_control_H2A.Z_rep2


title: 18H206


title: MK cultured with MSC rep1


title: MK cultured only rep3


title: KI-1

value: C57BL/6-Kindlin3-integrin mutant


title: 04H112 [re-analysis]

description: reanalysis of GSM1203311


title: MK cultured only rep4


title: WT1OXLDL


title: 05H050 [re-analysis]

description: reanalysis of GSM1203313


title: MK cultured only rep2


title: KI-2


title: 18H182


title: MK cultured only rep1


title: 04H133 [re-analysis]

description: reanalysis of GSM1203312


title: KI-2OXLDL


title: 18H195


title: 18H194


title: 18H175


title: 18H166


title: ABCs#2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on a NovaSeq6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. An Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: spleen

value: B cell

value: MRL/lpr

value: CD19+B220hiAA4.1-CD21lo CD23-CD11c+ B cells (no stimulation)


title: PROP2

treatment_protocol: In our experimental design, RNA was extracted from GL261 cells at 24 hours post-treatment with 1 uM of sodium chloride or propionate

value: tumor

value: sodium propionate


title: 18H156

value: Bone marrow


title: 03H041 [re-analysis]

description: reanalysis of GSM1203307

value: acute myeloid leukemia


title: KI-1OXLDL

value: bone marrow-derived macrophages


title: 03H119 [re-analysis]

description: reanalysis of GSM1203309


title: 02H066 [re-analysis]

description: reanalysis of GSM1203306


title: ABCs#1


title: ABCs#3


title: PROP1


title: PROP3


title: 03H116 [re-analysis]

description: reanalysis of GSM1203308


title: 04H024 [re-analysis]

description: reanalysis of GSM1203310


title: CTRL2

value: sodium chloride


title: 18H151

value: Acute myeloid leukemia


title: CTRL3


title: 02H053 [re-analysis]

description: reanalysis of GSM1203305

value: unstranded


title: 18H146

value: Blood


title: dHuh7.5-NTCP_Mock_3

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: Library name: 75-Mock-3

data_processing:
Raw data acquisition (HiSeq Control Software, HCS, HD 3.4.0.38) and base calling (Real-Time Analysis Software, RTA, 2.7.7) was performed on-instrument
Base calls were converted into lane-specific, multiplexed, unaligned BAM files suitable for long-term archival (IlluminaBasecallsToMultiplexSam, 2.19.2-CeMM).
Archive BAM files were demultiplexed into sample-specific, unaligned BAM files (Illumi-naSamDemux, 2.19.2-CeMM).
NGS reads were mapped to the Genome Reference Consortium GRCh38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR, 2.7.5a) utilizing the “basic” ensembl transcript annotation from version e100 (April 2020) as reference transcriptome.
STAR was run with options recommended by the ENCODE project. NGS read alignments overlapping ensembl transcript features were counted with the Bioconductor (3.11) Genomic Alignments (1.24.0) package. Transcript-level counts were aggregated to gene-level counts and the Bioconductor DESeq2 (1.28.1) package was used to test for differential expression based on a model using the negative binomial distribution.
Assembly: hg38
Supplementary files format and content: tab-separated file includes normalized counts of protein-coding genes for each sample

growth_protocol: 10% FCS-supplemented DMEM (dHuh7.5-NTCP cells) and 10% FCS-supplemented William's E medium (dHepaRG cells)

extract_protocol:
Total intracellular RNAs were extracted with the “Monarch, nucleic acid purification kit” according to the manufacturer’s instructions (New England Biolabs)
RNA-seq libraries were prepared with the Illumina Stranded mRNA kit.

treatment_protocol: HuH7.5-NTCP cells were differentiated with 2% of DMSO for 1 week without splitting the cells. HepaRG cells were differentiated in 1.8% DMSO for 4 weeks without splitting the cells. Both cell lines were then stimulated of not with IFNα-2a (500 UI/mL) for 8h.

value: Mock


title: FOB#2

value: CD19+B220hiAA4.1-CD23+ B cells (no stimulation)


title: CTRL1


title: 18H141


title: Nr4a1#3

value: retorovirally Nr4a1 transduced B cells stimulated with BAFF, IL-21, R848, aIgM


title: WTHYP2

city: Boston

first: Shashi

last: Kant

state: MA

address: 4 Blackfan Circle, Room 614

department: Cardiovascular Medicine

institute: Brigham Women's Hospital

description: Library name: Sample 11

data_processing:
Novogene Bioinformatics Institute
Tophat2 algorithm
Assembly: Mapping reads against the transcriptome, Mapping full Length reads to exon, mapping the partial reads to two exons
Supplementary files format and content: xls file inlcude FPKM values for each samples

source_name: Lung

growth_protocol: MLEC growth media supplemented with a 1:1 mixture of DMEM (Life Technology Thermo, 11885-084;) and Ham’s F-12 (Life Technology Thermo, 11765-054, Waltham, MA), 20% fetal bovine serum, 50 mg of endothelial mitogen, 50 mg/mL heparin, 100 units/mL penicillin, and 100 μg/mL streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNeasy plus kit (Qiagen, 74136, Germantown, MD)
NEBNext Ultra™ RNA Library Prep Kit

treatment_protocol: The monolayers of WT and Mlk2-/-Mlk3-/- primary endothelial MLECs were exposed to normoxia (21% O2) or hypoxia (1% O2, Airgas, Radnor, PA) for 90 minutes

value: Lung

value: Primary Endothelial Cells

value: Lung Enodthelial cells

value: WildType

value: Hypoxia -90 Minutes


title: WTHYP3

description: Library name: Sample 12


title: WT3

description: Library name: Sample 9


title: FOB#1

value: spleen

value: B cell

value: MRL/lpr


title: WTHYP1

description: Library name: Sample 10


title: dHuh7.5-NTCP_Mock_2

description: Library name: 75-Mock-2


title: Nr4a1#2


title: 18H152


title: FOB#3


title: 18H137

value: Bone marrow


title: 18H138


title: Nr4a1#1


title: 18H119


title: WT2

description: Library name: Sample 8


title: dHuh7.5-NTCP_IFN_1

description: Library name: 75-IFN-1

value: IFNa


title: dHuh7.5-NTCP_IFN_3

description: Library name: 75-IFN-3


title: dHuh7.5-NTCP_IFN_2

description: Library name: 75-IFN-2


title: empty#3

value: retorovirally mock transduced B cells stimulated with BAFF, IL-21, R848, aIgM


title: dHuh7.5-NTCP_Mock_1

description: Library name: 75-Mock-1


title: 18H131

value: Acute myeloid leukemia


title: WT1

description: Library name: Sample 7


title: MLKHYP3

description: Library name: Sample 6

value: MLK2 MLK3 Knockout


title: empty#1


title: 18H118


title: MLKHYP2

description: Library name: Sample 5


title: dHepaRG_Mock_3

description: Library name: RG-Mock-3

source_name: HepaRG

value: HepaRG


title: 18H104


title: MLK3

description: Library name: Sample 3


title: dHepaRG_Mock_2

description: Library name: RG-Mock-2

value: Mock


title: dHepaRG_Mock_1

description: Library name: RG-Mock-1


title: naïve#2

value: CD43 negative cells


title: dHepaRG_IFN_3

description: Library name: RG-IFN-3


title: 18H094

value: Blood


title: MLKHYP1

description: Library name: Sample 4

value: Lung


title: macrophage, CARΔ-M.TNF-a, rep4

description: Sample 28

growth_protocol: Bone marrow macrophages were maintained in DMEM supplemented with 10% Fetal bovine serum (FBS), 1X penicillin and streptomycin, 2mM glutamine, 1XNon-Essential Amino Acid (NEAA), and 10ng/ml macrophage colony-stimulating factor (M-CSF) in humidified atmosphere with 5% CO2 at 37C.

treatment_protocol: S1-4 are samples without any treatment. S5-8 are samples stimulatedbyLPS and IFN-r, S9-12 are samples stimulated by IL4 and IL13, S13-16 are samples transduced with the intact CAR, S17-20 are samples transduced with the intact CAR and stimulated by TNF-a, S21-24 are samples transduced with the truncated CAR, S21-28 are samples transduced with the truncated CAR and stimulated by TNF-a.

value: macrophage

value: truncated CAR and TNF-α


title: MLK1

description: Library name: Sample 1

value: Primary Endothelial Cells

value: Lung Enodthelial cells


title: 18H093


title: naïve#1

value: spleen


title: 18H072


title: macrophage, CARΔ-M.TNF-a, rep3

description: Sample 27


title: dHepaRG_IFN_1

description: Library name: RG-IFN-1


title: MLK2

description: Library name: Sample 2


title: 18H089


title: KDR 144h Ebs rep1

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

data_processing:
Fastq sequencing files were trimmed, processed and analyzed following the regular MAGeCKFlute pipeline (Wang et al., 2019 Nat Methods). gRNA abudance was calculated by quantifying gRNAs detected in KDR/FLK1+ cells (starting timepoint) versus gRNAs detected in CD45 BFP bone marrow cells (primary or secondary transplantation).
Assembly: mm10
Supplementary files format and content: Excel file containing the counts for every gRNA of the library in KDR cells (time 0) and bone marrow cells from either primary or secondary transplant
Library strategy: CRISPR screen

source_name: KDR+ cells Ebs 144h

extract_protocol:
Genomic DNA (gDNA) from cells containing gRNA library (KDR or bone marrow cells) was extracted using Qiagen DNeasy Blood and Tissue Kits (Qiagen). gRNAs integrated into gDNA were amplified using TAKARA PrimeSTAR polymerase and library was constructed using the same TAKARA Prime Star enzyme
Library construction was prepared as previously described in Joung et al. 2017 (https://doi.org/10.1038/nprot.2017.016). genomic DNA (gDNA) was sequenced using Illumina sequencer HiSeq 2500 (1x50bp)

value: KDR+ cells Ebs 144h


title: dHepaRG_IFN_2

description: Library name: RG-IFN-2


title: empty#2

value: B cell


title: macrophage, CARΔ-M.TNF-a, rep2

description: Sample 26

data_processing:
Short-read sequencing was performed on the Novaseq X platform (Illumina) with 150bp pair-end reads. Library sequencing quality was determined using FastQC (Babraham Bioinformatics: www.bioinformatics.babraham.ac.uk/).
Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore (Babraham Bioinformatics). STAR was used to align reads to mouse genome mm10 using ENSEMBL gene annotations as a guide.
Read counts data corresponding to ENSEMBL gene annotations were generated the STAR flag --quantMode GeneCounts. Multiqc was used to verify quality metrics. All analyses were performed in the R Statistical Environment with tidyverse.
Briefly, counts data were background corrected and normalized for library size using edgeR. DGE was determined using the QLFtest (BH MTC p <0.05).
Gene lists were functionally annotated with Gene Ontology (GO), REACTOME and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (adjusted p value <0.05) using the cluster Profiler package
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes matrix table for each Sample
Supplementary files format and content: Excel file includes logFC, pValue, FDR, ect for each Sample

value: Bone marrow


title: 18H062

state: QC


title: naïve#3


title: ICGC_PA56_HiSeq4000

city: Heidelberg

first: Konstantin

last: Okonechnikov

state: Germany

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center

data_processing:
10X data: reads aligned, assigned to cells and gene expression counts computed with CellRanger v2.1.0
DROP-seq,C1 data: reads aligned with STAR, gene expression counts per cell computed with FeatureCount
Filtering of low quality cells performed with Seurat
Assembly: hg19, mm10
Supplementary files format and content: Gene expression matrix (raw)

source_name: Tumor

extract_protocol:
Nuclei from frozen tissue were isolated using the optimized protocol described on the original article.
See protocol column per each sample.
snRNA-seq

value: Tumor

tag: tumor class

value: PA

tag: protocol

value: male

tag: tumor location

value: Cerebellum


title: CD45 BFP Bone marrow 1ary Transplant 4 weeks rep1

source_name: mESC-KDR-Derived transplanted cells

tag: cell type

value: mESC-KDR-Derived transplanted cells


title: KDR 144h Ebs rep2


title: 18H063

tag: tissue

value: Acute myeloid leukemia


title: 18H058


title: CD45 BFP Bone marrow 2ary Transplant 16 weeks rep1


title: B062_004_H1013_DropSeq

organism:
Homo sapiens
Mus musculus

source_name: PDX

value: PDX

value: GBM

value: Drop-seq


title: B062_004_H1013_FluidigmC1

value: Fluidigm C1


title: 18H049

value: Blood


title: CD45 BFP Bone marrow 2ary Transplant 12 weeks rep3


title: 18H053


title: macrophage, CARΔ-M, rep2

description: Sample 22

extract_protocol:
RNA was isolated from mouse macrophages using Ambion 463 RiboPure RNA Purification Kit (AM1924, Thermo Fisher).
Poly-A selected mRNA libraries were generated using the Illumina stranded mRNA Prep Kit (20040534, Illumina) and validated with the Agilent Tapestation 4200 and qPCR before sequencing.

value: macrophage

value: truncated CAR


title: 18H047


title: CD45 BFP Bone marrow 2ary Transplant 12 weeks rep2


title: 18H045


title: B062_004_H1013_10X


title: macrophage, CAR.M.TNF-a, rep3

description: Sample 19

value: intact CAR and TNF-α


title: 18H030


title: macrophage, CARΔ-M.TNF-a, rep1

description: Sample 25

value: truncated CAR and TNF-α


title: macrophage, CARΔ-M, rep1

description: Sample 21


title: macrophage, CARΔ-M, rep3

description: Sample 23


title: A-PDK1KO heart tissue 4 [H333]

city: Kobe

first: Manabu

last: Nagao

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe University

description:
KO4
H333

data_processing:
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38). Clean reads were mapped to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0). Quantification of gene expression level was performed by using featureCounts (Version 1.6.3) to count reads mapped to each gene.
Assembly: mm10
Supplementary files format and content: excel file including FPKM values for each sample

source_name: heart

extract_protocol:
The mice were sacrificed in a randomly-fed state at the age from 10-11 weeks. The tissues were collected and snap frozen in liquid nitrogen, subsequently stored at -80℃ until further analysis.
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7).

value: heart

tag: genotype

value: Adipocyte-specific PDK1 knockout


title: UV_SM3, sample RNA22

city: Hull

first: Lauric

last: Feugere

address: Cottingham Road

department: Biological and Marine Sciences

country: United Kingdom

institute: University of Hull

description: Sampling immediately after DNA damage/repair following 24 hours in Stress Metabolites at 27°C

data_processing:
The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1.
Reads were filtered and trimmed using fastp v0.23.1, to remove low quality reads, polyG, polyX, and Illumina adapter sequences. Default parameters were used along with --dup_calc_accuracy 3 --trim_poly_g --trim_poly_x. Reads associated from all four UV treatments showed low-quality and UV-induced RNA degradation which led to high duplication levels. Such reads were deduplicated via fastp using the "--dedup" argument.
Reads were aligned to the zebrafish reference genome using STAR v2.6.1
Reads were counted by gene using STAR v2.6.1 (--runMode alignReads --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattributes Standard)
Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2.
Assembly: primary genome assembly GRCz11.104 (http://ftp.ensembl.org/pub/release-104/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna_sm.primary_assembly.fa.gz and http://ftp.ensembl.org/pub/release-104/gtf/danio_rerio/Danio_rerio.GRCz11.104.gtf.gz)
Supplementary files format and content: The files with "RNA**_ReadsPerGenes.fastp.D.tab" (where ** is RNA number and D indicates that reads were deduplicated) are read counts per gene obtained from STAR, which were used in DESeq2 for differential expression analysis.

organism: Danio rerio

source_name: 20 pooled individuals of 1-dpf whole-body embryos

growth_protocol: Zebrafish eggs were sanitized with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish (wild-type AB) maintained at 27°C, with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes (one embryo per tube) containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol. At the end of the experimental treatments, embryos were subjected to a DNA damage/repair assay (UV) before sampling.

extract_protocol:
Randomized embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations, and followed by a DNAse I digestion step and a sodium acetate clean-up.
Total RNA samples were processed to prepare cDNA libraries using the Illumina TruSeq stranded mRNA kit.

treatment_protocol: Two temperature protocols were used, either (i) a control constant temperature of 27°C, or (ii)  thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27, 29, 32, 29, and 27°C, with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium (fresh medium free of metabolites or stress medium with stress metabolites, SM) and incubated with their temperature protocols for 24 hours, from 11 am (once they reached the stage of 2-3.3 hours post fertilization) to 11 am on the next day. At 1 day post fertilization, embryos from each treatment were subjected to UVB for 6 min to induce strong DNA damage; immediately followed by 15 min of UVA exposure, to induce partial repair via UVA-activated repair enzymes. UV-exposed embryos were sampled immediately after the 6+15 min of UV damage/repair assay (by pools of 20 per condition, and snap-frozen at -80°C before total RNA extraction). This resulted in 12 treatments in a factorial design of TS x SM; with two factors: TS (heat stress vs control at 27°C), and SM (stress metabolites from heat-stressed embryos vs fresh medium free of metabolites) within the UV group.

tag: line

value: AB

value: Wild-type

value: 1 day post fertilization

tag: temperature

tag: medium

value: stress metabolites


title: macrophage, CARΔ-M, rep4

city: Westmead

first: Jianwei

institute: The Westmead Institute for Medical

description: Sample 24

value: Bone marrow

tag: treatment


title: ICGC_GBM61_HiSeq4000

value: Tumor

tag: Sex

value: female

value: Hemispheric


title: macrophage, CAR.M.TNF-a, rep4

description: Sample 20


title: UV_TS3, sample RNA39

description: Sampling immediately after DNA damage/repair following 24 hours in Fresh medium with repeated heat stress

value: 20 pooled individuals of 1-dpf whole-body embryos

value: heat stress

value: fresh medium


title: UV_C3, sample RNA38

description: Sampling immediately after DNA damage/repair following 24 hours in Control (fresh medium at 27°C)


title: A-PDK1KO heart tissue 3 [H332]

description:
KO3
H332


title: UV_TS1, sample RNA21


title: 18H027

value: Acute myeloid leukemia


title: A-PDK1KO heart tissue 2 [H329]

description:
KO2
H329


title: A-PDK1KO heart tissue 5 [H337]

description:
KO5
H337


title: UV_TS2, sample RNA23


title: A-PDK1KO heart tissue 1 [H326]

description:
KO1
H326


title: 18H016

value: Blood


title: CD45 BFP Bone marrow 2ary Transplant 12 weeks rep4

value: mESC-KDR-Derived transplanted cells


title: CD45 BFP Bone marrow 2ary Transplant 12 weeks rep1


title: macrophage, CAR.M.TNF-a, rep1

description: Sample 17

value: macrophage

value: intact CAR and TNF-α


title: macrophage, CAR.M.TNF-a, rep2

description: Sample 18


title: PDK1 flox/flox heart tissue 4 [H334]

description:
Ctrl4
H334

value: heart

value: PDK1 flox/flox


title: macrophage, CAR.M, rep4

description: Sample 16

value: intact CAR


title: UV_C2, sample RNA20

value: AB

value: Wild-type

value: 1 day post fertilization


title: 17H154


title: macrophage, M2, rep4

description: Sample 12

value: Bone marrow

value: IL-4 and IL-13


title: PDK1 flox/flox heart tissue 3 [H331]

description:
Ctrl3
H331


title: macrophage, CAR.M, rep1

description: Sample 13


title: 17H210


title: UV_SM2, sample RNA19

value: stress metabolites


title: macrophage, CAR.M, rep3

description: Sample 15


title: PDK1 flox/flox heart tissue 5 [H335]

description:
Ctrl5
H335


title: macrophage, M2, rep2

description: Sample 10


title: 17H105


title: 17H125


title: macrophage, CAR.M, rep2

description: Sample 14


title: 17H177


title: 17H209


title: 17H155


title: UV_SM1, sample RNA16

value: 20 pooled individuals of 1-dpf whole-body embryos


title: macrophage, M2, rep3

description: Sample 11


title: UV_TS+SM2, sample RNA17

description: Sampling immediately after DNA damage/repair following 24 hours in Stress Metabolites with repeated heat stress

value: heat stress


title: PDK1 flox/flox heart tissue 2 [H330]

description:
Ctrl2
H330


title: 18H006


title: Zr1Zr2_KO4_CD

first: Xuyun

last: Zhao

state: Shanghai

address: South Chongqing Road

department: Medical school

institute: Shanghai Jiaotong University

data_processing:
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Liver

extract_protocol:
RNA were extracted from brown adipose tissue using  Trizol method.
1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 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. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Liver

value: Zrsr2 and Zrsr5 Liver KO


title: macrophage, M1, rep4

last: Chen

address: 176 Hawkesbury Rd

description: Sample 8

value: LPS and IFN-γ


title: PDK1 flox/flox heart tissue 1 [H328]

description:
Ctrl1
H328


title: UV_C1, sample RNA14

value: fresh medium


title: UV_TS+SM3, sample RNA18


title: 17H065

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters
Strand orientation is reverse, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

value: Acute myeloid leukemia


title: Zlike_2

city: 湖北省 / 武汉市 / 洪山区

first: 京明

last: 李

address: 狮子山街1号华中农业大学

institute: 华中农业大学

description:
Library name: Sample 8
column name in raw_counts_All_Sample.xlsx: Zlike_2
Slike vs Zlike fpkm1 degseqfc1 padj0.05.xlsx

data_processing:
Brassica_napus.ZS11.v0.genome.fa
Raw reads were processed using fastp.
Reads were aligned to brassica napus reference genome （Brassica_napus.ZS11.v0.genome.fa）using hisat2.
FeatureCounts was used to count the number of paired mapping reads for each gene.
Assembly: Brassica_napus.ZS11.v0.genome.fa
Supplementary files format and content: The tabular file contains the raw counts for each sample

organism: Brassica napus

source_name: apical meristems

growth_protocol: experimental station

extract_protocol: Toal RNA was extracted by using RNAprep Pure Plant Kit (Tiangen Biotech) from apical meristems with three replications

treatment_protocol: no treatment

value: apical meristems

tag: cell line

value: Zlike

value: WT


title: macrophage, M1, rep1

description: Sample 5

source_name: Bone marrow

value: macrophage


title: Slike_3

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 12
column name in raw_counts_All_Sample.xlsx: Slike_3
Slike vs Zlike fpkm1 degseqfc1 padj0.05.xlsx

value: Slike

value: mutant


title: Zr1Zr2_KO2_CD

value: Zrsr2 and Zrsr3 Liver KO


title: Slike_2

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 11
column name in raw_counts_All_Sample.xlsx: Slike_2
Slike vs Zlike fpkm1 degseqfc1 padj0.05.xlsx


title: 17H043

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Stranded sequencing libraries were prepared from total RNA using the NEBNext PolyA mRNA Magnetic Isolation Module.

value: Blood


title: UV_TS+SM1, sample RNA13

value: AB

value: Wild-type

tag: time

value: 1 day post fertilization


title: 17H093


title: 17H075

value: Bone marrow


title: macrophage, M1, rep3

description: Sample 7


title: Zr1Zr2_KO3_CD

value: Liver

value: Zrsr2 and Zrsr4 Liver KO


title: GFP2_CD


title: Zr1Zr2_KO1_CD

value: Zrsr2 and Zrsr2 Liver KO


title: macrophage, M1, rep2

description: Sample 6

value: LPS and IFN-γ


title: GFP4_CD


title: Zlike_3

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 9
column name in raw_counts_All_Sample.xlsx: Zlike_3
Slike vs Zlike fpkm1 degseqfc1 padj0.05.xlsx


title: Slike_1

city: 湖北省 / 武汉市 / 洪山区

address: 狮子山街1号华中农业大学

description:
Library name: Sample 10
column name in raw_counts_All_Sample.xlsx: Slike_1
Slike vs Zlike fpkm1 degseqfc1 padj0.05.xlsx


title: macrophage, M2, rep1

description: Sample 9

value: IL-4 and IL-13


title: GFP3_CD


title: 17H037

value: Acute myeloid leukemia


title: macrophage, control, rep4

description: Sample 4

value: No treatment


title: GFP1_CD

value: WT