title: Spleen from TMEV-infected mice on day 4_5


title: ExpTcell_Act_T_24hrs_3

status: Public on Mar 20 2024

type: SRA

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

library_source: transcriptomic

data_processing:
Fastqc
Trimming of reads using trimmomatic and fastp
Hisat2 alignment using Ensemble Grch38
Raw Gene ocunt generation using htseq-count program
Assembly: Grch38
Supplementary files format and content: htseq-Count text fiile

molecule: total RNA

organism: Homo sapiens

source_name: Expanded T cells

growth_protocol: T cell expansion was done by activating PBMCs with PHA and IL2 in T cell media for 12 days. T cells were sustained with IL2 throughout the expansion. Experiment was performed on day 13.

extract_protocol: Advanta™ RNA-Seq NGS Library Prep Kit and 48.Atlas™ IFC (Fluidigm)

treatment_protocol: On day 13, expanded T cells were either non-activated or activated with CD3/CD28 DynaBeads (Gibco) for 24 hours. This was followed by treatment (or not) with 200 µM of pregnenolone for 2 or 24 hours.

tag: cell type

value: PBMC-derived expanded T cells

tag: t cell activation

value: Yes

tag: pregnenolone (200 µm) treatment

tag: time point

tag: biological replicate

tag: technical replicate


title: Spleen from TMEV-infected mice on day 4_1

city: Osakasayama

first: Ijaz

last: Ahmad

state: Osak/Kansai

address: 377-2 Onohigashi

department: Department of Microbiology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Basecalls were performed, using CASAVA on Linux
The raw sequence data were aligned to reference genome, Mus musculus GRCm38.75, downloaded from ENSEMBLE, using the Spliced Transcripts Alignment to a Reference (STAR).
The read count data were normalized by DEG elimination strategy (DEGES), using “R” and the package “tag count comparison (TCC).”
Assembly: mm10
Supplementary files format and content: An Excel file includes the read count data normalized with DEGES.

organism: Mus musculus

source_name: Spleen

extract_protocol:
Total RNA was isolated from the platelets, using the RNeasy Mini Kit (Qiagen, Valencia, CA) and TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA), according to the manufacturer’s instruction. The Quality of RNA was examined using NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Female SJL/J mice (5 wk old, 15–17 g) were inoculated intracerebrally with 2 × 10^5 PFUs of TMEV (Daniels' strain). As a control, age-matched female SJL/J mice were injected with 20 μL PBS intracerebrally. We collected the spleens on 4, 7, and 35 days post infection. We also collected blood from the carotid artery, using the syringes prefilled with 0.1 mL ACD buffer (Sigma-Aldrich, St Louis, MO), centrifuged the blood at 118 g for 8 min and obtained platelet-rich plasma, followed by platelet isolation with centrifugation at 735 g for 10 min. Platelets were resuspended to PBS (pH 7.37–7.38) very slowly and gently.

tag: strain

value: SJL/J

tag: Sex

value: Female

tag: tissue

value: Spleen

tag: genotype

value: Wild type

tag: treatment

value: Intracerebral TMEV infection

tag: time

value: 4 days post infection


title: 26a_beforePRI-724

type: RNA

city: Tokyo

first: Juntaro

last: Matsuzaki

address: 1-5-30 Shibakoen, Minato-ku

institute: Keio University Faculty of Pharmacy

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner 3000 (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale. Experimental batch effect was removed using Partek Genomics Suite 7.19.1125.

source_name: Plasma

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from EVs suspended in 300uL PBS using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

treatment_protocol: Plasma EVs were isolated from 1 mL of plasma via the TIM4-affinity method, using the MagCapture Exosome Isolation Kit PS (Wako, Osaka, Japan), according to the manufacturer's instruction.

tag: gender

value: M

tag: age

tag: virus

value: HCV

tag: child-pugh

value: A

tag: lsm

tag: molecule type

value: miRNA


title: 25b_afterPRI-724


title: Spleen from control mice on day 4_5

value: Intracerebral PBS injection

value: 4 days post injection


title: shNR4A3_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep1

city: Dublin

first: Eoin

middle: P

last: Cummins

state: Dublin

address: UCD Conway Institute of Biomolecular and Biomedical Research, UCD Belfield

department: Conway Institute/School of Medicine

country: Ireland

institute: University College Dublin

data_processing:
Raw data quality was evaluated with Fast QC, and per base quality score distribution plotted
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: .txt file format of raw counts

source_name: Human monocytic leukaemia_ THP1

growth_protocol: The appropriate number of shNT, shNR4A2 and shNR4A3 THP-1 cells were counted, centrifuged at 1,200rpm (290xg) and the supernatant was removed. Cells were transferred to an environmental gas chamber (37℃, 5%/10% CO2) and resuspended in buffered DMEM media supplemented with 10% FBS, 1% P/S. at a concentration of 750,000 cells/ml (3 million cells/ 4 mls media on 60mm plastic petri dishes). Cells were incubated for 2 hours. LPS-stimulated cells were treated with 2.5ug/ml LPS  for a further 2 hours before lysis.

extract_protocol:
Cells were collected and total mRNA was extracted using the Omega EZNA Total RNA Kit I, as per the manufacturer’s instructions.
cDNA library preparation was performed with polyA selection using Illumina HiSeq, 2x150bp configuration, single index, per lane. ~350M raw paired-end reads per lane. Library preparation and sequencing were performed by Genewiz (Germany).

treatment_protocol: Cells were treated +/- LPS for 2hrs in their respective CO2 chamber

tag: cell line

value: Human monocytic leukaemia_ THP1

tag: lentiviral particle_transduction

value: NR4A3 targeting shRNA

value: 10% CO2 + LPS


title: ExpTcell_Act_T_24hrs_4

tag: cell type

value: PBMC-derived expanded T cells

tag: t cell activation

tag: pregnenolone (200 µm) treatment

tag: time point


title: 25a_beforePRI-724


title: 23b_afterPRI-724

value: HBV


title: ExpTcell_NA_UT_24hrs_1_rep2

value: No

tag: biological replicate

tag: technical replicate


title: shNR4A3_THP1 10% CO2_rep3


title: Spleen from control mice on day 4_4

tag: strain

value: SJL/J

tag: Sex

value: Female

tag: tissue

tag: genotype


title: ExpTcell_NA_UT_24hrs_1_rep1


title: Spleen from control mice on day 4_3

value: Spleen

value: Wild type

tag: treatment

tag: time


title: shNR4A3_THP1 10% CO2_rep2


title: 23a_beforePRI-724

tag: gender

tag: age

tag: virus

tag: child-pugh


title: ExpTcell_NA_UT_0hrs_2_rep1


title: ExpTcell_Act_T_2hrs_3_rep2

value: Yes


title: 22b_afterPRI-724

value: M

tag: lsm

tag: molecule type


title: shNR4A3_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

tag: cell line

tag: lentiviral particle_transduction

value: 5% CO2 + LPS


title: Spleen from control mice on day 4_2


title: Spleen from control mice on day 4_1


title: shNR4A3_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep2


title: 22a_beforePRI-724

value: HCV

value: A


title: ExpTcell_NA_UT_2hrs_3_rep2

tag: cell type

tag: t cell activation

tag: pregnenolone (200 µm) treatment

tag: time point


title: Platelets from TMEV-infected mice on day 35_6

source_name: Platelets

tag: strain

tag: Sex

value: Platelets

value: Intracerebral TMEV infection

value: 35 days post infection


title: Platelets from TMEV-infected mice on day 35_7

tag: tissue

tag: genotype


title: 21b_afterPRI-724

value: B

value: miRNA


title: shNR4A3_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep1

value: Human monocytic leukaemia_ THP1

value: NR4A3 targeting shRNA

tag: treatment


title: ExpTcell_Act_T_2hrs_4

value: PBMC-derived expanded T cells

tag: biological replicate

tag: technical replicate


title: shNR4A3_THP1 5% CO2_rep3


title: ExpTcell_Act_UT_2hrs_4

value: No


title: Platelets from TMEV-infected mice on day 35_5

value: SJL/J

value: Female

tag: time


title: 21a_beforePRI-724

tag: gender

tag: age

tag: virus

value: HBV

tag: child-pugh


title: 18b_afterPRI-724

tag: lsm

tag: molecule type


title: ExpTcell_Act_UT_24hrs_1

tag: cell type

tag: t cell activation

value: Yes


title: shNR4A3_THP1 5% CO2_rep2

tag: cell line

tag: lentiviral particle_transduction


title: shNR4A3_THP1 5% CO2_rep1


title: shNR4A3_THP1 10% CO2_rep1


title: Platelets from TMEV-infected mice on day 35_4

tag: strain

tag: Sex

value: Wild type


title: ExpTcell_Act_UT_2hrs_2

tag: pregnenolone (200 µm) treatment

tag: time point


title: ExpTcell_Act_UT_24hrs_4

tag: biological replicate


title: ExpTcell_NA_T_2hrs_2_rep1

tag: technical replicate


title: ExpTcell_NA_UT_2hrs_3_rep1


title: 18a_beforePRI-724

value: M


title: Platelets from TMEV-infected mice on day 35_2

tag: tissue

tag: genotype

tag: treatment

tag: time


title: 17a_beforePRI-724

tag: gender

tag: age

tag: virus

value: HCV

tag: child-pugh


title: Platelets from TMEV-infected mice on day 35_3


title: shNR4A2_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

value: NR4A2 targeting shRNA

value: 10% CO2 + LPS


title: shNR4A2_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep2


title: shNR4A2_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep1


title: Platelets from control mice on day 35_7

value: Platelets

value: Intracerebral PBS injection

value: 35 days post injection


title: ExpTcell_NA_T_24hrs_4

tag: cell type

tag: t cell activation


title: ExpTcell_NA_UT_0hrs_4_rep2


title: Platelets from TMEV-infected mice on day 35_1

value: Intracerebral TMEV infection

value: 35 days post infection


title: Platelets from control mice on day 35_6


title: 17b_afterPRI-724

value: A

tag: lsm

tag: molecule type

value: miRNA


title: ExpTcell_NA_UT_2hrs_2

value: PBMC-derived expanded T cells

value: No


title: shNR4A2_THP1 10% CO2_rep1

tag: cell line

value: Human monocytic leukaemia_ THP1

tag: lentiviral particle_transduction


title: Platelets from control mice on day 35_5

tag: strain

value: SJL/J

tag: Sex

value: Female


title: ExpTcell_NA_UT_2hrs_1

tag: pregnenolone (200 µm) treatment

tag: time point

tag: biological replicate

tag: technical replicate


title: Platelets from control mice on day 35_4

tag: tissue

tag: genotype

value: Wild type

tag: treatment

tag: time


title: ExpTcell_NA_UT_0hrs_4_rep1


title: shNR4A2_THP1 10% CO2_rep3


title: 15b_afterPRI-724

tag: gender

value: M

tag: age

tag: virus

value: HBV

tag: child-pugh


title: 14b_afterPRI-724

tag: lsm

tag: molecule type


title: Platelets from control mice on day 35_3


title: ExpTcell_NA_UT_0hrs_1

tag: cell type

tag: t cell activation


title: shNR4A2_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

tag: cell line

tag: lentiviral particle_transduction

value: NR4A2 targeting shRNA

value: 5% CO2 + LPS


title: 14a_beforePRI-724


title: shNR4A2_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep2


title: 12b_afterPRI-724

value: B


title: ExpTcell_NA_T_24hrs_1

tag: pregnenolone (200 µm) treatment

value: Yes

tag: time point


title: ExpTcell_Act_UT_2hrs_3_rep1

tag: biological replicate

tag: technical replicate


title: Platelets from control mice on day 35_2

tag: strain

tag: Sex

tag: tissue

value: Platelets

tag: genotype

value: Intracerebral PBS injection

value: 35 days post injection


title: 11a_beforePRI-724

tag: gender

tag: age

value: HCV

value: A


title: shNR4A2_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep1

tag: treatment


title: 11b_afterPRI-724

tag: virus

tag: child-pugh

tag: lsm

value: miRNA


title: shNR4A2_THP1 10% CO2_rep2


title: 15a_beforePRI-724

tag: molecule type


title: MCF10A Cells, Mutant R323, rep3

city: Riverside

first: Ernest

last: Martinez

address: 900 University Ave.

department: Biochemistry

country: USA

institute: University of California Riverside

data_processing:
Trimmed sequence reads were mapped to a hg38 index with the inclusion of mouse c-MYC cDNA sequence and transcript/gene annotations with STARv.2.7.9.a
Read count extraction was performed with featureCounts v.1.6.4.
Assembly: hg38 w/ inclusion of mouse c-MYC cDNA and transcript/gene annotations
Supplementary files format and content: tab-delimited text files include read-count values for each sample

growth_protocol: MCF10A cells were grown under adherent conditions as recommended by supplier (ATCC)

extract_protocol:
RNA was extracted using the Direct-zol RNA MiniPrep Plus kit ( Zymo Research, Irvine, CA, USA). RNA was quantified using Thermoscientific Nanodrop Onec spectrophotometer and quality was assessed using Agilent 2100 bioanalyzer.
RNA sequencing libraries were prepared with Kapa RNA mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol
stranded mRNA-seq

tag: cell line

tag: cell type

value: Normal Mammary Epithelial Cells


title: 10b_afterPRI-724


title: MCF10A Cells, Mutant R323, rep2


title: Platelets from TMEV-infected mice on day 7_6

value: Intracerebral TMEV infection

tag: time

value: 7 days post infection


title: shNR4A2_THP1 5% CO2_rep2

value: Human monocytic leukaemia_ THP1

tag: lentiviral particle_transduction


title: MCF10A Cells, Mutant R323, rep1


title: 10a_beforePRI-724


title: shNR4A2_THP1 5% CO2_rep1


title: MCF10A Cells, Mutant R158, rep3


title: 12a_beforePRI-724


title: Platelets from TMEV-infected mice on day 7_3

value: SJL/J

value: Female

value: Wild type


title: Platelets from TMEV-infected mice on day 7_4


title: MCF10A Cells, Mutant R158, rep2


title: shNT_control_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

value: non-target shRNA

value: 10% CO2 + LPS


title: shNT_control_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep2


title: 07b_afterPRI-724

value: F

value: HBV

value: B


title: Platelets from control mice on day 35_1

value: Platelets

value: Intracerebral PBS injection


title: shNR4A2_THP1 5% CO2_rep3

value: NR4A2 targeting shRNA


title: Platelets from TMEV-infected mice on day 7_1


title: shNT_control_THP1 10% CO2_rep3


title: Platelets from TMEV-infected mice on day 7_5


title: 06b_afterPRI-724

value: M

value: HCV

value: A


title: 07a_beforePRI-724

value: miRNA


title: MCF10A Cells, Mutant R158, rep1

value: Normal Mammary Epithelial Cells


title: shNT_control_THP1 10% CO2 + LPS (2.5ug/ml) (2hrs)_rep1

value: Human monocytic leukaemia_ THP1


title: Platelets from control mice on day 7_5

value: SJL/J

value: 7 days post injection


title: MCF10A Cells, Mutant R149, rep2


title: 06a_beforePRI-724


title: shNT_control_THP1 10% CO2_rep2


title: 02a_beforePRI-724


title: MCF10A Cells, Mutant R149, rep3


title: Platelets from control mice on day 7_4

value: Female

value: Wild type


title: shNT_control_THP1 10% CO2_rep1

value: non-target shRNA


title: 02b_afterPRI-724

value: F


title: MCF10A Cells, Wild Type, rep3

value: WT


title: MCF10A Cells, Mutant R149, rep1


title: shNT_control_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep3

value: 5% CO2 + LPS


title: shNT_control_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep2


title: MCF10A Cells, Wild Type, rep2


title: Platelets from control mice on day 7_2

value: Platelets


title: Platelets from control mice on day 7_1

value: Intracerebral PBS injection


title: MCF10A Cells, Wild Type, rep1


title: Platelets from TMEV-infected mice on day 4_5

value: Intracerebral TMEV infection

value: 4 days post infection


title: MCF10A Cells, Empty, rep2

value: E


title: Platelets from control mice on day 7_3


title: Platelets from TMEV-infected mice on day 4_4


title: shNT_control_THP1 5% CO2_rep1


title: Platelets from TMEV-infected mice on day 4_3


title: shNT_control_THP1 5% CO2 + LPS (2.5ug/ml) (2hrs)_rep1


title: MCF10A Cells, Empty, rep1


title: shNT_control_THP1 5% CO2_rep3


title: Platelets from TMEV-infected mice on day 4_6


title: PDX MG69, 50 mg/kg Futibatinib, replicate3

city: boston

first: Yuanli

last: Zhen

address: 185 cambridge street

department: cancer center

institute: mgh

data_processing:
For paired-end sequencing,image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
For single-end sequencing, read counts for individual genes were produced using count feature in HTSeq v. 0.6.0 (PMID: 35561197). Differential expression analysis was performed using the edgeR package v. 3.36.0 (PMID: 19910308) after normalizing read counts and including only genes with count per million reads (CPM) > 1 for one or more samples.
Assembly: For paired-end sequencing, homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. For single-end sequencing, RNA-seq reads were mapped to the hg19 reference genome using STAR v. 2.3.0 (PMID: 23104886).
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: cholangiocarcinoma

extract_protocol:
RNA was extracted from cultured cells or tumor tissues from PDX under different treatment conditions using the Rneasy Mini plus Kit (QIAGEN) in accordance with the manufacturer-prescribed protocol.
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: cholangiocarcinoma

tag: dose

value: 50 mg/kg

value: 14 days

value: Futibatinib

tag: bio replicate


title: DonC_Restim_Leishmania

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: hg19
Supplementary files format and content: .gene.mmseq files contain counts per gene

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were differentiated into resting macrophages by ex vivo culture in RPMI 1640 medium (Sigma Aldrich) with 10% Human Serum. Trained immunity was induced by exposing cells to Leishmania braziliensis for 24 hours.

extract_protocol:
Total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

tag: individual

value: Monocyte

value: Leishmania exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: DonC_Restim_RPMI

value: RPMI media only for 6 days, then exposed to LPS for 4 hours


title: PDX MG69, 50 mg/kg Futibatinib, replicate2


title: Platelets from TMEV-infected mice on day 4_1

tag: strain

value: SJL/J

tag: Sex

value: Female

value: Wild type


title: MCF10A Cells, Empty, rep3

value: Normal Mammary Epithelial Cells

tag: genotype


title: Platelets from TMEV-infected mice on day 7_2

tag: tissue

value: 7 days post infection


title: DonC_d6_Leishmania

value: Leishmania exposed for 24 hours, rested in media alone for 5 days


title: HUVEC cells - hypoxia_rep1

city: Shanghai

first: Qing-Wei

last: Zhang

address: Pujian Road 160

country: China

institute: Renji Hospital

description: Gene expression after hypoxia treatment for 24 hours

hyb_protocol: These labeled cDNA samples were used as probes to hybridize to microarrays for 17 h at 65°C using an Agilent Expression Hybridization Kit in hybridization chamber gasket slides (Agilent).

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Scanned images were imported into Agilent Feature Extraction software for grid alignment and data analysis

source_name: HUVEC cells

label_protocol: 0.2 µg of total RNA were reversely transcribed into cDNA using an RNA Spike In Kit with one-color (Agilent) in the presence of 0.8 uL of Random Primer and 2 uL of Spike Mix.These cDNA samples were then cleaned and labeled in accordance with the Agilent human microarray (OE Biotech human ceRNA microarray, design ID:086188, Agilent, Santa Clara, CA, USA) analysis protocol using Low Input Quick-Amp Labeling Kit, one-color (Agilent).

growth_protocol: HUVECs were cultured in the Endothelial Cell Medium (ECM) (ScienCell, USA) medium. Both cell lines were grown in an incubator at 37°C and in a 5% CO2 humidified environment.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: HUVECs were cultured in the noxia environment with Endothelial Cell Medium (ECM) or hypoxia (1% O2) environment with ECM or noxia environment with glucose-free ECM

value: HUVEC

value: Hypoxia


title: HUVEC cells - glucose deprivation_rep2

description: Gene expression after glucose deprivation for 24 hours

value: Glucose deprivation


title: PDX MG69, 50 mg/kg Futibatinib, replicate1


title: Neonate3, periphery, rep2

city: Los Angeles

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

description: 10X Genomics, snATAC-seq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: calJac4
Supplementary files format and content: Tab-separated values files and matrix files

organism: Callithrix jacchus

source_name: Retina

extract_protocol:
Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. They were dissociated in papain, followed by antibody staining and beads-enrichment or FACS sorting .
Foveal and peripheral retina tissues were dissected from neonatal and adult marmoset retinas. The foveal piece (~1.5mm in diameter) of the retina containing the whole fovea area was dissected out and dissociated into individual cells for high throughput droplet-based single cell RNA sequencing (scRNA-seq, 10x Genomics). The peripheral area (any area 5mm away from the foveal center) was also dissociated into a single cell suspension and underwent two enrichment procedures. We first used CD73, a photoreceptor marker, to label photoreceptors and used a microbeads-conjugated secondary antibody to deplete all the CD73 labeled cells (1). Second, we enriched RGCs and ACs with CD90 positive selection via fluorescence-activated cell sorting (FACS). The peripheral cells after CD73 depletion or CD90 enrichment were used to generate scRNA-seq libraries (10X Genomics). Libraries were sequenced on the Illumina HiSeq 2500 platform. The peripheral retinal tissues of an adult marmoset were snap frozen with dry ice. Nuclei were isolated with ice-cold Nuclei EZ lysis buffer and resuspended with 1%BSA/1X PBS. Nuclei were stained with anti-NeuN-PE (Millipore) for 30min at 4C. After washing and resuspension, the nuclei solution was additionally stained with Dyecycle Ruby (Thermo Fisher) before sorting. NeuN-positive and Dyecycle-positive nuclei were sorted via FACS. The sorted nuclei were used to generate single nuclei sequencing (snRNA-seq) libraries (10X Genomics) and were sequenced on the Illumina NovaSeq S4 platform.Frozen foveal and peripheral retinas were retrieved from a -80 °C freezer and placed on ice. Nuclei from these frozen samples were separately isolated using Lysis Buffer and Nuclei Isolation Columns from the Chromium Nuclei Isolation Kit (10X Genomics) following the Manufacturer’s User Guide. The isolated nuclei were then resuspended in Resuspension Buffer (10X Genomics). ScATAC-seq libraries were generated from the recovered nuclei using the Chromium Next GEM Single Cell ATAC Reagent v2 Kit (10X Genomics). The quantity and quality of the scATAC-seq libraries were evaluated using Qubit fluorometers (Thermo Fisher) and Tapestation (Agilent). ScATAC-seq libraries were sequenced on the Illumina Novaseq X Plus 10B platform.

value: Retina

value: Retinal cell types


title: DonC_d6_RPMI

value: RPMI media only, collected at 6 days post culture


title: Platelets from control mice on day 4_5

value: Platelets

value: Intracerebral PBS injection

value: 4 days post injection


title: Platelets from TMEV-infected mice on day 4_2

value: Intracerebral TMEV infection

value: 4 days post infection


title: shNT_control_THP1 5% CO2_rep2

value: Human monocytic leukaemia_ THP1

value: non-target shRNA


title: HUVEC cells - glucose deprivation_rep3


title: PDX MG69, vehicle, replicate2

value: cholangiocarcinoma

value: 14 days

value: vehicle


title: Neonate3, fovea, rep2

description: 10X Genomics, snATAC-seq


title: Platelets from control mice on day 4_4

value: SJL/J

value: Female

value: Wild type


title: DonC_d1_Leishmania

value: Monocyte

value: Leishmania exposed, collected at 24 hours post culture


title: PDX MG69, vehicle, replicate1


title: DonC_d1_RPMI

value: RPMI media only, collected at 24 hours post culture


title: Platelets from control mice on day 4_3


title: HUVEC cells - glucose deprivation_rep1

value: HUVEC

value: Glucose deprivation


title: Neonate3, periphery, rep1

description: 10X Genomics, snATAC-seq

value: Retina

value: Retinal cell types


title: Adult3, periphery, NeuN

description: 10X Genomics, snRNA-seq


title: Neonate3, fovea, rep1

description: 10X Genomics, snATAC-seq


title: HUVEC cells - hypoxia_rep2

value: Hypoxia


title: Platelets from control mice on day 4_2

value: Platelets

value: Intracerebral PBS injection

value: 4 days post injection


title: PDX MG212, 1 mg/kg pemigatinib, replicate 3

value: cholangiocarcinoma

value: 11 days

value: pemigatinib


title: HUVEC cells - control_rep1

description: Gene expression for controls

value: Control


title: DonC_d0

value: Baseline monocyte, attached to dish for 1  hour


title: HUVEC cells - control_rep3

description: Gene expression for controls


title: PDX MG212, 1 mg/kg pemigatinib, replicate 2


title: E11 cells, DMSO

city: Minato City

first: Kensuke

last: Sekiguchi

state: Please Select

address: 3-19-18 Nishishinbashi

institute: Jikei University

data_processing:
The quality control of the sequenced raw reads was analyzed. Overall reads' quality, total bases, total reads, GC (%) and basic statistics were calculated.
Biases in analysis were reduced by removing artifacts such as low-quality reads, adaptor sequences, contaminant DNA, or PCR duplicates.
Trimmed reads were mapped to the reference genome with HISAT2, a splice-aware aligner.
Assembly: mm10
Supplementary files format and content: Processed data files include raw counts, FPKM values, TPM values for each sample.

source_name: Kidney

growth_protocol: Mycoplasma-free E11 podocytes were propagated in 10 U/mL murine interferon-γ at 33°C and then differentiated by culture for 10-14 days at 37°C in the absence of interferon-γ28.

extract_protocol:
RNA was harvested using Trizol (Thermo).
TruSeq stranded mRNA was utilized in the preparation of RNA libraries for RNA-seq.

treatment_protocol: ROCK2 in hibition in podocytes were established by using a chemical inhibitor of ROCK2.

value: Kidney

value: Podocytes

value: DMSO


title: HUVEC cells - control_rep2

description: Gene expression for controls


title: DonB_Restim_Leishmania

value: Monocyte

value: Leishmania exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: E11 cells, SLx

value: SLx


title: KO87, chew diet, rep5

city: St. Louis

first: Irfan

last: Lodhi

state: MISSOURI

address: 660 S. Euclid Ave.

department: Endocrinology, Metabolism and Lipid Research

institute: Washington University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected
Assembly: mm10
Supplementary files format and content: space delimited text files include RPKM value for each feature and sample.

source_name: liver

growth_protocol: Control or ACOX1-LKO mice were feeding with chew diet in room temperature for 10 weeks.

extract_protocol:
Liver RNA was isolated using PureLinkRNA kit from Invitrogen.
RNA-seq libraries were indexed, pooled according to library kit manufacturer’s protocol.

value: liver

value: Chew diet

value: 10 weeks


title: DonB_Restim_RPMI

value: RPMI media only for 6 days, then exposed to LPS for 4 hours


title: PDX MG212, 1 mg/kg pemigatinib, replicate 1

description:
MG212-Pemi-1
This is a paired-end experiment but only the forward read file (R1) was available for submission to GEO/SRA.


title: DonB_d6_Leishmania

value: Leishmania exposed for 24 hours, rested in media alone for 5 days


title: CD45+ sorted tumor, L-fucose treated, day 21 VDJ

city: Tampa

first: Dongliang

last: Du

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

data_processing:
Sequencing reads were mapped against mm10 mouse transcriptome and processed for UMI counting using Cell Ranger (v3.0, 10X Genomics). Barcodes with UMI counts were imported to Seurat v4.0(Stuart et al., 2019) for downstream analysis. Cells with less than 200 genes detected, with greater than 10% mitochondrial UMIs, or with complexity score (log10GenesPerUMI) less than 0.8 were filtered out; genes detected in less than three cells were also excluded. Doublets were detected using Scrublet(Wolock et al., 2019), DoubletFinder(McGinnis et al., 2019), and scDblFinder(Germain et al., 2021), using 0.08% doublet rate for every 1000 cells. Cells identified as doublets by more than one method were removed. Raw UMI counts were log normalized and the top 5000 variable genes were detected in each sample separately. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring function. Individual mice samples were further integrated to remove batch effects using IntegrateData function (Hao et al., 2021) in Seurat with anchor.features =8000. Scaled z-scores for each gene were calculated using ScaleData regressing against total reads count, mitochondrial UMIs percentage, cell cycle phases, and log10GenesPerUMI. Principal component analysis was performed on the integrated data and a shared nearest neighbor (SNN) graph was constructed using the first 40 principle components. Clusters were identified using the by Louvain clustering (Blondel et al., 2008) implemented in FindClusters function at resolution=0.8. Uniform manifold approximation and projection (UMAP) was used to visualize gene expression and clusters. Differential expression analysis for each cluster was performed using FindAllMarkers function in Seurat with default settings. Clusters were further annotated by comparing differential genes with markers previously associated with T cells (Cd3e, Cd3d, Cd3g), B cells (Cd79a, Cd79b, Cd19), NK cells (Gzma, Klrb1c, Ncr1), cDC1 (Xcr1, Clec9a, Itgae, Batf3), cDC2 (Lilrb4a, Itgax, Csf1r, Mgl2), mregDC (Fscn1, Ccl22, Cacnb3, Ccr7, Fabp3), monoDC (Cd7, Atp1b1, Clec10a, Cd209d), Macrophages (C1qc, C1qb, Apoe), Monocytes (Plac8, Ly6c2, Arg1), Neutrophils (S100a9, S100a8, Mmp9), and Mast cells (Cpa3, Hdc, Ifitm1) (Supplementary Figure 6c). For marker gene bubble plot, gene-level average expression was calculated for each cluster and then Z-score normalized.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: SW1 melanoma tumors

extract_protocol:
For single-cell RNA sequencing of intratumoral immune cells, 4-6-weeks-old C3H/HeJ mice were injected subcutaneously into the right flank with 1x106 SW1 melanoma cells. After 10 days, a pretreatment mouse cohort (n=3) was sacrificed, and the harvested tumors were subjected to scRNAseq as the day 0 of L-fuc treatment timepoint. The remaining mice were administered either control (n=6) or 100nM L-fuc (n=6)-supplemented water ad libitum as previously described(Lau et al., 2015;Lester et al., 2023) for 7 or 21 days (tumor endpoint for harvest). Upon sacrifice, tumors were removed and CD45+ cells were isolated through sorting.
Tumors were harvested at 0, 7 or 21 days after the start of L-fuc treatment, and subjected to scRNAseq analyses by 10X Genomics Chromium Single Cell Controller for single-cell RNA-sequencing library preparation (10X Genomics, Pleasanton, CA). Reverse transcription was then performed on encapsulated individual cell droplets to generate cDNA and generate cDNA libraries. These libraries were sequenced using an Illumina NextSeq 500 instrument using v2.5 flow cells; a 10X Genomics CellRanger software was used for alignment and gene counting.

treatment_protocol: 4-6-week-old female C3H/Hej mice were injected with 1x10^5 SW1 cells subqutaneously into the right flank. After 10 days, the mice were supplied with either control (n=5) or 100mM L-fuc (n=5)-supplemented water ad libitum.

value: SW1 melanoma tumors

value: Lymphocytes

value: Intratumoral CD45+ cells

tag: time point

value: day 21

value: L-fucose water ad libitum


title: KO68, chew diet, rep3

tag: treatment


title: CD45+ sorted tumor, L-fucose treated, day 7 VDJ

value: day 7


title: CD45+ sorted tumor, control treated, day 7 VDJ

value: control water ad libitum


title: Platelets from control mice on day 4_1

value: SJL/J

value: Female

value: Platelets

value: Wild type

value: Intracerebral PBS injection

value: 4 days post injection


title: KO67, chew diet, rep2

value: liver

value: Chew diet


title: PDX MG212, vehicle, replicate 3

value: cholangiocarcinoma

value: 11 days

value: vehicle


title: DonB_d6_RPMI

value: Monocyte

value: RPMI media only, collected at 6 days post culture


title: PDX MG212, vehicle, replicate 2

description:
MG212-Vehicle-2
This is a paired-end experiment but only the forward read file (R1) was available for submission to GEO/SRA.


title: KO66, chew diet, rep1

value: 10 weeks


title: DonB_d1_RPMI

value: RPMI media only, collected at 24 hours post culture


title: PDX MG212, vehicle, replicate 1


title: ICC13-7 cells, 75 nm Futibatinib, 24 hours, replicate 3

value: Cholangiocarcinoma cell

value: 75 nm

value: 24 hours

value: Futibatinib


title: DonB_d1_Leishmania

value: Leishmania exposed, collected at 24 hours post culture


title: CD45+ sorted tumor, control treated, day 21 VDJ

value: SW1 melanoma tumors

value: Lymphocytes

value: Intratumoral CD45+ cells

value: day 21

value: control water ad libitum


title: DonB_d0

value: Baseline monocyte, attached to dish for 1  hour


title: WT95, chew diet, rep5

value: liver

value: WT

value: Chew diet


title: CD45+ sorted tumor, control treated, day 0 VDJ

value: day 0


title: CD45+ sorted tumor, L-fucose treated, day 7 RNA

value: day 7

value: L-fucose water ad libitum


title: WT91, chew diet, rep4

value: 10 weeks


title: ICC13-7 cells, 75 nm Futibatinib, 24 hours, replicate 2

value: Cholangiocarcinoma cell

value: 75 nm


title: CD45+ sorted tumor, L-fucose treated, day 21 RNA


title: DonA_Restim_Leishmania

value: Monocyte

value: Leishmania exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: ICC13-7 cells, 75 nm Futibatinib, 24 hours, replicate 1

value: 24 hours

value: Futibatinib


title: KO86, chew diet, rep4


title: WT88, chew diet, rep3


title: ICC13-7 cells, 75 nm Futibatinib, 12 hours, replicate 3

value: 12 hours


title: DonA_Restim_RPMI

value: RPMI media only for 6 days, then exposed to LPS for 4 hours


title: WT70, chew diet, rep2


title: DonA_d6_Leishmania

value: Leishmania exposed for 24 hours, rested in media alone for 5 days


title: ICC13-7 cells, 75 nm Futibatinib, 12 hours, replicate 2


title: WT69, chew diet, rep1


title: CD45+ sorted tumor, control treated, day 21 RNA

value: SW1 melanoma tumors

value: Lymphocytes

value: Intratumoral CD45+ cells

value: day 21

value: control water ad libitum


title: ICC13-7 cells, 75 nm Futibatinib, 12 hours, replicate 1


title: CD45+ sorted tumor, control treated, day 0 RNA

value: day 0


title: F1PreSet2S3: Bone Marrow-derived LSK cells from Prediseased mice

city: Athens

first: Αnastasia

last: Filia

address: Soranou Efessiou 4

country: Greece

institute: BRFAA

library_source: genomic

data_processing:
Raw reads were trimmed with Trim Galore! (v0.6.4) using the options –rrbs, –illumina and the default value for –quality (Phred score: 20).
This way, quality trimming is performed first, and adapter trimming is carried in a second round.
Further analysis of fastq files was performed with Bismark (v0.23.1) using the Bowtie2 dependency in three individual steps, genome preparation of mm10, alignment and methylation information extraction.
The bismark.cov.gz files produced from the latter step were then used in R with the methylKit package for further analysis, specifically to detect Differentially Methylated Regions (DMRs).
Assembly: mm10
Supplementary files format and content: text file which includes percentage of methylation per sample in the genome split in 1000bp tiles

molecule: genomic DNA

growth_protocol: HSPC were sorted from the F1-L BM and spleen, either treated with β-glucan or PBS.

extract_protocol: Libraries for RRBS were prepared according to a protocol as previously described (Luetke-Eversloh et al., 2014) with minor modifications.

treatment_protocol: Female 3-months-old NZBW/F1 mice were injected i.p. with either 1mg of  β-glucan peptide in 200uL of PBS or 200uL PBS  as control every 15 days, till the age of 6 months old.

tag: condition

value: Prediseased mice

value: hematopoietic stem and progenitor cells


title: ICC13-7 cells, 75 nm Futibatinib, 4 hours, replicate 3

value: Cholangiocarcinoma cell

value: 4 hours


title: DonA_d1_Leishmania

value: Monocyte

value: Leishmania exposed, collected at 24 hours post culture


title: hippocampus_HFFD_HFFD+HPH-6

city: Xi'an

first: Shuqing

address: West Changan Avenue

institute: Shaanxi Normal University

data_processing:
Next, we used Trimmomatic v0.38 to trim linker reads and filter low-quality reads to obtain Clean Reads. The Clean Reads were then mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6) using HISAT2 software. Subsequently, the comparison completion Clean Reads were assembled into transcripts. FeatureCounts software was used to calculate the expression level of each transcript in each sample and analyze the gene expression level by FPKM
Assembly: mm10
Supplementary files format and content: tab-delimited excel file includes raw counts for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted using a Trizol kit
A fragmentation buffer was added to randomly fragment the mRNA, and then use mRNA as a template to reverse-transcribe into cDNA. Double-stranded cDNA was purified using AMPure XP beads, end-repaired, and ligated to Illumina sequencing adapters to obtain the final cDNA library
The cDNA library was sequenced using Illumina Novaseq6000.

value: hippocampus

value: HFFD+HPH


title: F1PreSet2S2: Bone Marrow-derived LSK cells from Prediseased mice


title: hippocampus_HFFD_HFFD+HPH-5


title: DonA_d1_RPMI

value: RPMI media only, collected at 24 hours post culture


title: ICC13-7 cells, 75 nm Futibatinib, 4 hours, replicate 2

value: 75 nm

value: Futibatinib


title: F1PreSet2S1: Bone Marrow-derived LSK cells from Prediseased mice


title: ICC13-7 cells, 75 nm Futibatinib, 4 hours, replicate 1


title: PARDS-5

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality checks were performed using FastQC (v0.11.8), summarised with MultiQC (v1.9). Reads were then subsampled. Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (v2.7.6a) with default parameters. The counts of the aligned reads corresponding to exons were obtained using featureCounts program against the exon annotations obtained from the ensembl database (annotation file Homo_sapiens.GRCh38.98.gtf). MA plots, JSIs and PCA were performed as further quality checks.
The resulting expression values were normalised using quantile normalisation [Bolstad2003] and noise was removed using noisyR count matrix approach [Moutsopoulos2021].
Differential expression analysis was performed using edgeR (v3.28.1) [Robinson2010] and DESeq2 1.26.0 [Love2014].
The visualisation, and community accessible overview were complied using bulkAnalyseR [Moutsopoulos2021].
Enrichment analysis on the set of differentially expressed genes against a background of all genes expressed in the dataset using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.9) [Raudvere2009].
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: count matrix containing raw gene expression

growth_protocol: PSC-CMs were grown in serum free media (CMD-BSA or RPMI supplemented with B27) supplemented with 10% patient serum

extract_protocol: GenElute Mammalian total RNA Miniprep Kit

treatment_protocol: All serum samples were obtained from different patients and media with serum was refreshed every 48 hours

value: pluripotent stem cells derived cardiomyocytes (PSC-CMs)

tag: treated with

value: Plasma

tag: donor disease status

value: ARDS


title: F1PreDC: Bone Marrow-derived LSK cells from Prediseased mice


title: ICC13-7 cells, DMSO, replicate 3

value: 24 hours

value: DMSO


title: CD45+ sorted tumor, control treated, day 7 RNA

value: SW1 melanoma tumors

value: Lymphocytes

value: Intratumoral CD45+ cells

value: day 7

value: control water ad libitum


title: DonA_d0

value: Monocyte

value: Baseline monocyte, attached to dish for 1  hour


title: hippocampus_HFFD_HFFD+HPH-3

value: hippocampus


title: PARDS-4


title: ICC13-7 cells, DMSO, replicate 2

value: Cholangiocarcinoma cell


title: F1PreDA2: Bone Marrow-derived LSK cells from Prediseased mice

value: Prediseased mice

value: hematopoietic stem and progenitor cells


title: F1PreDA1: Bone Marrow-derived LSK cells from Prediseased mice


title: PARDS-3


title: hippocampus_HFFD_HFFD+HPH-2

value: HFFD+HPH


title: DonA_d6_RPMI

value: RPMI media only, collected at 6 days post culture


title: F1LupSet2S4: Bone Marrow-derived LSK cells from Lupus mice

value: Lupus mice


title: hippocampus_HFFD_HFFD+HPH-1


title: PARDS-2

value: pluripotent stem cells derived cardiomyocytes (PSC-CMs)

value: Plasma

value: ARDS


title: MHCC-97H cells, shNT_3

city: Wenzhou

first: Liang

last: Xu

state: Zhejiang

address: Chashan Higher Education Zone

department: School of Laboratory Medicine and Life Sciences

institute: Wenzhou Medical University

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:hisat2-2.2.1) 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-2.1.6) 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.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). 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 (NEB, cat.m0280, USA) 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 NovaseqTM 6000 following the vendor's recommended protocol.

value: liver

value: hepatocellular carcinoma cell

value: WT


title: PARDS-1


title: F1LupSet2S3: Bone Marrow-derived LSK cells from Lupus mice


title: hippocampus_HFFD_HFFD-5

value: HFFD


title: PCOV-5

value: Severe COVID


title: MHCC-97H cells, shNT_1


title: hippocampus_HFFD_HFFD+HPH-4


title: hippocampus_HFFD_HFFD-4


title: F1LupSet2S2: Bone Marrow-derived LSK cells from Lupus mice


title: PCOV-4


title: MHCC-97H cells, shRRP15_3

value: RRP15 knockdown


title: hippocampus_HFFD_HFFD-3


title: F1LupSet2S1: Bone Marrow-derived LSK cells from Lupus mice


title: 10 nM 1,25(OH)2D3, 24 h, Ind26

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description:
VitaminD_Ind26
24 h 10 nM 1,25D
125D_Ind26

data_processing:
Read alignment using STAR v2.7.2a using defualt parameters
Quantification using FastQC v0.11.9 and Featurecounts v2.0.1 using default parameters
Filtering for expressed protein coding genes and read counts normalization via EdgeR v4.0.14 (TMM-normalized CPM)
Assembly: hg38, Aligned to Ensembl annotation version 111, final annotation (via Biomart) to Ensembl version 111.38
Supplementary files format and content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)

source_name: peripheral blood mononuclear cells (PBMC)

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: Treatment for 24 h either with 1,25(OH)2D3 (10 nM) or solvent (0.1% EtOH).

tag: subject status

value: Healthy Individuals


title: MHCC-97H cells, shRRP15_2

tag: cell line


title: PCOV-3

tag: cell type


title: 10 nM 1,25(OH)2D3, 24 h, Ind23

description:
VitaminD_Ind23
24 h 10 nM 1,25D
125D_Ind23

value: peripheral blood mononuclear cells (PBMC)


title: hippocampus_HFFD_HFFD-2

value: hippocampus


title: ICC13-7 cells, DMSO, replicate 1

value: Cholangiocarcinoma cell

tag: time

value: 24 hours

value: DMSO


title: PCOV-2


title: MHCC-97H cells, shRRP15_1


title: hippocampus_HFFD_HFFD-1


title: 10 nM 1,25(OH)2D3, 24 h, Ind12

description:
VitaminD_Ind12
24 h 10 nM 1,25D
125D_Ind12


title: hippocampus_HFFD_HFFD-6


title: MHCC-97H cells, shNT_2


title: hippocampus_chow_diet_Control-6

value: Control


title: SC-7

source_name: Serum

value: Serum

value: COVID negative


title: 10 nM 1,25(OH)2D3, 24 h, Ind11

description:
VitaminD_Ind11
24 h 10 nM 1,25D
125D_Ind11


title: hippocampus_chow_diet_Control-5


title: 10 nM 1,25(OH)2D3, 24 h, Ind10

description:
VitaminD_Ind10
24 h 10 nM 1,25D
125D_Ind10


title: hippocampus_chow_diet_Control-4


title: hippocampus_chow_diet_Control-3


title: Infected, salt, shoot, biol rep 3

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

country: Spain

institute: CBGP (UPM-INIA/CSIC)

data_processing:
Novogene Novogene Co., LTD Genomics Service (Cambridge, UK)
Original image data files from the Illumina platform were transformed to sequenced reads by CASAVA base recognition.
Sequence reads were trimmed for the adaptor sequence/low-quality reads were deleted using a Novogene in-house script (quality parameter limit: 0.05)
Trimmed sequence reads were mapped against the TAIR10 Arabidopsis genome using hisat2 v2.0.5.
Read count extraction and normalization was performed using HTSeq v0.6.1 with ‐m union parameter.
Assembly: TAIR10 Arabidopsis genome
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Shoots

growth_protocol: Seedlings were grown vertically for seven days on 0.5x MS medium. Then, they were transferred to solidified Plant Nutrition Medium. Root and shoot tissue was harvested after seven days of co-cultivation.

extract_protocol:
DNA-free total RNA was extracted by employing the phenol/chloroform method described by Oñate-Sánchez & Vicente-Carbajosa, 2008, BMC Res. Notes.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations.

treatment_protocol: Each seedling was either mock-infected (50 µl water) or inoculated with 50 µl of a solution containing 2 x 105 spores ml-1.

value: Shoots

value: Fusarium sp. K-23 infected, Salt


title: Infected, salt, shoot, biol rep 2


title: Infected, salt, shoot, biol rep 1


title: Mock, salt, shoot, biol rep 3

value: Salt


title: 10 nM 1,25(OH)2D3, 24 h, Ind08

description:
VitaminD_Ind08
24 h 10 nM 1,25D
125D_Ind08


title: SC-4

value: pluripotent stem cells derived cardiomyocytes (PSC-CMs)


title: Mock, salt, shoot, biol rep 2


title: hippocampus_chow_diet_Control-2


title: SC-3


title: 10 nM 1,25(OH)2D3, 24 h, Ind07

description:
VitaminD_Ind07
24 h 10 nM 1,25D
125D_Ind07


title: Mock, salt, shoot, biol rep 1


title: hippocampus_chow_diet_Control-1


title: PCOV-1

value: Plasma


title: Infected, shoot, biol rep 3

value: Fusarium sp. K-23 infected


title: 10 nM 1,25(OH)2D3, 24 h, Ind06

description:
VitaminD_Ind06
24 h 10 nM 1,25D
125D_Ind06


title: 10 nM 1,25(OH)2D3, 24 h, Ind05

description:
VitaminD_Ind05
24 h 10 nM 1,25D
125D_Ind05


title: SB-6

value: Mild  COVID


title: SC-6


title: SB-5


title: 10 nM 1,25(OH)2D3, 24 h, Ind09

description:
VitaminD_Ind09
24 h 10 nM 1,25D
125D_Ind09


title: 10 nM 1,25(OH)2D3, 24 h, Ind04

description:
VitaminD_Ind04
24 h 10 nM 1,25D
125D_Ind04


title: Infected, shoot, biol rep 2


title: SC-5


title: PD3

first: Jiaoyao

last: Ma

state: Shanghai

address: No. 130, Dong'an Road, Xuhui District

institute: Fudan University

data_processing:
Fastq files were trimmed with Trimmomatic.
Clean reads were mapped to the mouse reference genome (mm10) using HISAT2, followed by transcript assembly using HTSeq and differential gene expression analysis using DESeq2.
Genes with adjusted p-values < 0.05 and fold change > 1.5 were marked as significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: raw counts for each Sample

source_name: inner ear organoid

growth_protocol: The inner ear organoid was cultured in low-attachment 24-well plates (Corning). The culture medium was composed of DMEM/F12 Glutamax supplemented with penicillin/streptomycin, N2, B27, EGF (20 ng/mL), bFGF (10 ng/mL),  IGF (50 ng/mL) and CHIR99021 (3 μM, Sigma), all from Thermo Fisher Scientific except CHIR99021 .

extract_protocol:
RNA was harvested using QIAzolLysisReagent (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA-Seq libraries of organoids were prepared with the  Illumina Stranded mRNA Prep kit (Ligation, Illumina).

treatment_protocol: The organoids were treated with PD0325901(1 μM, Sigma) or the same volume of DMSO, and the culture media were changed every 2 days.

value: inner ear organoid

value: epithelial cells

value: WT

value: 1 μM PD for 10 days


title: PD2


title: Infected, shoot, biol rep 1


title: PD1


title: Control3

value: same volume of DMSO for 10 days


title: 10 nM 1,25(OH)2D3, 24 h, Ind03

description:
VitaminD_Ind03
24 h 10 nM 1,25D
125D_Ind03

value: Healthy Individuals

value: peripheral blood mononuclear cells (PBMC)


title: SB-2


title: Mock, shoot, biol rep 3

value: Control


title: 10 nM 1,25(OH)2D3, 24 h, Ind02

description:
VitaminD_Ind02
24 h 10 nM 1,25D
125D_Ind02


title: Control2


title: SE-7

value: Serum

value: Severe COVID


title: SB-1


title: HUVEC cells - hypoxia_rep3

description: Gene expression after hypoxia treatment for 24 hours

value: HUVEC

value: Hypoxia


title: 10 nM 1,25(OH)2D3, 24 h, Ind01

description:
VitaminD_Ind01
24 h 10 nM 1,25D
125D_Ind01


title: SB-3


title: 0.1% EtOH, 24 h, Ind26

description:
Control_Ind26
24 h 0.1% EtOH
EtOH_Ind26

value: 0.1% ethanol for 24 h


title: 0.1% EtOH, 24 h, Ind23

description:
Control_Ind23
24 h 0.1% EtOH
EtOH_Ind23


title: Mock, shoot, biol rep 2

value: Shoots


title: Control1


title: PDX MG69, vehicle, replicate3

value: cholangiocarcinoma

value: 14 days

value: vehicle


title: SE-6

value: pluripotent stem cells derived cardiomyocytes (PSC-CMs)


title: Mock, shoot, biol rep 1


title: SE-5


title: Infected, salt, root, biol rep 3

source_name: Roots

value: Roots

value: Fusarium sp. K-23 infected, Salt


title: 0.1% EtOH, 24 h, Ind11

description:
Control_Ind11
24 h 0.1% EtOH
EtOH_Ind11


title: Infected, salt, root, biol rep 2


title: SE-3


title: SE-4


title: Infected, salt, root, biol rep 1


title: 0.1% EtOH, 24 h, Ind10

description:
Control_Ind10
24 h 0.1% EtOH
EtOH_Ind10


title: Mock, salt, root, biol rep 3

value: Salt


title: SE-2


title: Mock, salt, root, biol rep 2


title: LL2_NRF2KO.1 [N1D8.1]

city: Indianapolis

first: Ana

middle: S

last: Leal

state: IN

address: 980 W Walnut St

department: Department of Medicine

institute: Indiana University

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Read pseudo-alignment was completed with Kallisto read-mapping software v0.48.0
Tximport v1.26.1 R package was used to adjust count data for transcript length as counts per million (Length-scaled transcripts per million).
Gene ID annotated using Ensemble Mus Musculus GRChm39
Assembly: GRCm39
Supplementary files format and content: .txt file containing annotated length-scaled counts per million

growth_protocol: All LL2 cell lines were cultured in DMEM medium (Corning™) with 10% fetal bovine serum (FBS, VWR) and 1% Penicillin Streptomycin (Pen/Strep). Cells were cultured at 37C and 5% CO2.

extract_protocol:
RNA was isolated using Rneasy Miniprep Kit (Qiagen) per the manufacturer's protocol.
Total RNAs with a 260/280 ratio > 2.0 and 260/230 ratio >1.9 were submitted in biologic triplicates to the Van Andel Research Institute Genomics Core, who prepared libraries from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA).

value: Lung Cancer Cell Line

value: NRF2 KO


title: SE-1


title: 0.1% EtOH, 24 h, Ind09

description:
Control_Ind09
24 h 0.1% EtOH
EtOH_Ind09

value: Healthy Individuals

value: peripheral blood mononuclear cells (PBMC)


title: LL2_NRF2KO.2 [N1D8.2]


title: 0.1% EtOH, 24 h, Ind08

description:
Control_Ind08
24 h 0.1% EtOH
EtOH_Ind08


title: Mock, salt, root, biol rep 1


title: 0.1% EtOH, 24 h, Ind12

description:
Control_Ind12
24 h 0.1% EtOH
EtOH_Ind12


title: M_53_P

city: Melbourne

first: Jeremy

last: Anderson

address: 50 Flemington Rd, Parkville

department: Infection and Immunity

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the limma-voom pipeline. Genes with low expression (CPM <1) were removed from analysis, leaving expression data for 14,574 genes. limma-voom was used to normalise count data and determine gene expression differences between group comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .counts.txt files contain counts per gene

source_name: Cord blood

extract_protocol:
mRNA were extracted using the QIAGEN Rneasy mini-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 100ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

treatment_protocol: Samples were left unstimulated or stimulated with RSVA or RSVB for 24h

value: Cord blood mononuclear cells

tag: stimulation

value: Unstimulated

tag: preterm/term

value: Preterm

tag: gender

value: M


title: Infected, root, biol rep 2

value: Fusarium sp. K-23 infected


title: 0.1% EtOH, 24 h, Ind07

description:
Control_Ind07
24 h 0.1% EtOH
EtOH_Ind07

value: 0.1% ethanol for 24 h


title: 0.1% EtOH, 24 h, Ind06

description:
Control_Ind06
24 h 0.1% EtOH
EtOH_Ind06


title: LL2_NRF2KO.3 [N1D8.3]


title: Infected, root, biol rep 1


title: M_51_P

tag: individual


title: M_52_P

value: F


title: 0.1% EtOH, 24 h, Ind05

description:
Control_Ind05
24 h 0.1% EtOH
EtOH_Ind05


title: M_50_P


title: LL2_KEAPKO1.2 [K2B12.2]

value: KEAP KO #1


title: LL2_KEAPKO1.3 [K2B12.3]


title: 0.1% EtOH, 24 h, Ind04

description:
Control_Ind04
24 h 0.1% EtOH
EtOH_Ind04


title: LL2_KEAPKO1.1 [K2B12.1]


title: H3K18lac-L2C-G+N-L_rep1

value: Control


title: 0.1% EtOH, 24 h, Ind03

description:
Control_Ind03
24 h 0.1% EtOH
EtOH_Ind03


title: H3K18lac-L2C-G+N-L_rep2


title: M_49_P


title: LL2_KEAPKO2.1 [K3A3.1]

value: KEAP KO #2


title: M_48_P


title: Infected, root, biol rep 3

value: Roots


title: LL2_KEAPKO2.3 [K3A3.3]


title: M_47_P


title: 0.1% EtOH, 24 h, Ind02

description:
Control_Ind02
24 h 0.1% EtOH
EtOH_Ind02


title: 0.1% EtOH, 24 h, Ind01

description:
Control_Ind01
24 h 0.1% EtOH
EtOH_Ind01


title: M_46_P


title: LL2_KEAPKO3.1 [K3F10.1]

value: KEAP KO #3


title: cpl2-2, repl3

city: Singapore

first: Yu

state: Singapore

address: 1 Research Link national university of singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and lowqualityreads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The whole sequence was aligned to a single exon. The sequencing sequence was piecewise aligned to two exons of the genome. The sequencing sequence was segmented and aligned to more than three (including three) exons of the genome
Supplementary files format and content: genome TAIR10
Supplementary files format and content: xls file with gene count

growth_protocol: 23 ± 2°C, long days (16 hr light/8 hr dark)

extract_protocol:
The aerial parts of 9-day-old wild-type and cpl2-2 seedlings grown under LDs were harvested for total RNA extraction using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used to construct the library

value: seedlings

tag: age

value: CPL2 knock out

value: 23 ± 2°C, long days


title: cpl2-2, repl2


title: cpl2-2, repl1


title: M_45_P


title: HIV-C

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Single cell GE+Cell surface protein

data_processing:
Cell Ranger Suite (v3.1.0, https://support.10xgenomics.com) with refdata-cellranger-GRCh38-3.0.0 transcriptome as a reference was used to map reads on human genome (Hg38) using STAR.109 Samples from eight PLWH on ART and eight PLWoH controls were combined and cells expressing fewer than 500 genes and genes that were not expressed in at least one cell were discarded. There were 61,114 cells left after initial quality control. Seurat v3110 was used for clustering, marker identification, and visualization. Cell types were predicted against five human datasets as references using SingleR111 and a consensus resolution of clusters into six immune cell types was made. Of these, the B cell cluster (5,186 cells) was subset and re-clustered. Gene expression was used to investigate if the sub-clusters were all indeed B cells. Two sub-clusters lacked in expression of known B cell markers and instead expressed genes associated with dendritic cells and T cells, likely due to spill over from neighboring clusters and/or ambient RNA. These were excluded from the analysis. The R package scCustomize was used to visualize gene expression of select markers as estimated kernel densities.
Assembly: Hg38
Supplementary files format and content: cellRanger count matrix, feature, cell-ids

source_name: PBMCs

extract_protocol:
Samples were uniquely barcoded using TotalSeq-B human hashtag antibodies (BioLegend, San Diego, CA), as per manufacturer’s directions, to allow for sample multiplexing for the 10x Genomics Chromium Controller single-cell platform (10x Genomics, Pleasanton, CA). Specifically, 2 million PBMC of each sample were first blocked with Human TruStain FcX (BioLegend; catalog #422301), then incubated with 40ng of various anti-human hashtag antibodies carrying unique cell barcodes and 12-100ng of various CITE-seq antibodies, each previously optimized by flow cytometry. TotalSeq-B human CITEseq antibodies (BioLegend) used to subtype immune cells in the downstream data were: anti-human CD14 (#367145), anti-human CD16 (#302063), anti-human CD19 (#302263), anti-human CD20 (#302361), anti-human CD27 (#302851), anti-human CD3 (#300477), anti-human CD38 (#356639), anti-human CD4 (#300565), anti-human CD56 (#362561), anti-human HLA-DR (#307661), anti-human CD45RA (#304161), and anti-human CD8 (#344757). After washing and dead cell exclusion using EasySep™ Dead Cell Removal (Annexin V) Kit (Stem Cell; catalog #17899), a 10x G chip lane was super-loaded with a multiplexed pool of four uniquely barcoded samples, at a total of 40,000 single cells per lane with expected target recovery of 50%, five lanes were loaded in total.  Single-cell droplets were generated using the Chromium Next GEM single cell 3’ kit v3.1 (10x Genomics) on the 10x Genomics Chromium Controller.
cDNA synthesis and amplification, library preparation, and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics), according to the manufacturer’s instructions. Overall library size was determined using the Agilent Bioanalyzer 2100 and the High Sensitivity DNA assay, and libraries were quantitated using KAPA real-time PCR.
Each library consisting of four pooled samples was sequenced on the NextSeq 500 (Illumina) using a 75 base pair cycle sequencing kit (Illumina) and a paired-end run with the following run parameters: 28 base pair x 8 base pair (index) x 55 base pair.

value: PBMCs


title: LL2_KEAPKO3.2 [K3F10.2]

value: Lung Cancer Cell Line


title: HIV-D

description: Single cell GE+Cell surface protein


title: M_44_P

value: Cord blood mononuclear cells


title: WT, repl3

source_name: Col

value: WT Col


title: LL2_KEAPKO3.3 [K3F10.3]


title: HIV-A

description: Single cell GE+Cell surface protein


title: M_42_P

value: Unstimulated

value: Preterm


title: M_43_P


title: LL2_WT.2 [aWT.2]

value: WT


title: H3K18lac-L2C-G+N-L+A_rep2


title: M_41_P


title: WT, repl2


title: WT, repl1


title: LL2_KEAPKO2.2 [K3A3.2]


title: LL2_WT.1 [aWT.1]


title: NA_GBM_5_Far

city: Groningen

first: Anna

middle: Pilar

last: Ainslie

address: Antonius Deusinglaan, 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Sequencing read alignement Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the Lexogen BlueBee Genomics Platform
Trimmed sequence reads were mapped to GRCh38 using the Lexogen BlueBee Genomics Platform
Read count extraction and CPM normalization were performed using RStudio, DEG analysis was performed using the function "edgeR"
Assembly: hg38
Supplementary files format and content: tab-delimited text files of raw read counts

source_name: Brain

extract_protocol:
RNA was harvested from human brain tissue using the Qiagen RNA Lipid Tissue kit.
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) following manufacturer's protocols.

tag: disease

value: Glioblastoma multiforme

value: Brain

tag: brodmann area

tag: Sex

value: Male

tag: biomaterial provider

value: From NIH NeuroBioBank Maryland


title: Vivo-ADSCs3

city: chongqing

first: Chao

last: Wang

address: 136 zhongshan NO.2 road,yuzhong

institute: Children's hospital of chongqing medical university

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Assembly: Rnor_6.0
Supplementary files format and content: processsed data.xslx, count and fpkm values

organism: Rattus norvegicus

source_name: adipose tissue

growth_protocol: Subcutaneous inguinal adipose tissues were harvested from GFP-transgenic rats and then digested with 0.075% type 2 collagenase.  The digested cells were resuspended in DMEM/F12 containing 10% fetal bovine serum (FBS) (Gibco, USA) and 1% penicillin-streptomycin solution. ADSCs were incubated at 37°C in a humidified atmosphere containing 5% CO2. The medium was changed every 2 days, and adherent cells were passaged at a ratio of 1:2 until 80-90% confluence with TrypLE Express solution (Gibco, USA)

extract_protocol:
Total RNA was extracted by Trizol reagent according to manufacture' instruction.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’ s instructions.

treatment_protocol: Con-ADSCs: the 4th passage ADSCs isolated from GFP transgenic rat adipose tissue. Vitro-ADSCs: the 4th passage ADSCs traditionally cultured and passaged in a incubator, and collected at the same time point of the Vivo-ADSCs group. Vivo-ADSCs: the 4th passage ADSCs injected into adipose tissues of nude mice and re-isolated after 7 day of injection

tag: tissue

value: adipose tissue

value: primary ADSCs

value: Mesenchymal stem cells

tag: group

value: Vivo-ADSCs


title: HIV-B

description: Single cell GE+Cell surface protein


title: NA_GBM_4_Far

value: Female

value: From NIH NeuroBioBank Sepulveda


title: M_38_P

institute: Murdoch Children's Research Institute

value: F


title: Vivo-ADSCs1


title: DKAA-1-WT2h1

city: Saint Louis

first: Ruben

last: Nava

state: MO

address: 4590 Children’s Place

department: Department of Surgery

institute: Washington University in St Louis

data_processing:
Alignment, Cell Ranger V6, aligned to mm10 transcriptome
QC and Filtering, Seurat V4
Unsupervised Clustering, Seurat V4
Assembly: mm10
Supplementary files format and content: cellranger expression matrix

source_name: lung

extract_protocol:
Orthotopic left lung transplantation was performed from a B6 (CD45.2) donor into a B6 (CD45.1) recipient. Grafts were stored for 60 minutes at 4 ˚C with an additional 45 minutes at 28˚C prior to transplantation. The left lung was allowed to reperfuse for either 2 hours or 3 days prior to sacrifice and lung harvest. For the naïve sample, the left lung was harvested from a naïve B6 mouse. Single cell suspension was prepared as described above. For each sample, cells from two mice were pooled and were stained with CD45.2 (clone 104; Biolegend), CD45.1 (clone A20; Biolegend) and DAPI (BD Biosciences, 564907). Flow cytometric analysis and sorting were performed on a BD FACS Melody cell sorter.
Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics and Chromium Single Cell 3ʹ Reagent v1.1 kit from 10X Genomics

value: lung

tag: strain

tag: treatment

value: B6>B6 transplant 2h reperfusion


title: NA_GBM_2_Far


title: Vitro-ADSCs3

value: Vitro-ADSCs


title: DKAA-7-WT3d1

value: B6>B6 transplant 3d reperfusion


title: LL2_WT.3 [aWT.3]

value: Lung Cancer Cell Line

tag: genotype


title: M_37_P

value: Cord blood mononuclear cells

value: Unstimulated

value: Preterm

value: M


title: NA_GBM_3_Far

value: Glioblastoma multiforme

value: Brain

value: From NIH NeuroBioBank Maryland


title: Vitro-ADSCs2

value: adipose tissue

tag: cell line

value: primary ADSCs

value: Mesenchymal stem cells


title: Vitro-ADSCs1

tag: cell type


title: M_34_P


title: NA_GBM_4_Near2

value: Female

value: From NIH NeuroBioBank Sepulveda


title: DKAA-1-CTRL1

value: lung

value: naive


title: M_40_P

value: F


title: NA_GBM_1_Far


title: M_36_P


title: NA_GBM_5_Near2

value: Male


title: M_35_P


title: MDSC_DAB

city: Toronto

first: Tracy

last: McGaha

state: Ontario

address: 610 University Ave

department: Immunology

country: Canada

institute: University Health Network

description: 10x Genomics

data_processing:
Cellranger v7.0.0 with underlying Martian v4.0.8. was used to process the Chromium single cell GEX sequencing data
cellranger count was ran using SC5P-R2 chemistry, a reference transcriptome of refdata-gex-mm10-2020-A
Seurat v4.3.0 was on R v4.1.2  to preprocess the count matrix, and MNN was used for integrating the two samples
Code for preprocessing the 10x data can be found in the data availability statement of the associated paper
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: R rds file

source_name: Bone marrow

growth_protocol: Bone marrow cells differentiated in vitro into MDSC with 50 ng/mL GM-CSF and 50 ng/mL IL-6 for 4 days.

extract_protocol:
Single cell suspension of DMSO- or DAB-treated MDSC were washed twice in PBS and filtered through a 100μm cell strainer. Cell were then resuspended in PBS+0.04% BSA and loaded into the 10X Chromium Controller using the Chromium Next GEM Single Cell 5’ Kit v2 (10x Genomics).
Protocol number CG000331 RevB from 10X Genomics (User Guide, Chromium Next GEM Single Cell 5’ Reagent Kits v2, Dual Index) was used.

treatment_protocol: MDSC were differentiaed in presence of 1.5 μM Dabrafenib or matching volume of Dimethyl sulfoxide (DMSO).

value: Bone marrow

value: Myeloid-derived suppresor cells

value: 10 weeks

value: 1.5 μM  Dabrafenib


title: Vivo-ADSCs2

value: Vivo-ADSCs


title: NA_GBM_2_Near2

value: Glioblastoma multiforme


title: NA_GBM_3_Near2

value: Brain


title: M_31_P

value: Cord blood mononuclear cells

value: Unstimulated

value: Preterm


title: Control_5_Far

value: Unaffected control

value: From NIH NeuroBioBank Maryland


title: Con-ADSCs2

value: adipose tissue

value: primary ADSCs

value: Mesenchymal stem cells

value: Con-ADSCs


title: M_30_P

value: M


title: MCC progenitors, Emi2 mutant, Stage 26 Exp2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were mapped to v2 of the Xenopus laevis 9.2 genome using RNA-STAR. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
The aligned reads were then counted, normalized, and tested for differential expression using the HOMER software package from UCSD and edgeR. Differentially expressed genes were defined as having a false discovery rate (FDR) <0.05 and a log2 fold change >1 when comparing two experimental conditions.
For visualization purposes, RNA-seq reads were also mapped to the Xenopus laevis genome with bowtie2 and loaded as tracks into the IGV browser.
Genome_build: Xenopus laevis 9.2
Supplementary_files_format_and_content: Excel table containing normalized counts and differential expression statistics.

organism: Xenopus laevis

source_name: MCC progenitors

growth_protocol: Fertilized Xenopus eggs were injected with Cas9 protein along with a gRNA directed agains Emi2 to generate FO mutants.

extract_protocol:
At the equivalent of stage 17 and stage 26, total RNA was extracted using the proteinaseK method, followed by phenol:chloroform extraction, precipitation in 4M LiCl, resuspension in buffer, phenol-chloroform extraction, and ethanol precipitation.
RNAseq libraries were constructed with Illumina Truseq RNA Sample Preparation kit v2 according to the manufacturer’s instructions and sequenced on a HiSeq 2500 at 1x50 base pairs to a depth of 20-40 million reads.
Each RNAseq condition was performed in triplicate, using animal caps isolated from different females on different days.

treatment_protocol: Both wildtype and emi2 mutant embryos were injected at the 2-4 cell stage with an inducible multicilin (multicilin fused to the human glucocorticord receptor ligand binding domain).  At stage 10, skin progenitors were isolated (40 animal caps/sample) and treated with dexmethasone at stage 11 to induce multicilin activity, which converts most if not all of the cells into MCC progenitors.

value: Emi2 mutant

tag: Stage

value: Stage 26

value: MCC progenitors

tag: replicate


title: M_33_P

tag: stimulation

tag: preterm/term

value: F


title: lps4

city: Nanjing

first: Lu

address: 87 Dingjiaqiao Road

department: Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine

institute: Zhongda Hospital, School of Medicine, Southeast University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads per sample were generated.
Raw reads of fastq format were firstly processed using fastp (Shifu C, et al., Bioinformatics, 2018) and the low-quality reads were removed to obtain the clean reads.
The clean reads were mapped to the mouse genome (GRCm38) using HISAT2 (Kim D, et al., Nature Methods, 2015).
Transcript abundance was quantified by the fragments per kilobase million (FPKM), FPKM of each gene was calculated using a protocol from Roberts A et al., Genome Biology, 2011.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: monocyte

growth_protocol: Monocytes were isolated from tibias and femurs of C57BL/6J mice by negative selection using an EasySep Mouse Monocyte Isolation Kit (Stemcell technologies, Canada) following the manufacturer's procedures. The cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, USA), and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) 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 VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions.

treatment_protocol: Cells were treated with N-EC-EVs (ctr group) or L-EC-EVs (lps group) for 24 h.

value: monocyte

value: L-EC-EVs (lps group) for 24h


title: M_32_P

tag: individual

tag: gender


title: Control_4_Far

tag: disease

value: Brain

tag: age

value: Female


title: GBM, replicate 1, scATACseq

city: Los Angeles

first: Mingyi

last: Zhang

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

description: 10x Genomics

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the Cell Ranger ATAC pipeline
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: incisor

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Freshly collected proximal mouse incisor from control and Gli1-CreER;Arid1bfl/fl mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes. The prepared cells were tested for viability before process the extraction of nucleus. Cells viability  higher than 80% were used for the scATACseq.
Library was performed according to the manufacter's introduction (Chromium Next GEM Single Cell ATAC v1.1 ).

value: incisor

value: TMX induction


title: Ctrl, replicate 1, scATACseq

description: 10x Genomics

value: Control


title: MDSC_DMSO

description: 10x Genomics

value: Bone marrow

value: Myeloid-derived suppresor cells

tag: Sex

value: 10 weeks

value: DMSO


title: GBM, replicate 1, scRNAseq

description: 10x Genomics

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the CellRanger pipeline version 4.0
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
Freshly collected proximal mouse incisor from control and Gli1-CreER;Arid1bfl/fl mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes. The prepared cells were tested for viability before process the extraction. Cells viability  higher than 75% were used for the scRNAseq.
Library was performed according to the manufacter's introduction (Chromium Next GEM Single Cell 3ʹ v3.1 ).


title: MCC progenitors, Emi2 mutant, Stage 26 Exp3


title: NA_GBM_1_Near2

value: Glioblastoma multiforme

tag: brodmann area

tag: biomaterial provider

value: From NIH NeuroBioBank Maryland


title: lps3


title: Control_3_Far

value: Unaffected control

tag: tissue


title: M_28_T

value: Cord blood mononuclear cells

value: Unstimulated

value: Term

value: M


title: Con-ADSCs3

value: adipose tissue

value: primary ADSCs

value: Mesenchymal stem cells

tag: group

value: Con-ADSCs


title: MCC progenitors, Wildtype, Stage26 Exp3

value: Wildtype

value: Stage 26

value: MCC progenitors


title: MCC progenitors, Emi2 mutant, Stage 26 Exp1

value: Emi2 mutant


title: lps2

tag: strain

value: monocyte

tag: treatment

value: L-EC-EVs (lps group) for 24h


title: Control_2_Far

value: Brain

value: Female


title: M_27_T


title: MCC progenitors, Wildtype, Stage 26 Exp2

tag: genotype


title: Con-ADSCs1

tag: cell line

tag: cell type


title: lps1


title: Ctrl1, replicate 1, scRNAseq

description: 10x Genomics

value: incisor

value: Control

value: TMX induction


title: Control_1_Far

value: Unaffected control

value: Male

value: From NIH NeuroBioBank Maryland


title: MCC progenitors, Emi2 mutant, Stage 17 Exp3

tag: Stage

value: Stage 17

tag: replicate


title: M_29_T

value: Cord blood mononuclear cells

tag: stimulation

value: Unstimulated

tag: preterm/term

value: Term

value: M


title: M_25_T

tag: individual

tag: gender


title: MCC progenitors, Wildtype, Stage 26 Exp1

value: Wildtype

value: Stage 26

value: MCC progenitors


title: M_26_T


title: ctr4

value: monocyte

value: N-EC-EVs (ctr group) for 24h


title: ctr3


title: Control_4_Near2

tag: disease

value: Brain

tag: age

value: Female


title: Control_3_Near2

tag: brodmann area

tag: Sex


title: M_23_P

value: Preterm


title: Control_2_Near2

tag: tissue

tag: biomaterial provider


title: MCC progenitors, Emi2 mutant, Stage 17 Exp2

value: Emi2 mutant


title: ctr1

tag: strain


title: ctr2

tag: treatment


title: M_24_T

value: F


title: MCC progenitors, Wildtype, Stage 17 Exp3

tag: genotype


title: M_21_T


title: MCC progenitors, Wildtype, Stage 17 Exp2


title: M_20_T


title: E10.5 Msx1+ mesenchymal progenitors, replicate 1, scRNAseq

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

description: 10x Genomics

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
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: hindlimb buds

extract_protocol:
About 20 hindlimb buds were dissected from E10.5 Msx1-P2A-tdTomato mice. These limb buds were dissociated into single cells first and resuspended in PBS with 1% BSA. The sorted Msx1+ cells were both counted and adjusted to the concentration of about 1 × 10^6/ml. Then the suspension was centrifuged at 550g for 5 min at 4°C and repeated twice. Cells were counted and cell viability was confirmed by Countess II Automated Cell Counter (Thermo Fisher, Cat# AMQAX1000).
Samples were then used for single-cell RNA sequencing (scRNA-seq) with the 10× Genomics system (Library preparation and sequencing were performed by Berry Genomics Inc, Beijing).

value: Goblet cells

value: hindlimb buds

tag: cell population

value: Msx1+ cells

tag: developmental stage


title: RNaseL-/-, irradiation, rep3 [RL_KO_IR_3]

city: Beijing

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

description: Bone marrow was taken from RNaseL-/- mice 6 hours after total-body irradiation

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow

growth_protocol: Murine bone marrow was dissected and extracted 6 hours after total-body irradiation, then lysed with TRIzol reagent.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6N mice, which genotype is wildtype or RNaseL-/-, were performed total-body irradiation at a dose of 6Gy(a dose rate of 69 cGy/min) by a 60Co irradiator.

value: bone marrow

value: RNaseL-/-

value: Ionizing radiation


title: M_19_T

tag: cell type

value: Cord blood mononuclear cells

value: Unstimulated

value: Term

value: M


title: Control_5_Near2

value: Unaffected control

value: Male

value: From NIH NeuroBioBank Maryland


title: RNaseL-/-, irradiation, rep2 [RL_KO_IR_2]


title: M_18_T


title: MCC progenitors, Wildtype, Stage 17 Exp1

value: Wildtype

tag: Stage

value: Stage 17

value: MCC progenitors

tag: replicate


title: WS, PB-Mac, 1

city: Chiba

first: Naoya

last: Takayama

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Graduate School of Medicine

institute: Chiba University

data_processing:
Genomic coordinates of RTEs, along with their names, classes, and families, were downloaded from the UCSC Genome Browser using the Table Browser with “group” set to “Repeats” and “track” set to “RepeatMasker”
Each RTE was assigned reads obtained from the mapped RNA-seq samples within its genomic coordinates.
Read counts were normalized using limma.
Differentially expressed RTEs between sample groups were calculated using limma-voom.
Assembly: hg19

source_name: Peripheral blood-derived macrophages

extract_protocol:
Total RNA from untreated or oxLDL-treated healthy-, WS-, and gcWS-iMφs was isolated using an RNeasy Micro Kit (QIAGEN)
~10 ng total RNA was used as input for cDNA conversion using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (cat. #634890, Clontech, Takara). cDNA was fragmented using an S220 Focused-ultrasonicator (Covaris). The cDNA library was then amplified using a NEBNext® Ultra™ DNA Library Prep Kit for Illumina (cat. #E7370L, New England Biolabs).

value: Peripheral blood-derived macrophages


title: WS, PB-Mac, 2


title: K700K,AAVS1-KO,erythroid-differentiated,rep1

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

data_processing:
A genome annotation (UCSC hg19/GRCh37) was created by combining the UCSC knownGene (PMID: 24270787), Ensembl 71 (PMID: 23203987), and MISO v2.0 (PMID: 21057496) annotations. Transcriptome mapping was accomplished using RSEM v1.2.4 (PMID: 21816040) with the argument ‘‘-v 2’’ which indicates Bowtie invocation (PMID: 19261174). Unaligned reads were mapped to the genome with TopHat v2.0.8b (PMID: 19289445), and to a custom annotation which includes all gene-level pairwise combinations of annotated 5’ and 3’ splice sites. The combined RSEM/Bowtie and TopHat alignments were inputted to MISO v2.0 (PMID: 21057496) to quantify isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text-file includes raw isoform counts for each sample: isoform.expression.5.txt

source_name: CD34+ Cord Blood

extract_protocol:
CD34+ cells from cord blood were CRISPR/Cas9-edited to introduce an endogenous SF3B1 K700E mutation (SF3B1 K700E/+) or have no mutation (SF3B1 +/+; AAVS1 edited as a negative control)and expanded in culture.  2 days after editing, BFP+ CD34+ cells were sorted into Trizol and RNA isolated. The remainder of CD34+ cells were differentiated into erythroid cells for 7 days. BFP+ CD71+ CD235a+ erythroid cells were sorted into Trizol and RNA isolated.
Poly(A)-selected, strand-specific (dUTP method) Illumina libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) (input of 10 ng RNA was used for samples with >10 ng available; for samples with <10 ng available, entire amount was used for library prep) l and sequenced on the Illumina HiSeq 2000 to obtain∼60-80M paired-end 151 bp reads per sample.

value: CD34+ Cord Blood


title: MCC progenitors, Emi2 mutant, Stage 17 Exp1

value: Emi2 mutant


title: RNaseL-/-, irradiation, rep1 [RL_KO_IR_1]


title: Wildtype, irradiation, rep3 [WT_IR_3]

description: Bone marrow was taken from wildtype mice 6 hours after total-body irradiation


title: M_17_T

state: Victoria

tag: stimulation

tag: preterm/term


title: Healthy, PB-Mac, 2


title: Healthy, PB-Mac, 1


title: K700K,AAVS1-KO,erythroid-differentiated,rep2


title: Control_1_Near2

value: Brain


title: K700K,AAVS1-KO,non-differentiated,rep2


title: M_15_T

tag: individual

tag: gender

value: F


title: Wildtype, irradiation, rep2 [WT_IR_2]

value: bone marrow


title: M_14_T


title: gcWS, iMac, oxLDL, pos, 3

description: iPS_macrophage_limma_lcpm_padj0.01_lfc1.txt

source_name: iPSC-derived macrophages

value: iPSC-derived macrophages

value: oxLDL


title: M_16_T

value: Cord blood mononuclear cells

value: Unstimulated


title: Wildtype, irradiation, rep1 [WT_IR_1]

value: Ionizing radiation


title: K700K,AAVS1-KO,non-differentiated,rep1


title: gcWS, iMac, oxLDL, pos, 2


title: RNaseL-/-, control, rep3 [RL_KO_3]

description: Bone marrow was taken from RNaseL-/- mice

value: RNaseL-/-

value: No treatment


title: K700E,GPATCH8-KO,erythroid-differentiated,rep2


title: M_13_T

value: Term

value: M


title: gcWS, iMac, oxLDL, pos,1


title: K700E,GPATCH8-KO,erythroid-differentiated,rep1


title: RNaseL-/-, control, rep2 [RL_KO_2]


title: RNaseL-/-, control, rep1 [RL_KO_1]


title: WS, iMac, oxLDL, pos, 4


title: K700E,GPATCH8-KO,non-differentiated,rep2


title: WS, iMac, oxLDL, pos, 3


title: K700E,AAVS1-KO,erythroid-differentiated,rep2


title: K700E,GPATCH8-KO,non-differentiated,rep1


title: WS, iMac, oxLDL, pos, 2


title: M_11_T


title: Wildtype, control, rep3 [WT_3]

description: Bone marrow was taken from wildtype mice

value: Wildtype


title: M_9_T


title: M_10_T


title: M_12_T


title: Healthy, iMac, oxLDL, pos, 2


title: Wildtype, control, rep2 [WT_2]


title: M_5_P

value: Preterm


title: WS, iMac, oxLDL, pos,1


title: Healthy, iMac, oxLDL, pos, 3


title: ob_ob_ETS_3

city: Seoul

first: Seung Min

last: Jeong

address: 222, Banpo-daero, Seocho-gu

department: Department of Biochemistry

country: South Korea

institute: College of Medicine, The Catholic University of Korea

description: allograft tumor from C57BL/6J-ob/ob, post chemotherapy

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell from allograft tumor (B16F10 cell)

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: post chemotherapy


title: M_4_T


title: K700E,AAVS1-KO,non-differentiated,rep1

value: CD34+ Cord Blood


title: Wildtype, control, rep1 [WT_1]


title: ob_ob_ETS_4


title: K700E,AAVS1-KO,erythroid-differentiated,rep1


title: K700E,AAVS1-KO,non-differentiated,rep2


title: M_3_T