title: agu79_Family232_48hpf_noc2l-/-_7

city: Sagamihara City

first: Kenta

last: Watai

state: Kanagawa

address: 5-10-1 Fuchinobe

country: Japan

institute: Aoyamagakuin University

description:
Library name: sample48
RNA from single larva at 48 hpf
watai_148_L15_S48

data_processing:
Read 1 reads were processed with fastp (version 0.21.0) (S. Chen et al. 2018) using the following command: “ fastp --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31”. The trimmed reads were then mapped to a zebrafosh mRNA refferece Danio_rerio.GRCz11.cdna.all.fa, using BWA mem (version 0.7.17-r1188) (W. Chen et al. 2013) with the default parameters. The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0) (Patro et al. 2017).
Assembly: Danio_rerio.GRCz11.cdna.all.fa
Supplementary files format and content: csv-delimited text file includes rawcnt values for each Sample

organism: Danio rerio

source_name: Whole organism

growth_protocol: The zebrafish (Danio rerio) strains RIKEN WT (RW) was maintained under a 14-h light/10-h dark cycle. The water temperature was kept at 28°C ± 1°C and water quality conditions were maintained according to The Zebrafish Book (University of Oregon Press) and the Guide for the Care and Use of Laboratory Animals 8th edition (National Research Council, 2011).

extract_protocol:
At each developmental stage (24 hpf, 36 hpf, and 48 hpf), 6-9 embryos were individually placed into 1.5 mL tubes. To each tube, 200 µL of TRI Reagent-LS was added and the contents were vortexed. Subsequently, 40 µL of chloroform was added, followed by vortexing, and the tubes were left to stand at room temperature for 15 minutes to allow phase separation into an aqueous phase, interphase, and organic phase. The aqueous phase, which contains RNA, was transferred to a new 1.5 mL tube, mixed by inversion with 100 µL of isopropanol, and left to stand for 10 minutes to precipitate the RNA. After centrifugation (12,000 × g, 2°C, 10 minutes), the supernatant was removed, and the RNA was recovered as a pellet. The pellet was washed twice with 75% ethanol and eluted in 10 µL of nuclease-free water (NFW; Cosmo Bio Co., Ltd.).
3’ mRNA-Seq were conducted according to the Lasy-Seq ver. 1.1 protocol (https://sites.google.com/view/lasy-seq/) (Kamitani et al. 2019; Kashima et al. 2021). Briefly, total RNA was reverse transcribed using an RT primer with index and SuperScript IV reverse transcriptase (Thermo Fisher Scientific, Waltham, MA, USA). Then, all RT mixtures of the samples were pooled and purified using an equal volume of AMpure XP beads (Beckman Coulter, Brea, CA, USA) according to the manufacturer’s instructions. Second strand synthesis was conducted on the pooled samples using RnaseH (5 U/μL, Enzymatics, Beverly, MA, USA), and DNA polymerase I (10 U/μL, Enzymatics, Beverly, MA, USA). To avoid the carryover of large amounts of rRNAs, the mixture was subjected to Rnase treatment using Rnase T1 (Thermo Fisher Scientific, Waltham, MA, USA). Then, purification was conducted with a 0.8× volume of Ampure XP beads. Fragmentation, end-repair, and A-tailing were conducted using 5× WGS Fragmentation Mix (Enzymatics, Beverly, MA, USA). The Adapter for Lasy-Seq was ligated using 5× Ligation Mix (Enzymatics, Beverly, MA, USA), and the adapter-ligated DNA was purified twice with a 0.8× volume of Ampure XP beads. After optimisation of PCR cycles for library amplification by qPCR using Evagreen, 20× in water (Biotium, Fremont, CA, USA) and the QuantStudio5 Real-Time PCR System (Applied Biosystems, Waltham, MA, USA), the library was amplified using KAPA HiFi HotStart ReadyMix (KAPA BIOSYSTEMS, Wilmington, MA, USA) on the ProFlex PCR System (Applied Biosystems, Waltham, MA, USA). The amplified library was purified with an equal volume of Ampure XP beads. One microliter of the library was then used for electrophoresis using a Bioanalyzer 2100 with the Agilent High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA) to check for quality. Then, sequencing of 150-bp paired-end reads was performed using HiSeq X Ten (Illumina, San Diego, CA, USA) by Macrogen, Inc. (Seoul, Korea).

value: Whole organism

value: noc2l -/-


title: agu79_Family232_48hpf_noc2l-/-_5

status: Public on Mar 27 2025

type: SRA

description:
Library name: sample46
RNA from single larva at 48 hpf
watai_146_L15_S46

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: GO_day14_totbulkRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_rep4

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
RNA-Seq datasets were aligned to the Mus musculus genome assembly (GRCm38/mm10 Dec. 2011) as single-end (Smart-Seq2 polyA datasets) or paired-end (total random primed datasets) using STAR (Dobin et al. 2013) with parameters “-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000”
RNA-Seq samples for hybrid Bl6 x JF1 F1 2-cell embryos were separately aligned to Bl6 and JF1 genomes obtained by injecting JF1 single-nucleotide polymorphisms (SNPs) into reference mm10 genome using previously published SNP table (Takada et al. 2013). RNA-seq reads were categorized as maternal (Bl6), paternal (JF1) or undefined based on minimal number of mismatches in alignments to both genomes.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated from BAM files using the function qExportWig from QuasR package selecting uniquely mapped reads. BigWig processed files for hybrid Bl6 x JF1 2-cell embryos were generated separately for maternal (files ending with MAT.bw), paternal (files ending with PAT.bw) and total alignments normalized by total number of mapped allelic reads (MAT and PAT) or total number of mapped reads.

organism: Mus musculus

source_name: growing oocyte day 14

extract_protocol:
After removing the zona-pellucida by treating with acid tyrode’s solution, oocytes and F1 hybrid 2-cell embryos were washed in PBS supplemented with 0.05% Polyvinyl alcohol and lysed in Smartseq2 lysis buffer.
Libraries were prepared by Smartseq2 protocol. cDNAs were prepared by oligo dT based reverse transcription and template switching using Superscript II reverse transcriptase followed by the pre-amplification PCR using KAPA HiFi HotStart ReadyMix PCR Kit and the purification using AMPure Xp beads. 1ng of pre-amplified cDNA was tagmented by Tn5 transposase and adapter-ligated fragments were amplified with adding Nextera XT indexes followed by the purification using AMPure XP beads. Libraries with different indexes were pooled and submitted to sequencing. For total RNA sequencing GOs were isolated from the d14.0 mice. 60-80 oocytes were pooled and frozen in 100μl of Buffer RL. 4 and 3 biological replicates were prepared for ctrl and Kdm2aKOKdm2bKO, respectively. RNA was purified by using Single Cell RNA Purification Kit (NORGEN; 51800). Libraries were prepared according to Illumina Stranded total RNA-seq protocol with Illumina IDT DNA/RNA UDI indexes.

tag: cell type

value: growing oocyte day 14

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ

tag: strain


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_22

molecule: polyA RNA

source_name: growing oocyte day 9

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: ZT8-old-3

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

data_processing:
Primary analysis of raw sequencing datasets was performed using the nf-core/rnaseq v3.6 pipeline (https://doi.org/10.5281/zenodo.7998767).
Raw FastQ files were quality and adapter trimmed with Trim Galore v0.6.7. (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Ribosomal RNA reads were filtered out with SortMeRNA v 4.3.476.
Cleaned reads were aligned with STAR v2.6.1d77 against the GRCh38 genome from the Ensembl 108 database and expression for annotated genes was quantified using Salmon v1.5.278 in mapping-based mode.
Assembly: GRCm39
Supplementary files format and content: raw counts as caluclated by STAR v.2.7.6a in --quantMode GeneCounts

source_name: lung

growth_protocol: Male specific pathogen-free C57BL/6J young adult mice (2-month-old, 20-25g) and elderly mice (18-month-old, 35-45 g) were fed a standard rodent chow (SAFE A04, SAFE, Augy, France) with water ad libitum and housed in a 12-h light/dark cycle.

extract_protocol:
A frozen piece of lung was resuspended in 500 µL of TRIzol and RNA were extracted following the manufacturer protocol. RNA extracts were clean up with Macherey-Nagel nucleospin RNA column.
The quality of RNA was evaluated with a Bioanalyzer (Agilent Technologies) and the Agilent RNA 6000 nano kit. Only RNAs with RNA Integrity Number (RIN) over 7 were used. 200ng of RNA were used for library construction followed by 100 bp paired-end sequencing performed by DNBSEQ technology and DNA nanoballs.

treatment_protocol: Lungs from young mice and old mice were harvested at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20 (n=4-5/group), were perfused with 10 mL ice-cold PBS through using the right cardiac ventricule route. Lungs were incubated in RNA later for 10 minutes at room temperature, frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: lung

tag: timepoint

tag: age

value: old

tag: number (zt)


title: ZT8-old-1


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_21


title: agu79_Family232_48hpf_noc2l-/-_6

description:
Library name: sample47
RNA from single larva at 48 hpf
watai_147_L15_S47


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_19


title: GO_day14_totbulkRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_rep2


title: GO_day14_totbulkRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_rep3


title: HaCaT: keratinocyte SCC BCC cell line

city: Boston

first: Tomonori

last: Oka

state: MA

department: CBRC

country: USA

institute: Massachusetts general hospital

data_processing:
The QC for the RNA samples was performed using Qubit and Bioanalyzer instruments.
Libraries were then prepared using NEBNext Ultra II non-directional RNA Library Prep kit
Library quality and concentration were assessed with Labchip and qPCR.
Libraries were sequenced on Novaseq6000 using PE150 sequencing.
Base calling was done with bcl2fastq.
Data was trimmed to remove low quality reads and adapter reads. Remaining reads were mapped to the reference genome using STAR, followed by calculation of FPKM.
genome build: Human genome/GRCh38
processed data files format and content: FPKM values

organism: Homo sapiens

source_name: HaCaT

extract_protocol: Used RNAeasy mini kit (Qiagen) and followed instruction

value: human normal keratinocyte cell line

tag: cell line

value: HaCaT


title: Kert: keratinocyte SCC BCC cell line

source_name: KERTr

value: Kert


title: agu79_Family232_48hpf_noc2l-/-_3

description:
Library name: sample44
RNA from single larva at 48 hpf
watai_144_L15_S44


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_20


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_18


title: ZT8-young-5

value: young


title: ZT8-young-4


title: GO_day14_totbulkRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_rep1


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_17


title: ZT8-young-3


title: agu79_Family232_48hpf_noc2l-/-_4

description:
Library name: sample45
RNA from single larva at 48 hpf
watai_145_L15_S45


title: agu79_Family232_48hpf_noc2l-/-_1

description:
Library name: sample42
RNA from single larva at 48 hpf
watai_142_L15_S42


title: agu79_Family232_48hpf_noc2l-/-_2

description:
Library name: sample43
RNA from single larva at 48 hpf
watai_143_L15_S43


title: N3

city: Beijing

first: Nianchen

last: Liu

address: No. 95 Yong'an Road, Xicheng District, Beijing

country: China

institute: Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical Universit

description: Library name: N3

data_processing:
SOAPnuke V2.3
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: read counts and FPKM values for each Sample

source_name: colon

extract_protocol:
Extracting Total RNA with Trizol
Total RNA was processed using mRNA enrichment method, reverse transcribed and subjected to PCR using specific primers. The PCR product was thermally denatured into single strands, and then a bridge primer was used to circularize the single stranded DNA to obtain a single stranded circular DNA library.

treatment_protocol: The anal 1/3 segment of the mouse colon was excised, frozen in liquid nitrogen, and stored at -80°C.

value: colon

value: WT

tag: treatment

value: normal control


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_15


title: N4

description: Library name: N4


title: agu79_Family232_48hpf_noc2l+/+_9

description:
Library name: sample41
RNA from single larva at 48 hpf
watai_141_L15_S41

value: noc2l +/+


title: agu79_Family232_48hpf_noc2l+/+_8

description:
Library name: sample40
RNA from single larva at 48 hpf
watai_140_L15_S40


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_16


title: ZT8-young-1


title: ZT4-old-4


title: agu79_Family232_48hpf_noc2l+/+_7

description:
Library name: sample39
RNA from single larva at 48 hpf
watai_139_L15_S39


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_13


title: D6

description: Library name: D6

value: AOM/DSS modeling


title: ZT4-old-5


title: N2

description: Library name: N2


title: agu79_Family232_48hpf_noc2l+/+_5

description:
Library name: sample37
RNA from single larva at 48 hpf
watai_137_L15_S37

value: Whole organism


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_12


title: agu79_Family232_48hpf_noc2l+/+_6

description:
Library name: sample38
RNA from single larva at 48 hpf
watai_138_L15_S38


title: D2

description: Library name: D2


title: ZT4-old-3


title: D5

description: Library name: D5


title: ZT4-old-2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_11


title: agu79_Family232_48hpf_noc2l+/+_4

description:
Library name: sample36
RNA from single larva at 48 hpf
watai_136_L15_S36


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_10


title: ZT8-young-2


title: C5

description: Library name: C5

value: creatine supplementiom


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_14


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_9


title: agu79_Family232_48hpf_noc2l+/+_3

description:
Library name: sample35
RNA from single larva at 48 hpf
watai_135_L15_S35


title: D7

description: Library name: D7


title: ZT4-old-1


title: ZT4-young-5


title: agu79_Family232_48hpf_noc2l+/+_2

description:
Library name: sample34
RNA from single larva at 48 hpf
watai_134_L15_S34


title: C4

description: Library name: C4


title: agu79_Family232_48hpf_noc2l+/+_1

description:
Library name: sample33
RNA from single larva at 48 hpf
watai_133_L15_S33


title: ZT4-young-4


title: C3

description: Library name: C3


title: C2

description: Library name: C2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_7


title: agu79_Family232_36hpf_noc2l-/-_9

description:
Library name: sample32
RNA from single larva at 36 hpf
watai_132_L15_S32

value: noc2l -/-


title: ZT4-young-2


title: agu79_Family232_36hpf_noc2l-/-_8

description:
Library name: sample31
RNA from single larva at 36 hpf
watai_131_L15_S31


title: PdgfraCreER;MN1:BEND2;AI14-1-R2

first: wei

last: Shi

address: Chinese Institute for Brain Research, Beijing(CIBR), Jianzan Building, No.26, Science Park Road, Zhongguancun Life Science Park, Changping District, Beijing, China

institute: Chinese institute for brain research

description: Library name: Sample4

data_processing:
Sequencing reads from RNA-seq of OPC cells were trimmed with Trimmomatic 0.39 and aligned to mouse reference genome (GRCm38/mm10) using Salmon (1.8.0). Gene expression matrix was acquired by Tximport . Genes with Reads<10 in all samples were excluded. Heatmap analysis was performed with R (https://www.R-project.org/) using Heatmap. Each gene was normalized to its maximum value across different samples.
Assembly: GRCm38/mm10
Supplementary files format and content: csv file for counts.

source_name: brian

extract_protocol:
Brains of neonatal mice were extracted and transferred into 60mm dishes with 1X Lo Ovo buffer (1% BSA in DPBS, Sigma-Aldrich #A3803) and pial membranes were carefully removed. All procedures were done at room temperature, unless otherwise stated. Forebrains from individual neonatal mice were cut into chunks and placed in papain (20U/mL in EBSS, Worthington #LK003176，Worthington #LK003188) and DNase (200U/mL in ddH2O, Worthington #LK003170) in 1X Lo Ovo. Tissue chunks were digested for 30 min at 37 °C, then washed by 1X Lo Ovo for 2-3 times and triturated by 5 mL pipette and P-1000 pipetman. The cells were centrifuged for 15 min at 300 x g, then discarded supernatant and resuspended cell pellets with 1X Lo Ovo. Cells were kept on ice before sorting. For fluorescence-activated cell sorting (FACS), the cells were incubated with DAPI (1μg/mL, Sigma-Aldrich #D9542) for 10 min and then sorted using the BD FACSAria Fusion Flow Cytometer (BD Biosciences). After gating on morphology and singlets, DAPI-negative (live) and tdTomato+ cells were collected into a 5mL tube (Eppendorf #30119401) containing 1X Lo Ovo.
Cells were immediately lysed in lysis buffer, then reverse transcribed to cDNA and amplified using Single Cell Full Length mRNA-Amplificatoin Kit (Vazyme, N712). cDNA libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-TD503) according to the manufacturer’s instructions. cDNA libraries were sequenced on an MGISEQ-2000 platform using a 100bp paired-end setting.

value: brian

value: Pdgfra lineage

value: Intraperitoneal Injection of tamoxifen at P0 and P1,sacrifice at P4


title: ZT4-young-3

value: lung


title: PdgfraCreER;MN1:BEND2;AI14-1-R1

description: Library name: Sample3


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_6

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: ZT4-young-1


title: PdgfraCreER;AI14-1-R2

description: Library name: Sample2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_4


title: agu79_Family232_36hpf_noc2l-/-_7

description:
Library name: sample30
RNA from single larva at 36 hpf
watai_130_L15_S30


title: ZT0-old-5

value: old


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_3


title: agu79_Family232_36hpf_noc2l-/-_6

description:
Library name: sample29
RNA from single larva at 36 hpf
watai_129_L15_S29


title: ZT0-old-4


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_8


title: PdgfraCreER;AI14-1-R1

description: Library name: Sample1


title: ZT0-old-3


title: agu79_Family232_36hpf_noc2l-/-_4

description:
Library name: sample27
RNA from single larva at 36 hpf
watai_127_L15_S27


title: agu79_Family232_36hpf_noc2l-/-_5

description:
Library name: sample28
RNA from single larva at 36 hpf
watai_128_L15_S28


title: TREx293_MN1-CXXC5_rep2

description: Library name: Sample10

data_processing:
Sequencing reads from RNA-seq of TREx293 cells were aligned to the Human reference genome (GRCh38) using Hisat2 (v2-2.1.0)54 with default parameters. The resulting data were converted and sorted with Samtools (v1.0.1)55. Expression values of each gene were quantified as transcripts per million (TPM) using featureCounts (v2.0.0)56.
Assembly: hg38
Supplementary files format and content: txt files include counts for each sample

growth_protocol: TREx293 cells were grown at 37 ℃ in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, GEMINI 900108).

extract_protocol:
Total RNA was extracted using trizol reagent. The integrity of the total RNA was determined with a Bioanalyzer 2100 or 2200 (Agilent).
cDNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme). cDNA libraries were sequenced on DNBSEQ-T7 platform using a 150bp paired-end setting.

treatment_protocol: Stable cell lines were generated by cloning BEND2 chimera cDNAs, which were tagged with a 3×HA epitope, into the pcDNA5/FRT/TO vector. This was followed by co-transfecting these constructs with the pOG44 plasmid (1:9 ratio) into T-RexTM293 cells. Subsequently, the transfected cells were subjected to stringent selection using a combination of 10 μg/mL Blasticidin and 100 μg/mL Hygromycin for 7-14 days. Doxycycline was used to induce gene expression.

value: MN1-CXXC5 knockin


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_1


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_5


title: TREx293_MN1-CXXC5_rep1

description: Library name: Sample9


title: ZT0-old-2


title: agu79_Family232_36hpf_noc2l-/-_3

description:
Library name: sample26
RNA from single larva at 36 hpf
watai_126_L15_S26


title: TREx293_MN1-BEND2_rep2

description: Library name: Sample8

value: MN1-BEND2 knockin


title: agu79_Family232_36hpf_noc2l-/-_2

description:
Library name: sample25
RNA from single larva at 36 hpf
watai_125_L15_S25


title: ZT0-young-5

value: young


title: ZT0-old-1


title: TREx293_MN1-BEND2_rep1

description: Library name: Sample7


title: H460, non-responder, rep 2

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

description:
Library name: H460 non-responder_2
17_S17

data_processing:
Sequences were trimmed with TrimGalore and standard settings
Sequences were aligned with hisat2 (standard settings) on grcm38
Reads were counted by summarizeOverlaps
Assembly: grch38
Supplementary files format and content: semicolon separated file contains the raw transcript counts

source_name: lung-derived

growth_protocol: Tumor cells are maintained in RPMI 1640 medium with 10% FCS and 1% Penicillin/Streptomycin mix, 37°C, 5% CO2

extract_protocol:
RNA was isolated according to manufacturer’s protocol (NucleoSpin® RNA II (MACHEREY-NAGEL GmbH & Co. KG, Düren, 244 Germany)). Concentration and quality of RNA was measured with Qubit (Invitrogen, Waltham, MA, 245 USA) and Agilent Bioanalyzer DNA HS (Agilent, Santa Clara, CA USA)
Libraries were construced with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

treatment_protocol: Tumor cells were stimulated with conditioned supernatants for 8h, 37°C, 5%CO2.

value: lung-derived

value: tumor

value: treated with non-responder supernatant


title: ZT0-young-4


title: ZT0-young-3


title: H460, non-responder, rep 1

description:
Library name: H460 non-responder_1
16_S16


title: TREx293_MN1_rep1

description: Library name: Sample5

value: MN1 knockin


title: agu79_Family232_36hpf_noc2l+/+_8

description:
Library name: sample23
RNA from single larva at 36 hpf
watai_123_L15_S23

value: Whole organism

value: noc2l +/+


title: H460, non-responder, rep 3

description:
Library name: H460 non-responder_3
18_S18


title: TREx293_MN1_rep2

description: Library name: Sample6


title: H460, responder, rep 3

description:
Library name: H460 responder_3
15_S15

value: treated with responder supernatant


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_2


title: H460, responder, rep 2

description:
Library name: H460 responder_2
14_S14


title: agu79_Family232_36hpf_noc2l+/+_7

description:
Library name: sample22
RNA from single larva at 36 hpf
watai_122_L15_S22


title: TREx293_CTRL_rep2

description: Library name: Sample4

value: WT


title: ZT0-young-2


title: agu79_Family232_36hpf_noc2l+/+_6

description:
Library name: sample21
RNA from single larva at 36 hpf
watai_121_L15_S21


title: H460, responder, rep 1

description:
Library name: H460 responder_1
13_S13


title: agu79_Family232_36hpf_noc2l+/+_5

description:
Library name: sample20
RNA from single larva at 36 hpf
watai_120_L15_S20


title: ZT0-young-1


title: TREx293_CTRL_rep1

description: Library name: Sample3


title: H460, control, rep 3

description:
Library name: H460 control_3
12_S12

value: untreated


title: agu79_Family232_36hpf_noc2l-/-_1

description:
Library name: sample24
RNA from single larva at 36 hpf
watai_124_L15_S24

value: noc2l -/-


title: TREx293_BEND2_rep2

description: Library name: Sample2

value: BEND2 knockin


title: AthRoot_cpd_cpd_Rep5

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using catadapt
Trimmed sequence reads were mapped to Arabidopsis Thaliana genome using STAR
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include read counts for each sample

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen) according to manufacturer's protocol
RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat no. E7760), according to the manufacturer’s protocol.

value: Root

value: cpd


title: agu79_Family232_36hpf_noc2l+/+_4

description:
Library name: sample19
RNA from single larva at 36 hpf
watai_119_L15_S19


title: TREx293_BEND2_rep1

description: Library name: Sample1


title: H460, control, rep 1

description:
Library name: H460 control_1
10_S10


title: AthRoot_cpd_cpd_Rep4


title: agu79_Family232_36hpf_noc2l+/+_2

description:
Library name: sample17
RNA from single larva at 36 hpf
watai_117_L15_S17


title: agu79_Family232_36hpf_noc2l+/+_3

description:
Library name: sample18
RNA from single larva at 36 hpf
watai_118_L15_S18


title: AthRoot_cpd_cpd_Rep3


title: FaDu, non-responder, rep 3

description:
Library name: FaDu non-responder_3
9_S9

source_name: pharynx-derived

value: pharynx-derived

value: FaDu


title: FaDu, non-responder, rep 2

description:
Library name: FaDu non-responder_2
8_S8


title: AthRoot_cpd_cpd_Rep1


title: AthRoot_cpd_cpd_Rep2


title: agu79_Family232_24hpf_noc2l-/-_9

description:
Library name: sample15
RNA from single larva at 24hpf
watai_115_L15_S15


title: agu79_Family232_36hpf_noc2l+/+_1

description:
Library name: sample16
RNA from single larva at 36 hpf
watai_116_L15_S16


title: FaDu, non-responder, rep 1

description:
Library name: FaDu non-responder_1
7_S7


title: agu79_Family232_24hpf_noc2l-/-_8

description:
Library name: sample14
RNA from single larva at 24hpf
watai_114_L15_S14


title: AthRoot_Grafted_cpd_WT_Rep5


title: AthRoot_Grafted_cpd_WT_Rep4


title: FaDu, responder, rep 2

description:
Library name: FaDu responder_2
5_S5


title: H460, control, rep 2

description:
Library name: H460 control_2
11_S11


title: FaDu, responder, rep 1

description:
Library name: FaDu responder_1
4_S4


title: agu79_Family232_24hpf_noc2l-/-_6

description:
Library name: sample12
RNA from single larva at 24hpf
watai_112_L15_S12


title: agu79_Family232_24hpf_noc2l-/-_7

description:
Library name: sample13
RNA from single larva at 24hpf
watai_113_L15_S13


title: AthRoot_Grafted_cpd_WT_Rep3


title: agu79_Family232_24hpf_noc2l-/-_5

description:
Library name: sample11
RNA from single larva at 24hpf
watai_111_L15_S11


title: Sebastian biol rep 3

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

data_processing:
Paired-end reads were mapped against the Barley Morex_V3 genome (Mascher et al., 2021; https://doi.org/10.1093/plcell/koab077) using STAR version 2.7.3a (Dobin et al., 2013; https://doi.org/10.1093/bioinformatics/bts635).
Quantification at gene level was done using STAR with the –quantMode GeneCounts option.
Assembly: GCA_904849725.1
Supplementary files format and content: Raw gene level read counts

organism: Hordeum vulgare

source_name: 7-day-old above ground parts

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacturers’ instructions.
RNA sequencing libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions.

treatment_protocol: The above ground parts, including the shoot apex, of 7 day old plants were harvested. Leaf 1 was removed, and the basal centimetre of the shoot apex snap frozen in liquid nitrogen. Three biological replicates were collected for each genotype. Each biological replicate is a pool of 6 individual plants.

value: above ground parts

value: 7 days old

value: Sebastian


title: AthRoot_Grafted_cpd_WT_Rep2


title: Sebastian biol rep 2


title: FaDu, control, rep 1

description:
Library name: FaDu control_1
1_S1

value: tumor


title: FaDu, responder, rep 3

description:
Library name: FaDu responder_3
6_S6


title: Glioma-associated mesenchymal stem cell_glioma treatment_rep3

type: RNA

city: WUHAN

first: YIHAO

last: WANG

state: HUBEI

address: No. 1277 JIEFANG AVENUE

department: Department of Neurosurgery

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Gene expression data from glioma-associated mesenchymal stem cell under glioma treatment

hyb_protocol: Following fragmentation, the data were processed with GeneChip Hybridization Oven 645 and GeneChip Fluidics Station 450 using GeneChip Hybridization Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Workstation with GeneChip Data Collection Software.

label: biotin

source_name: Glioma-associated mesenchymal stem cell under glioma treatment

label_protocol: RNA were prepared according to the standard Affymetrix protocol using GeneChip WT PLUS Reagent Kit and GeneChip Hybridization Wash and Stain Kit.

growth_protocol: GA-MSCs extracted from glioblastoma specimens classified as WHO grade IV (confirmed by pathological examination) were cultured in T25 culture flasks. Once the cell density reached approximately 70%-80%.

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

treatment_protocol: The cells were treated with either DMEM (control condition) or GSC-CM (experimental condition). Each condition was tested in triplicate.

value: Brain


title: Glioma-associated mesenchymal stem cell_untreated_rep1

description: Gene expression data from untreated glioma-associated mesenchymal stem cell

source_name: Glioma-associated mesenchymal stem cell untreated


title: FaDu, control, rep 2

description:
Library name: FaDu control_2
2_S2


title: nal1 biol rep 3

value: nal1 (Sebastian)


title: AthRoot_Grafted_cpd_WT_Rep1


title: agu79_Family232_24hpf_noc2l-/-_4

description:
Library name: sample10
RNA from single larva at 24hpf
watai_110_L15_S10

value: Whole organism


title: agu79_Family232_24hpf_noc2l-/-_2

description:
Library name: sample8
RNA from single larva at 24hpf
watai_108_L15_S8


title: Sebastian biol rep 1


title: AthRoot_Grafted_WT_cpd_Rep5


title: Glioma-associated mesenchymal stem cell_glioma treatment_rep1


title: Glioma-associated mesenchymal stem cell_untreated_rep2


title: agu79_Family232_24hpf_noc2l-/-_3

description:
Library name: sample9
RNA from single larva at 24hpf
watai_109_L15_S9


title: Glioma-associated mesenchymal stem cell_untreated_rep3


title: AthRoot_Grafted_WT_cpd_Rep4


title: HR6_Z8KO2_1

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Assembly: hg19
Supplementary files format and content: TXT

source_name: BT474 cells

growth_protocol: Cells were cultured with RPMI1640+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a Kapa mRNA Hyper Prep kit (Roche).

treatment_protocol: Cells were transduced with lentivirus and selected with puromycin.

tag: knockout


title: AthRoot_Grafted_WT_cpd_Rep3


title: nal1 biol rep 2


title: AthRoot_Grafted_WT_cpd_Rep2


title: FaDu, control, rep 3

description:
Library name: FaDu control_3
3_S3


title: agu79_Family232_24hpf_noc2l-/-_1

description:
Library name: sample7
RNA from single larva at 24hpf
watai_107_L15_S7


title: HR6_Z8KO1_2


title: agu79_Family232_24hpf_noc2l+/+_6

description:
Library name: sample6
RNA from single larva at 24hpf
watai_106_L15_S6

value: noc2l +/+


title: Bonus biol rep 3

value: Bonus


title: AthRoot_Grafted_WT_cpd_Rep1


title: HR6_Z8KO2_2


title: Glioma-associated mesenchymal stem cell_glioma treatment_rep2


title: nal1 biol rep 1


title: AthRoot_Grafted_WT_WT_Rep5


title: Bonus biol rep 2


title: agu79_Family232_24hpf_noc2l+/+_4

description:
Library name: sample4
RNA from single larva at 24hpf
watai_104_L15_S4


title: HR6_2

value: Control


title: Bonus biol rep 1


title: agu79_Family232_24hpf_noc2l+/+_5

description:
Library name: sample5
RNA from single larva at 24hpf
watai_105_L15_S5


title: HR6_1


title: AthRoot_Grafted_WT_WT_Rep3


title: BT474T_2


title: HR6_Z8KO1_1


title: agu79_Family232_24hpf_noc2l+/+_2

description:
Library name: sample2
RNA from single larva at 24hpf
watai_102_L15_S2


title: AthRoot_Grafted_WT_WT_Rep4


title: blf13 biol rep 2

value: blf13 (Bonus)


title: AthRoot_Grafted_WT_WT_Rep1


title: BT474T_1


title: AthRoot_Grafted_WT_WT_Rep2


title: Blood sample from a female participant 316,  sample id 316, collected before COVID (COVID-19 positive).

status: Public on Mar 26 2025

type: genomic

city: Budapest

first: Zsolt

last: Radák

address: Alkotás Street 44, building L3

country: Hungary

institute: Research Center for Molecular Exercise Science, Hungarian University of Sports Science

hyb_protocol: Bisulfite-treated DNA was hybridized to the Infinium MethylationEPIC BeadChip (Illumina Inc., San Diego, CA) according to the manufacturer’s protocol, with a modification where 8 µL of bisulfite-treated DNA was used as the starting material.

scan_protocol: Arrays were scanned using the Illumina iScan System following the manufacturer’s instructions.

data_processing:
Raw intensity data from the Infinium MethylationEPIC array were processed using the R packages minfi, Meffil, and ewastools. Quality control included checking extension, hybridization, and bisulfite conversion. Samples with a call rate < 96% or at least 4% undetected probes were excluded. Probes with a detection p-value > 0.01 in at least 10% of samples were set as undetected. Probes with a bead number < 3 in at least 10% of samples were excluded. Data were normalized using the "noob" method in R.
Beta values were calculated as the ratio of methylated probe intensity to the sum of methylated and unmethylated probe intensities, adjusted for background signal.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Whole blood

label_protocol: Not applicable. The Infinium MethylationEPIC array uses direct hybridization without labeled nucleotides.

extract_protocol: Genomic DNA was extracted from whole blood samples and bisulfite-converted using the EZ-96 DNA Methylation MagPrep Kit (Zymo Research, Irvine, CA, USA) with the KingFisher Flex robot (Thermo Fisher Scientific). The bisulfite conversion followed the manufacturer’s protocol with modifications, including 15 µL MagBinding Beads and a cycle of 16 repetitions at 95°C for 30s, followed by 50°C for 1 hour. After the cycle, DNA was incubated for 10 min at 4°C.

tag: sentrix id

tag: sentrix position

value: Whole blood

value: COVID-19 positive


title: Blood sample from a female participant 315,  sample id 315, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 316,  sample id 113A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 311,  sample id 311, collected before COVID (COVID-19 negative).

value: COVID-19 negative


title: agu79_Family232_24hpf_noc2l+/+_1

description:
Library name: sample1
RNA from single larva at 24hpf
watai_101_L15_S1


title: Blood sample from a male participant 305,  sample id 102A, collected after COVID (COVID-19 positive).


title: agu79_Family232_24hpf_noc2l+/+_3

description:
Library name: sample3
RNA from single larva at 24hpf
watai_103_L15_S3


title: Blood sample from a female participant 303,  sample id 303, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 306,  sample id 103A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 315,  sample id 112A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 305,  sample id 305, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 299,  sample id 96A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 303,  sample id 100A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 299,  sample id 299, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 306,  sample id 306, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 298,  sample id 298, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 311,  sample id 108A, collected after COVID (COVID-19 negative).


title: Blood sample from a male participant 296,  sample id 93A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 293,  sample id 293, collected before COVID (COVID-19 positive).


title: blf13 biol rep 3


title: Blood sample from a female participant 293,  sample id 90A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 290,  sample id 290, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 296,  sample id 296, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 289,  sample id 289, collected before COVID (COVID-19 negative).


title: blf13 biol rep 1


title: Blood sample from a male participant 289,  sample id 86A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 286,  sample id 286, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 282,  sample id 282, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 285,  sample id 82A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 275,  sample id 275, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 279,  sample id 76A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 276,  sample id 276, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 298,  sample id 95A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 277,  sample id 74A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 282,  sample id 79A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 277,  sample id 277, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 274,  sample id 71A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 274,  sample id 274, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 275,  sample id 72A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 273,  sample id 273, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 271,  sample id 68A, collected after COVID (COVID-19 negative).


title: Blood sample from a male participant 272,  sample id 69A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 267,  sample id 267, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 290,  sample id 87A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 270,  sample id 67A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 270,  sample id 270, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 266,  sample id 266, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 286,  sample id 83A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 266,  sample id 63A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 267,  sample id 64A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 264,  sample id 264, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 285,  sample id 285, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 276,  sample id 73A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 263,  sample id 263, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 279,  sample id 279, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 272,  sample id 272, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 264,  sample id 61A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 273,  sample id 70A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 262,  sample id 262, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 260,  sample id 260, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 263,  sample id 60A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 262,  sample id 59A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 271,  sample id 271, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 260,  sample id 57A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 252,  sample id 252, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 252,  sample id 49A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 246,  sample id 43A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 244,  sample id 244, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 249,  sample id 46A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 240,  sample id 37A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 237,  sample id 237, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 244,  sample id 41A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 240,  sample id 240, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 235,  sample id 235, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 237,  sample id 34A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 232,  sample id 232, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 235,  sample id 32A, collected after COVID (COVID-19 negative).


title: Blood sample from a male participant 232,  sample id 29A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 231,  sample id 28A, collected after COVID (COVID-19 negative).


title: Blood sample from a male participant 230,  sample id 230, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 231,  sample id 231, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 229,  sample id 229, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 229,  sample id 26A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 220,  sample id 17A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 220,  sample id 220, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 222,  sample id 19A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 249,  sample id 249, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 222,  sample id 222, collected before COVID (COVID-19 negative).


title: Blood sample from a female participant 246,  sample id 246, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 219,  sample id 16A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 217,  sample id 217, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 216,  sample id 216, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 230,  sample id 27A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 217,  sample id 14A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 215,  sample id 12A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 214,  sample id 214, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 210,  sample id 210, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 214,  sample id 11A, collected after COVID (COVID-19 negative).


title: Blood sample from a male participant 216,  sample id 13A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 209,  sample id 209, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 219,  sample id 219, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 210,  sample id 7A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 208,  sample id 208, collected before COVID (COVID-19 positive).


title: Blood sample from a male participant 209,  sample id 6A, collected after COVID (COVID-19 positive).


title: Blood sample from a male participant 208,  sample id 5A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 206,  sample id 3A, collected after COVID (COVID-19 negative).


title: Blood sample from a female participant 206,  sample id 206, collected before COVID (COVID-19 negative).


title: Blood sample from a male participant 205,  sample id 2A, collected after COVID (COVID-19 positive).


title: Blood sample from a female participant 215,  sample id 215, collected before COVID (COVID-19 positive).


title: Blood sample from a female participant 211,  sample id 8A, collected after COVID (COVID-19 negative).


title: Wild-type

city: Tampa

first: Saulius

last: Sumanas

state: FL

address: 560 Channelside Dr

department: Department of Pathology and Cell Biology

institute: University of South Florida

description:
Library name: WT
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger Cloud Count software v9.0.0. Two separate sequencing runs were performed for each sample. The sequences from the two runs were combined using Cell Ranger Count v9.0.0. Sequences from wild-type and fli1b mutant samples were aggregated using Cell Ranger Aggr v9.0.0
Assembly: Zebrafish Zv11
Supplementary files format and content: Aggregated filtered feature HDF5 archive file and a related aggregation.csv file

source_name: whole embryo

extract_protocol:
fli1b-/- and wild-type embryos were obtained by the corresponding in-crosses of sibling parents that were either homozygous mutant (fli1b-/-) or wild-type (fli1b+/+). Approximately 40 embryos from each sample were manually dechorionated at approximately 23-24 hpf, then transferred into 1.5mL tubes. Whole embryos were then dissociated into a single-cell suspension by cold protease tissue dissociation protocol (Potter and Potter, 2019). All steps were performed on ice. Embryo water was removed and deyolking buffer was added (55mM NaCl, 1.8mM KCl, 1.25mM NaHCO3, in 1XPBS). Embryos were pipetted up and down until yolk was dissolved, then centrifugated at 300G for 1 min. Supernatant was aspirated and embryos were resuspended in 0.5X Danieau Buffer. This step was repeated and after the supernatant was aspirated, Bacillus lichenformis enzyme mix (1x FBS in PBS, 0.5mM of EDTA, 125 U/mL of DNase 1, 10mg/mL of Bacillus lichenformis) was prepared and added to embryos.  Embryos were incubated on ice for 20 mins and titrated 15 times every 2 min. Cell dissociation was monitored under microscope and once completed, centrifugation was performed at 1,200G for 5 min. Supernatant was discarded and pellet was resuspended in 10% FBS in PBS. Cells were then passed through 20-µm strainer, then washed with 500 ul of 10% FBS. Cells were then pelleted again at 1,200G for 5 min, washed once with 1ml of 10% FBS, and centrifuged at 1,200G for 5 min. Cells were resuspended in 250 ul of 10% FBS, then counted using a hemocytometer.
A suspension of approximately 16,000 cells (for each of genotype) was loaded onto the 10x Genomics Single Cell 3’ chip at the USF Genomics Core. Library was prepared according to the manufacturer's instructions (single cell 3' v3.1 protocol).

value: whole embryo

value: wt


title: Blood sample from a female participant 211,  sample id 211, collected before COVID (COVID-19 negative).


title: GBM, MGH66, Fresh

city: Philadelphia

first: Dana

last: Silverbush

state: PA

address: 421 curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented, and hybridized to the Illumina Infinium MethylationEPIC (850K) BeadChip according to the manufacturer’s standard protocol.

scan_protocol: Arrays were scanned using an Illumina iScan with standard Illumina scanner settings.

data_processing: Raw intensity data were processed using the minfi (or RnBeads) package in R. Background correction and normalization were applied.

source_name: GBM

label_protocol: Extracted genomic DNA was bisulfite converted using the Qiagen EpiTect Bisulfite Kit, following the manufacturer’s protocol.

extract_protocol: Genomic DNA was extracted from GBM tissue samples using:  - Fresh-frozen tissue: Qiagen DNeasy Blood & Tissue Kit, following the manufacturer’s protocol.  - FFPE tissue: Qiagen QIAamp DNA FFPE Tissue Kit, with deparaffinization and removal of formalin-induced modifications according to the manufacturer’s instructions.

value: GBM

value: MGMT methylated


title: GBM, MGH128, Fresh


title: shcontrol.input

city: Shaanxi

first: Li

last: Lei

state: Xi 'an

address: 277 Yanta West Road, Xi 'an, Shaanxi

institute: The First Affiliated Hospital of Xi'an Jiaotong University

description:
Library name: shcontrol.input
The raw data are being made available for controlled access in dbGaP

library_source: genomic

data_processing:
Raw reads containing adaptor sequences and those with ambiguous or low-quality bases at the beginning or end were trimmed using Trimmomatic(0.39).
The qualified reads from each sample were aligned to the assembled reference genome using BWA (0.7.17) with default parameters.
MACS2(V2.1.1) was used to call peaks with the pvaue ＜0.05 and annotated to the gene functional region.
Assembly: hg19
Supplementary files format and content: bigwig for each sample

source_name: RCC cell line

growth_protocol: SW839 cell line was grown in their respective media supplemented with 10% fetal bovine serum, 1000 U/ml penicillin and 100 μg/ml streptomycin, in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were treated with 1% PFA at 37 °C for 15 minutes, followed by the addition of 0.125 M glycine to quench the fixation reaction, with incubation for 5 minutes at room temperature. The cells were then washed with cold PBS supplemented with 1 mM PMSF and lysed using ChIP SDS lysis buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 1% SDS) containing protease and phosphatase inhibitors for 15 minutes on ice. DNA fragmentation within the desired range of 200–800 base pairs was achieved using an ultrasonic processor on ice.
ChIP-Seq

treatment_protocol: SW839 cell line was transfection with shTRIP4 plasmid to decrease the expression of TRIP4.

value: RCC cell line

value: shControl


title: GBM, MGH115, Fresh, rep 1

value: MGMT unmethylated


title: GBM, MGH106, Fresh


title: GBM, MGH102, Fresh


title: GBM, MGH115, FFPE, rep 2


title: GBM, MGH129, Fresh, rep 1


title: shTRIP4.p65

description:
Library name: shTRIP4.p65
The raw data are being made available for controlled access in dbGaP


title: GBM, MGH124, Fresh


title: shcontrol.p65

description:
Library name: shcontrol.p65
The raw data are being made available for controlled access in dbGaP


title: GBM, MGH105, FFPE


title: Fli1b_mutant

description:
Library name: MUT
10x Genomics


title: GBM, MGH129, FFPE, rep 2


title: chip-FOXO3-R_L1

city: Hangzhou

first: haixia

last: chen

state: Zhejiang

address: Research Building, School of Medicine, Zijingang Campus, Zhejiang University

institute: epartment of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine

description: Library name: chip-FOXO3-R_L1_1

data_processing:
Raw reads from ChIP-seq were trimmed using Trim Galore, and then the short reads were mapped to the human genome version hg38 with Bowtie2 (version 2.5.4)
BAM files containing mapped reads with PCR duplicates removed using SAMtools (version 1.20)
Peaks were called using MACS2
reads were processed into the BigWig file format from BAM output using bedtools (version 2.31.1)
MEME (Multiple EM for Motif Elicitation, version 5.0.3) Suite for motif-based sequence analyses
Heatmaps were generated using deeptools (version 3.5.5) computeMatrix reference-point-TSS and plotHeatmap functions.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Cells were cultured in DMEM (Sigma, D5796) containing 10% fetal bovine serum (Gibco) and 1% Penicillin- Streptomycin (NCM, #C100C5) at 37°C in a 5% CO2 humidified incubator,

extract_protocol:
HT1080 cells were seeded into 20 cm dishes. Formaldehyde was added directly to the medium to a final concentration of 1% and incubated for 20 minutes at room temperature. To quench the crosslinking reaction, 10x glycine was added for 5 minutes. The tubes were then sonicated on ice using a tip sonicator for 5 minutes (50% amplitude, 1-second on/1-second off intervals). The chromatin lysate was diluted with ChIP lysis buffer, and a 1% input sample was removed. Then, 5 μg of FOXO3a antibody (Affinity Biosciences, #AF3771) was added to the protein sample and incubated overnight at 4°C. Protein A/G magnetic beads were added and incubated for 2 hours at 4°C. The beads were sequentially washed with low salt, high salt, LiCl, and TE buffers. ChIP DNA was eluted at 62°C for 2 hours in 100 μl of elution buffer containing proteinase K, and the final products were obtained after purification (absin, #abs50034).
ChIP product was used for library preparation. The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptor_x0002_ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.

value: Human fibrosarcoma cells


title: GBM, MGH143, FFPE


title: Blood sample from a male participant 205,  sample id 205, collected before COVID (COVID-19 positive).


title: RNApolyII_L1

description: Library name: RNApolyII_L1_1


title: shTRIP4.input

description:
Library name: shTRIP4.input
The raw data are being made available for controlled access in dbGaP


title: chip-FOXO3-R-SRT_L1

description: Library name: chip-FOXO3-R-SRT_L1_1

value: RSL3 and SRT


title: chip-FOXO3-CTL_L1

description: Library name: chip-FOXO3-CTL_L1_1


title: IDC 3

city: Chengdu

first: Hong

last: Chen

state: Sichuan

address: Keyuan South Road

institute: West China Hospital, Sichuan University

description: Library name: Sample 23

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Assembly: hg38
Supplementary files format and content: csv files include raw counts for each Sample

source_name: breast

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: breast

value: Human ductal epithelial cells


title: IDC 2

description: Library name: Sample 22


title: IDC 5

description: Library name: Sample 25


title: IDC 1

description: Library name: Sample 21


title: IDC_DCIS 5

description: Library name: Sample 20


title: IDC_DCIS 4

description: Library name: Sample 19


title: IDC_DCIS 3

description: Library name: Sample 18


title: DCIS 2

description: Library name: Sample 7


title: DCIS 1

description: Library name: Sample 6


title: DCISM 4

description: Library name: Sample 14


title: IDC 4

description: Library name: Sample 24


title: DCISM 2

description: Library name: Sample 12


title: DCIS 4

description: Library name: Sample 9


title: DCIS 5

description: Library name: Sample 10


title: Normal 4

description: Library name: Sample 4


title: DCIS 3

description: Library name: Sample 8


title: Input_4B7_CutNRun

city: Cambridge

first: Sarah

middle: J

last: Horton

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample 3
CUTnRUN

data_processing:
Libraries that were deemed to pass minimum quality thresholds across all quality control metrics during initial quality assessment using FastQC were passed on to downstream analysis. Paired end reads were processed using the CUT&RUNTools pipeline (available at: https://github.com/fl-yu/CUT-RUNTools-2.0)
Assembly: hg38
Supplementary files format and content: BigWig files of uniquely mappable, counts-per-million normalised, high-confidence reads for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig
Supplementary files format and content: Peak-calling was carried out using MACS2 , with the narrow-peak setting and the following parameters (-p 0.05 -B --SPMR --keep-dup all). Black-listed regions were further filtered from the called peaks, and only peaks with a minimum q-value of 0.05 were retained.
Library strategy: CUT&Run

growth_protocol: 0.3 million cells per sample of 697WT and 697KI cell lines were harvested and washed in wash buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x cOmpleteTM EDTA-free PI).

extract_protocol:
As per the CUTnRUN manufacturer's recommendation (CUTANA™ CUT&RUN Protocol v2.0)
Library preparaTon was performed using the NEBNext Ultra II DNA library preparaTon kit for Illumina (NEB, E7645) according to manufacturer’s protocol. Library quality and molarity was measured by Qubit (ThermoFisher) and TapeStation (Agilent). Samples were 50-bp paired-end sequenced on the NovaSeq (Illumina) instrument (CRUK CI Genomics Core Facility).

tag: chip antibody


title: DCISM 1

description: Library name: Sample 11


title: Input_B5_ChIP

description:
Library name: Sample 4
ChIP-seq

data_processing:
Paired end reads were first trimmed for Trueseq adaptors using trimmomatic62 (version 0.36) with the following parameters (PE -phred33 ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25). Adaptor-trimmed reads were then aligned to the human genome version hg38 using Bowtie 263 (version 2.4.5) using the following parameters (--very-sensitive-local --phred33 -I 10 -X 700). Aligned reads in SAM format were converted to BAM format, sorted then indexed using Samtools64 (version 1.11). Duplicate reads in aligned BAM files were marked using the Picard tool MarkDuplicates, and the resulting duplicate reads were subsequently removed by Samtools.
Assembly: hg38
Supplementary files format and content: BigWig files of uniquely mappable, counts-per-million normalised, high-confidence reads for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig
Supplementary files format and content: Peak-calling was carried out using MACS2 , with the narrow-peak setting and the following parameters (-p 0.05 -B --SPMR --keep-dup all). Black-listed regions were further filtered from the called peaks, and only peaks with a minimum q-value of 0.05 were retained.

growth_protocol: 7 million 697WT and 697KI were harvested then cross-linked with 1% formaldehyde for 10min at RT, reacTon that was stopped by Glycine (final concentraTon 125 mM).

extract_protocol:
Cells were washed twice with ice-cold PBS and finally resuspended in cold PBS with 1x Protease inhibitors (PI) (Roche, 11836170001). After this step all buffers contained PI. Cell pellets were lysed with cell lysis buffer (10nM Tris-Cl, 10mM NaCl, 0.2% NP40) for 10min at 4°C. After centrifugaTon at 2400 rpm at 4°C, nuclei were resuspended in 100μl of SonicaTon buffer (0.5% SDS, 20mM Hepes, 5mM EDTA) and incubated on ice for 10min. ChromaTn was sheared by sonicaTon (three cycles of 30 s “ON” and 30 s “OFF”). Prior to immunoprecipitaTon, the sonicated chromaTn was diluted with 400μl of diluTon buffer (20mM Tris pH8.1, 2mM EDTA, 150mM NaCl, 1% TritonX100 and 0.01% SDS). ImmunoprecipitaTon was performed overnight in 20% Tx-100 using 2.5μg of anTbody (IgG, Proteintech, 30000-0-AP; H3, Cell Signalling Technology, 14269S and H3K27ac, AcTve moTf, 39133). Immunocomplexes were captured using the protein A (10002D) and protein G (10004D) Dynabeads (Invitrogen). After 4h, the immunocomplexes were magneTzed and repeatedly washed in the following buffers: RIPA buffer (20mM Hepes, 150mM NaCl, 1mM EDTA, 0.1% SDS, 1% Tx-100), RIPA-500 (20mM Hepes, 500mM NaCl, 1mM EDTA, 0.1% SDS, 1% Tx-100, 0.1% DOC) and LiCl wash buffer (10mM Tris-HCl, 1mM EDTA, 150mM LiCl, 0.5% NP40, 0.5% DOC).
Library preparaTon was performed using the NEBNext Ultra II DNA library preparaTon kit for Illumina (NEB, E7645) according to manufacturer’s protocol. Library quality and molarity was measured by Qubit (ThermoFisher) and TapeStation (Agilent). Samples were 50-bp paired-end sequenced on the NovaSeq (Illumina) instrument (CRUK CI Genomics Core Facility).


title: DCISM 5

description: Library name: Sample 15


title: CREBBP2_4B7_CutNRun

description:
Library name: Sample 1
CUTnRUN

value: CREBBP (Santa Cruz biotechnology, SC369, Lot:G1613)


title: Input_4B7_ChIP

description:
Library name: Sample 3
ChIP-seq


title: T,rep3

city: Shanghai

first: Baohui

last: Han

address: 227 South Chongqing Road

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Chest Hospital

description: Library name: T3

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: human

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human

value: Colorectal cancer


title: Normal 5

description: Library name: Sample 5


title: H3K27ac_B5_ChIP

description:
Library name: Sample 2
ChIP-seq

value: H3K27ac (Active motif, 39133)


title: Input_B5_CutNRun

description:
Library name: Sample 4
CUTnRUN


title: DCISM 3

description: Library name: Sample 13


title: CREBBP2_B5_CutNRun

description:
Library name: Sample 2
CUTnRUN


title: T,rep2

description: Library name: T2


title: Normal 3

description: Library name: Sample 3


title: IDC_DCIS 2

description: Library name: Sample 17


title: IDC_DCIS 1

description: Library name: Sample 16


title: T,rep1

description: Library name: T1


title: C,rep2

description: Library name: C2


title: C,rep3

description: Library name: C3


title: H3K27ac_4B7_ChIP

description:
Library name: Sample 1
ChIP-seq


title: TT_IP,rep2

description: Library name: TT2_IP

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2 (2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools (3.5.0)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: C,rep1

description: Library name: C1


title: TT_input,rep1

description: Library name: TT1_input


title: TT_IP,rep1

description: Library name: TT1_IP


title: TT_input,rep2

description: Library name: TT2_input


title: TC_IP,rep2

description: Library name: TC2_IP


title: TC_IP,rep1

description: Library name: TC1_IP


title: HT_input,rep2

description: Library name: HT2_input


title: HC_IP,rep2

description: Library name: HC2_IP


title: HT_IP,rep2

description: Library name: HT2_IP


title: HT_IP,rep1

description: Library name: HT1_IP


title: HC_input,rep2

description: Library name: HC2_input


title: HC_input,rep1

description: Library name: HC1_input


title: TC_input,rep1

description: Library name: TC1_input


title: AT,rep2

description: Library name: AT2

data_processing:
ATAC-seq reads were aligned to the hg38 reference genome using Bowtie2 (2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools (3.5.0)

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013).
Cells were  vehicle treated and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using AMPure Beads.DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.


title: AC,rep1

description: Library name: AC1


title: AT,rep1

description: Library name: AT1


title: SV-HUC1, treated, 24h, biol rep 4

city: Ljubljana

first: Tadeja

last: Kuret

state: Slovenia

address: Vrazov trg 2

department: Faculty of Medicine

country: Slovenia

institute: University of Ljubljana

description:
Library name: T4
T4

data_processing:
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including Hisat2, FeatureCounts and Novogene's wrapped scripts.
High quality reads were aligned to human (Ensembl GRCh38.p13) reference genome using Hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. The fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups (TNFα-treated vs. control; three replicates per group) was performed using DESeq2 R package (1.20.0). P value was calculated using the negative binomial distribution and the resulting p values were adjusted using the Benjamini-Hochberg’s approach for controlling the false discovery rate.
The clusterProfiler (v. 3.8.1) software was used for enrichment analysis of differentially expressed genes, including Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome database
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes counts for each gene for each sample (gene_count.txt)
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene for each sample (gene_fpkm.txt)
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene for each sample and diferential analysis of treated vs ctrl RT4 cells (treated_RT4vsCtrl_RT4_deg_all seq genes.txt)

growth_protocol: SV-HUC1 cells were grown in 75 cm2 cell culture flasks in basal media consisting of equal parts of advanced Dulbecco's modified Eagle's medium (A-DMEM) and F12 (HAM), supplemented with 5% fetal bovine serum (FBS), and 4 mM GlutaMAX  in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using Quick-RNA Microprep Kit (Zymo Research). Library preparation was performed by Novogene Co., Ltd, using at least 0.5 ug high-quality total RNA input per sample.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina following manufacturer’s recommendations

treatment_protocol: Cells were treated with 20 mU/ml glucose oxidase (GO) for 24h in cell culture media, untreated cells served as controls.

value: urothelial cells

value: glucose oxidase (20 mU/ml)


title: SV-HUC1, treated, 24h, biol rep 2

description:
Library name: T2
T2


title: SV-HUC1, treated, 24h, biol rep 3

description:
Library name: T3
T3


title: SV-HUC1, treated, 24h, biol rep 1

description:
Library name: T1
T1


title: SV-HUC1, control, 24h, biol rep 3

description:
Library name: C3
C3


title: SV-HUC1, control, 24h, biol rep 4

description:
Library name: C4
C4


title: TC_input,rep2

description: Library name: TC2_input


title: SV-HUC1, control, 24h, biol rep 2

description:
Library name: C2
C2


title: HT_input,rep1

description: Library name: HT1_input


title: SV-HUC1, control, 24h, biol rep 1

description:
Library name: C1
C1


title: 3262704_JWH006-C27_CTCF_RBR_R3

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: Library name: sample 6

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina). Raw reads were first trimmed using TrimGalore (v0.6.3) with parameters ‘--paired --retain_unpaired’
Filtered reads were then mapped to the Homo sapiens reference genome GRCm37.p13 using STAR (v2.7.9a). Gene-level read quantification was done using RSEM (v1.3.1)on the Gencode annotation v19 To identify the differentially expressed genes, normalization factors are first estimated using the trimmed mean of M values (TMM) and genes with CPM < 1 in all samples were removed
Next, the TMM normalization factors and raw counts were then used for the Limma-voom analysis using the “voom”, “lmFit” and “eBayes” functtions from the limma R package.
Assembly: hg19
Supplementary files format and content: gene-based raw counts and TPM tsv file

source_name: Blood

extract_protocol:
Total RNA was extracted from cells using Trizol (Thermo Fisher Scientific, 15596026) with the zymo RNA clean and concentrator kit 5 kit.
The RNA-seq library was constructed  for deep sequencing using a Novaseq system (illumina) for single-end 100-bp reads.

value: Blood

value: SEM

value: B-ALL


title: 3262703_JWH005-C27_CTCF_RBR_R2

description: Library name: sample 5


title: 3262700_JWH002-C27_CTCF_WT_R2

description: Library name: sample 2


title: 3262699_JWH001-C27_CTCF_WT_R1

description: Library name: sample 1


title: HC_IP,rep1

description: Library name: HC1_IP


title: 3262701_JWH003-C27_CTCF_WT_R3

description: Library name: sample 3


title: 3262702_JWH004-C27_CTCF_RBR_R1

description: Library name: sample 4


title: MIA PaCa-2 cells, TNFα treated, 24 hours, biological replicate 2

city: KALYANI

first: ANIKET

last: KUMAR

state: WEST BENGAL

address: Near Netaji Subhas Sanatorium Post Office

country: India

institute: NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS

description:
Library name: MIA PaCa-2_24hr_TNFα biol rep 2
Nascent RNA-seq
miapaca2_24hneg.ucsc.bigWig
miapaca2_24hpos.ucsc.bigWig

data_processing:
QC of the reads was done by FastQC v0.11.7. Adaptor trimming was performed by Trim Galore version 0.6.10
Reads were mapped to the hg38 genome using bowtie2 with default parameters.
Bigwig files for both strands were generated using the makeBigWig.pl with the  option “-strand” as described in the Homer package
Assembly: hg38
Supplementary files format and content: BigWig files for both strands were generated using the makeBigWig.pl with the  option “-strand” as described in the Homer package

molecule: nuclear RNA

source_name: Pancreas

growth_protocol: Human pancreatic ductal adenocarcinoma (PDAC) MIAPaCa-2 cells were maintained in DMEM with 10 % fetal bovine serum (FBS) and 1% penicillin and streptomycin (Pen/Strep) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
During the last hour of TNF-α (0h, 24h) treatment, 0.5 mM 5-Ethynyl Uridine (5-EU) was added to the cells and incubated for 1 hour at 37ºC. Sub-cellular fractionation was done and RNA was isolated from nuclear fraction using TRIzol LS reagent (Ambion, Life Technologies) from TNF-ɑ treated (24h) and untreated (0h, control) MIAPaCa-2 cells. The nascent RNAs were captured using the Click-iT kit (Invitrogen) following manufacturer's protocol. In brief, Biotin Azide was covalently linked to EU-RNA using click chemistry and nacsent RNAs were pulled down by streptavidin Dyna beads and submitted for sequencing.
The cDNA library was prepared using the KAPA RNA HyperPrep Kit [KR1351-v2.17] with RiboErase (HMR) library preparation kit following the manufacturer's protocol with a few modifications. In brief, for depletion of rRNA firstly streptavidin Dyna beads bound nascent RNA (SDBbnRNA) was hybridized with rRNA complementary DNA oligonucleotides followed by RNase H treatment. The rRNA depleted SDBbnRNA was captured using magnetic stand and the supernatant was collected and cleaned up using 2.2X KAPA Pure Beads followed by elution in DNase digestion master mix. This elute was then mixed with rRNA depleted SDBbnRNA which was separated earlier on magnetic separator device and proceeded for DNase treatment to remove rRNA and complementary DNA oligonucleotides duplex. DNase treated sample supernatant was then again collected and cleaned up using 2.2X KAPA Pure Beads as explained earlier and then eluted in diluted Fragment, Prime and Elute buffer and mixed with rRNA depleted, DNase treated SDBbnRNA. Henceforth, standard protocol was followed.

treatment_protocol: Cells were treated with 20 ng/ml recombinant TNF-α (Abclonal) for 0 hours (untreated) or 24 hours.

value: Pancreas

value: MIA PaCa-2

value: epithelial cell

value: TNFα


title: MIA PaCa-2 cells, TNFα untreated, biological replicate 2

description:
Library name: MIA PaCa-2_0hr_TNFα  biol rep 2
Nascent RNA-seq
miapaca2_0hneg.ucsc.bigWig
miapaca2_0hpos.ucsc.bigWig


title: MIA PaCa-2 cells, TNFα treated, 24 hours, biological replicate 1

description:
Library name: MIA PaCa-2_24hr_TNFα biol rep 1
Nascent RNA-seq


title: AC,rep2

description: Library name: AC2


title: A549 xenograft, with post-stress, rep5

city: Linz

first: Yong

last: Yu

state: Upper-Austria

address: Altenberger Straße 69

country: Austria

institute: Johannes Keppler University Linz

description: Library name: A549 PS 5

data_processing:
RNAseq reads were cleaned by Trimmomatic (0.39) to trim low-quality sequences and remove adapter sequences, ensuring high-quality reads for downstream analysis. Following the trimming, genomic alignment was performed by Hisat2 (2.2.1) using the hg38 (human) and mm10 (mouse) reference genomes to accurately map the reads to their respective genomes. After alignment, featureCounts (v2.0.6) to quantify gene expression by counting the number of reads that overlapped to each gene. For differential expression analysis, two robust statistical tools based on R (4.3.3) languague, DESeq2 and edgeR, were used to identify genes with significant differences in expression between conditions, ensuring comprehensive and reliable results through cross-validation of the findings from both methods.
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: A549 xenograft tumor

growth_protocol: A549 cells were cultured in DMEM containing 10% FBS and 1% P/S in an incubator with 37 ℃, 5% CO2, and 5 million cells were subcutaneously transplantated into nude mice to form xenografts.

extract_protocol:
Xenograft were isolated for total RNA extraction using TRIzol reagent. 1ug total RNA was used for library preparation.
RNA-seq libraries were prepared using Fast RNA-seq Lib Prep Kit V2 (Abclonal, Cat. No. RK20306)

treatment_protocol: Mice were not treated with stress(n=5), restrained 7 days before (Stress, n=5) A549 transplantation, or restrained 12 days after (Post-stress, n=5) A549 transplantation.

value: A549 xenograft tumor

value: Lung adenocarcinoma

value: with post-stress


title: A549 xenograft, with post-stress, rep1

description: Library name: A549 PS 1


title: A549 xenograft, with post-stress, rep2

description: Library name: A549 PS 2


title: Normal 2

description: Library name: Sample 2

value: breast

value: Human ductal epithelial cells


title: A549 xenograft, with post-stress, rep4

description: Library name: A549 PS 4


title: A549 xenograft, with stress, rep3

description: Library name: A549 stress 3

value: with stress


title: A549 xenograft, with stress, rep5

description: Library name: A549 stress 5


title: A549 xenograft, with stress, rep4

description: Library name: A549 stress 4


title: A549 xenograft, with stress, rep2

description: Library name: A549 stress 2


title: Normal 1

description: Library name: Sample 1


title: A549 xenograft, with stress, rep1

description: Library name: A549 stress 1


title: A549 xenograft, without stress, rep5

description: Library name: A549 ctr.5

value: no stress


title: A549 xenograft, without stress, rep3

description: Library name: A549 ctr.3


title: A549 xenograft, without stress, rep2

description: Library name: A549 ctr.2


title: A549 xenograft, without stress, rep4

description: Library name: A549 ctr.4


title: HEK293T cells,input,rep3

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

description:
Library name: sample9
Ribosomes removed RNA

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
All fastq files were aligned to the human reference genome hg38, using STAR v2.7.10b
Reads less than 30 in length were removed, and only the proper pair and uniquely mapped alignments were persisted for the downstream pipelines.
The m6A methylation peaks were identified utilizing the R package exomepeak2.
Bigwig files were generated using deeptools Python package. Score represents the Counts Per Million mapped reads of RNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: Bigwig include CPM values for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: HEK293T cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions
RNA libraries for the RNA input, collected supernatant and IP were constructed using a Ultra ll Directional RNA Library Prep Kit for llluminae (NEB) following the manufacturer’s protocol.

value: HEK293T cells


title: A549 xenograft, without stress, rep1

description: Library name: A549 ctr.1


title: HEK293T cells,input,rep2

description:
Library name: sample8
Ribosomes removed RNA


title: A549 xenograft, with post-stress, rep3

description: Library name: A549 PS 3


title: HEK293T cells,FHY1-M3_con_sgRNA,rep2

description:
Library name: sample4
Ribosomes removed RNA

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
All fastq files were aligned to the human reference genome hg38, using STAR v2.7.10b
Reads less than 30 in length were removed, and only the proper pair and uniquely mapped alignments were persisted for the downstream pipelines.
The m6A methylation peaks were identified utilizing the R package exomepeak2.
Bigwig files were generated using deeptools Python package. Score represents the Counts Per Million mapped reads of RNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: Bigwig include CPM values for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample
Library strategy: MeRIP-seq


title: HEK293T cells,input,rep1

description:
Library name: sample7
Ribosomes removed RNA


title: HEK293T cells,FHY1-M3_con_sgRNA,rep1

description:
Library name: sample3
Ribosomes removed RNA


title: HEK293T cells,FHY1-M3_non-target_sgRNA,rep1

description:
Library name: sample5
Ribosomes removed RNA


title: MIA PaCa-2 cells, TNFα untreated, biological replicate 1

description:
Library name: MIA PaCa-2_0hr_TNFα  biol rep 1
Nascent RNA-seq


title: HEK293T cells,FHY1-M3_ACTB_sgRNA,rep1

description:
Library name: sample1
Ribosomes removed RNA


title: HEK293T cells,FHY1-M3_ACTB_sgRNA,rep2

description:
Library name: sample2
Ribosomes removed RNA


title: Whole blood, COVID positive, rep 770

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

data_processing:
RNASeq-DE workflow (v1.0.0), available online at  https://github.com/Sydney-Informatics-Hub/RNASeq-DE
3’ adapter and polyA tails were trimmed from raw sequence reads with BBDuk (v37.89)
Quality checked, trimmed reads were aligned as pairs to the human reference genome, GRCh38 primary assembly and gene set release 106 (obtained from Ensembl) with STAR, setting –sjdbOverhand to 149
Sequencing batch level binary alignment (BAM) files were merged and indexed with SAMtools (v1.10) to obtain sample level BAMs.
HTSeq-count (v0.12.4) with -s reverse was used to obtain feature level raw counts.
Assembly: GRCh38
Supplementary files format and content: HTSeq-count output, containing raw counts per sample

extract_protocol:
Total RNA was isolated from whole blood samples stored and stabilized in PAXgene RNA tubes according to the manufacturer's guidelines (PreAnalytiX)
Libraries were prepared with 300ng of total RNA per sample using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (RZP) as per manufacturer instructions (Illumina, CA, USA).

value: Whole blood

tag: type of_infection

tag: country of_samples_collected

value: France

tag: gender

value: Male


title: Whole blood, COVID positive, rep 769

value: Australia


title: Whole blood, COVID positive, rep 765

value: Co-infection (Bac/Viral)


title: Whole blood, COVID positive, rep 768


title: Whole blood, COVID positive, rep 772


title: Whole blood, COVID positive, rep 763


title: Whole blood, COVID positive, rep 766


title: Whole blood, COVID positive, rep 761


title: Whole blood, COVID positive, rep 771


title: Whole blood, COVID positive, rep 762


title: Whole blood, COVID positive, rep 767


title: Whole blood, COVID positive, rep 764

value: Female


title: Whole blood, COVID positive, rep 760


title: Whole blood, COVID positive, rep 759


title: Whole blood, COVID positive, rep 758


title: HEK293T cells,FHY1-M3_non-target_sgRNA,rep2

description:
Library name: sample6
Ribosomes removed RNA


title: Whole blood, COVID positive, rep 756


title: Whole blood, COVID positive, rep 757


title: Whole blood, COVID positive, rep 755


title: Whole blood, COVID positive, rep 754


title: Whole blood, COVID positive, rep 751

value: Czech Republic


title: Whole blood, COVID positive, rep 752

value: Co-infection (Viral/Fungal)


title: Whole blood, COVID positive, rep 748


title: Whole blood, COVID positive, rep 750


title: Whole blood, COVID positive, rep 749


title: Whole blood, COVID positive, rep 746


title: Whole blood, COVID positive, rep 744


title: Whole blood, COVID positive, rep 753


title: Whole blood, COVID positive, rep 737


title: Whole blood, COVID positive, rep 745


title: Whole blood, COVID positive, rep 736


title: Whole blood, COVID positive, rep 742


title: Whole blood, COVID positive, rep 733

value: Co-infection (viral/viral)


title: Whole blood, COVID positive, rep 741


title: Whole blood, COVID positive, rep 743


title: Whole blood, COVID positive, rep 738


title: Whole blood, COVID positive, rep 735


title: Whole blood, COVID positive, rep 740


title: Whole blood, COVID positive, rep 734


title: Whole blood, COVID positive, rep 739


title: Whole blood, COVID positive, rep 731


title: Whole blood, COVID positive, rep 730


title: Whole blood, COVID positive, rep 728


title: Whole blood, COVID positive, rep 727


title: Whole blood, COVID positive, rep 729

value: Indonesia


title: Whole blood, COVID positive, rep 732

value: Coronavirus


title: Whole blood, COVID positive, rep 726


title: Whole blood, COVID positive, rep 725


title: Whole blood, COVID positive, rep 724


title: Whole blood, COVID positive, rep 722


title: Whole blood, COVID positive, rep 721


title: Whole blood, COVID positive, rep 723


title: Whole blood, COVID positive, rep 720


title: Whole blood, COVID positive, rep 719


title: Whole blood, COVID positive, rep 718


title: Whole blood, COVID positive, rep 747


title: Whole blood, COVID positive, rep 716


title: Whole blood, COVID positive, rep 712


title: Whole blood, COVID positive, rep 713


title: Whole blood, COVID positive, rep 711

value: Sepsis


title: Whole blood, COVID positive, rep 715


title: Whole blood, COVID positive, rep 714


title: Whole blood, COVID positive, rep 709


title: Whole blood, COVID positive, rep 710


title: Whole blood, COVID positive, rep 705


title: Whole blood, COVID positive, rep 708


title: Whole blood, COVID positive, rep 704


title: Whole blood, COVID positive, rep 703


title: Whole blood, COVID positive, rep 707


title: Whole blood, COVID positive, rep 706


title: Whole blood, COVID positive, rep 697


title: Whole blood, COVID positive, rep 700


title: Whole blood, COVID positive, rep 702


title: Whole blood, COVID positive, rep 690


title: Whole blood, COVID positive, rep 692


title: Whole blood, COVID positive, rep 691


title: Whole blood, COVID positive, rep 693


title: Whole blood, COVID positive, rep 717


title: Whole blood, COVID positive, rep 694


title: Whole blood, COVID positive, rep 696


title: Whole blood, COVID positive, rep 701


title: Whole blood, COVID positive, rep 698


title: Whole blood, COVID positive, rep 689


title: Whole blood, COVID positive, rep 688


title: Whole blood, COVID positive, rep 686


title: Whole blood, COVID positive, rep 683


title: Whole blood, COVID positive, rep 685


title: Whole blood, COVID positive, rep 687


title: Whole blood, COVID positive, rep 681


title: Whole blood, COVID positive, rep 682


title: Whole blood, COVID positive, rep 684


title: Whole blood, COVID positive, rep 680


title: Whole blood, COVID positive, rep 699


title: Whole blood, COVID positive, rep 679


title: Whole blood, COVID positive, rep 677


title: Whole blood, COVID positive, rep 695


title: Whole blood, COVID positive, rep 673


title: Whole blood, COVID positive, rep 674


title: Whole blood, COVID positive, rep 671


title: Whole blood, COVID positive, rep 678


title: Whole blood, COVID positive, rep 672


title: Whole blood, COVID positive, rep 669


title: Whole blood, COVID positive, rep 668


title: Whole blood, COVID positive, rep 663


title: Whole blood, COVID positive, rep 666


title: Whole blood, COVID positive, rep 667


title: Whole blood, COVID positive, rep 670


title: Whole blood, COVID positive, rep 662


title: Whole blood, COVID positive, rep 675


title: Whole blood, COVID positive, rep 664


title: Whole blood, COVID positive, rep 660


title: Whole blood, COVID positive, rep 658


title: Whole blood, COVID positive, rep 661


title: Whole blood, COVID positive, rep 657


title: Whole blood, COVID positive, rep 655


title: Whole blood, COVID positive, rep 656


title: Whole blood, COVID positive, rep 653


title: Whole blood, COVID positive, rep 676


title: Whole blood, COVID positive, rep 650


title: Whole blood, COVID positive, rep 651


title: Whole blood, COVID positive, rep 648


title: Whole blood, COVID positive, rep 646


title: Whole blood, COVID positive, rep 645


title: Whole blood, COVID positive, rep 647


title: Whole blood, COVID positive, rep 644


title: Whole blood, COVID positive, rep 649


title: Whole blood, COVID positive, rep 643


title: Whole blood, COVID positive, rep 665


title: Whole blood, COVID positive, rep 642


title: Whole blood, COVID positive, rep 640

value: Singapore


title: Whole blood, COVID positive, rep 639


title: Whole blood, COVID positive, rep 638


title: Whole blood, COVID positive, rep 641


title: Whole blood, COVID positive, rep 659


title: Whole blood, COVID positive, rep 654


title: Whole blood, COVID positive, rep 652


title: Whole blood, COVID positive, rep 633


title: Whole blood, COVID positive, rep 631


title: Whole blood, COVID positive, rep 628


title: Whole blood, COVID positive, rep 630


title: Whole blood, COVID positive, rep 627


title: Whole blood, COVID positive, rep 629


title: Whole blood, COVID positive, rep 626


title: Whole blood, COVID positive, rep 623


title: Whole blood, COVID positive, rep 622


title: Whole blood, COVID positive, rep 624


title: Whole blood, COVID positive, rep 621


title: Whole blood, COVID positive, rep 618

value: Co-infection (Viral/Viral)


title: Whole blood, COVID positive, rep 637


title: Whole blood, COVID positive, rep 619


title: Whole blood, COVID positive, rep 636


title: Whole blood, COVID positive, rep 620


title: Whole blood, COVID positive, rep 617


title: Whole blood, COVID positive, rep 612


title: Whole blood, COVID positive, rep 611


title: Whole blood, COVID positive, rep 613


title: Whole blood, COVID positive, rep 635


title: Whole blood, COVID positive, rep 614


title: Whole blood, COVID positive, rep 616


title: Whole blood, COVID positive, rep 610


title: Whole blood, COVID positive, rep 634


title: Whole blood, COVID positive, rep 615


title: Whole blood, COVID positive, rep 609


title: Whole blood, COVID positive, rep 608


title: Whole blood, COVID positive, rep 606


title: Whole blood, COVID positive, rep 625


title: Whole blood, COVID positive, rep 604


title: Whole blood, COVID positive, rep 603


title: Whole blood, COVID positive, rep 607


title: Whole blood, COVID positive, rep 601


title: Whole blood, COVID positive, rep 605


title: Whole blood, COVID positive, rep 632


title: Whole blood, COVID positive, rep 602


title: Whole blood, COVID positive, rep 598


title: Whole blood, COVID positive, rep 595


title: Whole blood, COVID positive, rep 592


title: Whole blood, COVID positive, rep 593


title: Whole blood, COVID positive, rep 591


title: Whole blood, COVID positive, rep 588


title: Whole blood, COVID positive, rep 587


title: Whole blood, COVID positive, rep 590


title: Whole blood, COVID positive, rep 583


title: Whole blood, COVID positive, rep 584


title: Whole blood, COVID positive, rep 586


title: Whole blood, COVID positive, rep 589


title: Whole blood, COVID positive, rep 585


title: Whole blood, COVID positive, rep 582


title: Whole blood, COVID positive, rep 580


title: Whole blood, COVID positive, rep 578


title: Whole blood, COVID positive, rep 581


title: Whole blood, COVID positive, rep 579


title: Whole blood, COVID positive, rep 600


title: Whole blood, COVID positive, rep 574


title: Whole blood, COVID positive, rep 597


title: Whole blood, COVID positive, rep 571


title: Whole blood, COVID positive, rep 575


title: Whole blood, COVID positive, rep 599


title: Whole blood, COVID positive, rep 573


title: Whole blood, COVID positive, rep 572


title: Whole blood, COVID positive, rep 596


title: Whole blood, COVID positive, rep 594


title: Whole blood, COVID positive, rep 570


title: Whole blood, COVID positive, rep 568


title: Whole blood, COVID positive, rep 567


title: Whole blood, COVID positive, rep 569


title: Whole blood, COVID positive, rep 566


title: Whole blood, COVID positive, rep 565


title: Whole blood, COVID positive, rep 560


title: Whole blood, COVID positive, rep 562


title: Whole blood, COVID positive, rep 561


title: Whole blood, COVID positive, rep 564


title: Whole blood, COVID positive, rep 577


title: Whole blood, COVID positive, rep 559


title: Whole blood, COVID positive, rep 576


title: Whole blood, COVID positive, rep 557


title: Whole blood, COVID positive, rep 558


title: Whole blood, COVID positive, rep 554


title: Whole blood, COVID positive, rep 556


title: Whole blood, COVID positive, rep 555


title: Whole blood, COVID positive, rep 553