title: HAP1 cells, WT, HSV1 infection, 10hpi, rep2

description: Library name: DUX4_wt_I2_10h


title: HAP1 cells, WT, mock, 8hpi, rep1

status: Public on Jan 27 2025

type: SRA

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

description: Library name: DUX4_wt_M1_8h

library_source: transcriptomic

data_processing:
Sequence reads were mapping to hg38 by STAR
Assembly: hg38
Supplementary files format and content: counts files were generated by featurecounts

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs) total RNA-seq

tag: cell line

tag: cell type

value: HAP1 cells

tag: genotype

value: WT

tag: treatment

value: Mock


title: 18791_EB_Atrial_d14

city: Nijmegen

first: Rebecca

middle: Regina

last: Snabel

state: Gelderland

address: Geert Grooteplein 26-28

department: Molecular Developmental Biology

country: Netherlands

institute: RIMLS

library_source: transcriptomic single cell

data_processing:
Using Seq2Science (PMID: 38025697) for filtering and mapping of the reads.
Mapping was performed with Kallisto | Bustools wrapper (PMID: 33795888), using the following setting: ‘--technology 1,8,16:1,0,8:0,0,0’.
One combined dataset was build using Seurat (PMID: 31178118) and the count assays from this object were saved here as separate spliced (sf) and unspliced (uf) matrices.
Assembly: GRCh38
Supplementary files format and content: Matrices of spliced (sf) and unspliced (uf) are saved as .mtx files, which need to be combined with the respective barcode.tsv and genes.tsv files to create column- and row-names for the matrix.

molecule: polyA RNA

source_name: hESC-derived cardiac cells

growth_protocol: Monolayer (Mon), Embryoid Body (EB) and Engineered Heart Tissue (EHT) cardiomyocyte differentiation cultures.

extract_protocol:
Wnt-modulating protocols culturing the cells for a max of 26 days, either with or without RA treatment at day 4.
SORT-seq/CEL-Seq2

treatment_protocol: Ventricular or atrial conditions were cultured, with atrial treated with Retinoic Acid (RA) at Day 4.

tag: tissue

value: hESC-derived cardiac cells

value: cardiomyocyte

value: Cmdifferentiation


title: C_5L_ZT22_F_MCC3804A272_S175

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

country: USA

institute: University of Pittsburgh

description: Library name: C_5L_ZT22_F_MCC3804A272_S175

data_processing:
FASTQC
HTSeq
DESeq2 normalization (median of ratios)
Cosinor modeling
Assembly: Mus musculus Ensembl GRCm38
Supplementary files format and content: .csv

organism: Mus musculus

source_name: Brain

extract_protocol:
A co-immunoprecipitation protocol was used as previously described in (Chandra et al., 2015; Becker-Krail et al., 2022; DePoy et al., 2024), with minor modifications. Briefly, tissue was homogenized and incubated overnight with an anti-hemagglutinin A (HA) antibody (Abcam, Cambridge, UK). HA-tagged ribosomes, conjugated to an anti-HA antibody, were then isolated using Dynabeads (Invitrogen, Waltham, MA, USA). RNA was extracted and purified using an EZNA RNA Isolation Kit (Omega Bio-Tek Total RNA Miniprep kit) with ENZA RNase-Free DNAase (Omega Bio-Tek, Norcross, GA, USA).
cDNA synthesis: SMART-seq HT kit; Library prep: Nextera Flex

value: Brain

value: Parvalbumin interneurons

value: Ribo-tag mice


title: HAP1 cells, WT, HSV1 infection, 8hpi, rep2

description: Library name: DUX4_wt_I2_8h


title: SFTS_1，replicate 1, scRNAseq

city: Hefei

first: Yin

last: Zhang

state: Anhui

address: No. 218 Jixi Rd

country: China

institute: First Affiliated Hospital of Anhui Medical University

description:
Library name: sample 1
10x Genomics

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Assembly: Ensembl_release109
Supplementary files format and content: The format of the raw data files is "fastq.gz"; The format of the processed data files is "expression.xls".

source_name: Peripheral blood

extract_protocol:
Perform high-throughput sequencing on the final libraries using Illumina NovaSeq X Plus. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA.

value: Peripheral blood

value: monocytes

tag: Sex

value: female


title: 18788_EHT_Ventricular_m11


title: HAP1 cells, WT, mock, 4hpi, rep1

description: Library name: DUX4_wt_M1_4h


title: 18786_Mon_Atrial_m12


title: 18785_Mon_Ventricular_m5


title: HAP1 cells, WT, HSV1 infection, 10hpi, rep1

description: Library name: DUX4_wt_I1_10h


title: C_5K_ZT_6_F2_MCC3804A264_S174

description: Library name: C_5K_ZT_6_F2_MCC3804A264_S174


title: HAP1 cells, WT, HSV1 infection, 6hpi, rep2

description: Library name: DUX4_wt_I2_6h


title: 18784_EB_Ventricular_d18


title: HAP1 cells, WT, HSV1 infection, 8hpi, rep1

description: Library name: DUX4_wt_I1_8h


title: C_5I_ZT6_M_MCC3804A306_S193

description: Library name: C_5I_ZT6_M_MCC3804A306_S193


title: HAP1 cells, WT, HSV1 infection, 4hpi, rep2

description: Library name: DUX4_wt_I2_4h


title: HAP1 cells, WT, HSV1 infection, 6hpi, rep1

description: Library name: DUX4_wt_I1_6h


title: C_5H_ZT2_M_MCC3804A283_S197

description: Library name: C_5H_ZT2_M_MCC3804A283_S197


title: HAP1 cells, KO, mock, 10hpi, rep2

description: Library name: DUX4_ko_M2_10h

value: DUX4 KO


title: HAP1 cells, KO, mock, 4hpi, rep2

description: Library name: DUX4_ko_M2_4h


title: C_5J_ZT14_F_MCC3804A271_S167

description: Library name: C_5J_ZT14_F_MCC3804A271_S167


title: HAP1 cells, WT, HSV1 infection, 4hpi, rep1

description: Library name: DUX4_wt_I1_4h


title: HAP1 cells, KO, mock, 8hpi, rep1

description: Library name: DUX4_ko_M1_8h


title: C_5G_ZT10_F_MCC3804A278_S160

description: Library name: C_5G_ZT10_F_MCC3804A278_S160


title: HAP1 cells, KO, mock, 8hpi, rep2

description: Library name: DUX4_ko_M2_8h


title: 18781_EHT_Ventricular_m5


title: HAP1 cells, KO, HSV1 infection, 8hpi, rep2

description: Library name: DUX4_ko_I2_8h


title: C_5F_ZT14_M_MCC3804A299_S199

description: Library name: C_5F_ZT14_M_MCC3804A299_S199


title: C_5D_ZT18_M_MCC3804A282_S190

description: Library name: C_5D_ZT18_M_MCC3804A282_S190


title: HAP1 cells, KO, mock, 10hpi, rep1

description: Library name: DUX4_ko_M1_10h


title: 18780_Mon_Ventricular_d14


title: 18778_EB_Atrial_d5


title: HAP1 cells, KO, mock, 6hpi, rep2

description: Library name: DUX4_ko_M2_6h


title: HAP1 cells, KO, mock, 6hpi, rep1

description: Library name: DUX4_ko_M1_6h


title: 18782_EHT_Atrial_m5


title: 18779_Mon_Ventricular_d10


title: HAP1 cells, KO, HSV1 infection, 10hpi, rep2

description: Library name: DUX4_ko_I2_10h


title: C_5E_ZT2_F_MCC3804A307_S200

description: Library name: C_5E_ZT2_F_MCC3804A307_S200


title: HAP1 cells, KO, mock, 4hpi, rep1

description: Library name: DUX4_ko_M1_4h


title: HAP1 cells, KO, HSV1 infection, 6hpi, rep2

description: Library name: DUX4_ko_I2_6h


title: C_5C_ZT10_M_MCC3804A269_S151

description: Library name: C_5C_ZT10_M_MCC3804A269_S151


title: 18783_Mon_Atrial_m5


title: HAP1 cells, KO, HSV1 infection, 4hpi, rep2

description: Library name: DUX4_ko_I2_4h


title: 18777_Mon_Ventricular_d5


title: HAP1 cells, KO, HSV1 infection, 10hpi, rep1

description: Library name: DUX4_ko_I1_10h


title: 18776_EHT_Atrial_m12


title: C_5B_ZT18_F_MCC3804A279_S168

description: Library name: C_5B_ZT18_F_MCC3804A279_S168


title: HAP1 cells, KO, HSV1 infection, 8hpi, rep1

description: Library name: DUX4_ko_I1_8h


title: HAP1 cells, KO, HSV1 infection, 6hpi, rep1

description: Library name: DUX4_ko_I1_6h


title: 18775_Mon_Ventricular_m11


title: HAP1 cells, KO, HSV1 infection, 4hpi, rep1

description: Library name: DUX4_ko_I1_4h


title: C_4K_ZT2_F_MCC3804A261_S150

description: Library name: C_4K_ZT2_F_MCC3804A261_S150


title: C_4J_ZT22_M_MCC3804A289_S184

description: Library name: C_4J_ZT22_M_MCC3804A289_S184


title: 18773_EHT_Atrial_m5


title: HeLa cells, CFIm25 siRNA-2, repeat 1

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

data_processing:
data processing steps were carried out by our recently published pipeline quantify-polyA (https://pubmed.ncbi.nlm.nih.gov/34255024/）
Assembly: hg38
Supplementary files format and content: bw files
Library strategy: 3'-seq

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM+10%FBS medium

extract_protocol:
total RNAs were extracted by TRIZOL REAGENT
3'-seq was prepared by lexogen 3'-seq kit

treatment_protocol: Cells were treated with negative control siRNA or CFIm25 siRNAs by lipofectamine RNAi max(Life technology)

value: HeLa cells

value: tumor cell line

value: CFIm25 KD

value: CFIm25 siRNA


title: HeLa cells, CFIm25 siRNA-2, repeat 2


title: 18774_Mon_Atrial_m12


title: HeLa cells, CFIm25 siRNA-1, repeat 1


title: HeLa cells, CFIm25 siRNA-1, repeat 2


title: 18772_EHT_Ventricular_m5


title: Patient #4 Lesional biopsy

city: Irvine

first: Christina

last: Kraus

state: CA

address: 118 Medical Surge 1

department: Dermatology

institute: University of California, Irvine

description:
10x Genomics
SC_LE4

data_processing:
FASTQ files were aligned utilizing 10x Genomics Cloud Cell Ranger Count v7.1.0.
Assembly: Each library was aligned to an indexed Human GRCh38 genome.
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Skin

extract_protocol:
Punch biopsies  were incubated in 5 U/mL dispase at 37℃ for 45 min. The epidermis was peeled from the dermis, cut into fine pieces, and incubated in 0.25% trypsin-EDTA with 50 μg/mL DNase I for 45 min at 37°C, quenched with fetal bovine serum, and passed through a 70 μM cell strainer. Dermis was minced and digested in 0.1% collagenase II and 0.1% collagenase V in RPMI 1640 with 50 μg/mL DNase I for 90 min at 37°C, and strained through a 70-μM  cell strainer. Dead cell removal was performed using a Dead Cell Removal Kit. Epidermal and dermal cells were then recombined and washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cells/µL.
Library generation was performed following the 10x Genomics Chromium Single Cell 3ʹ v3.1 Reagents Kit (following the CG000315 Rev E. user guide), where we targeted 10,000 cells per sample for capture.

value: Skin

tag: age

tag: biopsy location

value: Interlabial sulcus

tag: previous treatment

value: TCS, CI


title: HeLa cells, negative control siRNA, repeat 2

value: WT

value: negative control siRNA


title: C_4I_ZT6_M_MCC3804A302_S163

description: Library name: C_4I_ZT6_M_MCC3804A302_S163


title: 18771_EB_Atrial_d14

value: hESC-derived cardiac cells

value: cardiomyocyte

value: Cmdifferentiation


title: Patient #3 Lesional biopsy

description:
10x Genomics
SC_LE3

value: TCS


title: C_4H_ZT10_M2_MCC3804A265_S181

description: Library name: C_4H_ZT10_M2_MCC3804A265_S181

value: Brain

value: Parvalbumin interneurons

value: Ribo-tag mice


title: Patient #4 Non-lesional biopsy

description:
10x Genomics
SC_NL4

value: Labia minora


title: 18770_EB_Ventricular_d14


title: Patient #3 Non-lesional biopsy

description:
10x Genomics
SC_NL3


title: Patient #2 Lesional biopsy

description:
10x Genomics
SC_LE2


title: C_4G_ZT18_F_MCC3804A268_S143

description: Library name: C_4G_ZT18_F_MCC3804A268_S143


title: C_5A_ZT22_M3_MCC3804A284_S145

description: Library name: C_5A_ZT22_M3_MCC3804A284_S145


title: Patient #2 Non-lesional biopsy

description:
10x Genomics
SC_NL2


title: C_4F_ZT22_F_MCC3804A260_S142

description: Library name: C_4F_ZT22_F_MCC3804A260_S142


title: 18769_EB_Atrial_d8


title: Patient #1 Lesional biopsy

description:
10x Genomics
SC_LE1


title: Patient #1 Non-lesional biopsy

description:
10x Genomics
SC_NL1


title: C_4L_ZT10_M_MCC3804A280_S176

description: Library name: C_4L_ZT10_M_MCC3804A280_S176


title: HeLa cells, negative control siRNA, repeat 1

value: HeLa cells


title: 18768_EB_Ventricular_d8


title: N/TERT-2G keratinocytes, CXCL14 knockdown, rep3

first: Xing

last: Dai

address: 825 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

data_processing:
Raw data were processed to remove reads containing adapter, and remove reads containing ploy-N (>10% uncertain nucleotides) and low-quality reads (>50% of the bases with quality score <5).
Reference genome (hg38) and gene model annotation files were downloaded from UCSC genome database. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM values for each gene were calculated based on the length of the gene and the read count mapped to it.
Assembly: hg38
Supplementary files format and content: gene_count.xls include raw counts for each sample
Supplementary files format and content: gene_fpkm.xls include FPKM values for each sample
Supplementary files format and content: gene_fpkm_group.xls include FPKM values for each treatment group

growth_protocol: The N/TERT-2G keratinocytes were cultured in Keratinocyte SFM (1X) medium (Gibco, 17005042), and incubated at 37°C with 95% air / 5% CO2.

extract_protocol:
Total RNAs were isolated using the Quick-RNA™ Miniprep Kit (Zymo Research) following the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesizedusing random hexamer primers, followed by the second strand cDNAsynthesis using either dUTP for directional library or dTTP for non-directional library

treatment_protocol: At 40-50% confluency, the N/TERT-2G keratinoctes were transfected with 100 pmol/well (6-well plate) of ATF3 siRNA, APOE siRNA, CXCL14 siRNA, or negative control siRNA, using 5 μl/well (6-well plate) of Lipofectamine 2000 transfection reagent (Thermo Fisher Scientific), following the manufacturer's protocol. Six hours later, the medium was replaced with Keratinocyte SFM (1X) medium supplemented with Penicillin-Streptomycin (Gibco, 100 units/ml).

value: N/TERT-2G keratinocyte

value: Immortalized skin keratinocytes

value: CXCL14 Knockdown

value: Transfection with CXCL14-targeted siRNA


title: C_4E_ZT14_F_MCC3804A276_S144

description: Library name: C_4E_ZT14_F_MCC3804A276_S144


title: C_4D_ZT2_M_MCC3804A293_S154

description: Library name: C_4D_ZT2_M_MCC3804A293_S154


title: N/TERT-2G keratinocytes, CXCL14 knockdown, rep2

value: Skin


title: N/TERT-2G keratinocytes, ATF3 knockdown, rep3

value: ATF3 knockdown

value: Transfection with ATF3-targeted siRNA


title: 18766_EB_Ventricular_d5


title: N/TERT-2G keratinocytes, CXCL14 knockdown, rep1


title: C_4C_ZT18_M_MCC3804A310_S164

description: Library name: C_4C_ZT18_M_MCC3804A310_S164


title: N/TERT-2G keratinocytes, ATF3 knockdown, rep2


title: N/TERT-2G keratinocytes, APOE knockdown, rep3

value: APOE knockdown

value: Transfection with APOE-targeted siRNA


title: 18765_EB_Shared_d4

value: hESC-derived cardiac cells

value: cardiomyocyte


title: C_4B_ZT6_F_MCC3804A287_S169

description: Library name: C_4B_ZT6_F_MCC3804A287_S169


title: N/TERT-2G keratinocytes, APOE knockdown, rep2


title: N/TERT-2G keratinocytes, APOE knockdown, rep1


title: C_4A_ZT14_M_MCC3804A309_S156

description: Library name: C_4A_ZT14_M_MCC3804A309_S156


title: 18764_Mon_Ventricular_d4

value: Cmdifferentiation


title: N/TERT-2G keratinocytes, negative control, rep3

value: Negative control

value: Transfection with negative control siRNA


title: N/TERT-2G keratinocytes, negative control, rep2


title: C_3L_ZT22_F1_MCC3804A294_S162

description: Library name: C_3L_ZT22_F1_MCC3804A294_S162

value: Brain

value: Parvalbumin interneurons

value: Ribo-tag mice


title: N/TERT-2G keratinocytes, negative control, rep1

value: N/TERT-2G keratinocyte


title: 948_EB_Atrial_d21


title: 946_EB_Atrial_d14


title: HeLa cells, RNAPII ChIP sample, U2 AMO treated , repeat 2

description: U2 AMO treated RNAPII IP

library_source: genomic

data_processing:
The NovaSeq platform was utilized for sequencing these libraries, and all ChIP-Seq data processing and analysis were carried out following the ENCODE ChIP-Seq pipeline (https://www.encodeproject.org/data-standards/chip-seq/).
Assembly: hg38
Supplementary files format and content: bw files

molecule: genomic DNA

source_name: HeLa

growth_protocol: HeLa cells were obtained from ATCC and cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Thermo Scientific).

extract_protocol:
For the preparation of ChIP-Seq libraries, the ChIP-IT Express Enzymatic Shearing (Active Motif) was used to make input DNA.
For the preparation of ChIP-Seq libraries,  ChIP-Seq library preparation (Vazyme) kits were employed. The RNAPII antibodies were purchased from Santa Cruz Biotechnology (sc-47701-X)
IPed DNA library was prepared using ChIP-seq DNA library preparation kits (Vazyme)

treatment_protocol: Electroporation was performed using a Bio-Rad Gene pulser at 960 μF and 280 V. After electroporation, cells were cultured for 12 hours in 6 well plates with 2 ml DMEM.

value: HeLa

value: cancer cell line

value: U2 AMO treated


title: C_3K_ZT14_M1_MCC3804A267_S195

description: Library name: C_3K_ZT14_M1_MCC3804A267_S195


title: HeLa cells, input DNA, U2 AMO treated , repeat 2

description: U2 AMO treated input DNA


title: 18767_Mon_Ventricular_d8


title: HeLa cells, input DNA, U2 AMO treated , repeat 1

description: U2 AMO treated input DNA


title: C_3J_ZT2_M1_MCC3804A312_S180

description: Library name: C_3J_ZT2_M1_MCC3804A312_S180


title: N/TERT-2G keratinocytes, ATF3 knockdown, rep1

value: Skin

value: Immortalized skin keratinocytes


title: C_3I_ZT18_F1_MCC3804A275_S196

description: Library name: C_3I_ZT18_F1_MCC3804A275_S196


title: HT29 SIS ECM MatriSphere Day 7_Sample 5

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Reads were trimmed for adapters and low-quality bases using Cutadapt v1.18.
Reads were aligned to reference genomes (mm10 for mouse, hg38 for human) using STAR v2.7.0f in 2-pass mode.
Gene expression was quantified using RSEM 1.3.1 with the GENCODE_30 (mouse) and GENCODE_M21 (human) gene annotations.
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by different expression of genes analysis. Three samples did not pass QC, were excluded from downstream analysis, and are therefore excluded from this accession.
Preranked GSEA was performed using fGSEA and the HALLMARK collection was searched for both mouse and human datasets, with mouse genes being first converted to human orthologs for lookup using human databases.
Assembly: Human samples used hg38 & GENCODE_30. Mouse samples used mm10 & GENCODE_M21.
Supplementary files format and content: The CSV (.csv) files provided for all Raw Counts, DEG, & GSEA results (mouse & human).

growth_protocol: CRC Cells were grown in Roswell Park Memorial Institute (RPMI) media supplemented with L-glutamine (Thermo Fisher 11875119), 10% fetal bovine serum (Thermo Fisher 16000044), and 1% penicillin streptomycin (Thermo Fisher 15140122). Cells were maintained at 37°C with 5% CO2 humidified air.

extract_protocol:
After 7 days of culture, CRC spheroids were transferred to 5 mL tubes in batches of 10, the excess media was removed by pipetting, 1 mL of TRIzol (Invitrogen) was added to each sample, and the samples were stored at -80°C until further processing. Samples were thawed on ice and the RNA was extracted using the RNeasy Micro Kit (QIAGEN) in accordance with the manufacturer’s instructions.
All mRNA-seq samples were pooled within species and sequenced on NovaSeq 6000 SP using Illumina® Stranded mRNA Prep and paired-end sequencing.

treatment_protocol: Cells were seeded onto ULA U-bottom plates with or without SIS ECM and allowed to grow up to 7 days

value: colorectal carcinoma

value: ECM


title: HT29 SIS ECM MatriSphere Day 7_Sample 6


title: 945_EB_Ventricular_d14


title: 944_EB_Atrial_d12


title: HT29 SIS ECM MatriSphere Day 7_Sample 2


title: 943_EB_Ventricular_d12


title: C_3G_ZT10_F1_MCC3804A285_S153

description: Library name: C_3G_ZT10_F1_MCC3804A285_S153


title: HT29 Cells alone Spheroid Day 7_Sample 6

value: CA


title: 942_EB_Atrial_d10

value: hESC-derived cardiac cells


title: 947_EB_Ventricular_d21

value: cardiomyocyte


title: HT29 SIS ECM MatriSphere Day 7_Sample 3


title: HeLa cells, RNAPII ChIP sample, U2 AMO treated , repeat 1

description: U2 AMO treated RNAPII IP


title: HT29 Cells alone Spheroid Day 7_Sample 4


title: C_3D_ZT6_F1_MCC3804A143_S210

description: Library name: C_3D_ZT6_F1_MCC3804A143_S210


title: 941_EB_Ventricular_d10

value: Cmdifferentiation


title: HT29 Cells alone Spheroid Day 7_Sample 3


title: HT29 SIS ECM MatriSphere Day 7_Sample 1


title: HT29 Cells alone Spheroid Day 7_Sample 2


title: HT29 Cells alone Spheroid Day 7_Sample 1


title: 940_EB_Atrial_d8


title: C_3C_ZT10_M1_MCC3804A152_S219

description: Library name: C_3C_ZT10_M1_MCC3804A152_S219


title: 939_EB_Ventricular_d8


title: HT29 SIS ECM MatriSphere Day 7_Sample 4


title: C_3H_ZT6_M1_MCC3804A316_S149

description: Library name: C_3H_ZT6_M1_MCC3804A316_S149


title: C_3B_ZT14_F2_MCC3804A197_S260

description: Library name: C_3B_ZT14_F2_MCC3804A197_S260


title: R3_LTL331CL_siK2

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

data_processing:
Fastq files containing 150 bp paired-end reads were aligned to the GRCh38 reference genome with HiSat2 (v. 2.1.0) within the CHURP pipeline.
Subread (v. 1.4.6) was used to quantify gene expression with the Ensembl v100 GTF file (Homo_sapiens.GRCh38.100.gtf).
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided in the subread_counts.txt file
Supplementary files format and content: CPM vaues are provided in the LTL331CL_CPM.txt file

growth_protocol: LTL331CL cells were maintained in reconditional programming media as described (Ci et al. 2020 Cells)

extract_protocol:
Total RNA was extracted from cells using the ReliaPrep RNA miniprep system (Promega).
Total RNA was sent to Novogene (Sacramento, CA) for library prep and sequencing. Library prep was performed with the mRNA-seq Lib Prep Kit for Illumina (ABclonal, RK20302). Poly (A) capture was used during library prep to enrich for mRNA.

treatment_protocol: LTL331CL cells were electroporated with two independent siRNAs targeting KLF5, or control siRNA and seeded on 6-well plates for 72 hours before RNA isolation.

value: Prostate Cancer

value: siRNA targeting KLF5 (2)


title: R2_LTL331CL_siK2


title: 938_EB_Atrial_d7


title: R1_LTL331CL_siK2


title: 937_EB_Ventricular_d7


title: C_3F_ZT2_F1_MCC3804A187_S245

description: Library name: C_3F_ZT2_F1_MCC3804A187_S245

value: Brain


title: HT29 Cells alone Spheroid Day 7_Sample 5


title: R2_LTL331CL_siK1

value: siRNA targeting KLF5 (1)


title: R1_LTL331CL_siK1


title: C_2L_ZT14_F_MCC3804A185_S231

description: Library name: C_2L_ZT14_F_MCC3804A185_S231

value: Parvalbumin interneurons

value: Ribo-tag mice


title: R3_LTL331CL_siC

value: Control siRNA


title: 936_EB_Atrial_d5


title: C_2K_ZT6_F2_MCC3804A175_S214

description: Library name: C_2K_ZT6_F2_MCC3804A175_S214


title: R2_LTL331CL_siC


title: C_2J_ZT2_F_MCC3804A176_S222

description: Library name: C_2J_ZT2_F_MCC3804A176_S222


title: R1_LTL331CL_siC


title: 935_EB_Ventricular_d5


title: resistant_rna_c.1

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
H929_resistant_rnaseq_rep3
NM2021_0136

data_processing:
Adapters were trimmed with Cutadapt. UMIs were trimmed and collapsed using UMI-tools (16). Transcript expression was quantified using Salmon v1.6 (12). Differentially expressed genes were determined using R package DESeq2 and deemed significant if adjusted p-value < 0.05 and fold change > 2 (13). Pipeline and all code available at https://github.com/mukherjeelab/2024_oma-resistance
Assembly: GRCh38 v.26
Supplementary files format and content: comma separated file with gene counts

source_name: bone marrow

growth_protocol: Cells were cultured at 37 °C with 5% CO2 in RPMI 1640 medium containing 10% fetal bovine serum (Atlas Biologics), 100 U/mL penicillin, and 100  μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
For RNA-seq RNA was isolated using Trizol LS and ZYMO Directzol RNA microprep kit with on-column DNase I treatment. PolyA(+) RNA was selected from 500 ng of each input sample using the NEBNext Poly(A) mRNA magnetic isolation module. For ribo-seq cells were lysed in lysis buffer containing 1ug/mL cycloheximide. Lysates were treated  with 750 U RNase I (Invitrogen Ambion). The digestion was stopped with SUPERaseIN followed by recovery of monosomes with equilibrated Microspin S-400 HR (GE) columns. Trizol LS was added to the monosome-containing elution and RNA isolated with the ZYMO Directzol microprep kit with on-column DNase I treatment. The isolated RNA was depleted of rRNA using the siTOOls riboPOOLs kit for ribosome profiling. The samples were resolved on a 15% TBE-Urea PAGE gel and ribosome protected fragments 28-29 nt in size were extracted and recovered. RPFs were treated with T4-PNK.
RNA-seq libraries were prepared using KAPA RNA Hyper prep RNAseq library prep kit (Roche) with with dual-index adapters, followed by quality check of the final libraries by Qubit dsDNA HS assay and Tapestation High Sensitivity D1000 ScreenTape. Ribo-seq libraries were prepared using Qiagen QIAseq miRNA library prep kit with provided single index adapters.

treatment_protocol: To determine drug efficacy, drugs were printed into 96-well culture plates using the D300e Digital Dispenser (Tecan). 60,000 cells per well were incubated in triplicate for 96 h. CellTiter-Glo Luminescent Assay (Promega) was used to determine cell viability using a Glomax Multi Detection System (Promega).

value: bone marrow

value: B lymphocyte


title: 828_Mon_Ventricular_d14


title: resistant_rna_a.1

description:
H929_resistant_rnaseq_rep1
NM2021_0134


title: C_2I_ZT14_M2_MCC3804A150_S203

description: Library name: C_2I_ZT14_M2_MCC3804A150_S203


title: resistant_rna_b.1

description:
H929_resistant_rnaseq_rep2
NM2021_0135


title: parental_rna_b.1

description:
H929_parental_rnaseq_rep2
NM2021_0132


title: 826_Mon_Ventricular_d13


title: C_2H_ZT18F_MCC3804A179_S244

description: Library name: C_2H_ZT18F_MCC3804A179_S244


title: parental_rna_c.1

description:
H929_parental_rnaseq_rep3
NM2021_0133


title: C_2G_ZT18_M_MCC3804A182_S207

description: Library name: C_2G_ZT18_M_MCC3804A182_S207


title: R3_LTL331CL_siK1


title: parental_rna_a.1

description:
H929_parental_rnaseq_rep1
NM2021_0131


title: resistant_rna_c

description:
MM.1S_resistant_rnaseq_rep3
NM2021_0130

source_name: peripheral blood

value: peripheral blood

value: B lymphoblast


title: resistant_rna_a

description:
MM.1S_resistant_rnaseq_rep1
NM2021_0128


title: 824_Mon_Ventricular_d12


title: 822_Mon_Ventricular_d11


title: C_3A_ZT22_M1_MCC3804A156_S248

description: Library name: C_3A_ZT22_M1_MCC3804A156_S248


title: parental_rna_b

description:
MM.1S_parental_rnaseq_rep2
NM2021_0126


title: 934_EB_Shared_d4


title: parental_rna_a

description:
MM.1S_parental_rnaseq_rep1
NM2021_0125


title: C_2D_ZT22_F_MCC3804A173_S257

description: Library name: C_2D_ZT22_F_MCC3804A173_S257


title: C_2E_ZT6_M3_MCC3804A195_S246

description: Library name: C_2E_ZT6_M3_MCC3804A195_S246


title: resistant_ribo_c.1

description:
H929_resistant_riboseq_rep3
NM2021_0123

data_processing:
*library strategy: Ribo-seq
Adapters were trimmed with Cutadapt. UMIs were trimmed and collapsed using UMI-tools (16). Transcript expression was quantified using Salmon v1.6 (12). Differentially expressed genes were determined using R package DESeq2 and deemed significant if adjusted p-value < 0.05 and fold change > 2 (13). Pipeline and all code available at https://github.com/mukherjeelab/2024_oma-resistance
Assembly: GRCh38 v.26
Supplementary files format and content: comma separated file with gene counts


title: 820_Mon_Ventricular_d10


title: resistant_ribo_b.1

description:
H929_resistant_riboseq_rep2
NM2021_0122


title: resistant_ribo_a.1

description:
H929_resistant_riboseq_rep1
NM2021_0121


title: parental_ribo_b.1

description:
H929_parental_riboseq_rep2
NM2021_0119


title: C_2C_ZT22_M_MCC3804A165_S256

description: Library name: C_2C_ZT22_M_MCC3804A165_S256


title: 817_Mon_Ventricular_d9


title: parental_ribo_c.1

description:
H929_parental_riboseq_rep3
NM2021_0120


title: C_2B_ZT10_M_MCC3804A162_S235

description: Library name: C_2B_ZT10_M_MCC3804A162_S235


title: resistant_rna_b

description:
MM.1S_resistant_rnaseq_rep2
NM2021_0129


title: 816_Mon_Ventricular_d8


title: 815_Mon_Ventricular_d8


title: parental_rna_c

description:
MM.1S_parental_rnaseq_rep3
NM2021_0127


title: tissue_PET_3

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: Sample 16
Column name in  Raw_counts_tissue.csv and Normalized_counts_tissue.csv: tissue_PET_3

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to GRCh38 by hisat2 with default parameters
Raw counts were generated using featureCounts and then normalized by DEseq2
Assembly: GRCh38
Supplementary files format and content: Matrix tables with raw gene counts or normalized gene counts for every gene and every sample

source_name: endometrium

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA). Samples were frozen in a 2mL tube using liquid nitrogen, homogenized in 1.5ml of TRIZOL reagent for 2 min, and then allowed to rest horizontally for 5 min. After centrifugation at 12000g for 5 min at 4°C, the supernatant was collected and mixed with 0.3 mL chloroform/isoamyl alcohol (24:1). The mixture was vigorously shaken for 15 s and then centrifuged at 12000g for 10 min at 4°C. After centrifugation, the upper aqueous phase was mixed with an equal volume of isopropyl alcohol and was centrifuged at 13600g for 20 min at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL of 75% ethanol and air-dried for 5-10 min. RNA samples were dissolved in 25-100μL of DEPC-treated water. Total RNA was qualified and quantified using a NanoDrop (Thermo Fisher Scientific, MA, USA) and Agilent 2100 bioanalyzer (Agilent, CA, US).
Oligo (dT)-attached magnetic beads were utilized to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer (75mM KCl, 6mM MgCl2, 50mM Tris-HCl, pH 8.3). First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis. Afterward, a-Tailing Mix and RNA Index Adapters were added for end repair. The cDNA fragments were amplified by PCR and the resulting PCR products were purified by Ampure XP Beads. The purified products were dissolved in EB (10mM Tris-HCl, pH8.5) solution and were validated on the Agilent 2100 bioanalyzer for quality control. The double-stranded PCR products from the previous step were heat-denatured and circularized by the splint oligo sequence to generate the final library as single-strand circular DNA. The final library was amplified with phi29 to produce DNA nanoballs (DNB), each containing more than 300 copies of single molecule. The DNBs were then loaded into the patterned nanoarray, and single-end 50 base reads were generated by BGISEQ-500.

value: endometrium

value: Pre-eclampsia


title: parental_ribo_c

description:
MM.1S_parental_riboseq_rep3
NM2021_0117


title: C_2A_ZT2_M2_MCC3804A184_S223

description: Library name: C_2A_ZT2_M2_MCC3804A184_S223


title: parental_ribo_a.1

description:
H929_parental_riboseq_rep1
NM2021_0118


title: C_2F_ZT10_F_MCC3804A157_S255

description: Library name: C_2F_ZT10_F_MCC3804A157_S255


title: tissue_PET_2

description:
Library name: Sample 15
Column name in  Raw_counts_tissue.csv and Normalized_counts_tissue.csv: tissue_PET_2


title: 814_Mon_Ventricular_d7


title: C_1K_ZT10_M_MCC3804A166_S205

description: Library name: C_1K_ZT10_M_MCC3804A166_S205


title: C_1L_ZT6_F_MCC3804A186_S238

description: Library name: C_1L_ZT6_F_MCC3804A186_S238


title: 821_Mon_Ventricular_d11


title: tissue_PET_1

description:
Library name: Sample 14
Column name in  Raw_counts_tissue.csv and Normalized_counts_tissue.csv: tissue_PET_1


title: C_1J_ZT18_F2_MCC3804A149_S254

description: Library name: C_1J_ZT18_F2_MCC3804A149_S254


title: tissue_NT_3

description:
Library name: Sample 13
Column name in  Raw_counts_tissue.csv and Normalized_counts_tissue.csv: tissue_NT_3

value: NT


title: parental_ribo_a

description:
MM.1S_parental_riboseq_rep1
NM2021_0115


title: STROMA_MHHP100_3

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
The fastq files were demultiplexed using umi_tools (v1.0.0). The umi_tools whitelist function was used to whitelist the indexes. Then the umi_tools extract function was used to extract and mark the fastq sequence names with the UMI and indexes which were then used to demultiplex the data
STAR 2.7.9a was used to map the fastq files aginast human (hg38/GRCh38) and mouse (mm10/GRCm38) refernce genomes obtained from Ensembl
The aligned bam files were deduplicated with the umi_tools dedup function based on their UMI sequence
The deduplicated mapped reads were counted using featureCounts v1.5.1 with ensembl gene annotations, Homo_sapiens.GRCh38.101.gtf and Mus_musculus.GRCm38.86.gtf
Supplementary files format and content: Tab separated text files with raw gene counts

source_name: ovary

extract_protocol:
RNA was harvested using RNeasy micro and mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol

value: ovary

value: Primary human ovarian cells, patient 6

value: WT

value: MEHHP 100x


title: resistant_ribo_c

description:
MM.1S_resistant_riboseq_rep3
NM2021_0114


title: C_1I_ZT10_F_MCC3804A198_S209

description: Library name: C_1I_ZT10_F_MCC3804A198_S209


title: tissue_NT_2

description:
Library name: Sample 12
Column name in  Raw_counts_tissue.csv and Normalized_counts_tissue.csv: tissue_NT_2


title: STROMA_MHHP100_2

value: Primary human ovarian cells, patient 5


title: C_1H_ZT_14_F_MCC3804A158_S204

description: Library name: C_1H_ZT_14_F_MCC3804A158_S204

value: Brain


title: resistant_ribo_b

description:
MM.1S_resistant_riboseq_rep2
NM2021_0113


title: STROMA_MHHP100_1

value: Primary human ovarian cells, patient 4


title: tissue_NT_1

description:
Library name: Sample 11
Column name in  Raw_counts_tissue.csv and Normalized_counts_tissue.csv: tissue_NT_1


title: organoid_PET_5

description:
Library name: Sample 10
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_PET_5

source_name: organoid

value: organoid


title: C_1G_ZT6_M_MCC3804A145_S226

description: Library name: C_1G_ZT6_M_MCC3804A145_S226

value: Parvalbumin interneurons

value: Ribo-tag mice


title: parental_ribo_b

description:
MM.1S_parental_riboseq_rep2
NM2021_0116


title: STROMA_MHHP_3

value: MEHHP 1x


title: C_1F_ZT2_F2_MCC3804A200_S225

description: Library name: C_1F_ZT2_F2_MCC3804A200_S225


title: organoid_PET_4

description:
Library name: Sample 9
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_PET_4


title: STROMA_MHHP_2


title: C_1E_ZT14_M3_MCC3804A190_S208

description: Library name: C_1E_ZT14_M3_MCC3804A190_S208


title: calu3-1d_2

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

institute: Helmholtz Center for Infection Research

data_processing:
bacterial cells: cutadapt
host cells: STAR aligner
all sample: bowtie2
featureCounts
Assembly: NC_002516.2, GRCh38.p13
Supplementary files format and content: reads per gene

source_name: Day 1 uninfected control 2

growth_protocol:
bacterial cells: Planktonic cultures in DMEM & Calu-3 ALI cultures
host cells: Air-liquid interface (ALI)

extract_protocol:
all samples: RNeasy Mini Kit & Qiashredder columns
all samples: NEBNext Ultra II Directional RNA library prep kit

treatment_protocol:
bacterial cells: Planktonic cultures in DMEM & Calu-3 ALI cultures + tobramycin treated
host cells: Controls & infected with PAO1 + tobramycin treated

value: Epithelial

value: wild type


title: STROMA_MHHP_1


title: organoid_PET_3

description:
Library name: Sample 8
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_PET_3


title: calu3-1d_1

source_name: Day 1 uninfected control 1


title: calu3-5d_3

source_name: Day 5 uninfected control 3


title: 813_Mon_Ventricular_d7

value: hESC-derived cardiac cells

value: cardiomyocyte

value: Cmdifferentiation


title: organoid_PET_2

description:
Library name: Sample 7
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_PET_2

value: Pre-eclampsia


title: organoid_PET_1

description:
Library name: Sample 6
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_PET_1


title: calu3-5d_2

source_name: Day 5 uninfected control 2


title: STROMA_EQUI100_3

value: ovary

value: Equimolar mixture 100x


title: STROMA_EQUI100_2

value: WT


title: organoid_NT_5

description:
Library name: Sample 5
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_NT_5

value: NT


title: C_1C_ZT22_M3_MCC3804A161_S228

description: Library name: C_1C_ZT22_M3_MCC3804A161_S228


title: calu3-5d_1

source_name: Day 5 uninfected control 1


title: resistant_ribo_a

description:
MM.1S_resistant_riboseq_rep1
NM2021_0112

value: peripheral blood

value: B lymphoblast


title: STROMA_EQUI100_1

value: Primary human ovarian cells, patient 4


title: STROMA_EQUI_3

value: Primary human ovarian cells, patient 6

value: Equimolar mixture 1x


title: organoid_NT_4

description:
Library name: Sample 4
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_NT_4

value: organoid


title: C_1A_ZT22_F_MCC3804A142_S202

description: Library name: C_1A_ZT22_F_MCC3804A142_S202

value: Brain

value: Parvalbumin interneurons

value: Ribo-tag mice


title: Sample 30

city: Kalyani

first: Kartiki

middle: V.

last: Desai

state: West Bengal

address: N.S.S kalyani

country: India

institute: National Institute of Biomedical Genomics

data_processing:
NovaSeq software used for base calling and FASTQC was used for quality check.
Sequence reads were trimmed for adaptor sequence using CutAdapt, and masked for low-complexity or low-quality sequence, then mapped with the human genome (GrCh38.1) by Hisat2.0 with parameters  -q -x -1 -2 -S
Aligned sequences were processed by Featurecounts package to get transcript specific counts with parameters -p s 2 -t -g
Assembly: GrCh38.1
Supplementary files format and content: Tab-delimited text files include single normalized count matrix from featureCounts for each Sample

source_name: Serum derived Evs

extract_protocol:
EV RNA was isolated by EXOQUICK® Exosome isolation and RNA purification kit for serum/plasma (System Biosciences,CA) and was reverse transcribed to make amplified cDNA by SMART seq v4 ultra-low input RNA kit (Takara Bio Inc, USA).
Low Input Library Prep Kit v2 (Takara Bio Inc, USA). DNA unique Dual index kit was used to combine libraries for sequencing (Takara Bio Inc, USA).  NOVASEQ 6000 was used for sequencing to generate 25 million paired end reads per sample.

value: Serum derived Evs

value: Healthy


title: Sample 29


title: organoid_NT_3

description:
Library name: Sample 3
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_NT_3


title: STROMA_EQUI_2

value: Primary human ovarian cells, patient 5


title: Edaravone dexborneol_3

city: Xinxiang

first: Han

address: 601 Jinsui Road, Hongqi District, Xinxiang City, Henan Province

institute: Xinxiang Medical University

description: Library name: EDB_3

data_processing:
Cutadapt was used to trim adapter sequences/low-quality reads, allowing 20% base mismatch.
The filtered reads were aligned to the reference genome using HISAT2 software.
HTSeq statistics were used to align the Read Count value of each gene as the original gene expression.
Read counts was normalized to log2-counts per million with the functions calcNormFactors and voom from the R package
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file includes readcount data for each sample

organism: Rattus norvegicus

source_name: Striatal tissue

extract_protocol:
RNA was extracted using TRIzol reagent (DP424, Tiangen) according to the manufacturer’s instruction.
RNA-seg libraries were prepared by Personal Biotechnology Co., Ltd.

value: Striatal tissue


title: Edaravone dexborneol_2

description: Library name: EDB_2


title: STROMA_EQUI_1

value: ovary


title: Sample 28


title: Sample 27


title: organoid_NT_1

description:
Library name: Sample 1
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_NT_1


title: STROMA_EPIDEM100_3

value: Epidemiological mixture 100x


title: C_1B_ZT18_M_MCC3804A192_S224

description: Library name: C_1B_ZT18_M_MCC3804A192_S224

source_name: Brain


title: Sample 26

value: Tumor


title: Edaravone dexborneol_1

description: Library name: EDB_1


title: in vitro cultured D7 blastocyst, manual cumulus denudation, rep5

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

description: Library name: MANUAL5

data_processing:
Paired-end read fastq files were quality checked with FastQC and preprocessed with fastp. The resulting files were pseudoaligned and quantified using kallisto against the reference transcriptome of Bos taurus
Assembly: Bos taurus ARS-UCD 1.3 Ensembl release 113
Supplementary files format and content: comma-delimited file with raw counts for each sample

organism: Bos taurus

extract_protocol:
Total RNA was extracted using a MagMAX mirVana Total Isolation Kit (Applied Biosystems, USA) following the manufacturer's instruction with minor modifications.
The RNA samples were quantified by Qubit RNA BR Assay (Thermo Fisher Scientific, Spain) and the RNA integrity was estimated using an RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent, USA), with a minimum RIN value of 8.4. RNA-seq libraries were prepared with a KAPA Stranded mRNA-seq Illumina Platforms Kit (Roche, Switzerland) following the manufacturer's recommendations. Briefly, 50–100 ng of total RNA was used for poly-A fraction enrichment with oligo-dT magnetic beads, after the mRNA fragmentation. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt-end double-stranded cDNA was 3′-adenylated, and Illumina platform-compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies, Spain) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with a DNA 7500 assay.

treatment_protocol: Manual or automatic cumulus denudation of bovine zygotes, followed by in vitro culture in SOF medium for seven days.

value: blastomera


title: Sample 25


title: organoid_NT_2

description:
Library name: Sample 2
Column name in  Raw_counts_organoid.csv and Normalized_counts_organoid.csv: organoid_NT_2

value: NT


title: STROMA_EPIDEM100_2

value: WT


title: in vitro cultured D7 blastocyst, manual cumulus denudation, rep4

description: Library name: MANUAL4


title: Intracerebral hemorrhage_2

description: Library name: ICH_2


title: Sample 24


title: Intracerebral hemorrhage_3

description: Library name: ICH_3


title: in vitro cultured D7 blastocyst, manual cumulus denudation, rep3

description: Library name: MANUAL3


title: STROMA_EPIDEM_3

value: Epidemiological mixture 1x


title: Sample 23


title: STROMA_EPIDEM100_1

value: Primary human ovarian cells, patient 4


title: in vitro cultured D7 blastocyst, manual cumulus denudation, rep2

description: Library name: MANUAL2


title: Sham_3

description: Library name: Sham_3


title: STROMA_EPIDEM_2


title: Sample 22


title: STROMA_EPIDEM_1


title: Sham_2

description: Library name: Sham_2


title: in vitro cultured D7 blastocyst, manual cumulus denudation, rep1

description: Library name: MANUAL1


title: Sham_1

description: Library name: Sham_1


title: Sample 21


title: STROMA_WQS100_3

value: Primary human ovarian cells, patient 6

value: WQS-mixture 100x


title: in vitro cultured D7 blastocyst, automatic cumulus denudation, rep5

description: Library name: AUTO5


title: Sample 20


title: Intracerebral hemorrhage_1

description: Library name: ICH_1


title: Sample 19


title: in vitro cultured D7 blastocyst, automatic cumulus denudation, rep4

description: Library name: AUTO4


title: Rat,saline2-TMJ,3days

city: Chongqing

first: Cong

last: Yu

address: No. 426 Songshi North Road, Yubei District

department: Anesthesiology

institute: The stomatology hospital affiliated chongqing medical university

description: Library name: RVM-CON-2

data_processing:
1.Quality control Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp (v0.21.0) software to filter the sequencing data to get high quality sequence（ Clean Data ） for further analysis .
2.Reads mapping The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2. 1.0.
3. Differential expression analysis we used StringTie(v2. 1.5) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq2 (v1.30.1) with screened conditions as follows: expression difference multiple |log2FoldChange|>1, significant padj≤0.05.  At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
4.GO and KEGG enrichment analysis we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using cluster Profiler to perform GO enrichment analysis on the differential genes, calculate P-value by hypergeometric distribution method (the standard of significant enrichment is padj≤0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler (v3.18. 1) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with padj≤0.05.
Assembly: mRatBN7.2
Supplementary files format and content: gene_fpkm.txt

source_name: rostral ventromedial medulla

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies,CA,USA)
1.  Sample qualification and quantification Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after the  total  RNA  was   qualified  and   quantified  as  follows:  (1)  RNA  purity   and concentration  were   then  examined  using  NanoDrop   spectrophotometer   (Thermo Scientific) and Qubit 4.0; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system. 2.  Library preparation Three  micrograms  of  RNA  were  used   as  input  material   for  the  RNA  sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.   Fragmentation   was   carried   out   using   divalent   cations   under   elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment  Selection.  After  purification  and  fragment  selection,  the  products  were amplified and enriched by PCR. Qubit was used for quantitative . The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded  circular  DNA.  Single-stranded  circular  DNA  is   amplified  by  a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative. 3.  Sequencing After library preparation , the sequencing library was sequenced on DNBSEQ-T7 with PE150 model at Bioyi Biotechnology Co.,Ltd. (Wuhan, China).

value: rostral ventromedial medulla

value: Bilateral TMJ 50uL saline Injection


title: C_1D_ZT2_M_MCC3804A163_S242

description: Library name: C_1D_ZT2_M_MCC3804A163_S242

data_processing:
FASTQC
HTSeq
DESeq2 normalization (median of ratios)
Cosinor modeling
Assembly: Mus musculus Ensembl GRCm38
Supplementary files format and content: .csv

value: Brain

value: Parvalbumin interneurons

value: Ribo-tag mice


title: STROMA_WQS100_2

value: Primary human ovarian cells, patient 5


title: Sample 18

value: Serum derived Evs


title: in vitro cultured D7 blastocyst, automatic cumulus denudation, rep3

description: Library name: AUTO3


title: Sample 17


title: STROMA_WQS_3

value: ovary

value: WQS-mixture 1x


title: Rat,saline3-TMJ,3days

description: Library name: RVM-CON-3


title: Rat,CFA3-TMJ,3days

description: Library name: RVM-CFA-3

value: Bilateral TMJ 50uL CFA Injection


title: STROMA_WQS100_1


title: in vitro cultured D7 blastocyst, automatic cumulus denudation, rep2

description: Library name: AUTO2

value: blastomera


title: STROMA_WQS_2


title: Sample 16

value: Tumor


title: in vivo collected D7 blastocyst, rep5

description: Library name: VIVO5

source_name: in vivo collected D7 blastocyst

value: in vivo collected D7 blastocyst


title: Rat,CFA2-TMJ,3days

description: Library name: RVM-CFA-2


title: in vivo collected D7 blastocyst, rep4

description: Library name: VIVO4


title: Sample 15


title: STROMA_WQS_1

value: WT


title: Sample 14


title: Sample 13


title: 22_Col_13DAP_3

city: Geneva

first: Lena

last: Hyvärinen

state: Geneva

address: 30, Quai Ernest-Ansermet

department: Plant Sciences

country: Switzerland

institute: University of Geneva

data_processing:
The galaxy plateform was used to process the data (usegalaxy.org). Several tools were used to obtain Differential Expression Genes (DEGs). If not mention, the default settings of the tools were applied.
First, the data were concatenated with concatenate multiple datasets tools . Fastp was used to remove bad quality sequences. Then, FastQ groomer was used to convert data to the appropriate format to subsequental analysis.
HISAT2 was used to align the sequences to Arabidopsis thaliana genome (https://www.ncbi.nlm.nih.gov/datasets/genomes/?taxon=3702) with the following details: single library end, unstrained, report aligments tailored for transcript assemblers including StringTie
StringTie (unstranded, 50bp length) was used to count and annotated the reads. Finally, DeSeq2 was used to identify the DEGs.
An excel file with the DEGS of each comparison resemble all the data
Assembly: https://www.ncbi.nlm.nih.gov/datasets/genomes/?taxon=3702
Supplementary files format and content: tabular files generated from StringTie with gene ID and read counts associated used by DeSeq2
Supplementary files format and content: excel file with the DEGs of all possible transcriptome comparisons

organism: Arabidopsis thaliana

source_name: endosperm-seedcoat

growth_protocol: All plants were grown in standard conditions, meaning at 21–23°C, 16 hr/8 h day/night photoperiod, light intensity of 120-130 µmol/m2s, humidity of 70% (22°C treatment). At bolting, flowers just before blooming were taggeted and this tag represents pollination event (0DAP). At 11 DAP, WT and myb107-2 developing seeds from tagged siliques from 3-4 different plants were dissected to isolate the seedcoat and endosperm. The same day, plant were transfered for a 6h cold treatment or a 48h cold treatment or kept at 22°C for the 13 DAP WT sample. The same isolation procedure was done for all the samples.

extract_protocol:
Total RNA was isolated as previously described in Piskurewicz and Lopez-Molina, 2011. Briefly, a 8M LiCl buffer was used for extraction, then precipitated RNA was solubilized in a buffer prior chloroform-phenol extraction and precipitated again with ethanol. Between 13.5 and 21.0 ng/ul total RNA was extracted per samples (Qbit measurement).
TruSeq mRNA stranded kit

treatment_protocol: Cold treamtent was performed in these conditions: 13°C, 16 h/8 h day/night photoperiod, light intensity of 120-130 µmol/m2s, humidity of 60-65%

value: endosperm-seedcoat

tag: ecotype

value: Col

tag: developmental stage

value: 13 DAP

value: 22degree C


title: STROMA_DMSO_2

value: DMSO


title: Rat,CFA1-TMJ,3days

description: Library name: RVM-CFA-1

value: rostral ventromedial medulla


title: STROMA_DMSO_3

value: Primary human ovarian cells, patient 6


title: Rat,saline1-TMJ,3days

description: Library name: RVM-CON-1

value: Bilateral TMJ 50uL saline Injection


title: in vivo collected D7 blastocyst, rep3

description: Library name: VIVO3


title: STROMA_DMSO_1

value: Primary human ovarian cells, patient 4


title: in vivo collected D7 blastocyst, rep2

description: Library name: VIVO2


title: KGN_MHHP100_3

value: Granulosa cancer cell line KGN

value: MEHHP 100x


title: 22_Col_13DAP_2


title: 48h_myb107_11DAP_3

value: 11 DAP

value: 48h 13degree C


title: CC-NfL, replicate 4

city: South San Francisco

first: Mitchell

last: Rezzonico

address: 1 DNA Way

institute: Genentech

description:
Library name: Sample 12
SAM24400401

data_processing:
The fastq sequence files for all RNA-seq samples were filtered for read quality (keeping reads where at least 70% of the cycles had Phred scores ≥ 23), and ribosomal RNA contamination. The remaining reads were aligned to the mouse reference genome (GRCm38) using the GSNAP alignment tool.
These steps, and the downstream processing of the resulting alignments to obtain read counts were implemented in the Bioconductor package HTSeqGenie.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Microglia

growth_protocol: Primary microglia cultures were prepared from P1-2 mouse brains dissected in HBSS. Cells were dissociated with 0.25% trypsin for 10 min at 37C followed by 3 washes in DMEM and filtered through a 70 mm strainer (Falcon, 352350). Cells were plated in 150 cm BioCoat PDL flasks (Corning, 354538). Next day cells were washed with PBS and replenished with fresh DMEM media supplemented with 10% FBS and 1% Pen/Strep. After 10-13 days flasks were shaken for 2 hours at 175 rpm at 37C, media was then collected and spun down at 700g for 5 min to pellet microglia. Microglia were plated in 24-well plates at 50,000 cells per well in DMEM supplemented with 10% FBS and 2.5 ng CSF1 per well (R&D Systems, 416-mL). All experiments were done within 2-4 days following microglia plating.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Total RNA was quantified with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on TapeStation 4200 (Agilent Technologies).
RNA-seq libraries were prepared using the Truseq Stranded mRNA Kit (Illumina). Libraries were quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on a NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: Microglia were treated with either full length NfL (5µg), coiled-coil NfL (5µg) or a vehicle control for 24 hours.

tag: strain

value: Microglia

value: Coiled-coil NfL

tag: batch


title: in vivo collected D7 blastocyst, rep1

description: Library name: VIVO1

value: blastomera

value: in vivo collected D7 blastocyst


title: in vitro cultured D7 blastocyst, automatic cumulus denudation, rep1

description: Library name: AUTO1


title: FL-NfL, replicate 4

description:
Library name: Sample 11
SAM24400400

value: WT

value: Full length NfL


title: 48h_myb107_11DAP_2

value: endosperm-seedcoat

value: Col


title: Sample 11

value: Serum derived Evs

value: Tumor


title: 22_Col_13DAP_1

value: 13 DAP

value: 22degree C


title: KGN_MHHP100_1

value: ovary


title: 48h_myb107_11DAP_1


title: Sample 10


title: Sample 9


title: Sample 12


title: KGN_MHHP100_2

value: Granulosa cancer cell line KGN


title: KGN_MHHP_3

value: MEHHP 1x


title: 48h_Col_11DAP_3

value: 11 DAP


title: Sample 8


title: CC-NfL, replicate 3

description:
Library name: Sample 9
SAM24400397


title: KGN_MHHP_2


title: Sample 7


title: FL-NfL, replicate 3

description:
Library name: Sample 8
SAM24400396


title: Sample 6


title: Vehicle, replicate 3

description:
Library name: Sample 7
SAM24400395

value: Vehicle


title: KGN_EQUI100_3

value: Equimolar mixture 100x


title: 48h_Col_11DAP_1

value: 48h 13degree C


title: Sample 5


title: CC-NfL, replicate 2

description:
Library name: Sample 6
SAM24400393

value: Microglia

value: Coiled-coil NfL


title: Sample 4


title: KGN_EQUI100_2

value: WT


title: Vehicle, replicate 4

description:
Library name: Sample 10
SAM24400399


title: KGN_EQUI100_1


title: 6h_Col_11DAP_2

value: 6h 13degree C


title: Vehicle, replicate 2

description:
Library name: Sample 4
SAM24400391


title: 6h_Col_11DAP_1

value: endosperm-seedcoat


title: Sample 2


title: 6h_Col_11DAP_3

value: Col


title: CC-NfL, replicate 1

description:
Library name: Sample 3
SAM24400389


title: 22_myb107_11DAP_3


title: KGN_EQUI_2

value: Equimolar mixture 1x


title: KGN_EQUI_3


title: Sample 1

value: Serum derived Evs

value: Tumor


title: 48h_Col_11DAP_2


title: KGN_MHHP_1


title: 22_myb107_11DAP_2

value: 22degree C


title: KGN_EQUI_1

value: ovary


title: FL-NfL, replicate 1

description:
Library name: Sample 2
SAM24400388

value: Full length NfL


title: 22_myb107_11DAP_1


title: Vehicle, replicate 1

description:
Library name: Sample 1
SAM24400387


title: KGN_EPIDEM100_3

value: Granulosa cancer cell line KGN

value: Epidemiological mixture 100x


title: HeLa cells, U2 AMO transfected, repeat 1

data_processing:
data were processed with our published pipeline QuantifyPoly(A) PMID: 34255024
Assembly: hg38

source_name: HeLa cell line

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS

extract_protocol:
Total RNAs were extracted with Trizol reagent
polyA+ RNA-seq library was prepared using standard illumina RNA-seq library preparation kit

treatment_protocol: cells were transfected with U2 AMO

value: HeLa cell line

value: HeLa

value: U2 AMO treated


title: Sample 3


title: 22_Col_11DAP_3

value: 11 DAP


title: KGN_EPIDEM100_2


title: HeLa cells, U2 AMO transfected, repeat 2


title: NIH3T3 cells, U2 AMO transfected-2

extract_protocol:
Total RNAs were extracted with Trizol reagent
3'-seq were prepared using 3'-seq kit (Lexogen, 016.24)


title: CC-NfL, replicate 3, scRNAseq

description:
Library name: Sample 10
SAM24406681

data_processing:
Cell Ranger mkfastq (v6.0.1, 10x Genomics) was used to generate demultiplexed FASTQ files. Reads were aligned to the mouse GRCm38 reference genome and gene counts were quantified as UMIs using Cell Ranger count (v6.0.1, 10x Genomics).
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain: Hippocampus

extract_protocol:
Mice were deeply anesthetized with 2.5% avertin (2,2,2-tribromoethanol (0.5 ml/25 g body weight) and perfused with ice-cold PBS. Both hippocampi were immediately dissected and chopped into 1-2 mm2 pieces in 2 ml ice-cold Hibernate A minus calcium (HACA, BrainBits). Tissue pieces were collected by centrifuging at 300 x g for 2 min in a round-bottom 2 ml tube and added with enzyme mixes from Neural Tissue Dissociation Kit (P) (Miltenyi 130-092-628) following the manufacturer’s manual with slight modifications. Each tissue sample was added into 2 ml pre-warmed Enzyme mix 1 with 5 mg/ml actinomycin D (Sigma-Aldrich A1410) and incubated on a rotator for 15 min at 37C. After adding Enzyme mix 2, samples were gently triturated with wide-orifice pipette tips, incubated for 10 min, gently triturated with regular pipette tips, incubated for another 10 min, and gently triturated with gradual addition of 10 ml ice-cold Hibernate A Low Fluorescence medium (HALF, BrainBits). Cell suspensions were filtered through 70 mm strainers (Miltenyi 130-098-462) and then centrifuged at 300 x g for 10 min at 4C. Cell pellets were carefully resuspended with wide-orifice pipette tips in HALF containing 5% FBS, with Calcein Violet AM (Thermo Fisher C34858) and propidium iodide (Thermo Fisher P1304MP) at 1 mg/ml each for live/dead FACS with BD FacsAria Fusion sorters. Sorted live single cell suspensions were collected into HALF containing 5% FBS. Cell suspensions were adjusted to 2,000 cells/ml by centrifugation at 300 x g for 10 min at 4C and resuspension in HALF containing 5% FBS. Cell viability and density were confirmed again by Trypan Blue staining and counting with Bio-Rad Tc10 counter. The single cell suspensions with viability >75% were proceeded for library preparation.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics PN-1000121 and PN-1000120) were used for library preparation according to the manufacturer’s user guides. Cell-RT mix was prepared to aim for 8,000 cells per sample and applied to Chromium Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Q33230) and profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies 5067-4626).

value: male

value: 11 weeks old

value: Coiled-coil NfL


title: FL-NfL, replicate 3, scRNAseq

description:
Library name: Sample 9
SAM24406679

value: WT


title: NIH3T3 cells, U2 AMO transfected-1


title: KGN_EPIDEM100_1


title: 22_Col_11DAP_1

value: endosperm-seedcoat

value: Col


title: 293 cells, U2 AMO transfected-2


title: K002000258_91866

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

description: Library name: KO100_K002000258_91866

data_processing:
Reads were mapped to the mm9 reference genome using bowtie2 v.2.3 (-k 4 -X2000 –local)
Duplicates were removed with samtools v.1.19. Unmapped reads, reads mapping at low quality (MAPQ <30), reads mapping to chrM, and any unpaired reads were removed.
BigWig files were created with deeptools v.3.5.1
Assembly: mm9
Supplementary files format and content: bam/BigWig

source_name: brain

growth_protocol: pRGCs were isolated from controland GemC1KO/KO newborn mice and plated in poly-D-lysine coatedT25 flasks. The cells were cultured under proliferating conditions(DMEM-high glucose, 10% FBS, 1% penicillin/streptomycin)

extract_protocol:
Pellets were resuspended in lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL) immediately followed by 10 min centrifugation at 4 degrees , resuspension in transposition buffer for 30 min at 37_x000E_C, and purification using the DNA Clean & Con- centrator kit (Zymo; D4014) as per manufacturer's instructions
Trans- posed DNA was eluted in a 10 μL volume and amplified by PCR with Nextera (Illumina) primers; a maximum of 10 PCR cycles was used. Library quality control was carried out using the Agilent 2200 Tap- eStation System, before libraries were paired-end sequenced (75 bp read length) to a total of 25 million reads per sample.

value: brain

value: pRGC

value: radial glial cells

value: GemC1 Knock Out


title: Vehicle, replicate 3, scRNAseq

description:
Library name: Sample 7
SAM24406676

value: Vehicle


title: 22_Col_11DAP_2

value: 22degree C


title: 293 cells, U2 AMO transfected-1


title: KGN_EPIDEM_1

source_name: ovary

value: ovary

value: Granulosa cancer cell line KGN

value: Epidemiological mixture 1x


title: CC-NfL, replicate 2, scRNAseq

description:
Library name: Sample 6
SAM24406675


title: HeLa cells, U2 AMO transfected-2

source_name: HeLa

value: HeLa

value: U2 AMO treated


title: CC-NfL, replicate 1, scRNAseq

description:
Library name: Sample 5
SAM24406674

value: male


title: K002000258_91864

description: Library name: WT150_K002000258_91864

value: Wild Type


title: KGN_WQS100_3

value: WQS-mixture 100x


title: HeLa cells, U2 AMO transfected-1


title: FL-NfL, replicate 2, scRNAseq

description:
Library name: Sample 4
SAM24406673

value: WT

value: 11 weeks old

value: Full length NfL


title: K002000258_91863

description: Library name: WT100_K002000258_91863

value: brain


title: KGN_WQS100_2


title: Hela cell , U6 AMO, repeat 2

data_processing:
data processing steps were carried out using standard encode pipeline  https://www.encodeproject.org/rna-seq/
Assembly: hg38
Supplementary files format and content: bw files

growth_protocol: HeLa and HEK293 cells were obtained from ATCC and cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Thermo Scientific).

extract_protocol:
Total RNAs were extracted with Trizol
polyA+ RNA-seq library was prepared using standard illumina RNA-seq library preparation kit

treatment_protocol: AMO transfection was carried out by electroporation method. Electrophoration was performed using a Bio-Rad Gene pulser at 960 μF and 280 V. After electroporation, cells were cultured for 12 hours in 6 well plates.. The sequence of the 25-mer U6 AMO is 5’-TGCTAATCTTCTCTGTATCGTTCCA-3’. The sequence of the 25-mer U1 AMO is 5’-GGTATCTCCCCTGCCAGGTAAGTAT-3’. The sequence of control AMO is 5’-CCTCTTACCTCAGTTACAATTTATA-3’. AMOs were ordered from Gene Tools.

value: cancer cell line

value: U6 AMO

value: U6 AMO  treatment


title: mEBD6_WT_rep3

city: San Francisco

first: Carolyn

last: Sangokoya

address: 35 Medical Center Way

department: Pathology

institute: UCSF

description:
FINAL.11.2023.mmu.rseq.heat3.AJM.genes.rsem.matrix.final.tsv
FINAL.11.2023.mmu.rseq.heat3.NM.genes.rsem.matrix.final.tsv

data_processing:
For RNA-seq data, raw fastq files were filtered and preprocessed by quality trimming using FASTX-Toolkit (v0.0.14). Adapters were removed, collapsed on unique molecular identifiers using FASTX (v0.0.14) and cutadapt (v1.18).
RNA-seq read mapping and alignment with alignment to mm10 reference genome assembly was performed using STAR (v2.7.10a). Read count tables of transcriptome mapped reads were generated using the RSEM program (v1.3.30).
Quantification of RSEM counts and differential gene expression were performed using R packages edgeR (v.3.40.2) and DESeq2 (v.1.38.3), using the generated count matrices as input for each comparison.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes transcripts per million (TPM) values for each sample

source_name: embryonic stem cells

extract_protocol:
Total RNA was extracted using Trizol. Poly-A RNA was captured usuing magnetic oligo-dT beads. RNA-seq libraries were prepared usinig 100ng poly-A enriched RNA
after poly-A purification, RNA libraries for RNA-seq were prepared using KAPA RNA Hyperprep Kit following manufacturer's protocols. Quality control on final libraries was assessed by TapeStation fragment analysis prior to pooling. Equimolar amounts of libraries were pooled and sequenced on Illumina HiSeq 4000 and NovaSeq X instruments using standard protocols.

value: embryonic stem cells

value: EBD6 differentiation


title: KGN_EPIDEM_3

value: ovary


title: Vehicle, replicate 4, scRNAseq

description:
Library name: Sample 8
SAM24406677

value: Vehicle


title: KGN_WQS100_1

value: Granulosa cancer cell line KGN


title: Vehicle, replicate 2, scRNAseq

description:
Library name: Sample 2
SAM24406671


title: mEBD6_WT_rep2


title: Hela cell , U6 AMO, repeat 1

first: chengguo

address: No. 74 zhongshan 2rd road

institute: sysu

value: HeLa


title: KGN_EPIDEM_2

value: Epidemiological mixture 1x


title: Hela cell , U1 AMO, repeat 2

value: U1 AMO

value: U1 AMO treatment


title: K002000258_91865

description: Library name: KO150_K002000258_91865

value: pRGC

value: radial glial cells

value: GemC1 Knock Out


title: KGN_WQS_2

value: WT

value: WQS-mixture 1x


title: Hela cell , U1 AMO, repeat 1

value: cancer cell line

value: U1 AMO  treatment


title: Vehicle, replicate 1, scRNAseq

description:
Library name: Sample 1
SAM24406670

value: male

value: 11 weeks old


title: mEBD2_WT_rep3

description: FINAL.11.2023.mmu.rseq.heat3.AJM.genes.rsem.matrix.final.tsv

value: embryonic stem cells

value: EBD2 differentiation


title: KGN_WQS_3

value: ovary


title: FL-NfL, replicate 1, scRNAseq

description:
Library name: Sample 3
SAM24406672

value: Full length NfL


title: Ctrl 48

city: Boston

first: Leonardo

last: Riella

state: MA

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

description: Library name: Sample 48

data_processing:
We used Fatsp 0.22.0 63 to detect and trim the adaptor sequences and to keep only reads with a minimum of 60% of bases with a phred quality equals or greater than 15. After quality control, we estimated the transcription abundance with Salmon 1.9.064 using the reference mouse transcriptome and annotation GRCm39 from release M34-Ensembl 111 from the Gencode65 portal
Assembly: GRCm39
Supplementary files format and content: csv file includes VSD normalization by DESeq2

source_name: Spleen

extract_protocol:
Total RNA was isolated from flow-sorted spleen Tregs using RNAeasy Plus (Qiagen).
Dual-indexed libraries were generated using Takara/Clontech Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian reagents (Takara)

value: Spleen

value: Ctrl


title: KGN_WQS_1

value: Granulosa cancer cell line KGN


title: Hela cell , NC AMO, repeat 2

city: guangzhou

last: yao

value: HeLa

value: negative control

value: NC AMO treatment


title: mEBD2_WT_rep2


title: mEBD6_WT_rep1

value: EBD6 differentiation


title: Ctrl 47

description: Library name: Sample 47


title: mEBD2_WT_rep1

value: WT


title: Hela cell , NC AMO, repeat 1


title: KGN_DMSO_3

value: DMSO


title: Ctrl 46

description: Library name: Sample 46


title: KGN_DMSO_2


title: PAO1_calu3-1d_3

organism:
Pseudomonas aeruginosa
Homo sapiens

source_name: Day 1 - Infected with Pseudomonas aeruginosa PAO1

value: Epithelial

value: wild type

value: infected with Pseduomonas aeruginosa PAO1


title: Hela cell, RNAPII ChIP, U6 AMO repeat 2

description: we performed ChIP-seq in control and U6-AMO treated sample. For the preparation of ChIP-Seq libraries, the ChIP-IT Express Enzymatic Shearing (Active Motif) and ChIP-Seq library preparation (Vazyme) kits were employed. The RNAPII antibodies were purchased from Santa Cruz Biotechnology (sc-47701-X). This is RNAPII ChIP sample.

data_processing:
The NovaSeq platform was utilized for sequencing these libraries, and all ChIP-Seq data processing and analysis were carried out following the ENCODE ChIP-Seq pipeline (https://www.encodeproject.org/data-standards/chip-seq/).
Assembly: hg38
Supplementary files format and content: bw files

growth_protocol: HeLa cells were growin in DMEM medium supplemented with 10% FBS

extract_protocol:
cells were fixed, DNA were extracted following the kit manual (ChIP-IT Express Enzymatic Shearing (Active Motif) )
For the preparation of ChIP-Seq libraries, the ChIP-IT Express Enzymatic Shearing (Active Motif) and ChIP-Seq library preparation (Vazyme) kits were employed. The RNAPII antibodies were purchased from Santa Cruz Biotechnology (sc-47701-X).

treatment_protocol: ChIP-seqs were carried out after the cells were transfected with control or U6 AMO for 12 hour

value: cancer cell line

value: RNAPII ChIP

value: U6 AMO treatment


title: Ctrl 45

description: Library name: Sample 45


title: KGN_DMSO_1

value: ovary


title: Hela cell, RNAPII ChIP, U6 AMO repeat 1


title: Hela cell, RNAPII ChIP, NC AMO repeat 2


title: HsGC_MHHP100_3

value: Human primary granulosa cells, patient 3

value: MEHHP 100x


title: PAO1_calu3-1d_1


title: IL-2 43

description: Library name: Sample 43

value: Spleen


title: HsGC_MHHP100_2

value: Human primary granulosa cells, patient 2


title: HsGC_MHHP100_1

value: Human primary granulosa cells, patient 1


title: PAO1_calu3-5d_3

source_name: Day 5 - Infected with Pseudomonas aeruginosa PAO1


title: IL-2 42

description: Library name: Sample 42


title: FL-NfL, replicate 2

description:
Library name: Sample 5
SAM24400392

value: Microglia

value: Full length NfL


title: PAO1_calu3-5d_2


title: Hela cell, RNAPII ChIP, NC AMO repeat 1

value: HeLa

value: NC AMO treatment


title: PAO1_calu3-5d_1


title: HsGC_MHHP_3

value: WT

value: MEHHP 1x


title: IL-2 41

description: Library name: Sample 41


title: Hela cell, input, U6 AMO repeat 1

description: we performed ChIP-seq in control and U6-AMO treated sample. For the preparation of ChIP-Seq libraries, the ChIP-IT Express Enzymatic Shearing (Active Motif) and ChIP-Seq library preparation (Vazyme) kits were employed. The RNAPII antibodies were purchased from Santa Cruz Biotechnology (sc-47701-X). This is input sample.

value: U6  AMO treated input


title: HsGC_MHHP_2


title: Hela cell, input, NC AMO repeat 2

value: negative control input


title: HsGC_MHHP_1


title: NP-OVA_DEC_OVAboost_24h, GC B cell, HTO

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Library name: Tube_exprReferee4_1_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

data_processing:
Single-cell RNA-Seq and Hashtag-oligos (HTOs) UMI quantification were performed with CellRanger multi v7.1.0 (10x Genomics), using the Cellranger GEX reference mm10, and analyzed in R with Seurat v.4.3.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content > 10% and feature count < 200 or > 2.500 were excluded. Sample batches were then merged, scaled, and normalized with SCTransform. Single-cell BCR libraries were mapped to the Cellranger VDJ GRCm38 reference using CellRanger multi v7.1.0.
Assembly: mm10
Supplementary files format and content: CellRanger output files:  GEX_HTO_barcodes.tsv.gz, GEX_HTO_features.tsv.gz, GEX_HTO_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Library strategy: CITE-Seq

source_name: Lymph node

extract_protocol:
For single cell RNA sequencing, single cell suspensions were prepared from draining lymph nodes of immunized mice and treated mice. Single cell suspensions were indexed with TotalSeqC (BioLegend) cell surface antibodies. Gross or fractionated GC cells were purified by flow cytometry, pooled and loaded onto a Chromium Controller (10x Genomics).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the mid-Output Kit (150 paired end) for V-D-J analysis or onto an NOVAseq for pooled V-D-J and single  cell gene expression. Hashtag indexing was used to demultiplex the sequencing data and generate gene-barcode matrices, respectively.

value: Lymph node

value: GC B cells

value: B18hi DEC +/+

value: NP-OVA immunized, DEC-OVA boosted, doxycyline treated -24hr.


title: Hela cell, input, NC AMO repeat 1

value: cancer cell line


title: PAO1_calu3-1d_2

value: Epithelial

value: wild type

value: infected with Pseduomonas aeruginosa PAO1


title: IL-2 44

description: Library name: Sample 44

value: Spleen


title: RBD_bait_positive_mCherry_high_mRNA_DZ_mCherrylow, GC B cell, HTO

description:
Library name: Rebutal_4-5_Tube_D_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: mRNA vaccinated or RBD vaccinated, doxycycline treated -36hr.


title: Cocultured_Ef_Bio2

city: Gainesville

first: Ling Ning Kaylie

last: Lam

state: Florida

address: 1395 Center Dr

department: Oral Biology

institute: University of Florida College of Dentistry

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with illumina software bcl-convert (v4.2.4). Read mapping was performed with HISAT2. Read quantification was performed using Subread’s featureCounts. Read counts were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (CPM). Differential expression analysis was performed using edgeR’s glmQLFTest. Differentially expressed genes were considered using a cut-off of log2 fold change (between ≤-1 and ≥1) and p ≤ 0.05.
Assembly: Ref file: GCA_000172575.2; E. faecalis OG1RF GenBank: CP002621.1
Supplementary files format and content: Tab-separated value file containing counts for each sample separated by sample number
Supplementary files format and content: Combined tab-separated value file for all samples

organism: Enterococcus faecalis OG1RF

source_name: Co-cultured (Treatment) Bio2 T24

growth_protocol: Bacterial cultures are grown in MRS broth for 24 hours at 37 degrees with 5% carbon dioxide

extract_protocol:
Biofilm samples were pelleted at 4,000 x rpm for 10 min, then suspended in RNAprotect solution (Qiagen, Hilden, Germany) for 5 mins. Then, samples were pelleted at 4,000 x rpm for 10 min again for downstream RNA extraction. Subsequent RNA extraction steps were performed according to the manufacturer’s protocol using PureLink RNA mini kit (Thermofisher, Massachusetts, USA) with minor modifications. Briefly, samples were incubated with 30 mg ml-1 of lysozyme for 30 mins prior to extracting RNA. After extraction, RNA samples were further processed using Monarch RNA cleanup kit (New England Biolabs, Massachusetts, USA). Then, the extracted RNA was quality checked using the RNA ScreenTape on a TapeStation instrument (Agilent Technologies, USA). Every sample had a minimum RNA concentration of 25 ng/µL and a RINe value ≥8.0. Extracted RNA samples were sent to SeqCenter (Pennsylvania, USA) for library preparation, ribosomal RNA depletion, sequencing and downstream bioinformatic analysis.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: Compared to the single-species E. faecalis OG1RF control, the treated group is subjected to co-culturing with Lactobacillus crispatus

value: Transwell co-culture


title: Cocultured_Ef_Bio1

source_name: Co-cultured (Treatment) Bio1 T24


title: PBMCs, Severe patient 5 (4th week of infection) Feature Barcode

city: Seoul

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

department: Anatomy and Cell Biology

country: South Korea

institute: Seoul National University College of Medicine

description:
S5_4_FB
Feature_barcode_CITE-seq.csv

data_processing:
Library strategy: CITEseq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts

molecule: protein

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
PBMCs were purified from heparinized peripheral whole blood using a Ficoll-Histopaque gradient.
The user guide of Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10× Genomics, Pleasanton, CA, USA) was used to prepare the cDNA libraries for single-cell RNA sequencing (scRNA-seq) assay. To check the viability of the sorted cells, a Countess™ II FL Automated Cell Counter (Thermo Fisher Scientific) was used with trypan blue. About 10,000 cells for each sample were determined as target cells, and the master mix and single-cell suspensions were dispensed into a Chromium Next GEM G Chip (10× Genomics). For each sample, 5 L of supernatant cDNA was prepared, amplification master mix, SI-PCR primer, and index kit were added, and sample index PCR was performed in a thermal cycler. The clean-up process was performed using 1.2× SPRIselect reagent, and elution was performed with buffer EB.
Single cell RNAseq, TCR/BCR sequencing, CITEseq

tag: individual

value: Severe patient 5

tag: infection

tag: severity

value: Severe

tag: time

value: 4th week of infection


title: RBD_bait_positive_mCherry_high_mRNA_DZ_mCherrylow, GC B cell, 10x RNA

description:
Library name: Rebutal_4-5_Tube_D_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Single-cell RNA-Seq and Hashtag-oligos (HTOs) UMI quantification were performed with CellRanger multi v7.1.0 (10x Genomics), using the Cellranger GEX reference mm10, and analyzed in R with Seurat v.4.3.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content > 10% and feature count < 200 or > 2.500 were excluded. Sample batches were then merged, scaled, and normalized with SCTransform. Single-cell BCR libraries were mapped to the Cellranger VDJ GRCm38 reference using CellRanger multi v7.1.0.
Assembly: mm10
Supplementary files format and content: CellRanger output files:  GEX_HTO_barcodes.tsv.gz, GEX_HTO_features.tsv.gz, GEX_HTO_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv


title: PBMCs, Severe patient 5 (4th week of infection) BCR

description:
S5_4_B
BCR_seq_data.xlsx

data_processing:
Library strategy: BCR-seq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts

value: Peripheral blood mononuclear cells (PBMCs)


title: Single_species_Ef_Bio3

source_name: Control Single-species Bio3 T24

value: biofilm


title: HsGC_EQUI100_2

data_processing:
The fastq files were demultiplexed using umi_tools (v1.0.0). The umi_tools whitelist function was used to whitelist the indexes. Then the umi_tools extract function was used to extract and mark the fastq sequence names with the UMI and indexes which were then used to demultiplex the data
STAR 2.7.9a was used to map the fastq files aginast human (hg38/GRCh38) and mouse (mm10/GRCm38) refernce genomes obtained from Ensembl
The aligned bam files were deduplicated with the umi_tools dedup function based on their UMI sequence
The deduplicated mapped reads were counted using featureCounts v1.5.1 with ensembl gene annotations, Homo_sapiens.GRCh38.101.gtf and Mus_musculus.GRCm38.86.gtf
Supplementary files format and content: Tab separated text files with raw gene counts

extract_protocol:
RNA was harvested using RNeasy micro and mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol

value: ovary

tag: cell line

value: Human primary granulosa cells, patient 2

value: WT

value: Equimolar mixture 100x


title: RBD_bait_positive_mCherry_low_mRNA_DZ_mCherryhigh, GC B cell, HTO

description:
Library name: Rebutal_4-5_Tube_C_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: Lymph node

tag: cell type

value: GC B cells


title: Hela cell, input, U6 AMO repeat 2

value: HeLa

value: cancer cell line

tag: genotype

value: U6  AMO treated input

value: U6 AMO treatment


title: PBMCs, Severe patient 5 (4th week of infection) TCR

description:
S5_4_T
TCR_seq_data.xlsx

data_processing:
Library strategy: TCR-seq
Basecalls performed using bcl2fastq v2.20.0.422
scRNA reads were filtering and align to GRCh38 genome using CellRanger 4.0
Gene count was performed using CellRanger and loaded into single cell objects in Seurat package (v4.0)
Filtering out qualified cells based on the plot displaying the average gene expression versus -log10 p-value or versus mitochondrial gene counts.
Filtering out cell types by annotations based on DEGs, CITE-seq and BCR/TCR-seq.
Inegration was perforemd using Seurat package with the RPCA method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text, xlsx or csv files include cell infromation or normalized gene counts


title: PBMCs, Severe patient 5 (4th week of infection) 5' Expression

description:
S5_4_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: Single_species_Ef_Bio2

source_name: Control Single-species Bio2 T24


title: RBD_bait_positive_mCherry_low_mRNA_DZ_mCherryhigh, GC B cell, 10x RNA

description:
Library name: Rebutal_4-5_Tube_C_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: treatment

value: mRNA vaccinated or RBD vaccinated, doxycycline treated -36hr.


title: HsGC_EQUI_3

tag: tissue

value: Human primary granulosa cells, patient 3

value: Equimolar mixture 1x


title: Single_species_Ef_Bio1

source_name: Control Single-species Bio1 T24


title: NP-OVA_DEC_OVAboost_24h, GC B cell, 10x RNA

description:
Library name: Tube_expReferee4_1_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: B18hi DEC +/+

value: NP-OVA immunized, DEC-OVA boosted, doxycyline treated -24hr.


title: HsGC_EQUI_1

value: Human primary granulosa cells, patient 1


title: RBD_bait_negative_mCherry_high_mRNA_LZ_mCherrylow, GC B celll, HTO

description:
Library name: Rebutal_4-5_Tube_B_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: C3

city: Hangzhou City

first: M

middle: R

last: Y

address: Hangzhou Normal University, Hangzhou City, Zhejiang Province

institute: Hangzhou Normal University

description:
Library name: Sample9
FPKM.C3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: customers.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

organism: Pseudotaxus chienii

source_name: leaf

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

value: leaf

value: The leaves were treated with MeJA for 2 day


title: PBMCs, Severe patient 5 (2nd week of infection) BCR

description:
S5_2_B
BCR_seq_data.xlsx

value: Peripheral blood mononuclear cells (PBMCs)

value: Severe patient 5

value: Severe

value: 2nd week of infection


title: PBMCs, Severe patient 5 (2nd week of infection) Feature Barcode

description:
S5_2_FB
Feature_barcode_CITE-seq.csv


title: RBD_bait_negative_mCherry_low_mRNA_LZ_mCherryhigh, GC B cell, HTO

description:
Library name: Rebutal_4-5_Tube_A_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: Lymph node

value: GC B cells


title: HsGC_EPIDEM100_3

value: ovary

value: WT

value: Epidemiological mixture 100x


title: HsGC_EQUI100_3

value: Equimolar mixture 100x


title: RBD_bait_negative_mCherry_low_mRNA_LZ_mCherryhigh, GC B cell, 10x RNA

description:
Library name: Rebutal_4-5_Tube_A_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA vaccinated or RBD vaccinated, doxycycline treated -36hr.


title: HsGC_EPIDEM100_2

value: Human primary granulosa cells, patient 2


title: PBMCs, Severe patient 5 (2nd week of infection) 5' Expression

description:
S5_2_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: RBD_positive_gross, GC B cell/contaminant CD8 T cell, HTO

description:
Library name: 7_CTRL_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: GC B cells + contaminant CD8 T cells

value: wildtype, C57BL/6J

value: RBD vaccinated


title: HsGC_EPIDEM100_1

value: Human primary granulosa cells, patient 1


title: PBMCs, Severe patient 5 (2nd week of infection) TCR

description:
S5_2_T
TCR_seq_data.xlsx


title: Cocultured_Ef_Bio3

source_name: Co-cultured (Treatment) Bio3 T24

value: Transwell co-culture


title: HsGC_EQUI100_1


title: C2

description:
Library name: Sample8
FPKM.C2

value: leaf

value: The leaves were treated with MeJA for 2 day


title: PBMCs, Severe patient 5 (1st week of infection) Feature Barcode

description:
S5_1_FB
Feature_barcode_CITE-seq.csv

value: Peripheral blood mononuclear cells (PBMCs)

value: Severe patient 5

value: Severe

value: 1st week of infection


title: HsGC_EQUI_2

value: ovary

value: Equimolar mixture 1x


title: B3

description:
Library name: Sample6
FPKM.B3

value: The leaves were treated with MeJA for 1 day


title: B2

description:
Library name: Sample5
FPKM.B2


title: RBD_bait_negative_mCherry_high_mRNA_LZ_mCherrylow, GC B cell, 10x RNA

description:
Library name: Rebutal_4-5_Tube_B_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node

value: GC B cells


title: RBD_positive_gross, GC B cell/contaminant CD8 T cell, 10x RNA

description:
Library name: 7_CTRL_RNA
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: PBMCs, Severe patient 5 (1st week of infection) BCR

description:
S5_1_B
BCR_seq_data.xlsx


title: C1

description:
Library name: Sample7
FPKM.C1


title: B1

description:
Library name: Sample4
FPKM.B1


title: HsGC_EPIDEM_3

value: Human primary granulosa cells, patient 3

value: WT

value: Epidemiological mixture 1x


title: HsGC_EPIDEM_2

value: Human primary granulosa cells, patient 2


title: PBMCs, Severe patient 5 (1st week of infection) TCR

description:
S5_1_T
TCR_seq_data.xlsx


title: A3

description:
Library name: Sample3
FPKM.A3

value: CK


title: RBD_negative_gross, GC B cell, 10x RNA

description:
Library name: 6_CTRL_RNA
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: wildtype, C57BL/6J

value: RBD vaccinated


title: A2

description:
Library name: Sample2
FPKM.A2

value: leaf


title: mCherry_low, GC B cell, HTO

description:
Library name: Princeton_GC_B_mCherry_Lo_rep2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: NP-OVA immunized, doxycycline treated -36hr.


title: PBMCs, Severe patient 5 (1st week of infection) 5' Expression

description:
S5_1_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt

value: Peripheral blood mononuclear cells (PBMCs)

value: Severe patient 5


title: HsGC_WQS100_3

value: WQS-mixture 100x


title: PBMCs, Severe patient 4 (4th week of infection) Feature Barcode

description:
S4_4_FB
Feature_barcode_CITE-seq.csv

value: Severe patient 4

value: Severe

value: 4th week of infection


title: A1

description:
Library name: Sample1
FPKM.A1


title: mCherry_low, GC B cell, 10x RNA

description:
Library name: Princeton_GC_B_mCherry_Lo_rep2_RNA
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node


title: HsGC_WQS100_2

value: ovary


title: mCherry_high, GC B cell, HTO

description:
Library name: Princeton_GC_B_mCherry_HI_rep2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: GC B cells


title: PBMCs, Severe patient 4 (4th week of infection) TCR

description:
S4_4_T
TCR_seq_data.xlsx


title: HsGC_WQS100_1

value: Human primary granulosa cells, patient 1

value: WT


title: PBMCs, Severe patient 4 (4th week of infection) BCR

description:
S4_4_B
BCR_seq_data.xlsx


title: mCherry_high, GC B cell , 10x RNA

description:
Library name: Princeton_GC_B_mCherry_HI_rep2_RNA
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: HsGC_WQS_3

value: Human primary granulosa cells, patient 3

value: WQS-mixture 1x


title: PBMCs, Severe patient 4 (4th week of infection) 5' Expression

description:
S4_4_Exp
pbmc_meta.data.txt
pbmc_normalized_count_integrated.txt
T_cell_normalized_count_integrated.txt
T_cell_meta.data.txt
B_cell_normalized_count_integrated.txt
B_cell_meta.data.txt
Monocyte_normalized_count_integrated.txt
Monocyte_meta.data.txt
NK_cell_normalized_count_integrated.txt
NK_cell_meta.data.txt


title: RBD_negative_gross, GC B cell, HTO

description:
Library name: 6_CTRL_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: wildtype, C57BL/6J


title: mRNA, pif4_F_R1

city: Birmingham

first: Rory

last: Osborne

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

data_processing:
Reads were trimmed and aligned to TAIR10 using bowtie. Differential gene expression analysis was performed using DEseq2
Supplementary files format and content: Processed data files contain read counts (mRNA sequencing)

extract_protocol: RNA was isolated using Qiagen Rneasy extraction kit according to manufacturing instructions.

value: Whole rosette


title: PBMCs, Severe patient 4 (2nd week of infection) Feature Barcode

description:
S4_2_FB
Feature_barcode_CITE-seq.csv

value: 2nd week of infection


title: HsGC_EPIDEM_1

city: Stockholm

first: Anastasios

address: Hälsovägen 7c

institute: Karolinska Institute

value: Epidemiological mixture 1x