title: early erythroid cells, EZH2-shRNA, day 7, Input

data_processing:
Reads from the ChIP-seq data were compared to the reference genome hg19 using Bowtie2 version 2.3.5.1 software, and only unique and non-duplicate mapped reads were used for downstream analysis.
Samtools version 1.6 software3 was used to measure the coverage and depth of reads.
To check the reproducibility of ChIP-seq experiments, deeptools version 2.5.7 was used to generate correlation plots for all samples
Signal trace files in BigWig format were generated using deeptools software4 and normalized to 1 million reads for visualization.Deeptools software was also used to normalize signal intensity, map gene body, and flanking region heatmap.
Peaks and annotation were performed using ChIPseeker version 1.2.0
Assembly: hg19
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

source_name: cord blood

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-Seq libraries were constructed using Hiseq × Ten Reagent kit v2.5 (#FC-501-2501, Illumina) and then sequenced on an Illumina X-ten (E00487, Illumina).

value: cord blood

value: erythroid cells

value: EZH2 knockdown

tag: chip antibody


title: PEL_7d_1

status: Public on Jan 01 2024

type: SRA

city: Guangzhou

first: Mingfeng

last: Zhou

state: Guangdong Province

address: No.1838 Guangzhou Avenue North

department: Department of Neurosurgery

country: China

institute: Nanfang Hospital, Southern Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
Genome_build: ensemble97
Supplementary_files_format_and_content: PEL_1d_vs_PEL_7d_vs_Control_read_count.txt: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Hypothalamic SON+PVN

extract_protocol:
Hypothalamic SON and PVN tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina NovaSeq Platform was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: S-D

tag: tissue

value: Hypothalamic SON+PVN

tag: treatment

value: PEL

tag: time point

value: 7 days after PEL surgery


title: BC121

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
Data-no_QC-counts.tsv
Data-counts.tsv
Data-normed.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were alligned using Kallisto, and transcript level tpm values were summed up to gene level tpm values
Genome_build: GRCm38 version 95
Supplementary_files_format_and_content: tpm.tsv contains the transcript per million levels of each gene within each cell, in a tab deliminated matrix. Counts.tsv contains the kallisto, aligned pseudocounts of each gene within each cell, in a tab. deliminated matrix. no-QC-counts.tsv contains the same information as counts.tsv, but including cells that failed quality control

organism: Mus musculus

source_name: MGE derived interneuron within the dorsal CA1 pyramidal cell layer

growth_protocol: Pups were housed under standard conditions with parents until post-natal day 4.

extract_protocol:
Cell contents including mRNA were aspirated within a patch pipette from acute slices.
Nextera XT

treatment_protocol: No treatment.

tag: cell type

value: MGE derived interneuron

tag: condition

value: WT female

tag: Sex

value: female

tag: genotype

value: WT

tag: contamination

value: No

tag: age

value: Post natal day 4 (p4)


title: early erythroid cells, EZH2-shRNA, day 7, IP, rep3

city: zhengzhou

first: li

last: mengjia

address: Science Road 100, Zhengzhou, Henan, 450001, P.R.

institute: zhengzhou university

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: CD34+ cells were purified from cord blood by using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’s instructions. The purity of isolated CD34+ cells was 95% to 98%. The cell culture procedure was comprised of 3 phases, Composition of the base culture medium was Iscove’s Modified Dulbecco’s Medium, 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL Holohuman transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the first phase (day 0 to day 6), CD34+ cells at a concentration of 105 /mL were cultured in the presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 does not need to be added into the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106 /mL on day 11 and to 5×106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1 mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

treatment_protocol: The day of getting CD34+ cells was recorded as day 0. Lentivirus human CD34+ transduction at day 2. During the early stage erythroid development, we used an shRNA-mediated approach by using a tetracycline-inducible-GFP expression system, which can be induced by adding doxycycline (DOX) at day 3. During the terminal erythroid development, we added DOX at day 7 .

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (#9738)


title: BC120


title: Control_3

description: PEL_1d_vs_PEL_7d_vs_Control_read_count.txt

value: Control


title: BC119


title: B1S18A.input (EndoC_bH1, cytokine-treated)

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

data_processing:
The reads were trimmed for adapters and polyX tails, and filtered by sequencing Phred quality (>= Q15) using fastp.
Adapter-trimmed reads to the human genome using STAR aligner with the two-pass option.
Alignments were assigned to genomic features by using featureCounts. Multi-mapping reads were counted as fractions.
Assembly: hg38
Supplementary files format and content: CSV file includes gene counts for each Sample

source_name: EndoC_bH1 cells

extract_protocol:
High-quality total RNA (>200nt) was extracted using standard Trizol reagent (Invitrogen) according to manufacturer instructions and the resultant aqueous phase was mixed (1:1) with 70% RNA-free ethanol and added to Qiagen Rneasy mini kit columns (Qiagen) and the kit protocol was followed with DNA digestion on column step performed.
RNA libraries for RNA-seq were prepared Takara Pico-Input Strand-Specific Total RNA-seq for Illumina v2 Kit following manufacturer's protocols.

tag: cell line

value: beta cells

value: cytokine-treated

tag: disease

tag: gender

value: F

tag: clone

tag: bmi

tag: batch


title: Control_2


title: BC117

value: WT male

value: male


title: early erythroid cells, EZH2-shRNA, day 7, IP, rep1

value: cord blood

value: erythroid cells

value: EZH2 knockdown

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (#9736)


title: B1S19A.input (EndoC_bH1, cytokine-treated)


title: B1S18.input (EndoC_bH1, CTRL)

value: CTRL


title: BC116

value: MGE derived interneuron


title: BC115


title: dcM-SHR-IP-Rep2

city: Shenzhen

first: Chuanlin

last: Shi

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

description: IP with anti-m6A antibody (Synaptic Systems)

data_processing:
The MeRIP-seq raw data were processed through in-house perl scripts by removing the 5’ adapter, reads with more than 10% N and reads with more than 50% nucleotides with Qphred <= 5.
The clean reads were then mapped to the TAIR10 Arabidopsis genome using HISAT2
Enriched m6A peaks were identified by MACS2 using the corresponding input library as control
Assembly: The clean reads were then mapped to the TAIR10 Arabidopsis genome
Supplementary files format and content: tab-delimited text files include m6A peaks identified by MACS2

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: All Arabidopsis seeds were surface-sterilized by 75% alcohol for 1 min and 30% sodium hypochlorite for 10 min, and rinsed five times with sterile distilled water, then imbibed in sterile water at 4 °C for 2 days. The seeds were grown on half-strength Murashige and Skoog (MS) medium under a long-day photoperiod (16 h light/8 h darkness, at 22 °C) for ~10 days. The seedlings were then transferred to soil in growth chambers with the same conditions.

extract_protocol:
Total RNA from Arabidopsis inflorescences was isolated by TRIzol reagent, and 100 μg total RNA was polyA-selected to get ~2 μg intact mRNA using Dynabeads mRNA Purification Kit (Invitrogen).
All the isolated mRNA was chemically fragmented using NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). We aliquoted ~300 ng fragmented mRNA used as input for MeRIP-seq. The remaining fragmented mRNA was added into 500 μl IP buffer, incubated with 5 μg anti-m6A antibody (Synaptic Systems) and 5 μl of RNasin Plus RNase Inhibitor (Promega) and tumbled at 4 °C for 2 h. Then, the reaction mixture was incubated with protein A/G magnetic beads (MedChemExpress) and tumbled at 4°C for 1 h. Then, the reaction mixture was washed twice with IP buffer, twice with low-salt IP buffer, and twice with high-salt IP buffer at 4 °C for 10 min for each. After extensive washing, the m6A-enriched RNA was purified by TRIzol reagent with glycol blue coprecipitant (Invitrogen). All the input and IP RNA were used for RNA library construction using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: untreated

value: inflorescences

value: dcM-SHR

value: untreated


title: early erythroid cells, Scramble-shRNA, day 7, IP, rep3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (#9735)


title: early erythroid cells, Scramble-shRNA, day 7, IP, rep2

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (#9734)


title: Control_1

tag: strain

value: S-D

value: Hypothalamic SON+PVN

value: Control


title: B1S17A.m6A (EndoC_bH1, cytokine-treated)

tag: tissue

value: beta cells

value: cytokine-treated

value: F


title: early erythroid cells, Scramble-shRNA, day 7, IP, rep1

value: cord blood

tag: treatment

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (#9733)


title: B1S18A.m6A (EndoC_bH1, cytokine-treated)


title: dcM-SHR-IP-Rep1


title: dcM-SHR-input-Rep1

description: input


title: late erythroid cells, EZH2-shRNA, day 15, rep3

data_processing:
HTSeq6 was used to read the counts for each gene in each sample, and then FPKM (Fragments Per Kilobase Million Mapped Reads) was calculated to evaluate the expression leve
DEseq2 version 1.6.3 software7 (https://bioconductor.org/packages/3.0/bioc/html/DESeq2.html) and edgeR version 3.26.8 software8 (https://bioconductor.org/packages/3.9/bioc/html/edgeR.html) were used to identify differentially expressed genes from the data.
The GO and KEGG databases were used for the functional enrichment analysis.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA version 4.1.0 software9 (http://www.gsea-msigdb.org/gsea/downloads.jsp).
The original data were filtered and compared with the reference genome hg19.l.
Assembly: hg19
Supplementary files format and content: include RPKM values for each Sample

source_name: late erythroid cells

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 NovaSeq 5000/6000 S4 Reagent Kit (#A00358, Illumina) and sequenced on an Illumina X-ten (E00487, Illumina)following manufacturer's protocols.

value: late erythroid cells

value: EZH2 knockdown

value: erythropoiesis


title: B1S18.m6A (EndoC_bH1, CTRL)

value: CTRL


title: B1S17.m6A (EndoC_bH1, CTRL)


title: dcM-non-IP-Rep2

value: inflorescences

value: dcM-non


title: dcM-SHR-input-Rep2

description: input

value: dcM-SHR

value: untreated


title: early erythroid cells, EZH2-shRNA, day 7, IP, rep2

value: erythroid cells

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (#9737)


title: early erythroid cells, Scramble-shRNA, day 7, Input

value: Scramble-shRNA


title: B1S17A.input (EndoC_bH1, cytokine-treated)


title: BC114

value: MGE derived interneuron

value: WT male

value: male

value: WT

value: No

value: Post natal day 4 (p4)


title: BC113


title: B1S19.input (EndoC_bH1, CTRL)

value: beta cells

value: F


title: BC112

value: Mut male

value: Mut


title: late erythroid cells, EZH2-shRNA, day 15, rep2

value: late erythroid cells

value: EZH2 knockdown

value: erythropoiesis


title: dcM-non-input-Rep2

description: input

value: inflorescences

value: dcM-non

value: untreated


title: late erythroid cells, EZH2-shRNA, day 15, rep1


title: BC111


title: BC110


title: late erythroid cells, Scramble-shRNA, day 15, rep3

value: Control


title: dcdM-SHR-IP-Rep2

value: dcdM-SHR


title: B1S16.m6A (EndoC_bH1, CTRL)

value: CTRL


title: dcM-non-IP-Rep1


title: dcM-non-input-Rep1

description: input


title: B1S16A.m6A (EndoC_bH1, cytokine-treated)

value: cytokine-treated


title: BC108

value: MGE derived interneuron

value: male


title: late erythroid cells, Scramble-shRNA, day 15, rep2


title: BC109

value: No

value: Post natal day 4 (p4)


title: late erythroid cells, Scramble-shRNA, day 15, rep1


title: B1S16A.input (EndoC_bH1, cytokine-treated)

value: beta cells

value: F


title: dcdM-SHR-input-Rep2

description: input


title: BC107

value: Mut male

value: Mut


title: BC106

value: Mut female

value: female


title: LP2

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

description: pool of 100 embryos

data_processing:
The quality of fastq files of sequences data was checked with a FastQC tool
Illumina adapters were trimmed
Reads were mapped to the bovine reference genome using the Star
Read counts were determined using FeatureCounts program
Differentially expressed genes (DEGs) between sample groups were determined by edgeR-robust
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: preimplantation embryo

growth_protocol: in vitro embryo development

extract_protocol:
Qiagen  (RNAeasy micro kit)
TruSeq® mRNA Stranded Sample preparation kit

treatment_protocol: addition of recombinant Wnt5A

value: low performing sire

tag: developmental stage

value: 4 cell stage


title: B1S15A.input (Islets, cytokine-treated)

source_name: Islets

value: Islets

tag: cell type

value: M


title: B1S15A.m6A (Islets, cytokine-treated)


title: dcdM-SHR-IP-Rep1

value: inflorescences

value: dcdM-SHR

value: untreated


title: LP1

description: pool of 100 embryos


title: BC105

value: MGE derived interneuron

tag: condition


title: Col-IP-Rep2


title: B1S16.input (EndoC_bH1, CTRL)

value: CTRL


title: B1S17.input (EndoC_bH1, CTRL)


title: HP3

description: pool of 100 embryos

value: high performing sire


title: B1S15.m6A (Islets, CTRL)


title: B1S15.input (Islets, CTRL)


title: Col-input-Rep2

description: input


title: B1S14A.m6A (Islets, cytokine-treated)

value: cytokine-treated


title: Col-IP-Rep1


title: BC103

tag: Sex

value: No

value: Post natal day 4 (p4)


title: scFLIT_mixture

first: Yicong

last: Xu

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

description: The 40% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

data_processing:
The adapter sequences and low-quality reads were removed using fastp.
The processed reads were aligned to the genome using STAR.
The duplicate reads with identical sequences were removed using Picard.
The transcripts were assembled and quantified using HTSeq.
Assembly: hg38;mm10
Supplementary files format and content: Tab-separated matrix files of counts for bulk samples
Supplementary files format and content: HDF5 matrix files of counts for the single-cell samples

organism:
Homo sapiens
Mus musculus

source_name: Cell line

growth_protocol: The cells were cultured in RPMI 1640 medium or DMEM supplemented with 10% fatal bovine serum and 1% penicillin–streptomycin. Adherent cells were detached by 0.25% Trypsin-EDTA at 37℃ for 3min and quenched with growth medium. All the cells were maintained in 37℃ with 5% CO2.

extract_protocol:
The methanol fixed cells were kept in -20℃ for 30min and pelleted at 500×g for 5min at 4℃. After two further washes with 1ml of ice-cold wash-resuspension buffer I, permeabilized cells were resuspended in 20ul of ice-cold wash-resuspension buffer II.
The cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

treatment_protocol: The cultured cells were washed twice with 1ml of ice-cold PBS and resuspended in 200ul of ice-cold PBS, 800ul of methanol were added dropwise and gently mixed.

value: Cell line

value: Embryonic kidney cells;Embryonic fibroblast cells

tag: genotype

value: WT

value: Fixed by 40% methanol


title: B1S14A.input (Islets, cytokine-treated)


title: HP2

description: pool of 100 embryos


title: CHMm_rep2

city: Seoul

first: Je-Yoel

last: Cho

address: 1, Gwanak-ro, Gwanak-gu

department: Biochemistry

country: South Korea

institute: Seoul National University

data_processing:
To remove adaptors with low-quality reads and extract miRNA-specific sequence, cutadapt was used with options (--quality-base 33 -u 4 -m 22 -M 30 -f fastq -q 20 -O 6 -j 23 -a adapter-sequence
Before and after the trimming step, quality of sequenced reads was estimated using FastQC.
For known and novel miRNA analysis, miRDeep2 package was used. First, all filtered reads data were merged into one file for novel miRNA analysis. The merged data were converted to collapsed fasta-formatted file and aligned to reference genome using mapper.pl script with options (-e -h -j -m -p). Second, novel miRNAs were identified using miRDeep2.pl script. The identified mature and hairpin forms of novel miRNAs were extracted and combined with known forms of miRBase prepared previously. Finally, the expression values of known and novel miRNAs were calculated using the quantifier.pl script. The CPM (counts per million), which is counts scaled by total number of reads, was used for further analysis. To estimate data reproducibility between replicate samples, Pearson correlation values were calculated and visualized using correlation function in R.
Assembly: canFam3.1
Supplementary files format and content: text

organism: Canis lupus familiaris

source_name: CHMm

growth_protocol: Canine mammary gland adenocarcinoma cell lines (CHMp and CHMm) was grown in RPMI 1640 medium (Hyclone) containing 10% fetal bovine serum (FBS, Gibco) and gentamicin (50ug/ml).

extract_protocol:
Exosomes were purified from cells cultured under serum-free conditions using a combined method of ultrafiltration and ultracentrifuge. First, the culture supernatant was subjected to a differential centrifuge to eliminate cells, dead cells, and cell debris and sequential filtered with 0.45 and 0.22 μm. The filtered supernatant was concentrated using 10K Amicon-Ultra 15 Centrifugal Filter Units (Merck). Filtered units were ultracentrifuged for 80 min and washed with PBS. Exosomes for RNA isolation were lysed with Qiazol (Qiagen) and miRNeasy mini plus kit (Qiagen). Isolated small RNA fracation was directly performed small RNA sequencing.
Small RNA library was prepared using NEXTflex™ Small RNA-Seq Kit v3 following manufacturer's instructions.

treatment_protocol: At 70~80% confluency in 100mm culture dishes, cell were washed with PBS two times and RPMI media without FBS and antibiotics was replaced.

value: CHMm


title: BC101

value: Mut female

value: female

value: Mut

tag: contamination


title: B1S14.m6A (Islets, CTRL)

value: Islets

value: M

tag: age


title: dcdM-SHR-input-Rep1

description: input

value: inflorescences

value: dcdM-SHR

value: untreated


title: CHMp_rep2

source_name: CHMp

tag: cell line

value: CHMp


title: BC100

value: MGE derived interneuron

value: Mut male

value: male


title: B1S14.input (Islets, CTRL)

value: CTRL

tag: disease


title: BC104

value: No

value: Post natal day 4 (p4)


title: 770279 treatment Grp 4-NO RT+Iso for OX40+Ctrl CpG+Iso PD-1

city: Durham

first: Vincent

middle: Michael

last: Perez

state: NC

address: 25 Alexandria Wy

department: Translational reasearch

institute: Tempus AI

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger output generated data for sample.
Assembly: GRCm38
Supplementary files format and content: Count matrix and cell metadata from the 10X output after de-multiplexing.

source_name: p53/MCA sarcoma

extract_protocol:
Tumors were dissected from mice, minced, and digested using the Miltenyi Biotec tumor dissociation kit. Dissociated cells were prepared for fluorescence-activated cell sorting of CD45+ cells for single-cell RNA sequencing. Single-cell suspensions from sorted live CD45+ cells were loaded on a Chromium Controller (10x Genomics) to generate single-cell beads in emulsion, and scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3.1 Single Index Kit), Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and Single Index Kit T Set A (10x Genomics) following the manufacturer’s protocol
Single-cell barcoded cDNA libraries were qualified and quantified using Agilent Bioanalyzer. cDNA libraries were sequenced on an Illumina NextSeq 500 (Illumina). Read lengths were 26 bp for read 1, 8 bp for i7 index, and 98 bp for read 2. Ten thousand cells from each sample were sequenced with greater than 50,000 reads per cell as recommended by the manufacturer.

value: p53/MCA sarcoma

value: 129/SVJ WT


title: BC099


title: BC098


title: BC097


title: BC102

value: Mut female


title: B1S13A.m6A (Islets, cytokine-treated)

value: cytokine-treated

tag: gender


title: B1S13A.input (Islets, cytokine-treated)

tag: clone


title: Col-input-Rep1

description: input


title: B1S13.m6A (Islets, CTRL)

tag: bmi


title: 770267 treatment Grp 8-RT+iso for OX40+CpG+iso for PD-1

description: 10x Genomics

value: Grp 8-RT+iso for OX40+CpG+iso for PD-1


title: 770264 treatment Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics

value: Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1


title: B1S13.input (Islets, CTRL)

value: Islets

value: M

tag: batch


title: BC096

value: WT male

value: WT


title: HP1

description: pool of 100 embryos

value: high performing sire

value: 4 cell stage


title: 770238 treatment Grp 4-NO RT+Iso for OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics


title: BC095

value: MGE derived interneuron


title: 770271 treatment Grp 4-NO RT+Iso for OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics


title: BC094

value: male


title: B1S12A.m6A (Islets, cytokine-treated)

value: CTRL

value: F


title: 770232 treatment Grp 10- No RT+Iso for OX40+CpG+Iso for PD-1

description: 10x Genomics


title: B1S12A.input (Islets, cytokine-treated)


title: BC093

value: No

value: Post natal day 4 (p4)


title: 770203 treatment Grp 10- No RT+Iso for OX40+CpG+Iso for PD-1

description: 10x Genomics

value: p53/MCA sarcoma

value: 129/SVJ WT


title: B1S12.m6A (Islets, CTRL)


title: SER/t3_rep3

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 8.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Cell line, A549

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: DMEM + 10% Fetal bovine serum + 5 units/mL penicillin + 5 ug/mL Streptomycin + 100 ug/mL normocin

extract_protocol: QIAgen RNAeasy Kit

treatment_protocol: Cigarette Smoke Extract (CSE 6%)

tag: group

value: SER

tag: time


title: 770231 treatment Grp 10-NO RT+Iso for OX40+CpG+Iso for PD-1

description: 10x Genomics

tag: tissue


title: Ctrl/t3_rep3

value: Control


title: BC092


title: B1S12.input (Islets, CTRL)

tag: treatment


title: Ctrl/t3_rep4


title: Ctrl/t3_rep2


title: SER/t3_rep2


title: 770224 treatment Grp 10-NO RT+Iso for OX40+CpG+Iso for PD-1

description: 10x Genomics


title: BC091


title: 770223 treatment Grp 4-NO RT+Iso for OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics


title: BC090


title: 770216 treatment Grp 8-RT+iso for OX40+CpG+iso for PD-1

description: 10x Genomics

value: Grp 8-RT+iso for OX40+CpG+iso for PD-1


title: B1S11A.input (Islets, cytokine-treated)

value: Islets

value: cytokine-treated


title: BC089

value: WT male


title: SER/t3_rep4


title: B1S11.m6A (Islets, CTRL)


title: Ctrl/t3_rep1


title: 770240 treatment Grp 10-NO RT+Iso for OX40+CpG+Iso for PD-1

description: 10x Genomics


title: SER/t3_rep1


title: B1S10A.input (Islets, cytokine-treated)

value: M


title: Ctrl/t1_rep3


title: 770226 treatment Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics

value: Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1


title: BC088

value: WT


title: Ctrl/t1_rep4


title: B1S11.input (Islets, CTRL)


title: BC085

value: MGE derived interneuron

value: WT male with contaminants

value: Yes


title: BC084

value: male


title: 770225 treatment Grp 8-RT+iso for OX40+CpG+iso for PD-1

description: 10x Genomics


title: Ctrl/t1_rep2


title: SER/t1_rep3


title: 770227 treatment Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics


title: 770184 treatment Grp 8-RT+iso for OX40+CpG+iso for PD-1

description: 10x Genomics


title: B1S10A.m6A (Islets, cytokine-treated)

value: CTRL


title: BC086

value: Post natal day 4 (p4)


title: B1S11A.m6A (Islets, cytokine-treated)

value: F


title: 770200 treatment Grp 4-NO RT+Iso for OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics

value: p53/MCA sarcoma

value: 129/SVJ WT


title: B1S10.input (Islets, CTRL)


title: Ctrl/t1_rep1

value: Control


title: SER/t0_rep4

value: SER


title: SER/t1_rep2


title: SER/t1_rep4


title: BC083


title: BC087

value: No


title: B1S1.m6A (Islets, CTRL)

value: Islets


title: 770128 treatment Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics


title: BEAS-2B cells, shFer, rep1

city: Chongqing

first: Wang

last: Jiaqi

address: No. 30, Gaotanyan Street

institute: Army Medical University

description: FerKD BEAS-2B cells cultured in N2B27 medium

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2.
featureCount software was used to calculate gene expression from aligned bam files
R statistical package DESeq2 was used for differential expression analysis
Assembly: hg19
Supplementary files format and content: raw reads counts

growth_protocol: BEAS-2B cells were cultured on N2B27 medium.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.
RNA-seq transcriptome libraries were prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA), using 1μg of total RNA. Shortly, messenger RNA was isolated with polyA selection by oligo(dT) beads and fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol.

value: human normal lung epithelial cells

value: Fer knockdown


title: BC079

value: Mut male

value: Mut


title: BC082

value: MGE derived interneuron

value: WT male

value: WT


title: 770174 treatment Grp 8-RT+iso for OX40+CpG+iso for PD-1

description: 10x Genomics

value: Grp 8-RT+iso for OX40+CpG+iso for PD-1


title: SER/t1_rep1


title: BEAS-2B cells, shControl, rep2

description: CTL BEAS-2B cells cultured in N2B27 medium

value: CTL


title: BC081

value: male

value: Post natal day 4 (p4)


title: BEAS-2B cells, shFer, rep2


title: BEAS-2B cells, shControl, rep1


title: KO-YR714

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

country: France

institute: CNRS-Universite Paris Sud

data_processing:
Image analysis and base calling is performed using the Illumina Real Time Analysis (3.4.4) software with default parameters.
Pass-filtered reads were mapped using STAR 2.7.3a
Count table of the gene features was obtained using FeatureCounts
Statistics and Differential expression analysis done with EdgeR
Pathways analysis representation done with the GOPlot R package
Assembly: Ensembl genome assembly GRCm38.98
Supplementary files format and content: Tab-delimited text files of the raw counts

source_name: Retina

extract_protocol:
Total RNAs were extracted using the Rneasy mini kit (Qiagen) according to the manufacturer’s protocol. RNA yields and quality were determined using a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer.
Stranded RNA-Seq libraries were constructed from 100 ng of high-quality total RNA (RIN > 8) using the TruSeq Stranded mRNA Library Preparation Kit (Illumina)

value: Retina

value: 4OH-T at P10 and P14  to induce the expression of the recombinase


title: BC080


title: KO-YR713


title: B1S1.input (Islets, CTRL)

value: CTRL

value: F


title: KO-YR711


title: 770163 treatment Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1

description: 10x Genomics

value: p53/MCA sarcoma

value: 129/SVJ WT

value: Grp 2-RT+Iso OX40+Ctrl CpG+Iso PD-1


title: Ctrl/t0_rep4

value: Control


title: BC076

value: Mut male

value: No


title: P6_STING_ht_T

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

institute: Institut Imagine

description:
10x Genomics
SeuratObject_SAVI.rds

data_processing:
Sequencing reads were demultiplexed and aligned to the human reference genome (GRCh38, release 98, built from ensembl sources), using the CellRanger Pipeline v6.0
Unfiltered RNA UMI counts were loaded into Seurat v4 for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with fwith low number of features (Filters were defined based on the batch : STING1 : nFeature <300 ; STING2 and STING3 <500) or a mitochondrial content higher than 20%.
Data from each sample were normalized using sctransform, before batch correction using Seurat’s FindIntegratedAnchors, on the 3000 most variable features. To avoid over-aligning samples, a reciprocal principal component analysis (PCA) was used to find integration anchors
On the resulting integrated datasets, we computed the PCA on the 3000 most variable genes, before computing a UMAP on 20 PCs. Community detection was performed using the graph-based modularity-optimization Louvain algorithm from Seurat’s FindClusters function with a 1.2 resolution.
Cell types labels were assigned to resulting clusters based on a manually curated list of marker genes as well as previously defined signatures of the well-known PBMCs subtypes.(Monaco et al., 2019) Despite filtering for high quality cells, 11/34 clusters stood out as poor quality clusters and were removed from further analysis. They represented low UMI cells, dying cells, cycling cells, doublets, or contaminants (progenitor cells, basophils, platelets or megakaryocytes). A total of 112,060 cells were kept.
Transcriptomic signatures scores were calculated using Seurat’s AddModuleScore function
Assembly: GRCh38, release 98
Supplementary files format and content: h5 files contain the raw count matrix for each sample
Supplementary files format and content: the rds file contains the Seurat object of all integrated samples

source_name: Blood

extract_protocol:
Peripheral blood samples were collected on lithium heparin. Blood samples were centrifuged at 2300 rpm (1065g) for 10 minutes to collect supernatant (plasma), which was stored at -20°C. Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation (2200 rpm or 974g without break for 30 minutes) using Ficoll (Eurobio Scientific, Les Ulis, France). After centrifugation, the pellet was resuspended in Phosphate-buffered saline (PBS) (Thermo Fisher scientific, Illkirch, France) and cells were centrifuged at 1500 rpm (453g)  for 5 minutes. Finally, the pellet was frozen in a medium containing 90% of Fetal Bovine Serum (FBS) (GIBCO, Thermo Fisher scientific, Illkirch, France) and 10% of dimethyl sulfoxide (DMSO) (Sigma Aldrich, St. Quentin Fallavier, France), and stored in liquid nitrogen.  PBMCs were thawed according to 10X Genomics protocol.
The scRNA-seq libraries were generated using Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (for STING1) or v.3 (for STING2 and STING3) (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1000 cells/µL in PBS+0,04% and 20,000 cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR

value: Blood

value: PBMC

tag: disease group

value: SAVI

value: JAK-inhib

value: M


title: BC075

tag: cell type

value: MGE derived interneuron

value: Mut female

value: female

value: Mut


title: SER/t0_rep3

value: SER


title: BC078

tag: condition

value: male

value: Post natal day 4 (p4)


title: P5_STING

description:
10x Genomics
SeuratObject_SAVI.rds

value: no

value: Ped

tag: Sex


title: CTL-YR613

value: Retina

tag: genotype

value: Yapfl/fl

value: 4OH-T at P10 and P14


title: Ctrl/t0_rep3

value: Control


title: Ctrl/t0_rep1


title: BC074

tag: contamination

value: No


title: atf4a-/-;atf4b-/-;sec31anju221_7dpf_liver_rep2

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

data_processing:
Illumina bcl2fastq2-v 2.20.0.422 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.9.
High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10.
Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

organism: Danio rerio

source_name: liver

extract_protocol:
At 7dpf,  zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment.
NEBNext Single Cell_Low Input RNA Library Prep Kit for Illumina (NEB, Cat No.6420) was used with all 7dpf liver cell for the construction of sequencing libraries.

value: liver

value: Digested with 2.5percent trypsin


title: atf4a-/-;atf4b-/-;sec31anju221_7dpf_liver_rep1


title: SER/t0_rep1


title: BC073

tag: age


title: atf4a-/-;atf4b-/-;sec31anju221_7dpf_liver_rep3


title: P4_STING_ht

description:
10x Genomics
SeuratObject_SAVI.rds

value: Blood

value: PBMC

value: SAVI

value: M


title: BC077

value: MGE derived interneuron

value: Mut male

value: Mut


title: CTL-YR612


title: P6_STING_ht

description:
10x Genomics
SeuratObject_SAVI.rds


title: atf6-/-;sec31anju221_7dpf_liver_rep1


title: B1S10.m6A (Islets, CTRL)

value: Islets

tag: cell line

value: CTRL


title: atf6-/-;sec31anju221_7dpf_liver_rep3


title: atf6-/-;sec31anju221_7dpf_liver_rep2


title: P4_STING_ht_T

description:
10x Genomics
SeuratObject_SAVI.rds

value: JAK-inhib


title: BC072

value: Mut female

value: female

value: Post natal day 4 (p4)


title: IL4/IL13 pre-activation + 24 hour post-infection 4

city: Yokohama

first: Shiori

last: Maeda

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
The sequenced reads were processed using the MOIRAI pipeline. After filtering for ribosomal and low-quality reads, they were mapped to the mouse genome (mm9) using BWA version 0.5.9 (r16) to calculate gene expression.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: Bone marrow-derived macrophages

extract_protocol:
Cells were harvested and lysed with 700 μl of Qiazol and stored at minus 80 oC for RNA extraction. Total RNA was prepared using miRNAeasy kit. RNA quality was assessed by Bioanalyzer to ensure that RIN (RNA integrity number) is over 7.0, and A260/280 and A260/230 ratios are over 1.7.
Transcriptome analysis was performed by CAGE. The CAGE libraries were constructed using the published nAnT-iCAGE protocol.

tag: agent

value: Mycobacterium avium subsp. hominissuis (MAH) strain TH-135

tag: time point

value: 24 hour post-infection

tag: strain

value: BALB/c

value: Bone marrow-derived macrophages


title: Ctrl/t0_rep2

value: Control


title: P2_STING_ht

description:
10x Genomics
SeuratObject_SAVI.rds

value: Blood

value: PBMC

value: no


title: IL4/IL13 pre-activation + 24 hour post-infection 3


title: IL4/IL13 pre-activation + 24 hour post-infection 2


title: BC071

value: MGE derived interneuron

value: No


title: BC070

value: Mut


title: BC069


title: IL4/IL13 pre-activation + 24 hour post-infection 1


title: P1_STING_ht_T2

description:
10x Genomics
SeuratObject_SAVI.rds

value: SAVI

value: F


title: srebf2-/-;sec31anju221_7dpf_liver_rep2

value: liver

value: Digested with 2.5percent trypsin


title: CTL-YR615

value: Retina

value: Yapfl/fl

value: 4OH-T at P10 and P14


title: srebf2-/-;sec31anju221_7dpf_liver_rep3


title: IL4/IL13 pre-activation 3


title: P1_STING_ht_T

description:
10x Genomics
SeuratObject_SAVI.rds

value: JAK-inhib


title: IL4/IL13 pre-activation 4

value: BALB/c


title: BC068

value: Mut female

value: female

value: Post natal day 4 (p4)


title: srebf1-/-;sec31anju221_7dpf_liver_rep3


title: BC067


title: P2_STING_ht_T

description:
10x Genomics
SeuratObject_SAVI.rds

value: Blood

value: PBMC

value: M


title: IL4/IL13 pre-activation 2

value: Bone marrow-derived macrophages


title: srebf1-/-;sec31anju221_7dpf_liver_rep2


title: C9_mother_P1_STING

description:
10x Genomics
SeuratObject_SAVI.rds

value: CTRL

value: no


title: IL4/IL13 pre-activation 1


title: xbp1-/-;sec31anju221_7dpf_liver_rep3


title: BC064

value: MGE derived interneuron

value: WT male

value: male

value: WT

value: No


title: BC066

value: Mut


title: IFNgamma pre-activation + 24 hour post-infection 3

value: Mycobacterium avium subsp. hominissuis (MAH) strain TH-135

value: IFNgamma

value: 24 hour post-infection


title: srebf1-/-;sec31anju221_7dpf_liver_rep1

value: liver

value: Digested with 2.5percent trypsin


title: C8_aunt_P1_STING

description:
10x Genomics
SeuratObject_SAVI.rds

value: Blood

value: F


title: BC065

value: Mut female

value: female

value: Post natal day 4 (p4)


title: srebf2-/-;sec31anju221_7dpf_liver_rep1


title: xbp1-/-;sec31anju221_7dpf_liver_rep2


title: IFNgamma pre-activation + 24 hour post-infection 4

value: BALB/c

value: Bone marrow-derived macrophages


title: C7

description:
10x Genomics
SeuratObject_SAVI.rds

value: PBMC

value: CTRL

value: no


title: IFNgamma pre-activation + 24 hour post-infection 1


title: C11

description:
10x Genomics
SeuratObject_SAVI.rds

value: M


title: C2

description:
10x Genomics
SeuratObject_SAVI.rds

value: Adult


title: xbp1-/-;sec31anju221_7dpf_liver_rep1


title: C1

description:
10x Genomics
SeuratObject_SAVI.rds


title: C10

description:
10x Genomics
SeuratObject_SAVI.rds


title: BC063

value: MGE derived interneuron

value: WT male

value: male

value: WT

value: No


title: BC062


title: sec31anju221_7dpf_liver_rep2

value: liver

value: Digested with 2.5percent trypsin


title: BC060

value: WT female


title: sec31anju221_7dpf_liver_rep3


title: IFNgamma pre-activation 4

value: IFNgamma


title: BC061

value: female

value: Post natal day 4 (p4)


title: sec31anju221_7dpf_liver_rep1


title: D39_36h

description:
10x Genomics
SeuratObject_IFN.rds

data_processing:
Sequencing reads were demultiplexed and aligned to the human reference genome (hg38), and counted using the CellRanger Pipeline v6.0
Unfiltered RNA UMI counts were loaded into Seurat v4 for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with fewer than 750 features or a mitochondrial content higher than 20%
Data from each sample were normalized using sctransform, before batch correction using Seurat’s FindIntegratedAnchors, on the 3,000 most variable features. For computational efficiency, integration anchors were determined with a canonical correlation analysis, using all unstimulated samples as reference.
On the resulting integrated datasets, we computed the PCA on the 3000 most variable genes, before computing a UMAP. Community detection was performed using the graph-based modularity-optimization Louvain algorithm from Seurat’s FindClusters function with a 1.2 resolution.
Cell types labels were assigned to resulting clusters based on a manually curated list of marker genes as well as previously defined signatures of the PBMC subtypes (Monaco et al., 2019).Despite filtering for high quality cells, 7/36 clusters in the stood out as poor quality and were removed from further analysis. They represented low UMI cells, dying cells, cycling cells, doublets, or contaminants (progenitor cells, basophils, platelets or megakaryocytes). A total of 115,503 cells were kept
Transcriptomic signatures scores were calculated using Seurat’s AddModuleScore function
Assembly: GRCh38, release 98
Supplementary files format and content: h5 files contain the raw count matrix for each sample
Supplementary files format and content: the rds file contains the Seurat object of all integrated samples

extract_protocol:
Buffy coats from three healthy young male (19 to 22 years old) were obtained from the Etablissement Français du Sang. PBMCs were isolated using Ficoll (Eurobio Scientific, Les Ulis, France) density gradient and centrifugation at 800g without brakes for 25 minutes. Following centrifugation, cells were washed in wash buffer and centrifuged at 160g for 9 minutes at 4°C and the pellet was resuspended in 10mL of wash buffer. Cells were plated in 96-wells tissue culture plates, with 150,000 cells per wells in an initial volume of 125 μL. One plate was made for each donor for each timepoint to plate a total of 15 million cell per condition.
Cells were challenged with 25μL of  recombinant IFN-β (Human interferon beta 1a, mammalian, Catalog No 11410-2, PBL assay Science, USA) at 6000 IU/mL for a final concentration of 1000 U/mL per well, at one of several timepoints: 1h, 2h, 4h, 8h, 12h, 24h or 36h. Stimulations were done so that all cells, even unstimulated, would be kept a total of 36h in culture. After 36h of culture at 37°C, 5% of CO2, cells from the wells of each plate were collected, pooled, and counted. 10,000 cells were sent to scRNA-seq

value: Blood

tag: time of_stimulation

value: human recombinant IFN-β


title: P1_STING_ht

description:
10x Genomics
SeuratObject_SAVI.rds

value: PBMC

value: SAVI

value: F

tag: batch


title: IFNgamma pre-activation 3

value: BALB/c

value: Bone marrow-derived macrophages


title: D39_24h

description:
10x Genomics
SeuratObject_IFN.rds


title: IFNgamma pre-activation + 24 hour post-infection 2

value: Mycobacterium avium subsp. hominissuis (MAH) strain TH-135

value: 24 hour post-infection


title: IFNgamma pre-activation 2


title: BC058

value: MGE derived interneuron

value: WT


title: D39_12h

description:
10x Genomics
SeuratObject_IFN.rds


title: SER/t0_rep2

tag: group

value: SER


title: WT_7dpf_liver_rep2

value: liver

value: wild type

value: Digested with 2.5percent trypsin


title: BC057

value: WT female

value: female

value: No


title: 24 hour post-infection 3


title: WT_7dpf_liver_rep1


title: BC056

value: Post natal day 4 (p4)


title: BC059


title: D39_1h

description:
10x Genomics
SeuratObject_IFN.rds

value: Blood

value: PBMC

value: human recombinant IFN-β


title: Mouse Liver β-cateninΔ(ex3)/+ rep3

city: Beijing

first: Fangming

last: Liu

address: No.5 Dongdan 3 Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary_files_format_and_content: fpkm_expression_6_samples.txt

source_name: Mouse Liver β-cateninΔ(ex3)/+

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Liver

value: 8 week


title: D39_4h

description:
10x Genomics
SeuratObject_IFN.rds


title: 24 hour post-infection 2

value: Mycobacterium avium subsp. hominissuis (MAH) strain TH-135

value: BALB/c

value: Bone marrow-derived macrophages


title: Mouse Liver β-cateninΔ(ex3)/+ rep2


title: D39_0h_2

description:
10x Genomics
SeuratObject_IFN.rds


title: 12 hour post-infection 4

value: 12 hout post-infection


title: IFNgamma pre-activation 1

value: IFNgamma


title: D39_0h

description:
10x Genomics
SeuratObject_IFN.rds


title: WT_7dpf_liver_rep3

value: liver


title: Mouse Liver WT rep3

source_name: Mouse Liver WT

value: WT


title: Mouse Liver β-cateninΔ(ex3)/+ rep1


title: 12 hour post-infection 3


title: 24 hour post-infection 4

value: 24 hour post-infection


title: Mouse Liver WT rep2


title: 12 hour post-infection 2


title: D38_24h

description:
10x Genomics
SeuratObject_IFN.rds


title: 12 hout post-infection 1


title: 24 hour post-infection 1


title: D38_12h

description:
10x Genomics
SeuratObject_IFN.rds


title: 4 hour post-infection 4

value: 4 hour post-infection


title: CKO tac 2

city: hangzhou

first: Yuhao

last: Zhang

state: zhejiang

address: jiefang road 88

institute: Second Affiliated Hospital Zhejiang University School of Medicine

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample,Matrix table with raw gene counts for every gene and every sample

source_name: Heart tissue

growth_protocol: Hearts from wild type and Piezo1-Cko mice under sham or TAC surgery

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TAC surgery


title: CKO tac 1


title: D38_4h

description:
10x Genomics
SeuratObject_IFN.rds


title: 4 hour post-infection 3


title: D38_36h

description:
10x Genomics
SeuratObject_IFN.rds


title: D38_2h

description:
10x Genomics
SeuratObject_IFN.rds


title: patient RO3940 monocyte

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from patient RO3940 monocyte

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

source_name: monocytes

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: RNA was extracted from monocytes negatively selected from PBMC and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

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

tag: sampletype

value: ROT1D - recent onsite of T1D


title: D38_1h

description:
10x Genomics
SeuratObject_IFN.rds

tag: tissue


title: patient RO4339 monocyte

description: Gene expression data from patient RO4339 monocyte


title: CKO sham 2

tag: treatment

value: sham


title: patient RO4028 monocyte

description: Gene expression data from patient RO4028 monocyte


title: patient RO4381 monocyte

description: Gene expression data from patient RO4381 monocyte


title: 4 hour post-infection 2


title: CKO sham 1


title: 4 hour post-infection 1


title: Mouse Liver WT rep1


title: Uninfected 4


title: WT tac 2

value: wild type


title: D38_0h

description:
10x Genomics
SeuratObject_IFN.rds

value: Blood

value: PBMC


title: Uninfected 3


title: patient RO3630 monocyte

description: Gene expression data from patient RO3630 monocyte


title: WT sham 2


title: patient RO1037 monocyte

description: Gene expression data from patient RO1037 monocyte


title: patient RO4056 monocyte

description: Gene expression data from patient RO4056 monocyte


title: patient RO3593 monocyte

description: Gene expression data from patient RO3593 monocyte


title: patient RO980 monocyte

description: Gene expression data from patient RO980 monocyte


title: Uninfected 2


title: D34_24h

description:
10x Genomics
SeuratObject_IFN.rds

value: human recombinant IFN-β


title: D34_36h

description:
10x Genomics
SeuratObject_IFN.rds


title: patient RO1015 monocyte

description: Gene expression data from patient RO1015 monocyte


title: WT sham 1


title: D34_12h

description:
10x Genomics
SeuratObject_IFN.rds


title: D38_0h_2

description:
10x Genomics
SeuratObject_IFN.rds


title: Uninfected 1


title: D34_8h

description:
10x Genomics
SeuratObject_IFN.rds


title: RIBO_B.s_BY212_Cm_64_2

city: Amsterdam

first: Yaozu

last: Han

address: Science Park 904

country: Netherlands

institute: Unversity Of Amsterdam

description: 64 h Ribo-seq replicate 2

data_processing:
After deep sequencing, the raw sequence reads of both RPFs and unprotected mRNA fragments were uploaded into the Galaxy platform (https://usegalaxy.org/).
Using the Cutadapt tool (version 4.0+galaxy0), the 3’ adapter sequences were removed, and 18 to 34 nt-long reads were selected, which on average removes approximately 15% of the total reads.
After checking that the adapter has been removed from reads by using the FastQC tool (Galaxy Version 0.73+galaxy0), the Bowtie2 tool (Galaxy Version 2.4.2+galaxy0) was used to align reads to the B. subtilis genome sequence NC_000964.3 to generate SAM files, which link reads to their genomic position.
Assembly: Bacillus.fasta
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigwig file includes RPKM vaules of each sample
Library strategy: Ribo-seq

organism: Bacillus subtilis

source_name: Gram-positive bacterium cell

growth_protocol: Fresh transformants of BY212 were streaked out on LB plates containing 20 μg/ml kanamycin at 37 °C. The next day cells were scraped from the plate and resuspended in 0.9% NaCl and subsequently diluted into 40 ml B3 medium containing 20 μg/ml kanamycin to an OD600 of approximately 0.25, and grown at 30 °C for 88 h.

extract_protocol:
The culture was cryogenically pulverized to release intracellular substances. And the ribosome bound with RNA was pelleted by ultracentrifugation over a sucrose cushion. The ribosome bound with RNA was digested with micrococcal nuclease and then was ultracentrifuged over a 10-50% sucrose gradient. 30%, 40% and 50% sucrose fractions were collected and used for RNA extraction by using phenol/chloroform/isoamyl alcohol. Ribosome protected fragments (RPFs) were isolated form extracted RNA by electrophoresis on a TBE 7M Urea PAGE gel and used for construction of cDNA libraries.
1 µl of RNA fragments were used to measure the RNA concentration using the Qubit RNA HS assay kit (Thermo Fisher). Both for the RPF and the unprotected mRNA fragments sequencing libraries were constructed using the Small RNA Library Prep Set for Illumina (NEB), following the manufacturer's protocol.

treatment_protocol: 40 ml cultures were poured into 2 Falcon tubes (50 ml) containing each 20 ml crushed frozen PBS buffer and 1 mM (323 µg/ml) chloramphenicol.

value: Gram-positive bacterium cell

value: amylase production

value: Chloramphenicol


title: RIBO_B.s_BY212_Cm_64_1

description: 64 h Ribo-seq replicate 1


title: patient RO4126 monocyte

description: Gene expression data from patient RO4126 monocyte


title: BEC_Sox9cKO_3 [98]

city: Augusta

first: Sergei

last: Bombin

institute: Augusta University

description: total RNA, rRNA depletion, UMIs

data_processing:
Cogent NGS Analysis Pipeline  v2.0
Reads were demultiplexed  with CogentAP
demultiplexed and mapped to the GRCm39 reference using CogentAP
genes count matrix was calculated by CogentAP
counts were normalized using DESeq2 package v1.36.0
Assembly: GRCm39
Supplementary files format and content: CSV file with DESeq2 normalized counts for each sample

extract_protocol:
total RNA: RNAqueous Micro Kit (Ambion)
SMARTer Stranded Total RNA-seq Kit v3 Pico (Takara)

value: biliary epithelial cells


title: WT tac 1


title: BEC_Control_3 [94]

description: total RNA, rRNA depletion, UMIs


title: D34_4h

description:
10x Genomics
SeuratObject_IFN.rds


title: patient RO3509 monocyte

description: Gene expression data from patient RO3509 monocyte


title: RIBO_B.s_BY212_Cm_16_2

description: 16 h Ribo-seq replicate 2


title: BEC_Control_2 [1773]

description: total RNA, rRNA depletion, UMIs


title: patient LRS_PRO028 monocyte

description: Gene expression data from patient LRS_PRO028 monocyte

value: LRS - low risk healthy sibling


title: patient RO3504 monocyte

description: Gene expression data from patient RO3504 monocyte


title: RIBO_B.s_BY212_Cm_16_1

description: 16 h Ribo-seq replicate 1


title: BEC_Sox9cKO_2 [1770]

description: total RNA, rRNA depletion, UMIs


title: RNA_B.s_BY212_Cm_64

description: 64 h RNA-seq

data_processing:
After deep sequencing, the raw sequence reads of both RPFs and unprotected mRNA fragments were uploaded into the Galaxy platform (https://usegalaxy.org/).
Using the Cutadapt tool (version 4.0+galaxy0), the 3’ adapter sequences were removed, and 18 to 34 nt-long reads were selected, which on average removes approximately 15% of the total reads.
After checking that the adapter has been removed from reads by using the FastQC tool (Galaxy Version 0.73+galaxy0), the Bowtie2 tool (Galaxy Version 2.4.2+galaxy0) was used to align reads to the B. subtilis genome sequence NC_000964.3 to generate SAM files, which link reads to their genomic position.
Assembly: Bacillus.fasta
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigwig file includes RPKM vaules of each sample

extract_protocol:
RNA was extracted by using phenol/chloroform/isoamyl alcohol. Ribosomal RNA was depleted using MICROBExpress Bacterial mRNA Enrichment Kit (Thermo Fisher), according to the manufacturer’s protocol. purified mRNA was fragmented by Magnesium RNA Fragmentation Module (NEB) following the manufacturer’s protocol and used for construction of cDNA libraries.
1 µl of RNA fragments were used to measure the RNA concentration using the Qubit RNA HS assay kit (Thermo Fisher). Both for the RPF and the unprotected mRNA fragments sequencing libraries were constructed using the Small RNA Library Prep Set for Illumina (NEB), following the manufacturer's protocol.


title: D34_2h

description:
10x Genomics
SeuratObject_IFN.rds


title: D34_0h_2

description:
10x Genomics
SeuratObject_IFN.rds


title: patient RO1071 monocyte

description: Gene expression data from patient RO1071 monocyte


title: BEC_Sox9cKO_1 [178]

description: total RNA, rRNA depletion, UMIs


title: patient LRS_PRO023 monocyte

description: Gene expression data from patient LRS_PRO023 monocyte


title: BEC_Control_1 [177]

description: total RNA, rRNA depletion, UMIs


title: patient LRS_PRO024 monocyte

description: Gene expression data from patient LRS_PRO024 monocyte


title: RNA_B.s_BY212_Cm_16

description: 16 h RNA-seq


title: OE1_T_2

city: Shanghai

first: zhenjun

last: li

address: Beidi rd 2901

institute: Shanghai academy of agricultural sciences

data_processing:
Data were processed using the online platform of Majorbio Cloud Platform (www.majorbio.com)
SeqPrep was used to strip adaptors and/or merging paired reads with overlap into single reads (https://github.com/jstjohn/SeqPrep)
Sickle was used to remove low-quality reads (https://github.com/najoshi/sickle).
Cufflinks (Version 2.2.1) was used to assemble the clean data which were then mapped to the rice reference genome
Gene expression levels were determined with the Transcripts Per Million reads (TPM) method
Assembly: Rice Genome Annotation Project (http://rice.uga.edu/)
Supplementary files format and content: xlsx files include gene annotations and TPM values for each Sample

organism: Oryza sativa

source_name: whole-plant

growth_protocol: The rice seedlings were grown in the hydroponic medium for two weeks before 2-nitroaniline treatment.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen, USA). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Treatment started with the addition of 2-nitroaniline (0.8 mM) and seedlings were kept under standard physiological conditions at 25°C. After 8 h of treatment, samples were collected and stored at -80 °C.

value: whole-plant

value: ScOYE3-overexpressing line

value: treated with 2-nitroaniline


title: W5_Wildtype_FPKM

city: Vienna

first: Torben

last: Redmer

address: Veterinärplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Briefly, raw FASTQ files were subjected to quality check with FastQC (v0.11.5) and MultiQC (v1.4)59 and low-quality reads were trimmed using Trimmomatic (v0.36)60 and mapped to the reference mouse genome (Ensembl GRCm38) utilizing gene annotation (Ensembl v91) with STAR. Differential expression analysis was carried out in R (version 3.5.1) with DESeq2 package (v1.20.0)61 and limma package (v3.38.2)62.
Assembly: GRCm38
Supplementary files format and content: Raw_count

source_name: Prostate

extract_protocol: Briefly, prostates of 19 week old mice were dissected, processed to yield a single cell suspension and Epcam (CD326) positive cells were isolated by MACS using anti-CD326-biotin (13–5791-82, eBioscience). Epcam positive cells were collected by centrifugation at 300xg for 5 min at 4 °C and stored at -80 °C until further use. High-quality RNA (200 ng) as assessed by 4200 TapeStation System (Agilent) was used for library preparation according to the manufacturer’s instructions.

value: Prostate

value: EPCAM positive MACsed prostate epithelial cells

value: wt, Cre-expressing PE-cells


title: W4_Wildtype_FPKM


title: OE1_T_1


title: LASCPC-01, Ketotifen, Day3_1

first: Qi

last: Wang

state: Shanghai

address: Shanghai Pu Dong district, Dongfang Rd. No.1630

institute: Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Neuroendocrine Prostate Cancer

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

value: Neuroendocrine Prostate Cancer

value: NEPC cells

value: WT

value: Ketotifen


title: LASCPC-01, PBS, Day3_2

value: PBS


title: LASCPC-01, Ketotifen, Day3_2


title: D34_0h

description:
10x Genomics
SeuratObject_IFN.rds

value: Blood

value: PBMC


title: ZH11_T_2

value: wild-type


title: W3_Wildtype_FPKM


title: LASCPC-01, PBS, Day3_1


title: ZH11_T_1


title: bladder cancer specimen, 22612

city: New York

first: Li

address: 1 Gustave L. Levy Pl

institute: Icahn school of medicine at Mount Sinai

data_processing:
TPM value was quantified by kallisto program
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Bladder cancer specimen

extract_protocol:
Total RNA from UC tissue stored in RNAlater or embedded in OCT was isolated with the Qiagen miRNeasy Mini Kit (217084, Qiagen, Germantown, MD, USA), eluted in water and treated with DNAse, at The Biorepository and Pathology Core Facility at the Icahn School of Medicine at Mount Sinai.
Total RNA was sequenced at the Genomics Core Facility at Icahn School of Medicine at Mount Sinai. Agilent RNA Direct SureSelect XT V6 kit was used for library prep and NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) was used for sequencing.

tag: gender

value: F

value: Bladder cancer specimen

tag: disease state

value: Bladder cancer


title: OE1_2

value: whole-plant

value: untreated


title: W2_Wildtype_FPKM

tag: cell type


title: patient LRS_PRO020 monocyte

description: Gene expression data from patient LRS_PRO020 monocyte

value: LRS - low risk healthy sibling


title: OE1_1

value: ScOYE3-overexpressing line


title: bladder cancer specimen, 22605

value: M


title: P5_PTEN_single KO_FPKM

value: Prostate

value: EPCAM positive MACsed prostate epithelial cells

value: Pten deleted in prostate epithelium


title: bladder cancer specimen, 22171


title: W1_Wildtype_FPKM

value: wt, Cre-expressing PE-cells


title: patient LRS_PRO004 monocyte

description: Gene expression data from patient LRS_PRO004 monocyte


title: patient LRS_PRO002 monocyte

description: Gene expression data from patient LRS_PRO002 monocyte


title: P4_PTEN_single KO_FPKM


title: bladder cancer specimen, 22144


title: bladder cancer specimen, 21783


title: ZH11_2


title: ZH11_1


title: P3_PTEN_single KO_FPKM


title: patient LRS3537 monocyte

description: Gene expression data from patient LRS3537 monocyte


title: patient LRS3729 monocyte

description: Gene expression data from patient LRS3729 monocyte


title: patient LRS_PRO012 monocyte

description: Gene expression data from patient LRS_PRO012 monocyte


title: P2_PTEN_single KO_FPKM


title: P1_PTEN_single KO_FPKM


title: kidney, MPO-AAGN, replicate 1

city: Clayton

first: Peter

middle: James

last: Eggenhuizen

state: VIC

address: Monash Medical Centre, 246 Clayton Road

department: Medicine

country: Australia

institute: Monash University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-3.0.0
Supplementary files format and content: matrix.h5 files

source_name: kidney

extract_protocol:
Kidneys were collected and then digested in 5mg/mL collagenase D (Roche Diagnostics) and 100μg/mL DNase I (Sigma-Aldrich), in Hanks balanced salt solution without Ca2+ and Mg2+ (Sigma-Aldrich) for 30 minutes at 37℃. Cells were erythrocyte lysed with NH4Cl and filtered with 40μM filter (BD Bioscience). Dead cells and debris were removed using Dead Cell Removal Kit (Miltenyi) leaving alive cells that were counted on a hemocytometer with 0.4% trypan blue (Sigma-Aldrich). Single-cell concentration was adjusted to between 700-1200 single cells/μL in 0.04% BSA/PBS.
Cells were loaded onto a 10x Chromium Controller (10x Genomics) to perform single-cell partitioning and barcoding. scRNA-seq libraries were constructed using 10x Genomics Chromium Single Cell 3’ V3.1 chemistry according to the manufacturer’s instructions (10x Genomics). Sample quality was determined by CE integrity analysis by AATI Fragment Analyzer and fluorimetric quantitation by Qubit (Invitrogen).

treatment_protocol: Subcutaneous immunization in the base of tail with 20μg of recombinant mouse myeloperoxidase (rMPO) in Freund’s complete adjuvant, followed by a similar subcutaneous injection seven days later in the back of the neck in Freund’s incomplete adjuvant. Seven days later, mice received an i.v. injection of 1.5 mg of sheep anti-mouse glomerular basement membrane (GBM) globulin on 2 d consecutively. Mice were humanely killed 4 days after administration of anti-GBM globulin.

value: kidney

value: pre-clinical mouse model of MPO-AAGN


title: patient LRS_PRO022 monocyte

description: Gene expression data from patient LRS_PRO022 monocyte


title: kidney, healthy, replicate 2

treatment_protocol: no treatment

value: control


title: bladder cancer specimen, 19425


title: patient LRS2761 monocyte

description: Gene expression data from patient LRS2761 monocyte

value: PBMC


title: patient LRS2937 monocyte

description: Gene expression data from patient LRS2937 monocyte


title: J5_Jun/PTEN_double KO_FPKM

value: Jun/Pten deleted in prostate epithelium


title: patient LRS192 monocyte

description: Gene expression data from patient LRS192 monocyte


title: patient LRS2736 monocyte

description: Gene expression data from patient LRS2736 monocyte


title: bladder cancer specimen, 18859


title: bladder cancer specimen, 19639


title: J3_Jun/PTEN_double KO_FPKM


title: kidney, MPO-AAGN, replicate 2

value: wild-type


title: bladder cancer specimen, 18763

value: Bladder cancer specimen


title: pRP[Exp]-CMV>hOAS3[NM_006187.4]/FLAG_rep4

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
RNA-seq raw reads were reversely-stranded paired-end reads. The reads were trimmed for adapters and polyX tails, then filtered by sequencing Phred quality (>= Q15) using fastp. The count table was generated by aligning reads to the human transcriptome (Ensembl version 110) using kallisto and converting transcript counts to gene counts using tximport.
We kept genes that have counts per million (CPM) more than 0.49 in at least 4 samples, normalized counts by weighted trimmed mean of M-values (TMM), and applied limma-voom transformation to obtain normalized log2CPM.
Assembly: Human transcriptome (Ensembl version 110)
Supplementary files format and content: CSV of log2 counts per million

source_name: Cell lysates

growth_protocol: Normal EndoCs growth media

extract_protocol:
Trizol with Qiagen columns
Stranded mRNA Library (B05)
DNBSEQ Eukaryotic Strand-specific Transcriptome PE150

treatment_protocol: Collected 96h post over-expression

value: Cell lysates

tag: disease

value: Non-diabetic

tag: cell fraction

value: Whole cells

tag: plasmid


title: kidney, healthy, replicate 1

tag: genotype


title: bladder cancer specimen, 21753

value: F

tag: age

value: Bladder cancer


title: patient LRS156 monocyte

description: Gene expression data from patient LRS156 monocyte

value: LRS - low risk healthy sibling


title: pRP[Exp]-CMV>hOAS3[NM_006187.4]/FLAG_rep3

tag: cell line


title: J2_Jun/PTEN_double KO_FPKM

value: Prostate


title: bladder cancer specimen, 18418

value: M


title: patient LRS2619 monocyte

description: Gene expression data from patient LRS2619 monocyte


title: patient LRS_PRO013 monocyte

description: Gene expression data from patient LRS_PRO013 monocyte


title: J1_Jun/PTEN_double KO_FPKM

value: EPCAM positive MACsed prostate epithelial cells


title: bladder cancer specimen, 17766


title: patient LRS133 monocyte

description: Gene expression data from patient LRS133 monocyte


title: D39_2h

description:
10x Genomics
SeuratObject_IFN.rds

value: Blood

value: human recombinant IFN-β


title: J4_Jun/PTEN_double KO_FPKM


title: pRP[Exp]-CMV>hOAS3[NM_006187.4]/FLAG_rep1


title: A5_Jun_single KO_FPKM

value: Jun deleted in prostate epithelium


title: bladder cancer specimen, 17760


title: pRP[Exp]-CMV>hOAS2[NM_002535.3]/FLAG_rep4


title: pRP[Exp]-CMV>hOAS2[NM_002535.3]/FLAG_rep3


title: A1_Jun_single KO_FPKM


title: patient HRS_PRO021 monocyte

description: Gene expression data from patient HRS_PRO021 monocyte

value: HRS - high risk healthy sibling


title: patient LRS2389 monocyte

description: Gene expression data from patient LRS2389 monocyte

value: PBMC


title: pRP[Exp]-CMV>hOAS3[NM_006187.4]/FLAG_rep2


title: pRP[Exp]-CMV>hOAS2[NM_002535.3]/FLAG_rep2


title: A2_Jun_single KO_FPKM


title: patient HRS_PRO026 monocyte

description: Gene expression data from patient HRS_PRO026 monocyte


title: Her2/Neu mouse model cells,Day7plusDox,Bio1,run1

city: Philadelphia

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Bcl2fastq (Illumina output to fastq format)
Fastqc (Quality control)
STAR aligner (To align to mm10 genome)
FeatureCounts (For read counting)
DESeq2 (Differential expression analysis)
Assembly: mm10
Supplementary files format and content: Tab delimited text file with raw counts for each sample

source_name: Her2-dependent cells derived from theMTB/TANmouse model

extract_protocol:
RNA extraction using Rneasy mini kit (Qiagen)
Illumina TruSeq Stranded mRNA library prep for NeoPrep kit

value: Doxycycline

tag: timepoint

value: Day 7


title: patient HRS_PRO019 monocyte

description: Gene expression data from patient HRS_PRO019 monocyte


title: Gemcitabine + I-BRD9 scRNA-seq

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description: Gemcitabine + I-BRD9

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing data was aligned and quantitated using CellRanger (10x Genomics) and hg38 reference genome sequence. Raw gene expression matrices were then analysed using Seurat R package (v4.0.5). Quality control was performed individually for each sample. All cells with <500 detected genes were removed, as well as cells contained <600 unique molecular identifiers (UMIs) and >10% mitochondrial counts.
Assembly: hg38
IBRD9_all_samples_count_matrix_after_QC.csv

source_name: Pancreatic cancer cells

growth_protocol:
Cells were grown to 80% confluency, and treated by 1% formaldehyde for 20 min and ethylene glycol bis (EGS)(Thermo Fisher Scientific, cat.#21565) for 45 min.
Approximately 5x106 cells were used per sample and cross-linked with 1% formaldehyde for 15 minutes. Cross-linking was stopped by incubating samples with glycine at a final concentration of 0.125M for 5 minutes at room temperature, and the cells were washed with PBS followed by pelleting at 250g for 5 minutes.
Cells were washed once with PBS, collected in Cell Dissociation Buffer (Gibco 13150-016) or TrypLE and centrifuged at 300g for 3 min. The cell pellets were then resuspended in 2 ml of 4°C PBS and counted by haemocytometer for using 100,000 cells in the subsequent step.
Cells were grown to 80% confluency

extract_protocol:
Chromatin complexes were eluted from the beads by incubation with ChIP elution buffer (1% SDS+TE) at 65 °C for 1 hr. After that, proteinase K (Life Technologies, cat.#AM2548) was added to the elution reverse cross-linked chromatin complexes for overnight.
After centrifugation at 16,000g for 1 hour at 4°C, DNA pellets were washed once with ice-cold 70% ethanol, and finally air dried. ChIP samples were resuspended in 30µl and 1:10 of the samples were used  in  qPCR for verifying the ChIP samples.
Cells were centrifuged at 300g for 3 min, the supernatant aspirated, the cell pellet resuspended in 150 ul of Isotonic Lysis Buffer (10 mM Tris-HCl pH 7.5, 3 mM CaCl, 2 mM MgCl2, 0.32 M Sucrose and Protease Inhibitors, Roche), and incubated for 12 min on ice. Triton X-100 from a 10% stock was then added at a final concentration of 0.5%, the samples were vortexed briefly and incubated on ice for 6 min. The samples were centrifuged for 5 min at 400g at 4°C, and the cytoplasmic fraction removed from the nuclear pellet. The samples were resuspended gently in 625uL of PBS and transferred to a fresh 1.5 ml eppendorf tube. The nuclei were centrifuged at 1500g for 3 min at 4°C and the supernatant aspirated thoroughly from the nuclear pellet. This step was immediately followed by tagmentation (Nextera DNA Sample Preparation Kit for 24 Samples, FC-121-1030) by resuspending each sample in 100 µL Nextera mastermix (52.5 µl TD buffer, 42.5 µl of water and 5 µl of TDE1 per reaction). The nuclear pellet was resuspended thoroughly by pipetting and incubated at 37 °C for 1 hour shaking at 300rpm.
Total RNA was isolated by RNeasy RNA Extraction Kit (Qiagen) according to manufacturer’s guidelines. RNA was then eluted in 30µl of water and the concentration was measured using Nanodrop. The master mix was prepared as follows: 8µl 5x First-Strand Buffer (Invitrogen), 0.5µl Random primers (0.5 ug/ml) (Promega Cat. C1181), 1ul dNTP mix (10 mM each) (Promega Cat.U1515), 2 ul 0.1 M DTT, 0.5 ul RNase Out, 0.25 ul Superscript III Reverse Transcriptase (Life Technologies). 500 ng of total RNA into a separate tube with 11.75 ul   RNase-free water. RNA was heated to 65 ⁰C for 5 min and allowed to chill on ice for 2 min. 8.25 ul of the master mix were added to RNA. The reaction was incubated at 25 ⁰C for 10 min and then at 42⁰C for 50 min. The reaction was then inactivated by heating at 70 for 15 min.
After collection of cells, centrifuge at a speed not exceeding 400rcf (adjust the speed and centrifugation time according to the cell types). Carefully discard the supernatant and retain the cell precipitation. The cell pellet was resuspended by 1mL 1X PBS containing 0.04% BSA and the washing procedure was repeated twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single-cell dispersion suspension with a concentration close to the goal number. A type of wide-bore pipette tip was used in cell resuspension for a lower cell damage. If necessary, cell filter should be applied to remove cell debris and clusters (eg. 30μm MACS SmartStrainers and 40μm FlowmiTM Cell Strainer). Automatic cytometry was used to determine the cell concentration. And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number. If the calculated concentration is too high, adjust the liquid volume to the appropriate concentration and repeat counting once more.
Single-cell mRNA libraries were built using the Chromium Next GEM Single Cell 3’ Library Construction V3 Kit (10X Genomics) according to manufacturer’s protocol.

treatment_protocol:
PDAC tumor tissue is broken up into as small pieces as possible by using a scalpel. Using forceps, insert tissue to the 15ml falcon tube containing 10ml of primary growth medium + 2.5 mg/ml Collagenase IV + 2 mg/ml Dispase II + 1 mg/ml Trypsin Inhibitor + 1 unit/ml DNase I (NEB, Cat. no. M0303S) and incubate the tissue at 37°C with shaking speed at 50rpm for about 40 min. Repeatedly collect the dissociated cells at interval of 20 min to increase cell yield and viability.  Cell suspensions were filtered using a 70um cell strainer and red blood cells (RBC) were removed by RBC lysis buffer (Invitrogen, Cat. no. 1966634) with 1 unit/ml DNase I.
10 million of dual crosslinked A13A/A13D cells were used to generate one in-situ ChIA-PET library. Briefly, after cell lysis and nuclear lysis, cells were subjected to in-situ digestion with Alu I restriction enzyme for overnight. On the next day, A-tailing was performed using Klenow Fragment (3′>5′ exo-) (NEB, cat.#M0212L) and dATP (100 mM; NEB, cat.#N0440S) for 1 hr at room temperature.  In-situ ligation was performed using in-house bridge linker (F: 5′- /5Phos/CGCGATATC/iBIOdT/TATCTGACT -3′, R: 5′- /5Phos/GTCAGATAAGATATCGCGT -3′. HPLC purified, from Integrated DNA Technologies) and T4 DNA ligase (Thermo Fisher Scientific, cat.#EL0013) for RT 1 hr and then 16°C for overnight. The nucleus was sonicated into ~1 kb size. Then chromatin was precleared using protein G beads for 1 hr and immunoprecipitation was performed using anti-CTCF antibody (Abclonal, cat.# A1133) coated protein G beads (Life Technologies, cat. no. 10009D) for overnight. After that, proximity-ligated chromatin complexes were washed sequentially by low salt, high salt, LiCl buffer and TE buffer.
The pellet was re-suspended in 2ml ChIP Cell Lysis Buffer (CLB: 10 mM Tris pH8, 10 mM NaCl, 0.2% NP-40) and incubated for 10 minutes to lyse the plasma membranes. Nuclei were pelleted at 600g for 5 min, lysed in 1.25ml of ChIP Nuclear Lysis Buffer (NLB: 50 mM Tris pH8, 10mM EDTA, 1% SDS) for 10 minutes, and then 0.75ml of ChIP Dilution Buffer (DB: 20 mM Tris pH8, 2mM EDTA, 150mM NaCl, 0.01% SDS, 1% Triton X-100) was added to the samples. Chromatin was sonicated in 15ml Diagenode Bioruptor Pico water bath sonicator with an automated water cooling system, by performing 30 cycles of 30 seconds ON, 45 seconds OFF. This protocol resulted in the homogeneous generation of fragments of 100-400bp. Samples were clarified by centrifugation at 16000g for 10 minutes, and diluted with 3.5ml of DB. After pre-clearing with 10µg of non-immune IgG for 1h and 50µl of Protein G-Agarose for 2h, ChIP was performed overnight in rotation using specific antibodies (Table S2) or non-immune IgG as a control. After incubation for 1 hour with 30µl of Protein G-Agarose, beads were washed twice with ChIP Washing Buffer 1 (WB1: 20mM Tris pH8, 2mM EDTA, 50mM NaCl, 0.1% SDS, 1% Triton X-100), once with ChIP Washing Buffer 2 (WB2: 10mM Tris pH8, 1mM EDTA, 0.25M LiCl, 1% NP-40, 1% Deoxycholic acid), and twice with Tris-EDTA (TE: 10mM Tris pH8, 1mM EDTA). Precipitated DNA was eluted with 150µl of ChIP Elution Buffer (EB: 100mM NaHCO3) twice for 15 minutes at room temperature in rotation, and processed as follows in parallel with 300µl of sonicated chromatin non-used for ChIP (Input). Cross-linking was reverted by adding NaCl to a final concentration of 300mM for protein-DNA de-crosslinking and incubated at 65°C for 5 hours and 1µg RNase A (Sigma) to digest contaminating RNA. Finally, 60µg of Proteinase K (Sigma) were added overnight at 45°C. DNA was extracted by sequential phenol-chloroform and chloroform extractions, and precipitated overnight at -80°C in 100mM NaAcetate, 66% ethanol and 50µg of glycogen (Ambion) as a carrier.
Decant the digested tissue into a 15ml falcon with growth medium and spin at 300xg for 10mins to sediment single cells. Resuspend cells in primary growth media, count cells (live/dead) and divide sample into four treatments conditions: DMSO; I-BRD9 at 10µM final concentration; DMSO + Gemcitabine at 1µM final concentration; I-BRD9 + Gemcitabine. Transfer samples to Collagen I coated plates (Gibco, Cat no: A11428-01)? Cells are likely to bind to the well surface. NB! It in unclear how many cells will survive the whole process. Therefore, plate several wells and plate out as much sample as possible to reach high enough cell numbers.  Incubate cells with the four different conditions for 72 hours.

tag: method

value: single-cell RNA-seq

tag: factor


title: pRP[Exp]-CMV>hOAS2[NM_002535.3]/FLAG_rep1

value: Cell lysates


title: pRP[Exp]-CMV>hOAS1[NM_016816.4]/FLAG_rep4

value: Non-diabetic


title: Her2/Neu mouse model cells,Day7,Bio1,run1

value: Her2-dependent cells derived from theMTB/TANmouse model


title: pRP[Exp]-CMV>hOAS1[NM_016816.4]/FLAG_rep3

value: Whole cells


title: A4_Jun_single KO_FPKM


title: Gemcitabine scRNA-seq

description: I-BRD


title: SBS child 8 with PNAC

first: Siyang

last: Cheng

address: KongJiang Rd.1665

institute: Xinhua hospital

data_processing:
libraries were prepared from total RNA with ribosomal RNA depleted and were sequenced on the illumina NovaseqTM 6000 platform.
Sequence reads were trimmed with Cutadapt  and were aligned to human reference genome (GRCh38/hg38) using HISAT2 package.
Differentially expressed genes (DEGs) were identified with DESeq2 package.
Gene expression fold change (FC) ≥ 2 and false discovery rate (FDR) < 0.05 were set as the threshold for DEGs and subsequent functional analysis using Gene Ontology (GO)  and KEGG database.
Assembly: GRCh38/hg38
Supplementary files format and content: Excel files include FPKM values for each Sample

growth_protocol: Liver samples were obtained from 8 pediatric patients with short bowel syndrome (SBS) at the Department of Pediatric Gastroenterology and Nutrition.

extract_protocol:
Total RNA from livers and cells were extracted using TRIzol reagent according to the manufacturer’s instruction
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Patients were divided into two groups (n=4 each group) based on the presence of IFALD, which is defined as serum direct bilirubin greater than 2 mg/dL (34.2 mol/L) with PN longer than 90 days when other causes of liver disease have been excluded

value: IFALD

value: liver

value: Parenteral nutrition administration


title: Her2/Neu mouse model cells,Day3,Bio1,run1

value: Day 3


title: control scRNA-seq

description: control


title: Her2/Neu mouse model cells,Day28plusDox,Bio4,run1

value: Day 28


title: pRP[Exp]-CMV>hOAS1[NM_016816.4]/FLAG_rep2


title: SBS child 7 with PNAC


title: pRP[Exp]-CMV>hOAS1[NM_016816.4]/FLAG_rep1


title: I-BRD9 scRNA-seq

description: Gemcitabine


title: pRP[Exp]-CMV>ORF_Stuffer_rep4


title: Her2/Neu mouse model cells,Day28plusDox,Bio1,run1


title: SBS child 6 with PNAC


title: patient HRS_PRO014 monocyte

description: Gene expression data from patient HRS_PRO014 monocyte


title: pRP[Exp]-CMV>ORF_Stuffer_rep3


title: SBS child 5 with PNAC


title: SBS child 4 without PNAC

value: No IFALD


title: patient HRS_PRO015 monocyte

description: Gene expression data from patient HRS_PRO015 monocyte


title: pRP[Exp]-CMV>ORF_Stuffer_rep2


title: Her2/Neu mouse model cells,Day14plusDox,Bio1,run1

value: Day 14


title: Her2/Neu mouse model cells,Day28,Bio1,run1


title: pRP[Exp]-CMV>ORF_Stuffer_rep1


title: SBS child 3 without PNAC


title: Her2/Neu mouse model cells,Day14,Bio1,run1


title: patient HRS4190 monocyte

description: Gene expression data from patient HRS4190 monocyte


title: Her2/Neu mouse model cells,Day0,Bio3,run1

value: Day 0


title: patient HRS3849 monocyte

description: Gene expression data from patient HRS3849 monocyte

value: HRS - high risk healthy sibling


title: patient HRS3689 monocyte

description: Gene expression data from patient HRS3689 monocyte

value: PBMC


title: splenic sorted NK cells, knockout, rep3

city: Monash University

first: Harrison

last: Sudholz

address: 15 Innovation walk

department: Biochemistry and Molecular Biology

description: Column 7

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with RNAStar, followed by featureCounts and DESeq2 (standard parameters)
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: sorted splenic NK cells

extract_protocol:
bulk RNA was isolated from sorted, splenic NK1.1+ CD3- cells using the Nucleospin RNA isolation kit
MGIEasy V3 chemistry

value: sorted splenic NK cells

value: KO

value: Core fucose deficient NK cells (NK1.1+CD3-,PhoSL-)

value: Fut8 KO

value: NK cell enrichment


title: SBS child 1 without PNAC


title: patient HRS3238 monocyte

description: Gene expression data from patient HRS3238 monocyte


title: patient HRS3053 monocyte

description: Gene expression data from patient HRS3053 monocyte


title: Her2/Neu mouse model cells,Day1,Bio1,run1

value: Her2-dependent cells derived from theMTB/TANmouse model

value: Day 1


title: Her2/Neu mouse model cells,Day0,Bio1,run1


title: EC, MEF2C ChIP, C , bio rep 2

city: Sacramento

first: Julian

last: Halmai

state: CA

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

data_processing:
bowtie2/2.4.2 (Aligner)
samtools/1.15.1 (SAM to BAM)
sambamba0.6.7 (duplicate, unmapped removal)
macs3/3.0.0a6 (peak caller)
deeptools/3.5.1 (data visualization)
Assembly: Ensembl GRCh38
Supplementary files format and content: narrowPeak
Supplementary files format and content: bigWig

extract_protocol:
These ECs were cross-linked in 1% formaldehyde for 10 min at room temperature and the reaction was stopped with 0.125 M glycine. Cross-linked cells were lysed with ChIP lysis buffer (5 mM PIPES pH8, 85 mM KCl, 1% Igepal) with a protease inhibitor (PI) cocktail (Millipore Sigma, #11697498001). Nuclei were collected by centrifugation at 2000 rpm for 5 min at 4 °C and lysed in nuclei lysis buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS) supplemented with the PI cocktail. Chromatin was fragmented using the Bioruptor Pico (Diagenode, Denville, NJ) and diluted with 5 volumes RIPA buffer (50 mM Tris pH 7.6, 150 mM NaCl, 1 mM EDTA pH8, 1% Igepal, 0.25% deoxycholic acid). ChIP enrichment was performed by incubation with 3 µg MEF2C antibody (Abcam, #ab211493) or 2 µg normal rabbit IgG (ab46540, Abcam) for 16 h at 4 °C. Immune complexes were bound to 20 µl magnetic protein A/G beads (Biorad, Hercules, CA) for 2 h at 4 °C. Beads were washed 2 × with RIPA (Thermo Fisher Scientific, #J62524.AE) and 3 × with ChIP wash buffer (100 mM Tris pH8, 500 mM LiCl, 1% deoxycholic acid). The final wash was performed in ChIP wash buffer with 150 mM NaCl. Cross-links were then reversed by heating beads in 100 µl ChIP elution buffer (50 mM NaHCO3, 1% SDS) overnight at 65 °C. DNA was purified using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany).
Libraries were prepared by Novogene.

value: Dura6.9 iPSC derivatives

value: endothelial cells

tag: chip antibody

value: MEF2C shRNA


title: splenic sorted NK cells, knockout, rep1

description: Column 5


title: SBS child 2 without PNAC

value: liver

value: Parenteral nutrition administration


title: patient HRS2068 monocyte

description: Gene expression data from patient HRS2068 monocyte


title: splenic sorted NK cells, wild type, rep3

description: Column 4

value: WT

value: NK cells (NK1.1+CD3-)


title: Her2/Neu mouse model cells,Day7plusDox,Bio5,run5

value: Doxycycline

value: Day 7


title: patient HRS3636 monocyte

description: Gene expression data from patient HRS3636 monocyte

value: PBMC

value: HRS - high risk healthy sibling


title: patient HRS3326 monocyte

description: Gene expression data from patient HRS3326 monocyte


title: patient HRS_PRO010 monocyte

description: Gene expression data from patient HRS_PRO010 monocyte


title: EC, MEF2C ChIP, C , bio rep 1


title: EC, MEF2C  ChIP, A , bio rep 2

value: Control


title: splenic sorted NK cells, wild type, rep2

description: Column 3

value: sorted splenic NK cells


title: patient HC4181 monocyte

description: Gene expression data from patient HC4181 monocyte

value: uHC - unrelated healthy control


title: Her2/Neu mouse model cells,Day7plusDox,Bio3,run5


title: Her2/Neu mouse model cells,Day7plusDox,Bio4,run4


title: Her2/Neu mouse model cells,Day7plusDox,Bio2,run3


title: MGG4-Nes-low-3

city: Orsay

first: Giorgio

last: Seano

address: Bâtiment 110, Rue Henri Becquerel

department: INSERM U1021 - CNRS UMR3347

institute: Institut Curie

description:
MGG4_tpm.csv
D348-D347T29

data_processing:
The reads obtained were processed using the Curie Institute Nextflow RNA-seq analysis pipeline
reads quality was assessed using FastQC and mapped to the reference genome (hg19/GRCh37 or mm10/GRCm38 for GL261) using STAR software
raw reads count tables were generated using STAR
Software versions and full pipelines are available at https://github.com/bioinfo-pf-curie/RNA-seq/
Assembly: hg19, mm10
Supplementary files format and content: Matrix table with TPM gene counts for every gene and every sample (.csv)

source_name: brain

growth_protocol: cells were maintained in neurospheres using NeuroCult basal medium with NeuroCult proliferation supplement (STEMCELL technologies, #05751), 20ng/ml EGF, 20ng/ml bFGF, 5ug/ml heparin (STEMCELL Technologies, #07980) and gentamycin (Sigma) (NC complete media) in low attachment flasks (Corning, #3814)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using 100ng to 1ug of RNA using Illumina library structure (Stranded mRNA Library preparation, Illumina), according to the manufacturer’s instructions. For MGG4-BV samples only, SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian protocol was used. Samples were sequenced as 100bp paired-end runs on the Novaseq 6000 (Illumina).

treatment_protocol: In-vitro MGG4 cells were treated with 25uM of temozolomide for 3 days before RNA extraction. For in-vivo MGG4 samples, mouse were irradiated with 10 Gy using a X-ray irradiator, or treated with 10mg/kg of temozolomide. Tissue was harvested 7 days after treatment. MGG4-Nes, MGG18-Nes and GL261-Nes samples were FACS-sorted based on reporter expression before RNA extraction with no additional treatment. For co-culture experiment, MGG4 cells were co-cultured 3 days with brain blood vessels before isolation of tumor cells for RNA extraction.

value: brain

value: patient-derived glioblastoma cell line

tag: group

value: Nes-low


title: splenic sorted NK cells, knockout, rep2

description: Column 6

value: KO

value: Core fucose deficient NK cells (NK1.1+CD3-,PhoSL-)

value: Fut8 KO

value: NK cell enrichment


title: patient HC4078 monocyte

description: Gene expression data from patient HC4078 monocyte

tag: sampletype


title: INDYKD, 46

city: Copenhagen N

first: Morten

last: Scheibye-Knudsen

state: Copenhagen N

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

data_processing:
Python
Paired-end reads from 44 RNA-Seq samples were aligned to mm9 using bowtie2
Differential expression analysis was performed using a Salmon → tximeta → DESeq2
GSEA was performed directly on DESeq2 normalized counts
Assembly: mm9
Supplementary files format and content: DESeq2 normalized counts

source_name: cerebellum

extract_protocol:
RNA extraction with trizol-chloroform
Total RNA, rRNA depleted
libraries were prepared using the DNBseq protocol from BGI.

tag: tissue

value: cerebellum

tag: Sex

value: M

tag: strain

value: INDY

value: KD


title: Her2/Neu mouse model cells,Day7,Bio3,run2

value: Her2-dependent cells derived from theMTB/TANmouse model

value: Day 7


title: MGG4-Nes-low-2

description:
MGG4_tpm.csv
D348-D347T27


title: MGG4-Nes-high-2

description:
MGG4_tpm.csv
D348-D347T28

value: Nes-high


title: Her2/Neu mouse model cells,Day7,Bio5,run5


title: INDYKD, 45

tag: treatment


title: splenic sorted NK cells, wild type, rep1

description: Column 2

value: WT

tag: cell type

value: NK cells (NK1.1+CD3-)


title: CSBKD, 44

value: CSB