title: COBRA_8444K_LPS


title: Overexp_CS8M_Vessel_rep2

status: Public on Apr 01 2024

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: 2 µg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

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

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

molecule: total RNA

organism: Mus musculus

source_name: Microdissected structures/cells, lung vessels and septa compartment

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2 µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

growth_protocol: Lung samples are harvested from animals that were exposed to cigarette smoke for 3 months.

extract_protocol: Laser microdisected septa and vessel compartment; Qiagen Rneasy Micro Kit.

treatment_protocol: 3 months time point: Room Air (RA) or Cigarette Smoke (CS) Exposure; Wt, Fgf10+/-, Fgfr2b+/- animals.  Therapeutic approach: 8 months of RA / CS Exposure followed by 1 week of treatment (+/- doxycycline)

tag: fgf10 expression

value: overexpressing

tag: treatment

value: cigarette smoke

tag: compartment

value: Vessel


title: Control_CS8M_Vessel_rep5

value: wild-type


title: Control_CS8M_Vessel_rep3


title: Control_RA8M_Vessel_rep5

value: room air


title: Overexp_CS8M_Vessel_rep1


title: Control_CS8M_Vessel_rep4


title: Control_CS8M_Vessel_rep2


title: NaraCOVID_TP1_CD4_020_TCR

type: SRA

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

library_source: transcriptomic

data_processing:
Data processing of Bulk TCRseq was performed as described in Aoki et al. (Aoki et al., 2021).
Adapter trimming and quality filtering of sequencing data were performed using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. In MiXCR, filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system. The Variable (V) and Joining (J) segments of TCRs were represented in IMGT gene nomenclature. T-cell clones were determined as TCR reads with the same TCR V segment, J segment, and CDR3 nucleotide sequence.
Inter-sample contamination within samples using same UDIs were excluded by "Decontaminate" function of vdjtools with the parameter "-r 10".
For bulk TCRseq data, we regarded the CD4+-CD8+ overlapping clones in the same participant as contamination during T-cell isolation from PBMC because CD4+ and CD8+ T-cell repertoire are mutually exclusive (Aoki 2021). Thus, these overlapping clones were categorized into either CD4+ or CD8+ according to their dominance in CD4+ and CD8+ repertoire using VDJtools-1.2.1. The sequencing reads of bulk TCR-seq samples were normalized to 100,000 reads by the ?DownSample? command of VDJtools-1.2.1. To preserve the minor clonotypes, we performed the normalization ten times and pooled these down-sampled repertoire data for each sample, by ?JoinSamples? command of VDJtools-1.2.1.
Assembly: IMGT reference sequences of human TRA and TRB
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

organism: Homo sapiens

source_name: Peripheral blood T cells

extract_protocol:
PBMCs were isolated from whole blood with BD vacutainer CPT tubes (BD), resuspended in CELLBANKER 1 (Takara), and stored in -80°C
CD4+ and CD8+ T cells were magnetically isolated from PBMC. PBMC were thawed by warming frozen cryovials in a 37°C water bath. Cells were stained for 20 minutes at 4°C with 1st antibody mix (Antibody Mix 1 in Supplementary Table S1). After washing with MACS buffer [0.5% BSA (Nacalai), 2 mmol/L EDTA (NIPPON GENE) in PBS (Nacalai)], Cells were stained for 20 minutes at 4°C with 2nd antibody mix; BD IMag anti-PE Magnetic Particles-DM (Clone E31-1459, BD) and anti-APC-Biotin (clone APC003, BioLegend). Then, the cell suspension was diluted with MACS buffer and set on a magnet plate (DynaMag96SideSkirted, Veritas). The positive fraction was collected as CD4+ T cells. The negative fraction was stained with BD IMag Streptavidin Particles Plus-DM (BD) for 20 minutes at 4°C. Then, the cell suspension was diluted with MACS buffer and set on a magnet plate. The positive fraction was collected as CD8+ T cells and B cells. The counts of CD4+ T cells, CD8+ T cells, and B cells were determined using Flow-Count fluorospheres (Beckman) and a Cytoflex flow cytometer (Beckman) and FlowJo software (version 10.8.1; BD Biosciences).
Bulk TCR sequencing library was prepared according to the previous report (Aoki et al., 2023).  In brief, mRNA in T-cell lysates were captured by incubating with 10 ?L of Dynabeads M270 streptavidin (Thermo Fisher Scientific) bound to 2.5 pmol of BioEcoP-dT25-adapter primers for 30 minutes at room temperature under gentle rotation. mRNA-trapped beads were suspended in 10 µL of RT mix and incubated for 60 min at 42ºC to perform reverse transcription (RT) and template-switching. The composition of the RT mix was as follows; 1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2 (NIPPON GENE), 1 U/µL RNaseIn Plus RNase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1 µM of i5-TSO. To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed using KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), followed by the purification of PCR product using an AM Pure XP kit (Beckman Coulter) at a 0.7:1 beads-to-sample ratio. The third PCR was performed to amplify TCR libraries and add adaptor sequences for the next-generation sequencer. The third-PCR products were purified as second PCR. Final TCR libraries, whose lengths were about 600 base pairs, were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems), and size distribution was analyzed by Microchip Electrophoresis System MultiNA (Shimadzu). TCR libraries were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina) using NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles, Illumina). Only read2 contained the sequence regarding the definition of T-cell clones. Oligonucleotides and reaction conditions for library preparation were summarized in Table S2 and S3, respectively.

treatment_protocol: Thirty-eight healthcare workers (≥20 years old) at Nara Medical University in Japan received two doses of Pfizer-BNT162b2 vaccine between 10 March and 30 March 2021.

value: Three shots of Pfizer-BNT162b2 vaccine

tag: cell type

value: CD4+ T cells

tag: age

tag: Sex

value: female

tag: date

value: before receiving the first dose


title: COBRA_8444K_RPMI

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 100-bp paired end 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.txt files contain counts per gene

source_name: Adolescent Human Peripheral Blood

growth_protocol: We performed two cohort studies ('COBRA' for adolescents with obesity and 'PAID' for controls) and isolated PBMCs. Following PBMC isolation we further purified the monocytes using a magnetic bead isolation method (negative isolation)

extract_protocol:
500.000 cells of the monocyte-enriched cell suspension were used for RNA extraction (250.000 for medium stimulated, 250.000 for LPS stimulated). The cells were spun down at 500g for 5 minutes. Supernatant was removed and the cell pellet was resuspended with 500µL TrIzoL solution. The resuspended solution was stored at -80C until RNA isolation. RNA was isolated using RNeasy Micro Kit (Qiagen) with adaptation of the first step for TriZOL samples, according to manufacturer’s protocol, and included on column DNAse treatment.
RNA quality was assessed on the Agilent 2100 analyzer. cDNA library construction and sequencing were performed at Beijing Genomics Institute using the BGISEQ-500 platform with a starting input of 200ng. Libraries were sequenced on the BGISeq-500 platform generating an average of 20 million reads per sample.
To infer gene expression levels, RNA-seq reads were aligned to hg19 human transcriptome using Bowtie. Quantification of gene expression levels as RPKM was performed using MMSEQ. Reads/transcripts were normalized using DEseq2 and pair-wise comparisons were performed.

tag: tissue

value: Adolescent Human Peripheral Blood

tag: individual

value: Monocyte

tag: group

value: COBRA

value: Negatively selected circulating monocytes exposed to media in vitro for 4 hours


title: COBRA_2972E_LPS

value: Negatively selected circulating monocytes exposed to LPS in vitro for 4 hours


title: R3_ams_B22_TACGCTAGTT-TTAGTCTGCT

city: Urbana

first: Gene

middle: E.

last: Robinson

state: IL

address: 1206 W. Gregory Dr. M/C 195

department: Carl R. Woese Institute for Genomic Biology

country: USA

description: oral antagomir treatment

data_processing:
Aligned FASTQ files to honey bee genome and deformed wing virus reference with STAR 2.7.6a
Counts were generated with the "featureCounts" function in Subread 2.0.0
Assembly: HAv3.1

organism: Apis mellifera

source_name: whole brain

growth_protocol: Adult worker honey bees were collected from apiaries at the University of Illinois at Urbana-Champaign Bee Research Facility in Urbana, IL. All workers used were produced from colonies headed by queens inseminated with the sperm from a single drone.

extract_protocol:
Abdominal fat body: abdomens were separated from the bodies and placed in 500ul RNAlaterICE (Life Technologies) at -20ºC for 14 to 18 h. Abdomens were then opened and guts and sting apparatus gently removed. The remaining intact fat body tissue connected to the cuticle was placed in a 1.5ml tube and stored frozen (-80°C) until RNA extraction. Brains: bee heads were separated from the bodies and placed in a pure ethanol in a dissection dish chilled on dry ice to prevent RNA degradation during dissection. The cuticle of the anterior head capsule (frons) was removed and each head placed in 300ul of RNAlaterICE at -20ºC for 14 to 18 h. Heads were then opened, hypopharyngeal glands removed, and whole brain collected. Brains were place in 1.5ml tube and stored frozen (-80°C) until RNA extraction. Total RNA extraction for both abdominal fat body and whole brain was performed with miRNeasy Mini Kits (Qiagen) and C. elegans miR-39 spike-in (Qiagen) at the tissue homogenization step for other downstream analyses (qPCR).
RNA-Seq libraries were prepared with Kapa Hyper Stranded mRNA library kit (Roche). Libraries were pooled and sequenced on one S4 lane for 151 cycles  from both ends of the fragments on a NovaSeq 6000 (Illumina). Reads are 150 nt.

treatment_protocol: Age-matched, 1-day old adults workers were collected, paint-marked for identificiation, and replaced into a colony for typical development. As 3-days old, paint-marked bees were recaptured and food removed for 1 hr prior to oral treatment. For the antagomir treatment, bees were cold-anesthetized on wet ice, immobilized, and allowed to reanimate before being fed 1,000 pmol of antagomir (ame-miR-305 or missense construct) suspended in 4 ul of 30% sucrose solution. Bees were immediately placed in individual cages to prevent oral treatment sharing via trophallaxis and provisioned ad libitum with 30% sucrose to prevent the introduction of  plant factors in honey or pollen. Bees were placed in an incuabtor (34°C, 50% relative humidity) for 48h and then flash-frozen in liquid nitrogen.

tag: caste

value: worker

value: brain

value: antagomir-missense

tag: colony


title: R3_ams_B21_CAGGTCGTAA-TTATGCCTTC

institute: University of Illinois at Urbana-Champaign

description: oral antagomir treatment


title: R3_ams_B19_AGGCGTCTGA-CACAAGATCC

description: oral antagomir treatment


title: R3_ams_B20_ACTTACGAGG-GTTAATCGCT

description: oral antagomir treatment


title: Cntrl_198_LPS

value: control


title: NaraCOVID_TP1_CD4_017_TCR

value: male


title: Cntrl_148_LPS


title: NaraCOVID_TP1_CD4_018_TCR


title: Control_RA8M_Vessel_rep4

value: Vessel


title: Cntrl_148_RPMI


title: Overexp_CS8M_Vessel_rep4

value: overexpressing

value: cigarette smoke


title: Control_CS8M_Vessel_rep1

value: wild-type


title: R3_ams_B18_GCGTGACGTT-TAGAAGAGAG

description: oral antagomir treatment


title: NaraCOVID_TP1_CD4_016_TCR

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells


title: NaraCOVID_TP1_CD4_019_TCR

value: female

value: before receiving the first dose


title: WT_CS_Vessel_rep4


title: WT_CS_Vessel_rep5


title: Cntrl_256_LPS

value: Adolescent Human Peripheral Blood

value: Monocyte


title: R3_ams_B17_GTGTACTCAA-AAGCAACCTT

description: oral antagomir treatment


title: R3_ams_B16_CGAGTCCGTT-ACTACTGCGG

description: oral antagomir treatment


title: Cntrl_198_RPMI

value: Negatively selected circulating monocytes exposed to media in vitro for 4 hours


title: NaraCOVID_TP1_CD4_014_TCR


title: WT_CS_Vessel_rep3


title: NaraCOVID_TP1_CD4_015_TCR


title: Cntrl_256_RPMI


title: WT_RA_Vessel_rep5

value: room air


title: R3_ams_B15_TTGTAAGAGG-CAGCTGCTTC

description: oral antagomir treatment

value: worker


title: NaraCOVID_TP1_CD4_012_TCR


title: R3_ams_B13_CGATTGTTCT-TGGTTGTACA

description: oral antagomir treatment

value: brain


title: Cntrl_300_RPMI


title: NaraCOVID_TP1_CD4_013_TCR


title: NaraCOVID_TP1_CD4_011_TCR


title: R3_ams_B14_TCGGCTACTG-CACACAATAG

description: oral antagomir treatment

value: antagomir-missense


title: hMSCs_Ctrl-3

city: Guangzhou

first: Yan

last: Huang

address: No. 135, XIngang Street

country: China

institute: Sun Yat-sen University

data_processing:
CLC Genomics Workbench y 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequenceusing CLC genomic benchwork (parameter- Quality limit: 0.05)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human Mesenchymal stem cells

growth_protocol: DMEM/F12, 10% fetal bovine serum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RlA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

treatment_protocol: Rosa roxburghii fruit extracts were disolved in PBS to make 100 ug/mL stock. The final concentration is 100 ng/mL. PBS is added as the control.

value: human Mesenchymal stem cells

tag: genotype

value: WT

value: PBS control


title: R3_a305_FB24_TGCTTGTGGT-CCTCGGTAGT

description: oral antagomir treatment

source_name: abdominal fat body

value: fat body


title: Control_RA8M_Vessel_rep2

value: Vessel


title: NaraCOVID_TP1_CD4_010_TCR

value: male


title: Control_RA8M_Vessel_rep1

value: wild-type


title: hMSCs_Ctrl-2


title: NaraCOVID_TP1_CD4_008_TCR

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells


title: FGF10_CS_Vessel_rep5

value: knock-down

value: cigarette smoke


title: hMSCs_Ctrl-1


title: R3_a305_FB22_CGTCCATGTA-CGAGCACTTA

description: oral antagomir treatment


title: hMSCs_CL-3

value: Rosa roxburghii fruit extracts


title: R3_a305_FB23_CTAACTGCAA-CTACGATGTG

description: oral antagomir treatment


title: Control_RA8M_Vessel_rep3


title: NaraCOVID_TP1_CD4_007_TCR

value: before receiving the first dose


title: FGF10_CS_Vessel_rep3


title: Cntrl_300_LPS

value: Adolescent Human Peripheral Blood

value: Monocyte

value: control

value: Negatively selected circulating monocytes exposed to LPS in vitro for 4 hours


title: R3_a305_FB21_ACTGTCTATC-GTCCACGTTG

description: oral antagomir treatment

value: worker


title: FGF10_RA_Vessel_rep4

value: room air


title: R3_a305_FB20_GCCTGTCCTA-AGCGGTCTTC

description: oral antagomir treatment


title: NaraCOVID_TP1_CD4_006_TCR


title: hMSCs_CL-2

value: human Mesenchymal stem cells

value: WT


title: NaraCOVID_TP1_CD4_005_TCR


title: hMSCs_CL-1


title: R3_a305_FB19_GCAAGCACCT-CGTCAGGATA

description: oral antagomir treatment

value: fat body


title: R3_a305_FB18_TCCGCATAGC-TGCCTTGCGT

description: oral antagomir treatment


title: NaraCOVID_TP1_CD4_003_TCR

value: male


title: p320_U6DDR_Taq_Rep3

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

library_source: other

data_processing:
PCR-mediated template switching, involved the extraction and merging of barcodes from the paired-end sequencing library based on sequencing identification (ID). Paired barcodes underwent pairwise alignment and were compared with a reference barcode list to determine matched, switched, and randomly occurring errors.
The mapping of each paired library to the reference DNA template was executed using CRISPResso2 and stored in BAM files.
The ID and Cigar information were extracted and generated into TXT files, which were then merged with the matched file containing barcodes identified by ID.
Gene information was incorporated based on the sgRNA spacer sequence.
For the analysis of repair outcomes, it was assumed that the Double-Strand Breaks (DSB) occurred within ±10bps of the ideal break site. This implies that the deletion window must overlap with the DSB window, and all insertions must reside within this DSB window.
Assembly: hg19, pMCB320-DDR, pMCB320-RuDDR
Supplementary files format and content: tab delimited text files contain the pairwise alignment information including: the index, the barcode 1 (sequence_x), sequence identity (ID), length of barcode 1 (len_x), the barcode 2 or the spacer (sequence_y), length of barcode 2 (len_y), the reverse complement of barcode 2 (sequence_y_rcp) and the alignment score between barcode 1 and the barcode 2 (Align_score).
Supplementary files format and content: tab delimited text files contain the filtered, annotated mapping information including: the Index, the sequencing identity (ID), the barcode 1 (barcode), the barcode 2 or sgRNA spacer (seq_exp), the alignment score between barcode 1 and barcode 2 (Align_score), the gene name (Symbol), the mapping to a 362bp region of interest in the reference template (Cigar), the length of deletion (D_length),  the position of deletion (D_location), the length of insertion (I_insertion), the position of insertion (I_location).
Library strategy: Dual-barcode Repair-Seq

molecule: other

organism: Escherichia coli

source_name: Endura Electrocompetent cells

growth_protocol: K562-iCas9-DDR cell line was cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
DDR libraries were constructed through a two-step PCR process. In the initial PCR, outer layer primers (DDR-lib-F1 and DDR-lib-R1) were employed to amplify the regions of interest. Subsequently, in the second PCR, I5-DDR and I7-DDR primers were used to tag the libraries, which were then purified through electrophoresis and a gel-extraction kit.

treatment_protocol: G1/G0-arrested K562-iCas9-DDR cell lines were treated by 50 μM Palbociclib. The cycling and G1/G0-arrested cells were transduced with Cas12a plus DDR1-crRNA nucleoproteins to generated twined  DSBs in different compound-treated conditions.

tag: cell line

value: Endura Electrocompetent cells

value: Bacteria

value: recA13 supE44 ara-14 galK2 lacY1 proA2 rpsL20(StrR) xyl-5[lambda]- leu mtl-1 F- mcrB mrr hsdS20(rB-, mB-)

value: Transformation

tag: polymerase

value: Taq


title: FGF10_CS_Vessel_rep2

value: knock-down

value: cigarette smoke

value: Vessel


title: NaraCOVID_TP1_CD4_002_TCR

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells

value: before receiving the first dose


title: FGF10_CS_Vessel_rep4


title: FGF10_RA_Vessel_rep3


title: p320_U6DDR_Taq_Rep2


title: p320_U6DDR_Taq_Rep1


title: WT_RA_Vessel_rep4

value: wild-type


title: NaraCOVID_TP1_CD4_001_TCR


title: R3_a305_FB16_CTGTACGGTA-CGTACCTTCC

description: oral antagomir treatment

value: worker


title: p320_U6DDR_Plat_Rep3

value: Platinum


title: R3_a305_FB15_CTCTCGAGGT-TAAGGCATAG

description: oral antagomir treatment


title: p320_U6DDR_Plat_Rep2


title: FGF10_RA_Vessel_rep2

value: room air


title: WT_RA_Vessel_rep3


title: COVID_AIM_NonNV_CD8_040_TCR

data_processing:
Data processing of Bulk TCRseq was performed as described in Aoki et al. (Aoki et al., 2021).
Adapter trimming and quality filtering of sequencing data were performed using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. In MiXCR, filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system. The Variable (V) and Joining (J) segments of TCRs were represented in IMGT gene nomenclature. T-cell clones were determined as TCR reads with the same TCR V segment, J segment, and CDR3 nucleotide sequence.
Inter-sample contamination within samples using same UDIs were excluded by "Decontaminate" function of vdjtools with the parameter "-r 10".
The sequencing reads of samples were normalized to 16 times the cell count in each sample by the ?DownSample? command of VDJtools-1.2.1, and TCR clones with 15 or fewer reads were regarded as sampling noise and removed from the dataset.
Assembly: IMGT reference sequences of human TRA and TRB
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

extract_protocol:
PBMCs were isolated from whole blood with BD vacutainer CPT tubes (BD), resuspended in CELLBANKER 1 (Takara), and stored in -80°C.
AIM assay was performed on PBMC samples collected at P2, P3, and P8. PBMC were thawed by warming frozen cryovials in a 37°C water bath and resuspended in 10mL of in Culture Medium (CM) [10% fetal bovine serum (MP Bio Japan), 1% HEPES (Nacarai) and 1% penicillin/streptomycin (Nacarai) in RPMI-1640 medium (Nacarai)]. Cells were resuspended in 1mL of CM, then plated in 24-well plates and incubated overnight (about 16 hours) in an incubator at 37°C, with 5% CO2. After incubation, cells were then stimulated for 24 hours in stimulation medium [CM with BD FastImmune CD28/CD49d Costimulatory Reagent (final x100, BD Biosciences) and anti-human CD40 (final concentration of 0.5?g/mL, clone HB14, BioLegend)] with or without PepTivator SARS-CoV-2 Prot_S Complete (final concentration of 1 mg/mL, Miltenyi). 20 hours post-stimulation, an anti-CD107a-FITC antibody (final concentration of 5?g/mL, clone H4A3, BioLegend) was added to the culture. After four hours, cells were washed in PBS supplemented with 10% FBS (10% FBS/PBS). Cells were stained for 20 minutes at 4°C with antibody mix 2 (Supplementary Table S1). Cells were washed once in 10% FBS/PBS. AIM+ non-naïve CD4+, AIM- non-naïve CD4+, AIM+ non-naïve CD8+, and AIM- non-naive CD8+ cells were sorted using FACS Aria II or Aria III (BD Biosciences) and FACSDiva software (BD Biosciences, v8.0.1). AIM+ CD4+ T cells were defined by dual-expression of CD69 and CD40L. AIM+ CD8+ T cells were defined by expression of either CD107a or CD137. Nonviable cells were excluded from the analysis based on forward and side scatter profiles and propidium iodide staining (PI, Sigma-Aldrich). Data were analyzed using FlowJo software.
TCRseq libraries of AIM+ and AIM- non-naive T cells  were prepared for sample collected at P3. Bulk TCR sequencing library was prepared according to the previous report (Aoki et al., 2023).  In brief, mRNA in T-cell lysates were captured by incubating with 10 ?L of Dynabeads M270 streptavidin (Thermo Fisher Scientific) bound to 2.5 pmol of BioEcoP-dT25-adapter primers for 30 minutes at room temperature under gentle rotation. mRNA-trapped beads were suspended in 10 µL of RT mix and incubated for 60 min at 42ºC to perform reverse transcription (RT) and template-switching. The composition of the RT mix was as follows; 1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2 (NIPPON GENE), 1 U/µL RNaseIn Plus RNase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1 µM of i5-TSO. To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed using KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), followed by the purification of PCR product using an AM Pure XP kit (Beckman Coulter) at a 0.7:1 beads-to-sample ratio. The third PCR was performed to amplify TCR libraries and add adaptor sequences for the next-generation sequencer. The third-PCR products were purified as second PCR. Final TCR libraries, whose lengths were about 600 base pairs, were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems), and size distribution was analyzed by Microchip Electrophoresis System MultiNA (Shimadzu). TCR libraries were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina) using NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles, Illumina). Only read2 contained the sequence regarding the definition of T-cell clones. Oligonucleotides and reaction conditions for library preparation were summarized in Table S2 and S3, respectively.

value: Three doses of Pfizer-BNT162b2 vaccine

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD107a- and CD137-] T cells

value: 1 week after receiving the second dose


title: NaraCOVID_TP1_CD4_004_TCR

value: male


title: COVID_AIM_NonNV_CD8_038_TCR


title: R3_a305_FB14_TGTTCCTAGA-CGGTAAGTAA

description: oral antagomir treatment

value: fat body


title: R3_a305_FB17_CTTATGGCAA-ACGTCTCCTC

description: oral antagomir treatment


title: R3_a305_FB13_GAAGGCGTTC-GCTAGAGGTG

description: oral antagomir treatment


title: R3_a305_B24_ACACTGTGAA-GTCTAACAGA

description: oral antagomir treatment

value: brain


title: COVID_AIM_NonNV_CD8_031_TCR


title: FGF10_RA_Vessel_rep1


title: p320_U6DDR_Ph_Rep3

value: Endura Electrocompetent cells

value: Bacteria

value: recA13 supE44 ara-14 galK2 lacY1 proA2 rpsL20(StrR) xyl-5[lambda]- leu mtl-1 F- mcrB mrr hsdS20(rB-, mB-)

value: Transformation

value: Phusion


title: p320_U6DDR_Ph_Rep2


title: WT_RA_Vessel_rep2

value: Vessel


title: R3_a305_B23_CACACGCCAA-TATCTTCAGC

description: oral antagomir treatment


title: R3_a305_B22_GTTGGCGTCT-CTAGACTTCG

description: oral antagomir treatment


title: p320_U6DDR_Ph_Rep1


title: p320_U6DDR_Plat_Rep1


title: 4cell_H3K27ac_ChIP

city: Beijing

first: Lijia

last: Li

address: Haidian District

department: School of Life Science

institute: Tsinghua University

library_source: genomic

data_processing:
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, and STAR ChIP-seq tracks, gene expression table for RNA-seq data

molecule: genomic DNA

source_name: Preimplantation embryo

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd)

extract_protocol:
Cells or embyos were lysed in wash buffer.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

tag: strain

tag: chip-antibody

value: H3K27ac (Active Motif 39133)


title: COVID_AIM_NonNV_CD8_035_TCR

value: female


title: R3_a305_B21_TCACTTCATG-GTGGTCGCAA

description: oral antagomir treatment

value: worker


title: R3_a305_B20_CACGTAAGGT-CCTCTAAGCT

description: oral antagomir treatment


title: COVID_AIM_NonNV_CD8_012_TCR


title: IFN_78

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
IFN_78_Ctrl_M; IFN_78_Ctrl_F; IFN_78_1hrIFN_M; IFN_78_1hrIFN_F; IFN_78_2hrIFN_M; IFN_78_3hrIFN_M; IFN_78_3hrIFN_F
IFN_78_Ctrl_M:male; IFN_78_Ctrl_F:female; IFN_78_1hrIFN_M:male; IFN_78_1hrIFN_F:female; IFN_78_2hrIFN_M:male; IFN_78_3hrIFN_M:male; IFN_78_3hrIFN_F:female
IFN_78_Ctrl_M:PBS (100 μL); IFN_78_Ctrl_F:PBS (100 μL); IFN_78_1hrIFN_M:IFNa [10,000 U (10μL)]; IFN_78_1hrIFN_F:IFNa [10,000 U (10μL)]; IFN_78_2hrIFN_M:IFNa [10,000 U (10μL)]; IFN_78_3hrIFN_M:IFNa [10,000 U (10μL)]; IFN_78_3hrIFN_F:IFNa [10,000 U (10μL)]

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 and hash libraries were processed using cite-seq-count
Data analysis was performed using Seurat v3 pipeline. Low-quality cells were defined as those with less than 700 or more than 3000 unique genes, or those with >10% mitochondrial gene reads and were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peritoneal Cavity (PC), Spleen (Sp)

extract_protocol:
Immune cells were prepared by peritoneal cavity lavage (peritoneal cavity) or mechanical disruption (spleen), followed by staining with flourescent antibodies, hashing with Totalseq-A antibodies against MHCI and CD45, and flow sorting macrophages, B cells and CD4+ T cells into DMEM/2%FCS
Libraries were prepared according to the 10x 3’ (samples 1-8) and 10x3'v3 (samples 9-15) GEX protocol. Hash libraries were prepared according to the New York Genome Center’s cell hashing/CITEseq protocol.

value: Peritoneal Cavity (PC), Spleen (Sp)

value: Macrophages (PC); B, CD4+ T (Sp)

value: 5 weeks

tag: hashid

value: IFN_78_Ctrl_M:TATGCTGCCACGGTA; IFN_78_Ctrl_F:GAGTCTGCCAGTATC; IFN_78_1hrIFN_M:AAAGCATTCTTCACG; IFN_78_1hrIFN_F:CTTTGTCTTTGTGAG; IFN_78_2hrIFN_M:CTTGCCGCATGTCAT; IFN_78_3hrIFN_M:ACCCACCAGTAAGAC; IFN_78_3hrIFN_F:GGTCGAGAGCATTCA


title: IFN_GEX

description:
IFN_GEX_Ctrl_M; IFN_GEX_Ctrl_F; IFN_GEX_1hrIFN_M; IFN_GEX_1hrIFN_F; IFN_GEX_2hrIFN_M; IFN_GEX_2hrIFN_F; IFN_GEX_3hrIFN_M; IFN_GEX_3hrIFN_F
IFN_GEX_Ctrl_M:male; IFN_GEX_Ctrl_F:female; IFN_GEX_1hrIFN_M:male; IFN_GEX_1hrIFN_F:female; IFN_GEX_2hrIFN_M:male; IFN_GEX_2hrIFN_F:female; IFN_GEX_3hrIFN_M:male; IFN_GEX_3hrIFN_F:female
IFN_GEX_Ctrl_M:PBS (100 μL); IFN_GEX_Ctrl_F:PBS (100 μL); IFN_GEX_1hrIFN_M:IFNa (7.01μL); IFN_GEX_1hrIFN_F:IFNa (5.533μL); IFN_GEX_2hrIFN_M:IFNa (7.06μL); IFN_GEX_2hrIFN_F:IFNa (5.58μL); IFN_GEX_3hrIFN_M:IFNa (7.12μL); IFN_GEX_3hrIFN_F:IFNa (5.26μL)

value: IFN_GEX_Ctrl_M:ACCCACCAGTAAGAC; IFN_GEX_Ctrl_F:GGTCGAGAGCATTCA; IFN_GEX_1hrIFN_M:CTTGCCGCATGTCAT; IFN_GEX_1hrIFN_F:AAAGCATTCTTCACG; IFN_GEX_2hrIFN_M:CTTTGTCTTTGTGAG; IFN_GEX_2hrIFN_F:TATGCTGCCACGGTA; IFN_GEX_3hrIFN_M:GAGTCTGCCAGTATC; IFN_GEX_3hrIFN_F:TATAGAACGCCAGGC


title: R3_a305_B19_GTAGCTGTCG-TTAACGCAGA

description: oral antagomir treatment

tag: treatment


title: FBC: CD45+ cecum immunocytes, 101-day-old CTRL mouse (#1 and #2), 101-day-old Trpv1-ADC mouse (#1 and #2)

description:
4 samples (CD45+ ceum immunocytes from 2 CTRL and 2 Trpv1-ADC mice) were hashed together into a single 10X scRNA-seq run
FBC: CD45+ cecum immunocytes, 101-day-old CTRL mouse Replicate 1,  101-day-old CTRL mouse Replicate 2, 101-day-old Trpv1-ADC mouse Replicate 1, 101-day-old Trpv1-ADC mouse Replicate 2

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics).
Hash-by-cell matrices were computed using CITE-seq-count.
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Cecum

extract_protocol:
Immunocytes were released by dispase/collagenase II solution followed by filtering and washed in RPMI containing 5% fetal calf serum (FCS). Cells were then purified by fluorescence-activated cell sorting. Single cells were then sent to the Broad Institute Genomics Platform, which performed encapsulation following 10x Genomics protocols.
10x Genomics library prep, 3' v3 chemistry

value: Cecum

value: CD45+ immune cells

value: Trpv1-WT.B6 & Trpv1-Cre.B6

value: Male

value: AAV neonatal i.p. and CNO injection every other day for 7 times

tag: hashtag assignment

value: CTRL mouse #1 (Hash1), CTRL mouse #2 (Hash3), Trpv1-ADC mouse #1 (Hash7), Trpv1-ADC mouse #2 (Hash9)

tag: hashtag id

value: Hash1-ACCCACCAGTAAGAC, Hash3-CTTGCCGCATGTCAT, Hash7-GAGTCTGCCAGTATC, Hash9-TGCCTATGAAACAAG


title: FGF10_CS_Vessel_rep1

tag: fgf10 expression

value: knock-down

value: cigarette smoke

tag: compartment


title: R3_a305_B18_AATCACGACC-ACTTCTGGTG

description: oral antagomir treatment

value: brain


title: COVID_AIM_NonNV_CD8_008_TCR

value: Three doses of Pfizer-BNT162b2 vaccine

tag: cell type

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD107a- and CD137-] T cells

tag: age

tag: Sex

value: female

tag: date

value: 1 week after receiving the second dose


title: WT_CS_Vessel_rep2

value: wild-type

value: Vessel


title: COVID_AIM_NonNV_CD8_023_TCR

value: male


title: FGF10_CS_Septa_rep5

value: Septa


title: GEX: CD45+ cecum immunocytes, 101-day-old CTRL mouse (#1 and #2), 101-day-old Trpv1-ADC mouse (#1 and #2)

description:
4 samples (CD45+ ceum immunocytes from 2 CTRL and 2 Trpv1-ADC mice) were hashed together into a single 10X scRNA-seq run
GEX: CD45+ cecum immunocytes, 101-day-old CTRL mouse Replicate 1,  101-day-old CTRL mouse Replicate 2, 101-day-old Trpv1-ADC mouse Replicate 1, 101-day-old Trpv1-ADC mouse Replicate 2

tag: tissue

value: Cecum

value: CD45+ immune cells


title: COVID_AIM_NonNV_CD8_003_TCR


title: WT_RA_Vessel_rep1

value: room air


title: R3_a305_B17_CGCTAAGGCT-AACCGGCACA

description: oral antagomir treatment

tag: caste

value: worker

tag: colony


title: Thymocytes_Nsd2_KO_hetero_2

city: Setagaya

first: Tomoko

last: Kawai

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

data_processing:
The Illumina HiSeq X Ten generates raw images and base calling through an integrated primary analysis software called RTA 2(Real Time Analysis 2). The BCL (base calls) binary is converted into FASTQ using illumina package bcl2fastq2-v2.20.0.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0.
Fragments Per Kilobase of exon per Million reads mapped (FPKM) were calculated using cufflinks-2.2.1 .
Supplementary_files_format_and_content: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Thymocytes

extract_protocol:
B cells were isolated from spleen by EasySepTM Mouse B cell Isolation Kit (STEMCELL Technologies, Vancouver, Canada). Thymocytes were isolated from thymus. Total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany).
Libraries were prepared from 100ng of total RNA using NEBNext UltraII Directional RNA Library Prep Kit for illumina (New England BioLabs, Ipswich, MA, USA) according to manufacture’s protocol.

value: Thymocytes

value: 107 days

tag: genotype


title: WT_CS_Vessel_rep1


title: Control_CS8M_Septa_rep5


title: FGF10_CS_Septa_rep4

value: knock-down


title: R3_a305_B16_AAGCCTTAGA-TCATAACACG

description: oral antagomir treatment


title: FGF10_RA_Septa_rep4


title: COVID_AIM_NonNV_CD8_021_TCR


title: Control_RA8M_Septa_rep5


title: COVID_AIM_NonNV_CD8_002_TCR


title: Control_CS8M_Septa_rep4

value: cigarette smoke


title: Thymocytes_Nsd2_KO_hetero_1


title: COVID_AIM_AIM_CD8_040_TCR

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD107a+ or CD137+] T cells


title: R3_a305_B15_CTGACGTGAA-AGGCTATGTT

description: oral antagomir treatment

value: brain


title: R3_a305_B14_ATCGCCACTG-CTGACGTGAA

description: oral antagomir treatment


title: COVID_AIM_NonNV_CD8_005_TCR

value: Three doses of Pfizer-BNT162b2 vaccine

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD107a- and CD137-] T cells


title: COVID_AIM_NonNV_CD8_001_TCR

value: 1 week after receiving the second dose


title: Thymocytes_Nsd2_KI_homo

value: 90 days


title: Thymocytes_WT_2

value: wild type


title: R3_a305_B13_GGTCATCTCG-TCCGCATAGC

description: oral antagomir treatment


title: FGF10_RA_Septa_rep3


title: COVID_AIM_AIM_CD8_038_TCR

value: male


title: Thymocytes_Nsd2_KI_hetero_2

value: 110 days


title: R2_ams_FB28_ATGTCTCCGG-CGAATAAGAG

description: oral antagomir treatment

value: fat body

value: antagomir-missense


title: COVID_AIM_AIM_CD8_035_TCR

value: female


title: Thymocytes_Nsd2_KI_hetero_1


title: WT_RA_Septa_rep5

value: wild-type

value: room air

value: Septa


title: FGF10_RA_Septa_rep2

value: knock-down


title: Thymocytes_WT_1

value: Thymocytes


title: R2_ams_FB27_GGCCAGTGAA-CATTAGCAGA

description: oral antagomir treatment

value: worker


title: COVID_AIM_AIM_CD8_031_TCR

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD107a+ or CD137+] T cells


title: R2_ams_FB26_AACGTTGAGA-TTACCGACCG

description: oral antagomir treatment


title: COVID_AIM_AIM_CD8_027_TCR

value: Three doses of Pfizer-BNT162b2 vaccine


title: R2_ams_FB24_TTGGACATCG-GACCAGATTC

description: oral antagomir treatment


title: Splenic B cells_Nsd2_KO_hetero_2

description: Splenic B cells_Nsd2_KO_hetero_2

source_name: splenic B cells

value: B cells isolated from spleen

value: 107 days


title: Splenic B cells_Nsd2_KO_hetero_1

description: Splenic B cells_Nsd2_KO_hetero_1


title: COVID_AIM_AIM_CD8_021_TCR

value: 1 week after receiving the second dose


title: Control_RA8M_Septa_rep4


title: R2_ams_FB23_CCGATAACTT-GTATACGGAG

description: oral antagomir treatment


title: FGF10_RA_Septa_rep1


title: Splenic B cells_WT_2

description: Splenic B cells_WT_2

value: wild type


title: COVID_AIM_AIM_CD8_012_TCR

value: male


title: R2_ams_FB22_TCGACACGAA-CGGCTTGCAT

description: oral antagomir treatment


title: Splenic B cells_Nsd2_KI_homo

description: Splenic B cells_Nsd2_KI_homo

value: 90 days


title: WT_RA_Septa_rep3


title: WT_CS_Septa_rep5

value: cigarette smoke


title: WT_RA_Septa_rep4


title: WT_RA_Septa_rep2


title: COVID_AIM_AIM_CD8_023_TCR


title: COVID_AIM_NonNV_CD8_027_TCR

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD107a- and CD137-] T cells


title: Splenic B cells_Nsd2_KI_hetero_2

description: Splenic B cells_Nsd2_KI_hetero_2

value: 110 days


title: WT_CS_Septa_rep4


title: R2_ams_FB20_AGTGTTCGCC-TCACTTCATG

description: oral antagomir treatment

value: fat body

value: antagomir-missense


title: COVID_AIM_AIM_CD8_005_TCR


title: Splenic B cells_Nsd2_KI_hetero_1

description: Splenic B cells_Nsd2_KI_hetero_1


title: COVID_AIM_AIM_CD8_003_TCR


title: R2_ams_FB17_CGGAGTGTGT-CAGACGCCTT

description: oral antagomir treatment


title: COVID_AIM_AIM_CD8_002_TCR


title: seedling roots, Po_GAQ1-treatment, 24 h, rep 3

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

description:
Po_GAQ1_tomato_counts.txt
Po_GAQ1_tomato_fpkm.txt

data_processing:
Clean data (clean reads) were obtained, using in-house Perl scripts, by removing reads containing adapter, poly-N and reads that were otherwise low-quality. The Q20, Q30, GC-content and sequence duplication level of the clean data were determined.
These clean reads were then mapped to the reference genome sequence for the tomato cultivar ‘Heinz 1706’ genome version build SL4.0 by STAR aligner (v2.5.2b) [Dobin et al., 2013]. Only reads with either a perfect match or one mismatch were analyzed further and annotated based on the reference genome for the tomato cultivar ‘Heinz 1706’ genome version build SL4.0, and annotations from the International Tomato Annotation Group (ITAG) version ITAG4.0 [The Tomato Genome consortium, Hosmani et al., 2019].  Dobin, A.; Davis, C.A.; Schlesinger, F.; Drenkow, J.; Zaleski, C.; Jha, S.; Batut, P.; Chaisson, M.; Gingeras, T.R. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29, 15-21, doi:10.1093/bioinformatics/bts635. The_Tomato_Genome_Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485, 635-641, doi:10.1038/nature11119. Hosmani, P.S.; Flores-Gonzalez, M.; Geest, H.v.d.; Maumus, F.; Bakker, L.V.; Schijlen, E.; Haarst, J.v.; Cordewener, J.; Sanchez-Perez, G.; Peters, S.; et al. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. bioRxiv 2019, 767764, doi:10.1101/767764.
The percentage of uniquely mapped reads was at least 95% in all samples. HTSeq (v 0.5.4) [Ander et al., 2015] was used to count the number of reads mapped to each gene. Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).  Anders, S.; Pyl, P.T.; Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 2015, 31, 166-169, doi:10.1093/bioinformatics/btu638.
Assembly: tomato cultivar ‘Heinz 1706’ genome version build SL4.0 (https://solgenomics.net/ftp/tomato_genome/assembly/build_4.00/)
Supplementary files format and content: Po_GAQ1_tomato_counts.txt is a tab-separated text file with count data.
Supplementary files format and content: Po_GAQ1_tomato_fpkm.txt is a tab-separated text file with FPKM data.

organism: Solanum lycopersicum

source_name: seedling root

growth_protocol: Square 10 cm Petri dishes containing 20 mL of 1% water agar were used to germinate ten tomato (cv. Moneymaker) seedlings.

extract_protocol:
RNA was extracted using a Trizol-based method (Accurate Biology, China), and samples were stored at -80°C. The samples were ground in 2 mL tubes with liquid nitrogen, and 1 mL of TRIzol reagent (Accurate Biology, China) was added, mixed, and incubated for 5 min, and then 200 μL of chloroform was added, shaken, incubated for 5 min, and then centrifuged for 15 min at 12,000 x g at 4℃. The supernatant was transferred to a new tube, and an equal volume of pre-cooled isopropanol was added and mixed well, and then allowed to stand for 30 min at -80℃, and then centrifuged at 12,000 x g for 10 min at 4℃. The pellet was washed with 1 mL of 75% ethanol, and later dissolved in 30 μL of DEPC-treated water. RNA samples were analyzed by Nanodrop OD260/280 and OD260/230 to check the quantity and purity.
The sequencing libraries for transcriptome sequencing were made with 1.5 μg of total RNA by using the NEBNext® Ultra™ RNA Library Prep Kit from Illumina® (NEB, USA) following the manufacturer’s instructions. Poly-T oligo-attached magnetic beads were used to purify the mRNA, and the mRNA was fragmented with divalent cations and heat using the NEBNext First Strand Synthesis Reaction Buffer. Fragments of 200-250 bp were purified with the AMPure XP system (Beckman Coulter, USA), and then 3 μL of the USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min, then 5 min at 95°C, and then PCR was carried out with a high-fidelity DNA polymerase along with the Universal PCR primers and Index (X) Primer. The Agilent Bioanalyzer 2100 system was used to assess the quality of the purified PCR products and library. The sequencing was carried out on an Illumina NovaSeq 6000 platform by Beijing Allwegene Technology (China), and paired-end 150 bp reads were made. About ~40 M raw reads for each sample were made.

treatment_protocol: When seedlings reached a 1.5 cm root length, a 0.6 cm diameter mycelial plug of Po_GAQ1 was placed 0.5 cm from the tomato root tip, and incubated for 24 h at 25°C. For the control, the seedlings were not inoculated with a mycelial plug. A 1 cm portion of the root tip was cut using a scalpel blade (~20 seedling roots were pooled for each biological replicate), and the seedling root tip samples were flash-frozen in liquid nitrogen and then stored at -80°C. The experiment was performed with three biological replicates.

value: seedling root

value: cv. Moneymaker


title: COVID_AIM_AIM_CD8_008_TCR

value: female


title: R2_ams_FB14_GAATAATCGG-ATCTCCTGAA

description: oral antagomir treatment

value: worker


title: Control_CS8M_Septa_rep3

value: wild-type

value: Septa


title: seedling roots, Po_GAQ1-treatment, 24 h, rep 2


title: COVID_AIM_NonNV_CD4_040_TCR

value: Three doses of Pfizer-BNT162b2 vaccine

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD69- or CD40L-] T cells


title: COVID_AIM_AIM_CD8_001_TCR

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD107a+ or CD137+] T cells

value: 1 week after receiving the second dose


title: Overexp_CS8M_Septa_rep4

value: overexpressing


title: Overexp_CS8M_Septa_rep5


title: R2_ams_FB21_CTACGTTCTT-CAGGTCGTAA

description: oral antagomir treatment


title: Overexp_CS8M_Septa_rep3


title: R2_ams_B28_CTGGCGTATG-GTAACATTGG

description: oral antagomir treatment

value: brain


title: R2_ams_FB18_TTACCGACCG-TGTCAAGCGT

description: oral antagomir treatment


title: Control_CS8M_Septa_rep2

value: cigarette smoke


title: Splenic B cells_WT_1

description: Splenic B cells_WT_1

value: B cells isolated from spleen

value: 90 days

value: wild type


title: seedling roots, Po_GAQ1-treatment, 24 h, rep 1


title: R2_ams_B26_GAGGTTGTTA-CCAGTGCACA

description: oral antagomir treatment

value: antagomir-missense


title: seedling roots, control, 24 h, rep 3

value: seedling root

value: control


title: R2_ams_B27_AGAGTATCAG-ACCTGTATCC

description: oral antagomir treatment


title: COVID_AIM_NonNV_CD4_038_TCR

value: male


title: seedling roots, control, 24 h, rep 2

value: cv. Moneymaker


title: COVID_AIM_NonNV_CD4_035_TCR

value: female


title: COVID_AIM_NonNV_CD4_031_TCR


title: seedling roots, control, 24 h, rep 1


title: Control_CS8M_Septa_rep1

value: wild-type

value: Septa


title: R2_ams_B23_ACACTGGCTA-TCCAAGCAGG

description: oral antagomir treatment

value: worker


title: COVID_AIM_NonNV_CD4_027_TCR

value: Three doses of Pfizer-BNT162b2 vaccine

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD69- or CD40L-] T cells


title: R2_ams_B22_CACTTAGGCG-TAGGACCTCC

description: oral antagomir treatment


title: COVID_AIM_NonNV_CD4_023_TCR

value: 1 week after receiving the second dose


title: SMC3no_M_P3_rep1

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
150 bp x 150 bp
s9C_SMC3no_M_P3

data_processing:
library strategy: Capture-C
CapC-MAP was used for data processing, genomedigest was used to create a restriction site map for GRCg7b.
Target files for each oligo pool were generated with capClocation2fragment.
Reads were trimmed using cutadapt(v2.5) and mapped with bowtie(v1.2.2) CapC-MAP also uses samtools(v1.9) for processing and replicates were combined with combinereps.
Directionality analysis (min 3kb,max 250kb) used capturec-tools with captured_normalizedpileups as input and custom scripts used for plotting.
Assembly: GRCg7b
Supplementary files format and content: captured_normalizedpileup bedgraph files show piled-up intrachromosomal interaction counts for each target normalised to reads per million.

organism: Gallus gallus

source_name: Bursa

growth_protocol: RPMI 10% FBS, 1% Chicken serum. Cells were culutured at 39C at 5% CO2.

extract_protocol:
Cells were lyse with SDS, washed, and triton X100 is used to sequester the SDS. Then genomic DNA was digedted with DpnII.
NEBNext Ultra II DNA library prep kit for Illumina protocol
NG-Capture-C. 3C library constructed above were double-hybridized with oligo pools to enrich the fragments coverirng Z or 5 centromere regions.

treatment_protocol: Cells were maintained at the concentration between 0.1-1 X10^6/ml. In order to block cells at G2, cells were treated with 2µM 1NMPP1 for 13 h. Prometaphase cells were collected at 30 min  except for SMC2-AID cells which was 45 min after washout of 1NMPP1. In order to deplete either SMC2 or SMC3, 125-150 µM auxin were added for the last 3h of 1NMPP1 treatment and then after until haresting cells. Nocodazole was added in release media at 0.5 µg/ml if required. Cells were crosslinked with 1% formaldehyde for 10 min, quenched with glycine, rinced with PBS. Cell pellets were frozen down with dryice.

value: Bursa

tag: cell line

value: lymphoblast

value: female (ZW)

value: Oligo pool 3


title: COVID_AIM_NonNV_CD4_021_TCR


title: SMC3no_M_P2_rep1

description:
150 bp x 150 bp
s9B_SMC3no_M_P2

value: Oligo pool 2


title: R2_ams_B21_GATGGATACA-TACGGAACCG

description: oral antagomir treatment

value: brain

value: antagomir-missense


title: R2_ams_B18_GGCTGCACAA-AGAGGTCCGA

description: oral antagomir treatment


title: R2_ams_B20_ACCAAGCCAA-TACAAGGCGG

description: oral antagomir treatment


title: COVID_AIM_NonNV_CD4_008_TCR


title: R2_ams_B17_ACGCATACTT-TCTCGTACTT

description: oral antagomir treatment


title: R2_ams_B24_TGATACCAGA-TGTGAAGGCC

description: oral antagomir treatment


title: Overexp_CS8M_Septa_rep2

value: overexpressing

value: cigarette smoke


title: COVID_AIM_NonNV_CD4_012_TCR

value: male


title: SMC3no_M_P1_rep1

description:
150 bp x 150 bp
s9A_SMC3no_M_P1

value: Oligo pool 1


title: SMC3no_G2_P2_rep2

description:
150 bp x 150 bp
s8B_SMC3no_G2_P2


title: SMC3no_G2_P3_rep2

description:
150 bp x 150 bp
s8C_SMC3no_G2_P3


title: WT_CS_Septa_rep3

value: wild-type


title: COVID_AIM_NonNV_CD4_005_TCR


title: R2_ams_B14_TTGTCTATGG-GTGTACTCAA

description: oral antagomir treatment


title: COVID_AIM_NonNV_CD4_003_TCR


title: Control_RA8M_Septa_rep3

value: room air

value: Septa


title: Control_RA8M_Septa_rep2


title: R2_a305_FB27_GACGTCCAGA-GGTTGAATCT

description: oral antagomir treatment

value: worker

value: fat body


title: Overexp_CS8M_Septa_rep1


title: WT_CS_Septa_rep1


title: SMC3no_G2_P1_rep2

description:
150 bp x 150 bp
s8A_SMC3no_G2_P1


title: FGF10_CS_Septa_rep2

value: knock-down


title: WT_CS_Septa_rep2


title: R2_a305_FB26_CCTGAGTTAT-TGGCACTTCC

description: oral antagomir treatment


title: COVID_AIM_NonNV_CD4_002_TCR

value: Three doses of Pfizer-BNT162b2 vaccine

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD69- or CD40L-] T cells

value: 1 week after receiving the second dose


title: SMC3no_G2_P3_rep1

description:
150 bp x 150 bp
s7C_SMC3no_G2_P3

value: Bursa

value: lymphoblast

value: female (ZW)

value: Oligo pool 3


title: SMC3no_G2_P2_rep1

description:
150 bp x 150 bp
s7B_SMC3no_G2_P2

value: Oligo pool 2


title: WT_RA_Septa_rep1


title: COVID_AIM_NonNV_CD4_001_TCR


title: FGF10_CS_Septa_rep1

value: cigarette smoke


title: FGF10_CS_Septa_rep3


title: R2_a305_FB25_CTGCAATCGG-CGATGCAGAA

description: oral antagomir treatment


title: TCF23 KO E19.5_3

city: Nagoya

first: Hossam

middle: Hassan

last: Shawki

state: Aichi

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

institute: Nagoya City University

data_processing:
Galaxy platform version 23.1.rc1 (https://usegalaxy.eu/).
Quality of RNA sequences was checked by FastQC (Galaxy version 0.73).
The FASTQ files were mapped to the mm10 mouse genome using HISAT2 (Galaxy version 2.2.1).
The mapped reads were quantified using HTSeq-count (Galaxy version 0.9.1).
Differential expression was defined between TCF23 KO and WT using DESeq2 (Galaxy Version 2.11.40.7), withP<0.05 and adjusted for multiple testing correction using the Benjamini–Hochberg method.
Assembly: mm10
Supplementary files format and content: Normalized_values.tabular.txt: Tabular file includes RPKM values for each sample.
Supplementary files format and content: raw_count_*.tab: Tabular files include raw counts for each sample.

source_name: Myometrium

extract_protocol:
Total RNA was isolated using ISOGEN II (Nippon gene, Japan). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were prepared with an NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA) and MGI Easy RNA Directional Library Prep Set (MGI Tech Co. Ltd) according to the manufacturer’s instructions.

value: Myometrium

tag: developmental stage

value: TCF23 KO


title: COVID_AIM_AIM_CD4_038_TCR

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD69+ and CD40L+] T cells

value: male


title: TCF23 KO E19.5_1


title: COVID_AIM_AIM_CD4_040_TCR


title: TCF23 KO E19.5_2


title: SMC3no_G2_P1_rep1

description:
150 bp x 150 bp
s7A_SMC3no_G2_P1

value: Oligo pool 1


title: Control_RA8M_Septa_rep1

value: wild-type

value: room air

value: Septa


title: SMC2au_M_P2_rep2

description:
150 bp x 150 bp
s18B_SMC2au_M_P2


title: R2_a305_FB24_AATAGCCTCA-ACTAAGTCGG

description: oral antagomir treatment

value: worker

value: fat body


title: SMC2au_M_P3_rep2

description:
150 bp x 150 bp
s18C_SMC2au_M_P3


title: TCF23 WT E19.5_2

value: TCF23 WT


title: R2_a305_FB19_CCGATAGTCG-ACGTGAACAT

description: oral antagomir treatment


title: COVID_AIM_AIM_CD4_031_TCR

value: Three doses of Pfizer-BNT162b2 vaccine

value: 1 week after receiving the second dose


title: COVID_AIM_AIM_CD4_027_TCR


title: SMC2au_Mnoc_P3_rep2

description:
150 bp x 150 bp
s16C_SMC2au_Mnoc_P3

value: Bursa

value: lymphoblast

value: female (ZW)


title: SMC2au_M_P1_rep2

description:
150 bp x 150 bp
s18A_SMC2au_M_P1


title: COVID_AIM_AIM_CD4_023_TCR


title: R2_a305_FB21_CAAGATCGAA-AACCATCGAA

description: oral antagomir treatment


title: TCF23 WT E19.5_1


title: R2_a305_FB23_ATACGGATAG-CTCTGCGCTT

description: oral antagomir treatment


title: COVID_AIM_AIM_CD4_035_TCR

value: female


title: WT-4

city: Nashville

first: Jin

last: Chen

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

data_processing:
Raw sequencing data was filtered for low quality reads, high levels of unknown bases, and connector contamination, performed by BGI Americas.
Clean reads were aligned to the reference genome using HISAT, performed by BGI Americas
Clean reads were then aligned to reference genes using Bowtie2, performed by BGI Americas.
Assembly: GCF_000001635.26 GRCm38.p6
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, and read counts for each sample
Supplementary files format and content: tab-delimited text file includes differential expression statistical analyses for each gene

source_name: mouse primary microvascular endothelial cells harvested from lung of Raptor floxed mice

growth_protocol: Raptor floxed mouse pulmonary microvascular endothelial cells (MPMECs) were cultured on tissue culture plates coated with 0.1% gelatin in EGM-2 medium (Lonza).

extract_protocol:
RNA was extracted using RNAqueous Micro Total RNA Isolation Kit (Invitrogen), per manufacturer's instructions.
The library was constructed by polyA selection by BGI Americas.

treatment_protocol: Raptor floxed MPMECs were treated with Ad-CMV-b-Gal (LacZ, WT control) or Ad-Cre (CRE, Raptor KO) (Vector Biolabs) for 48 hours.

value: WT

tag: strain


title: R2_a305_FB18_ACTCCTGCCT-CTACGGACTC

description: oral antagomir treatment


title: SMC2au_Mnoc_P1_rep2

description:
150 bp x 150 bp
s16A_SMC2au_Mnoc_P1


title: WT-3

value: mouse primary microvascular endothelial cells harvested from lung of Raptor floxed mice


title: R2_a305_FB22_AGGCTCCTTC-TGCACGGATA

description: oral antagomir treatment


title: COVID_AIM_AIM_CD4_012_TCR

value: CD14- CD19- CD3+ [CD45RA- or CD27-] [CD69+ and CD40L+] T cells


title: SMC2au_Mnoc_P2_rep2

description:
150 bp x 150 bp
s16B_SMC2au_Mnoc_P2

value: Oligo pool 2


title: R2_a305_FB17_GGTTGATAGA-TCTGCTCCGA

description: oral antagomir treatment


title: TCF23 WT E19.5_3

value: Myometrium


title: COVID_AIM_AIM_CD4_005_TCR

value: male


title: SMC2au_Mnoc_P3_rep1

description:
150 bp x 150 bp
s13C_SMC2au_Mnoc_P3

value: Oligo pool 3


title: R2_a305_B27_GTCGCGGTTA-CTGGTGAGGT

description: oral antagomir treatment

value: brain


title: WT-1


title: SMC2au_Mnoc_P2_rep1

description:
150 bp x 150 bp
s13B_SMC2au_Mnoc_P2


title: R2_a305_FB15_TATCTTCAGC-CGAATATTGG

description: oral antagomir treatment

value: worker


title: COVID_AIM_AIM_CD4_003_TCR


title: Raptor KO-4

value: Raptor KO


title: SMC2au_G2_P3_rep2

description:
150 bp x 150 bp
s11C_SMC2au_G2_P3


title: SMC2au_Mnoc_P1_rep1

description:
150 bp x 150 bp
s13A_SMC2au_Mnoc_P1

value: Oligo pool 1


title: COVID_AIM_AIM_CD4_021_TCR

value: Three doses of Pfizer-BNT162b2 vaccine


title: COVID_AIM_AIM_CD4_001_TCR

value: 1 week after receiving the second dose


title: Raptor KO-3


title: R2_a305_FB16_TGCACGGATA-GTTGTCTGCG

description: oral antagomir treatment

value: fat body


title: SMC2au_G2_P2_rep2

description:
150 bp x 150 bp
s11B_SMC2au_G2_P2

value: Bursa

value: lymphoblast


title: R2_a305_B26_CGTTCTCTTG-CCACTTGGTG

description: oral antagomir treatment


title: COVID_AIM_AIM_CD4_002_TCR


title: WT-2


title: R2_a305_B24_TCCGACGATT-TGGTATCCGG

description: oral antagomir treatment


title: Raptor KO-2


title: COVID_AIM_AIM_CD4_008_TCR

value: female


title: SMC3no_M_P3_rep2

description:
150 bp x 150 bp
s10C_SMC3no_M_P3

value: female (ZW)


title: SMC2au_G2_P1_rep2

description:
150 bp x 150 bp
s11A_SMC2au_G2_P1


title: R2_a305_B25_AGGCTATGTT-CGGTGGACAT

description: oral antagomir treatment


title: R2_a305_B22_ATGGATCGAA-TTGCTGAGTT

description: oral antagomir treatment


title: SMC3no_M_P2_rep2

description:
150 bp x 150 bp
s10B_SMC3no_M_P2


title: SMC3no_M_P1_rep2

description:
150 bp x 150 bp
s10A_SMC3no_M_P1


title: LLC cells-WT-2

source_name: metastatic tumor cells collected from lung

value: LLC-GFP-luciferase

value: Lewis lung carcinoma

value: WT mouse


title: R2_a305_B21_CACAGAACGG-ATCACTCACA

description: oral antagomir treatment


title: Raptor KO-1

value: mouse primary microvascular endothelial cells harvested from lung of Raptor floxed mice


title: mPB HSPCs

city: NY

first: Tomer

last: Itkin

state: NY

address: 1300 York Avenue, A-869

department: Medicine

institute: Weill Cornell Medicine

data_processing:
cellranger-6.1.2 was used to demultiplex CMO IDs CMO301 (CB) and CMO311 (mPB)
Assembly: GRCh38-2020-A
Supplementary files format and content: File formats are in de-multiplexed h5 counts file

source_name: mPB HSPCs isolated from co-cultures

extract_protocol: Human CB and mPB HSPCs were harvested isolated and sorted. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resoerted and processed for 10X Chromium scRNA-seq analysis.

value: mobilized peripheral blood (mPB)

tag: time points

value: 48 hours post introduction in co-culture

tag: source

value: In vitro cultures


title: LLC cells-WT-4

value: metastatic tumor cells collected from lung


title: R2_a305_B23_GGTCTCACCT-TCAATCGTCT

description: oral antagomir treatment

value: worker

value: brain

tag: treatment


title: CB HSPCs

source_name: CB HSPCs isolated from co-cultures

value: cord blood (CB)


title: LLC cells-Raptor ECKO-4

value: Raptor endothelial cell knockout (ECKO) mouse


title: R2_a305_B19_TCTCTGTTAG-CACGAGTATG

description: oral antagomir treatment


title: Pt1 iPSC-HPCs, WTcontrol, stimulated_STF3

city: Sagamihara

first: Makoto

last: Otsu

state: Kanagawa

address: 1-15-1 Kitasato, Minami-ku

institute: Kitasato University School of Medicine

data_processing:
Genedata Profiler Genome (GPG) v 11.0.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using GPG workflow.
Trimmed sequence reads (100bp) were mapped to GRCh37/hg19 using GPG and STAR sotwares.
Read count extraction and normalization were performed using GPG and STAR workflow.
All the above procedures were performed by TAKARA Bio.
Assembly: hg19
Supplementary files format and content: Excel spreadsheet files include FPKM values and read counts for each sample

source_name: induced pluripotent stem cells

extract_protocol:
RNA was harvested using NucleoSpinRNA XS kit (MACHEREY-NAGEL). 1-10 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: hematopoietic progenitor cells

tag: patient

value: WT/WT


title: LLC cells-Raptor ECKO-2


title: LLC cells-WT-3


title: Halo-CAP-H2_CDK1as(biol rep1)_CENP-A_ChIP

description: 101 bp x 101 bp

data_processing:
Remove adapters with Cutadapt-1.18 --minimum-length 20 --nextseq-trim=20
Align to galGal7b reference with bwa mem
Convert to coverage file with deeptools bamCoverage -bs 1 --normalizeUsing BPM
Assembly: GRCg7b
Supplementary files format and content: BigWig

growth_protocol: DMEM, 10% FBS, 1% Chicken serum, betamercaptoethanol, penicillin and streptmycin. Cells were culutured at 38C at 5% CO2.

extract_protocol:
A nuclear fraction of cells was digested with MNase and solubulised with 0.5M NaCl. CENP-A containing nucleosomes were immunoprecipitated with custom-made CENP-A antibody.
ChIP-seq libraries were prepared either using NEBNext Ultra II prep (WT, SMC2, SMC3) or KAPA Hyper prep (CAP-H, CAP-H2).

treatment_protocol: asynchronous growth mainting the concentration between 0.2-1 X10^6/ml

value: Bursa

value: lymphoblast

tag: chip antibody

value: custome made anti CENP-A antibody


title: Pt1 iPSC-HPCs, KRASG13C, stimulated_STF3


title: Pt1 iPSC-HPCs, KRASG13C, stimulated_SF


title: LLC cells-WT-1

value: LLC-GFP-luciferase


title: R2_a305_B16_AGGCCTCACA-AACAGAACCT

description: oral antagomir treatment

source_name: whole brain


title: Pt1 iPSC-HPCs, KRASG13C, unstimulated


title: R2_a305_B18_GCAGCATTCC-TGTGGTATAC

description: oral antagomir treatment


title: CAP-H_Halo_CDK1as(biol rep1)_CENP-A_ChIP

description: 101 bp x 101 bp

value: female


title: Twints No2 with TB

city: Tongliao

first: Batudeligen

last: Batudeligen

address: 536 West Hollin River Street

institute: Affiliated Hospital of Inner Mongolia University for the Nationalities

description: gene expresson data from blood from Twins No1 without TB

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Total RNA

source_name: blood from Twins No2 with TB

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA

growth_protocol: A volume of 4 mL blood was added to the PAXgene Blood RNA Tube by venipuncture and EDTA-containing tube (2 mL)

extract_protocol: Total blood RNA was extracted using the PAXgene RNA Blood Mini Kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s instructions.

treatment_protocol: The blood was keeped and the total RNA were extaction.

value: blood


title: PPPE.251 post

status: Public on Mar 28 2024

city: Rochester

first: Sylvie

last: Girard

state: Minnesota

address: 200 First Street

institute: Mayo Clinic

description: 10X Genomics

data_processing:
The Chromium protocol was followed, including GEM generation and barcoding, followed by GEM-RT cleanup and cDNA amplification, gene expression library construction, and lastly, cell multiplexing library construction and sequencing.
Assembly: GRCh38 2020-A
Supplementary files format and content: tab-seperated values files and hierarchical data format version 5

source_name: Blood

extract_protocol:
Blood was diluted with PBS-10%FBS in a 1:1 ratio and added to Sepmate-50 tubes (Stemcell) containing 15mL Lymphoprep density gradient medium (StemCell). Tubes were centrifuged at 1200g for 10 minutes. PBMCs were collected and diluted with PBS for a final volume of 45mL and centrifuged at 300g for 10 mintues. Supernantants were removed and the pellet was resuspended with 10mL of PBS. A 10µl aliquot was taken and combined with 10µl trypan blue solution (Bio-Rad) for cell count on a Bright-Line hemacytometer (Hausser Scientific). The resuspended pellet was centrifuged at 400g for 10 minutes and the supernatant was discarded. Pellets were resuspended with FBS-10%DMSO at a final concentration of 2M cells/mL and aliquoted to be frozen down slowly at -80°C for 24-48 hours and then transferred to liquid nitrogen for long term storage.
Library was constructed according to manufacturer instructions (10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (dual index) with feature barcode technology) for cell multiplexing at the McGill Genome Cente

value: Blood

tag: condition

value: Control

value: PBMC


title: R2_a305_B17_TCACACGTGG-GACCTATACA

description: oral antagomir treatment

data_processing:
Aligned FASTQ files to honey bee genome and deformed wing virus reference with STAR 2.7.6a
Counts were generated with the "featureCounts" function in Subread 2.0.0
Assembly: HAv3.1

extract_protocol:
Abdominal fat body: abdomens were separated from the bodies and placed in 500ul RNAlaterICE (Life Technologies) at -20ºC for 14 to 18 h. Abdomens were then opened and guts and sting apparatus gently removed. The remaining intact fat body tissue connected to the cuticle was placed in a 1.5ml tube and stored frozen (-80°C) until RNA extraction. Brains: bee heads were separated from the bodies and placed in a pure ethanol in a dissection dish chilled on dry ice to prevent RNA degradation during dissection. The cuticle of the anterior head capsule (frons) was removed and each head placed in 300ul of RNAlaterICE at -20ºC for 14 to 18 h. Heads were then opened, hypopharyngeal glands removed, and whole brain collected. Brains were place in 1.5ml tube and stored frozen (-80°C) until RNA extraction. Total RNA extraction for both abdominal fat body and whole brain was performed with miRNeasy Mini Kits (Qiagen) and C. elegans miR-39 spike-in (Qiagen) at the tissue homogenization step for other downstream analyses (qPCR).
RNA-Seq libraries were prepared with Kapa Hyper Stranded mRNA library kit (Roche). Libraries were pooled and sequenced on one S4 lane for 151 cycles  from both ends of the fragments on a NovaSeq 6000 (Illumina). Reads are 150 nt.


title: Twints No2 without TB

source_name: bloodf rom Twins No2 without TB


title: Pt1 iPSC-HPCs, WTcontrol, stimulated_SF


title: PPPE.221 pp

description: 10X Genomics

value: Postpartum

tag: cell type


title: PPPE.192 pp

description: 10X Genomics


title: PPPE.243 post

description: 10X Genomics


title: LLC cells-Raptor ECKO-1

value: metastatic tumor cells collected from lung

value: Lewis lung carcinoma


title: PPPE.235 post

description: 10X Genomics


title: PPPE.255 pp

description: 10X Genomics


title: Pt1 iPSC-HPCs, WTcontrol, unstimulated


title: PPPE.254 post

description: 10X Genomics


title: PPPE.227 pp

description: 10X Genomics


title: PPPE.223 pp

description: 10X Genomics


title: R2_a305_B15_GCCGAACTTG-GATCTCGTCC

description: oral antagomir treatment

value: worker

value: brain


title: LLC cells-Raptor ECKO-3

value: Raptor endothelial cell knockout (ECKO) mouse


title: 24_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r12

status: Public on Mar 26 2024

city: Barcelona

first: Lina

last: Badimon

state: BARCELONA

address: Carrer de Sant Antoni Maria Claret, 167

department: ICCC-Cardiovascular Program

country: Spain

institute: Research Institut- HSCSP

description: Circualting miRNA data in presence of coronary calcium score

hyb_protocol: Hybridization was performed on Affymetrix miRNA 4.0 arrays and cartridges were incubated at 48°C with 60 rpm rotation for 48 h using Affymetrix Hybridization Oven 600. After, each array was washed and stained using the FS450_002 fluidics script in Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using the GeneChip scanner 3000 7G System

data_processing: The data were explored using the Transcriptome Analysis Console software (TAC 4.0) for data summarization and normalization by RMA+DABG procedure (implemented in TAC 4.0 software).

label: Biotin

source_name: Plasma

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Rev3) to label 8 ul of total RNA isolated with miRNeasy Serum/Plasma Advanced Kit (Qiagen Inc) from each sample, according to manufacturers instructions. RNA quantitation was not considered due to low levels of total RNA isolated from plasma.

growth_protocol: Familial hypercholesterolemia patients plasma (200uL) was used for isolation of circulating miRNAs

extract_protocol: To isolate plasma miRNAs, we used plasma from familial hypercholesterolemia patients and miRNeasy Serum/Plasma Advanced Kit (Qiagen Inc), according to manufacturer’s instructions.

treatment_protocol: No treatment

tag: disease state

value: Familial hypercholesterolemia

value: Patients carrying the heterozygous mutation in the LDLR gene

tag: coronary calcium score condition

tag: gender

value: Male

tag: age

value: Plasma


title: Twints No1 without TB

source_name: blood from Twins No1 without TB

tag: tissue


title: PPPE.183 post

description: 10X Genomics


title: PPPE.180 pp

description: 10X Genomics


title: 14_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r7


title: 10_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r5


title: 9_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r5

description: Circualting miRNA data in absence of coronary calcium score


title: 23_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r12

value: Female


title: 6_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r3


title: 20_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r10


title: 4_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r2


title: 2_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r1


title: 5_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r3


title: 21_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r11


title: 19_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r10


title: 22_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r11


title: Seminoma, patient 1, scRNA-seq

status: Public on Mar 21 2024

city: Giessen

first: Daniela

last: Fietz

address: Frankfurter Straße 98

institute: Justus Liebig University Giessen

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment, filtering and UMI counting. The UMI count table was used for further analysis.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Testis

extract_protocol:
Testis specimens were placed into cold PBS and transported on ice. Tissues were digested following the standard two step enzymatic isolation protocol. Briefly, specimens were digested with collagenase type IV for 5 min at 37 °C with gentle agitation, then shaken vigorously and incubated for another 3 min. The tubules were sedimented by centrifugation at 200× g for 5 min and washed with Hanks' Balanced Salt Solution (HBSS) before digestion with 4.5 mL 0.25% trypsin/ethylenediaminetetraacetic acid (EDTA) and 4 Kunitz unit (kU) DNase I. The suspension was triturated vigorously three to five times then incubated at 37 °C for 5 min. The process was repeated in 5 min increments for up to 15 min total. The digestion was stopped by adding FBS to a final concentration of 10%. Single testicular cells were obtained by filtering through 70 µm and 40 µm strainers to obtain single cell suspensions. The cells were pelleted by centrifugation at 600× g for 15 min and washed twice with PBS. Cell number was measured using a hemocytometer, and cells re-suspended in 1× PBS/0.4% BSA.
Single cell suspensions were loaded and run on the 10x Chromium Controller using Chromium Single Cell 3′ v3.1 reagents (10x Genomics PN-1000121). Sequencing libraries were prepared following the manufacturer’s instructions, using 13 cycles of cDNA amplification, followed by an input of ∼100 ng of cDNA for library amplification using 12 cycles. The resulting libraries were then sequenced on a 2 X 100 cycle paired-end run on Illumina HiSeq 2500 or Novaseq 6000 instruments.

value: Testis


title: 17_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r9


title: 16_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r8


title: 3_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r2


title: 15_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r8


title: 13_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r7


title: SR34 [WES]

city: Madison

first: Jack

last: Shireman

state: WI

address: 600 Highland Ave

institute: UW-Madison

description: center and peripheral included when available CR= central PR= peripheral RF= undefined

data_processing:
Alignment with GATK pipeline
Variant calling using GATK pipeline
variant annotation using funcotate
data visualization in R using standard packages
QC with Multi-QC
Assembly: HG38
Supplementary files format and content: .txt
Library strategy: Exome-Seq

source_name: Brain

extract_protocol:
extracted using Quiagen All Prep
Aligent sure select V6
Bulk Exome Sequencing (done by novogene)

treatment_protocol: Stereotatic Radiation

value: Brain

value: Brain Metastases

value: SRS


title: SR33 [WES]


title: SR31 [WES]


title: 8_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r4


title: 11_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r6


title: 7_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r4


title: 12_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r6


title: SR24 [WES]


title: SR23 [WES]


title: SR20 [WES]


title: SR22 [WES]


title: 1_FH-WO_CCS: Familial hypercholesterolemia patients without coronary calcium score_r1


title: 18_FH-W_CCS: Familial hypercholesterolemia patients with coronary calcium score_r9


title: Twints No1 with TB

description: gene expresson data from blood from Twins No1 with TB

source_name: blood from Twins No1 with TB

value: blood


title: Seminoma, patient 2, scRNA-seq


title: Mixed germ cell tumour, scRNA-seq


title: Embryonal carcinoma, scRNA-seq


title: SR17 [WES]


title: SR19 [WES]


title: SR18 [WES]


title: SR35 [WES]


title: SR36 [WES]


title: SR14 [WES]


title: SR12 [WES]


title: SR30 [WES]


title: SR32 [WES]


title: SR29 [WES]


title: SR28 [WES]


title: SR26 [WES]


title: SR25 [WES]


title: SR21 [WES]


title: SR05 [WES]


title: SR02 [WES]


title: NU00617 [WES]


title: SR15 [WES]


title: SR27 [WES]


title: NU00570 [WES]

description: center and peripheral included when available CD= central PD= peripheral DF= undefined


title: DMSO sample 2 [A5]

status: Public on Mar 13 2024

city: West Lafayette

first: Tony

last: Hazbun

state: Indiana

address: 201 South University Street

department: Borch Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
150-bp paired-end DNA samples were sequenced using an Illumina NovaSeq6000. Fastp  was used to quality-trim reads and eliminate Illumina TruSeq adaptor sequences. Reads were aligned to the C. auris NCBI reference genome version B11221 using STAR aligner (v2.7.10a) The read counts mapped to each gene were counted using FeatureCounts  (v2.1). The EdgeR  Bioconductor package (v3.16.5) was used to perform the differential expression analysis. The Benjamini-Hochberg method was used to adjust the P-values for multiple testing. The cutoff for the significant differential expression was chosen at a FDR of 0.05. DEGs were annotated by blasting the sequences of identified DEGs versus C. albicans SC5314 Genome Database with an e-value cutoff of 0.01. Cluster Profiler Bioconductor  package (v2.4.3) was used to perform Gene Ontology analysis of DEGs. The length of each gene in the related annotation GTF file and the number of reads mapped to each gene were used to generate FPKM values for each gene.
Assembly: C. auris NCBI reference genome version B11221

organism: Candidozyma auris

source_name: Candida cells

growth_protocol: C. auris was grown on YPD broth

extract_protocol:
Exponential C. auris AR0390 in RPMI 1640 medium were treated with DMSO (control), AmB (0.5 µg/ml), LNP (32 µg/ml), or the combination of AmB/LNP in triplicates for 3 hr at 35 °C. Candida cells were collected, washed three times with PBS, and the total RNA was extracted using a RiboPureTM-Yeast Kit (AmBion, AM1926, MA, USA) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Candida cells were treated with the tested drugs in RPMI media

value: Candida cells

value: DMSO 5 uL

tag: ng/ul

tag: total volume

value: 40 ul


title: DMSO sample 3 [A6]


title: SR11 [WES]

tag: cell line

tag: genotype


title: SR08 [WES]


title: SR06 [WES]


title: ETI41 (30min)

status: Public on Feb 29 2024

city: Suwon-si

first: Uisuk

last: Jeong

state: Gyeonggi-do

address: 206, World cup-ro

department: Molecular Science and Engineering

country: South Korea

institute: Ajou university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Ascites

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Ascites

value: macrophage cell line

value: WT

value: ETI41 (30min)


title: SR07 [WES]


title: non-treatment

value: non-treatment


title: SR04 [WES]


title: ETI60 (30min, pre-treatment), Imiquimod (2h, post treatment)


title: interscapular brown adipose tissue, 10day cold exposed, Mafbf/f, 1

city: Tsukuba

first: Michito

last: Hamada

state: Ibaraki

address: 1-1-1 Tennodai,

department: Department of Anatomy and Embryology

institute: University of Tsukuba

description: Single bam file generated for each sample using STAR, from paired-end two separate fastq files

data_processing:
STAR version=STAR_2.6.1a_08-27
Sequence read were alligned and mapped using default paramaters of STAR version STAR_2.6.1a_08-27
Read count performed by STAR
Normalization and DEG analysis done by edgeR tool
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each Sample

source_name: interscapular brown adipose tissue

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
Library construction and RNA seq peformed by University of Tsukuba, RNA seq service

value: interscapular brown adipose tissue

tag: strain

value: tissue

value: Mafbf/f

value: 10 days, 4 degree cold exposure


title: SR03 [WES]


title: ETI60 (30min)

value: ETI60 (30min)


title: NU01164 [WES]

value: Brain


title: NU00913 [WES]

value: Brain Metastases


title: SR09 [WES]

value: SRS


title: SR13 [WES]


title: ETI60 (30min, pre-treatment), Imiquimod (4h, post treatment)


title: NK_DMSO_rep3 (RNA-seq)

status: Public on Feb 28 2024

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS

data_processing:
Image analysis and base calling were performed using the NovaSeq Control Software, Real‑Time Analysis 3 (RTA) and bcl2fastq.
Raw seq files and trimmed files were quality cheked usinf fastQC.
Raw seq files were trimmed using trimmomaticSE.
Trimmed files were aligned to the human genome hg38 using tophat2 v2.1.1.
bigWig files were generated using bamCoverage 3.3.0 with RPKM normalization.
Aligned reads were counted using htseq-counts 2.0.2.
Differential expression was computed using edgeR with paired quasi-likelyhood F test.
Gene set enrichment analysis was performed using GSEA v4.2.0.
Assembly: hg38, GRCh38p12
Supplementary files format and content: Tab delimited file containing edgeR computed Fold Change and False Decision Rate and counts per million reads for each sample.
Supplementary files format and content: bigWig files with RPKM normalization and bin=10.

source_name: blood

growth_protocol: PBMCs were purified from either buffy coat of healthy blood donors using density-based centrifugation method (Histopaque 1077- H8889 Sigma-Aldrich). NK (CD56+/CD3-) were sorted using a BD FACS Aria IIu Cell sorter and cultured in RPMI medium + 10% fetal calf serum.

extract_protocol:
Total RNA was purified using GenElute Single Cell RNA Purification Kit (Sigma-Aldrich RNB300), treated with DNase I on column (Sigma- DNASE70-1SET). RNA quality was checked using a BioAnalyser Nano 6000 Chip (Agilent).
Libraries were prepared using SMART-Seq Stranded Kit (Takara Bio). The quality, size and concentration of cDNA libraries were checked using the High Sensitivity NGS kit Fragment Analyzer and qPCR (ROCHE Light Cycler 480).

treatment_protocol: Purified NK cells were treated with TAK-981 (100 nM) for 24 h.

value: blood

value: natural killer

value: DMSO


title: ETI41 (30min, pre-treatment), Imiquimod (4h, post treatment)


title: ETI41 (30min, pre-treatment), Imiquimod (2h, post treatment)


title: 0.25% DMSO (30min, pre-treat), Imiquimod (2h)


title: 0.25% DMSO (30min, pre-treatment), Imiquimod (4h)


title: NU00890 [WES]


title: MLL7 PDX AZD1775 Dasatinib day6 scRNAseq

status: Public on Feb 25 2024

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: RAW data not provided due to patient privacy concerns

data_processing:
PDX cell scRNA-seq data was processed and aligned with Cell Ranger (version 6.0) using GRCh38-2020-A genome as reference.
Cells were filtered with Cell Ranger 6.0.1 following alignment.
Assembly: GRCh38-2020-A
Supplementary files format and content: barcode annotation: filtered barcode annotation; feature annotation: filtered feature list; count matrix: filtered UMI count matrix

molecule: polyA RNA

source_name: hCD45pos hCD19pos mCD45neg cells from a NSG mice bone marrow

growth_protocol: NSG mice of 8-9 weeks were sublethally irradiated (250cGy). 24 hours after 2 million cells MLL-7 PDX were transplanted via tail vein injection. For combination treatments, as a second cell model 2 million RS4;11 cells were transplanted to non-irradiated animals.

extract_protocol:
Fresh bone marrow cells for day 5 sequentially treated ones, which were stained with Draq7 (BioLegend), hCD45 (BD Bioscience), and hCD19 (BioLegend), together with a PerCP/Cyanine5.5 anti-mouse CD45 (BioLegend). Approximately 20.000 alive/mCD45-/hCD45+/hCD19+ cells were sorted into a PBS (GE Healthcare Life Sciences) + 2% FBS (Thermo Scientific) coated tube and prepared for sequencing using the 10x Genomics platform at the Center for Translational Genomics, Lund University.
Chromium NEXT GEM Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index)

treatment_protocol: For combination treatments, animals were treated with 6 days of AZD1775 (MedChemExpress) at 120mg/kg alone or with Dasatinib for 3 days (MedChemExpress) at 50 mg/kg. Vehicle animals received 6 days of 5% DMSO, 40% PEG 300, 5% Tween 80 and 50% NaCl solution (all from Sigma-Aldrich) when 1 % of hCD45pos(BD Bioscience) hCD19pos (Biolengend) mCD45neg (Biolengend) cells were detected in peripheral blood. Animals were sacrificed by cervical dislocation 20 h after the last treatment.

value: KMT2A-r acute lymphoblastic leukemia

value: KMT2A::AFF1;MEF2D::PTMA; KMT2A::PTPRC and clonal mutations in FLGE3292G; FLT3I836del; METL575I; CHEK1I465T; CSF1RS422C

value: AZD1775 Dasatinib

tag: time


title: MLL7 PDX Vehicle (DMSO) day6 scRNAseq

value: hCD45pos hCD19pos mCD45neg cells from a NSG mice bone marrow


title: 0.25% DMSO (30min)

value: Ascites

value: macrophage cell line

value: WT


title: NK_TAK981_rep3 (RNA-seq)


title: SMC__Pat583

status: Public on Feb 14 2024

city: Daejeon

first: Jun Hyeong

last: Lee

address: 291 Daehak-ro, Yuseong-gu, Daejeon

institute: KAIST

description: *** Raw data not provided for this sample due to patient privacy concerns ***

data_processing:
The adapter sequences in the FASTQ file were trimmed out by Trimmomatic (v.0.39)
To filter out rRNA, SortMeRNA (v.2.1b) was used.
The filtered reads were aligned to the hg38 reference genome by the STAR aligner (v.2.7.6a) in two-pass basic mode with gencode annotation (v.35)
The aligned reads were then sorted by samtools (v.1.7) and the read counts were calculated by HTSeq
To quantify gene expression, the read counts were normalized in the TPM value.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample (Protein-coding genes only)

source_name: Lung cancer tissue

extract_protocol:
The AllPrep DNA/RNA Mini Kit (Qiagen, USA) was used to purify RNA from formalin-fixed paraffin-embedded (FFPE) or fresh tumor samples.
Library preparation was performed with either the TruSeq RNA Library Prep Kit v2 (Illumina, USA) or the TruSeq RNA Access Library Prep Kit (Illumina, USA), following the manufacturer’s instructions.

value: Lung cancer tissue

tag: ethnicity

value: Korean

tag: treatment outcome

value: Responder

value: PD-1/PD-L1 inhibitor


title: DMSO sample 1 [A4]

value: Candida cells

tag: treatment

value: DMSO 5 uL

value: 40 ul


title: NK_DMSO_rep2 (RNA-seq)

value: blood


title: SMC__Pat529

value: Non-responder


title: NK_TAK981_rep2 (RNA-seq)

value: natural killer


title: SMC__Pat580


title: SMC__Pat453


title: SMC__Pat433


title: in vivo RS4.11 AZD1775 Dasatinib scRNAseq

source_name: RS4;11 mixed lineage leukemia t(4;11) rearranged (MLLr) cells.hCD45pos hCD19pos mCD45neg cells from a NSG mice bone marrow.

value: KMT2A-r acute lymphoblastic leukemia


title: NK_DMSO_rep1 (RNA-seq)

value: DMSO


title: SMC__Pat377


title: SMC__Pat401


title: SMC__Pat333


title: SMC__Pat581


title: SMC__Pat579


title: SMC__Pat327


title: SMC__Pat582


title: SMC__Pat391


title: SMC__Pat487


title: in vivo RS4.11 Vehicle scRNAseq

value: RS4;11 mixed lineage leukemia t(4;11) rearranged (MLLr) cells.hCD45pos hCD19pos mCD45neg cells from a NSG mice bone marrow.


title: SMC__Pat301


title: MLL7 PDX AZD1775 (Wee1i) day6 scRNAseq

value: hCD45pos hCD19pos mCD45neg cells from a NSG mice bone marrow

value: KMT2A::AFF1;MEF2D::PTMA; KMT2A::PTPRC and clonal mutations in FLGE3292G; FLT3I836del; METL575I; CHEK1I465T; CSF1RS422C


title: SMC__Pat486


title: SMC__Pat445


title: NK_TAK981_rep1 (RNA-seq)


title: in vivo RS4.11 AZD1775 scRNAseq


title: SMC__Pat399


title: SMC__Pat350


title: SMC__Pat344


title: SMC__Pat483


title: SMC__Pat418


title: SMC__Pat315


title: SMC__Pat355


title: SMC__Pat459


title: SMC__Pat294


title: SMC__Pat248


title: SMC__Pat292


title: SMC__Pat287


title: SMC__Pat223


title: SMC__Pat260


title: SMC__Pat222


title: SMC__Pat358


title: SMC__Pat246


title: SMC__Pat523


title: SMC__Pat478


title: SMC__Pat206


title: SMC__Pat512


title: SMC__Pat515


title: SMC__Pat462


title: SMC__Pat527


title: SMC__Pat494


title: SMC__Pat514


title: SMC__Pat501


title: SMC__Pat516


title: SMC__Pat372


title: SMC__Pat293


title: SMC__Pat306


title: SMC__Pat208


title: SMC__Pat573


title: SMC__Pat352


title: SMC__Pat541


title: SMC__Pat264


title: SMC__Pat385


title: SMC__Pat374


title: SMC__Pat456


title: SMC__Pat334


title: SMC__Pat469


title: SMC__Pat251


title: SMC__Pat363


title: SMC__Pat297


title: SMC__Pat442


title: SMC__Pat421


title: SMC__Pat233


title: SMC__Pat380


title: SMC__Pat397


title: SMC__Pat441


title: SMC__Pat386


title: SMC__Pat436


title: SMC__Pat179


title: SMC__Pat437


title: SMC__Pat440


title: SMC__Pat476


title: SMC__Pat431


title: SMC__Pat455


title: SMC__Pat427


title: SMC__Pat480


title: SMC__Pat178


title: SMC__Pat439


title: SMC__Pat284


title: SMC__Pat446


title: SMC__Pat416


title: SMC__Pat347


title: SMC__Pat376


title: SMC__Pat438


title: SMC__Pat177


title: SMC__Pat326


title: SMC__Pat217


title: SMC__Pat323


title: SMC__Pat324


title: SMC__Pat412


title: SMC__Pat253


title: SMC__Pat342


title: SMC__Pat394


title: SMC__Pat340


title: SMC__Pat185


title: SMC__Pat189


title: SMC__Pat182


title: SMC__Pat138


title: SMC__Pat176


title: SMC__Pat239


title: SMC__Pat241


title: SMC__Pat132


title: SMC__Pat243


title: SMC__Pat215


title: SMC__Pat204


title: SMC__Pat181


title: SMC__Pat130


title: SMC__Pat128


title: SMC__Pat129


title: SMC__Pat219


title: SMC__Pat249


title: SMC__Pat126


title: SMC__Pat230


title: SMC__Pat237


title: SMC__Pat125


title: SMC__Pat224


title: SMC__Pat123


title: SMC__Pat121


title: SMC__Pat124


title: SMC__Pat240


title: SMC__Pat118


title: SMC__Pat119


title: SMC__Pat116


title: SMC__Pat117


title: SMC__Pat113


title: SMC__Pat221


title: SMC__Pat109


title: SMC__Pat107


title: SMC__Pat111


title: SMC__Pat232


title: SMC__Pat104


title: SMC__Pat103


title: SMC__Pat105


title: SMC__Pat110


title: SMC__Pat106


title: SMC__Pat102


title: SMC__Pat100


title: SMC__Pat422


title: SMC__Pat97


title: SMC__Pat229


title: SMC__Pat98


title: SMC__Pat101


title: SMC__Pat214


title: SMC__Pat96


title: SMC__Pat211


title: SMC__Pat213


title: SMC__Pat414


title: SMC__Pat115


title: SMC__Pat89


title: SMC__Pat88


title: SMC__Pat108


title: SMC__Pat86


title: SMC__Pat87


title: SMC__Pat85


title: SMC__Pat84


title: SMC__Pat203


title: SMC__Pat200


title: SMC__Pat199


title: SMC__Pat99


title: SMC__Pat78


title: SMC__Pat197


title: SMC__Pat195


title: SMC__Pat196


title: SMC__Pat71


title: SMC__Pat90


title: SMC__Pat193


title: SMC__Pat188


title: SMC__Pat194


title: SMC__Pat190


title: SMC__Pat186


title: SMC__Pat65


title: SMC__Pat187


title: SMC__Pat184


title: SMC__Pat192


title: SMC__Pat63


title: SMC__Pat180


title: SMC__Pat58


title: SMC__Pat202


title: SMC__Pat56


title: SMC__Pat62


title: SMC__Pat173


title: SMC__Pat172


title: SMC__Pat170


title: SMC__Pat61


title: SMC__Pat174


title: SMC__Pat57


title: SMC__Pat169


title: SMC__Pat55


title: SMC__Pat201


title: SMC__Pat171


title: SMC__Pat59


title: SMC__Pat69


title: SMC__Pat165


title: SMC__Pat163


title: SMC__Pat161


title: SMC__Pat162


title: SMC__Pat159


title: SMC__Pat156


title: SMC__Pat155


title: SMC__Pat154


title: SMC__Pat168


title: SMC__Pat167


title: SMC__Pat153


title: SMC__Pat157


title: SMC__Pat166


title: SMC__Pat160


title: SMC__Pat164


title: SMC__Pat151


title: SMC__Pat142


title: SMC__Pat148


title: SMC__Pat152


title: SMC__Pat158


title: SMC__Pat145


title: SMC__Pat146


title: SMC__Pat144


title: SMC__Pat137


title: SMC__Pat140


title: SMC__Pat510


title: SMC__Pat149


title: SMC__Pat134


title: SMC__Pat143


title: SMC__Pat147


title: SMC__Pat141


title: SMC__Pat133


title: SMC__Pat139


title: SMC__Pat135


title: SMC__Pat547


title: SMC__Pat567


title: SMC__Pat549


title: SMC__Pat150


title: SMC__Pat532


title: SMC__Pat131


title: SMC__Pat564


title: SMC__Pat539


title: SMC__Pat127


title: SMC__Pat122


title: SMC__Pat575


title: SMC__Pat136


title: SMC__Pat507


title: SMC__Pat307


title: SMC__Pat556


title: SMC__Pat578


title: SMC__Pat546


title: SMC__Pat120


title: SMC__Pat563


title: SMC__Pat553


title: SMC__Pat112


title: SMC__Pat551


title: SMC__Pat552


title: SMC__Pat513


title: SMC__Pat536


title: SMC__Pat545


title: SMC__Pat558


title: SMC__Pat378


title: SMC__Pat373


title: SMC__Pat562


title: SMC__Pat538


title: SMC__Pat560


title: SMC__Pat526


title: SMC__Pat559


title: SMC__Pat557


title: SMC__Pat282


title: SMC__Pat91


title: SMC__Pat521


title: SMC__Pat114


title: SMC__Pat535


title: SMC__Pat499


title: SMC__Pat93


title: SMC__Pat92


title: SMC__Pat94


title: SMC__Pat354


title: SMC__Pat81


title: SMC__Pat530


title: SMC__Pat83


title: SMC__Pat485


title: SMC__Pat451


title: SMC__Pat80


title: SMC__Pat79


title: SMC__Pat76


title: SMC__Pat75


title: SMC__Pat77


title: SMC__Pat82


title: SMC__Pat74


title: SMC__Pat572


title: SMC__Pat341


title: SMC__Pat73


title: SMC__Pat70


title: SMC__Pat72


title: SMC__Pat577


title: SMC__Pat64


title: SMC__Pat68


title: SMC__Pat576


title: SMC__Pat60


title: SMC__Pat565


title: SMC__Pat566


title: SMC__Pat519


title: SMC__Pat548


title: SMC__Pat42


title: SMC__Pat53


title: SMC__Pat49


title: SMC__Pat52


title: SMC__Pat40


title: SMC__Pat66


title: SMC__Pat48


title: SMC__Pat39


title: SMC__Pat47


title: SMC__Pat45


title: SMC__Pat35


title: SMC__Pat32


title: SMC__Pat36


title: SMC__Pat41


title: SMC__Pat544


title: SMC__Pat381


title: SMC__Pat37


title: SMC__Pat54


title: SMC__Pat33


title: SMC__Pat46


title: SMC__Pat31


title: SMC__Pat44


title: SMC__Pat50


title: SMC__Pat28


title: SMC__Pat29


title: SMC__Pat43


title: SMC__Pat26


title: SMC__Pat30


title: SMC__Pat24


title: SMC__Pat22


title: SMC__Pat21


title: SMC__Pat38


title: SMC__Pat20


title: SMC__Pat51


title: SMC__Pat18


title: SMC__Pat34


title: SMC__Pat17


title: SMC__Pat15


title: SMC__Pat16


title: SMC__Pat14


title: SMC__Pat13


title: SMC__Pat11


title: SMC__Pat10


title: SMC__Pat8


title: SMC__Pat9


title: SMC__Pat12


title: SMC__Pat1


title: SMC__Pat5


title: SMC__Pat4


title: SMC__Pat6


title: SMC__Pat2


title: SMC__Pat3


title: SMC__Pat27