title: R61_H3K27ac_NeuN-_rep2

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

country: France

institute: CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Assembly: mm10
Supplementary files format and content: wig files
Supplementary files format and content: wig files

source_name: Striatum

extract_protocol:
Chromatin was extracted from NeuN+ and NeuN- sorted nuclei from R6/1 and WT mice by sonication and divided to allow immunoprecipitation of the same extract with H3K27ac, H3K27me3 antibodies and Input controls (1 million nuclei per ChIP was used). ChIPseq was performed as described by Alcala-Vida et al. (2021) using antibodies targeting H3K27ac (ab4729, Abcam) and H3K27me3ac (C15410195, diagenode). Briefly, nuclei were suspended in Sonication buffer (50mM HEPES pH7.9, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC, 0.1% SDS, 1x PIC) and sonicated to obtain DNA fragments < 500 bp using Covaris E220Ultrasonicator (Covaris). The soluble chromatin fraction was pretreated with protein A Agarose/Salmon Sperm DNA (16-157, Sigma-Aldrich) for 45 min at 4 °C. Subsequently, samples were incubated overnight at 4 °C with corresponding primary antibodies. Protein A Agarose/Salmon Sperm DNA was then added and the mixture was incubated for 3h at 4 °C in a shaker. Agarose beads were washed, protein–DNA complexes were eluted from the beads and de-crosslinked overnight with RNAse A at 65 °C. Proteins were eliminated by 2 h incubation at 45 °C with Proteinase K, and DNA recovered using Qiagen MiniElute PCR Purification Kit.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with Qubit (Invitrogen). ChIP-seq libraries were prepared from 2 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode), according to manufacturer’s instructions. Illumina compatible indexes were added through PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt® AMPure® XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: Striatum

value: female

value: H3K27ac: ab4729, Abcam


title: Pig dorsal skin, 2 weeks, wounded and treated with PBS

status: Public on Jan 08 2025

type: SRA

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Base calls were converted to reads using the 10X Cell Ranger implementation of mkfastq and then aligned against the Sscrofa11.1 reference genome.
For quality control, scRNA-seq cell barcodes were restricted to those with 1000-5000 reads and less than 10% of their transcriptome from mitochondrial genes. Batch correction was performed to the 16 week data at the sample-level using anchor-based transfer in Seurat.
Assembly: Sus_scrofa.Sscrofa11
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Sus scrofa

source_name: dorsal skin wound

extract_protocol:
Skin wounds from porcine skin and xenografted human skin at POD 14 were harvested and mechanically digested with sharp dissecting scissors (n = 6 per condition). Tissue was then added to an enzymatic digestion solution consisting of Collagenase II (ThermoFisher, Cat:17101015) and IV (ThermoFisher, Cat:17104019) in DMEM-F12 (GIBCOTM, Fischer Scientific, Hampton, NH). Samples were digested on an orbital shaker at 150 rpm for 90 minutes at 37oC. FACS buffer was added to quench the digest and samples were filtered through 70 μm cell strainers. Samples were then centrifuged at 1500 for 5 minutes at 4°C and then filtered a second time using 40 μm cell strainers. scRNA-seq was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines. Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.
Transcriptomic samples were prepared from pooled single-cell suspensions using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, Chromium Single Cell B Chip Kit, and Chromium i7 Multiplex Kit (10X Genomics, cat# 1000075, 1000073, and 120262).

tag: tissue

value: dorsal skin wound

tag: cell type

value: all cells (unsorted)

tag: genotype

value: Red duroc

tag: treatment

value: PBS, 2 weeks


title: Pig dorsal skin, wounded and treated with Verteporfin

library_source: transcriptomic single cell

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against the Cell Ranger human reference genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample. For both human and porcine datasets, a maximum percent mitochondrial RNA cutoff of 15% was employed. Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis
Assembly: Sus_scrofa.Sscrofa11 (pig) and hg38 (human xenograft)

extract_protocol:
Skin wounds from porcine skin at 16 weeks and xenografted human skin at POD 14 were harvested and mechanically digested with sharp dissecting scissors (n = 6 per condition). Tissue was then added to an enzymatic digestion solution consisting of Collagenase II (ThermoFisher, Cat:17101015) and IV (ThermoFisher, Cat:17104019) in DMEM-F12 (GIBCOTM, Fischer Scientific, Hampton, NH). Samples were digested on an orbital shaker at 150 rpm for 90 minutes at 37oC. FACS buffer was added to quench the digest and samples were filtered through 70 μm cell strainers. Samples were then centrifuged at 1500 for 5 minutes at 4°C and then filtered a second time using 40 μm cell strainers.
scRNA-seq was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

tag: strain

value: Red durac


title: Patient sample 73

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: P_73
Targeted RNA-Seq

data_processing:
Raw read counts received from HTG Molecular Diagnostics, Inc. are first bach effect corrected using combat R package and subsequntly normalized using edgeR Bioconductor package.
Supplementary files format and content: Data matrix with sample ID in rows and log2 normalized expression values in columns in a comma separated text file.

organism: Homo sapiens

source_name: FFPE

extract_protocol: Patient tissue samples were obtained during standard of care treatment from various clinical timepoints and were sent to HTG Molecular Diagnostics, Inc. for targeted sequencing using their HTG EdgeSeq Oncology Biomarker Panel (OBP) consisting of 2549 cancer-associated genes. Raw data was assembled from five batches of separate HTG runs

value: FFPE


title: Patient sample 72

description:
Library name: P_72
Targeted RNA-Seq


title: R61_H3K27ac_NeuN+_rep2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: Sex

tag: chip antibody


title: Pig dorsal skin, wounded and treated with PBS


title: SHARP_KO_eV_2

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
The fastq files were quality and adapter trimmed using TrimGalore.
The fastq files were aligned using Hisat2.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 with a q-value cutoff < 0.0001. Peaks had be conserved in both replicates.
Assembly: hg19
Supplementary files format and content: Peaks as .bed files (generated from both replicates, and linked to the corresponding *_1 sample records)
Supplementary files format and content: Normalized coverage tracks as .bigwig files

source_name: HeLa

growth_protocol: Human HeLa cells were grown at 37°C with 5% CO2 in DMEM medium supplemented with 2% FCS and penicillin/streptomycin.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907).
Lybrary-prep kit for ChIP-Seq: Diagenode MicropPlex Library Preparation kit v3.

tag: cell line

value: HeLa

value: RBPSUH (D10A4) XP Rabbit mAb (Cell Signaling #5313)


title: Pig dorsal skin, 8 weeks, wounded and treated with PBS

value: PBS, 8 weeks


title: Patient sample 71

description:
Library name: P_71
Targeted RNA-Seq


title: Pig dorsal skin (unwounded)


title: WT_H3K27ac_NeuN-_rep2

value: Wild-type


title: Patient sample 70

description:
Library name: P_70
Targeted RNA-Seq


title: SHARP_KO_36_HaloRBPJ_WT_2


title: Patient sample 69

description:
Library name: P_69
Targeted RNA-Seq


title: WT_H3K27ac_NeuN+_rep2


title: Input_R61_NeuN-_rep2

value: No antibody


title: SHARP_KO_36_HaloRBPJ_WT_1


title: Patient sample 74

description:
Library name: P_74
Targeted RNA-Seq


title: SHARP_KO_eV_for_36_1


title: Input_R61_NeuN+_rep2


title: Patient sample 68

description:
Library name: P_68
Targeted RNA-Seq


title: Patient sample 67

description:
Library name: P_67
Targeted RNA-Seq


title: Input_SHARP_KO_eV_for_36


title: Input_WT_NeuN+_rep2


title: SHARP_KO_36_Halo_only_1


title: Patient sample 66

description:
Library name: P_66
Targeted RNA-Seq


title: Patient sample 65

description:
Library name: P_65
Targeted RNA-Seq


title: SHARP_KO_36_2


title: SHARP_KO_36_1


title: R61_H3K27me3_NeuN+_rep2

value: H3K27me3:C15410195, Diagenode


title: Patient sample 64

description:
Library name: P_64
Targeted RNA-Seq


title: SHARP_KO_eV_1


title: WT_H3K27me3_NeuN-_rep2


title: Patient sample 63

description:
Library name: P_63
Targeted RNA-Seq


title: Patient sample 62

description:
Library name: P_62
Targeted RNA-Seq


title: SHARP_KO_30_Halo_only_2


title: R61_H3K27me3_NeuN-_rep1

value: male


title: Input_WT_NeuN-_rep2


title: control_rep4

type: RNA

city: Solna

first: Monika

last: Ehnman

address: Karolinska University Hospital, Akademiska stråket 1

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description:
ctrl_4
RD control, biological rep 4

hyb_protocol: Hybridization, washing and staining was carried out on Affymetrix GeneChip Clariom D human arrays (Affymetrix, Thermo Fisher Scientific), using Affymetrix GeneChip® Fluidics Station 450, according to the manufacturer’s protocol.

scan_protocol: Extracted RNA (4 replicates/condition) was labeled and amplified (one cycle amplification) according to Affymetrix™ GeneChip Expression Analysis Technical Manual. Chips were scanned using the GeneChipTM Scanner 3000.

data_processing: Data analysis was performed using Expression Console Software (v1.4.1). Raw data was background corrected, normalized, summarized and log2 transformed using the Robust Multi-array Average (RMA) algorithm.

label: biotin

source_name: RD control

label_protocol: Biotinylated DNA targets were prepared from 150 ng total RNA using the GeneChip WT Plus Reagent Kit (Affymetrix, Thermo Fisher Scientific) according to the manufacturer's instructions.

growth_protocol: Cells were kept at 37 °C in a humidified 5% CO2 atmosphere. Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS, 2 mmol/L glutamine, 100 U/mL penicillin, and 100 ug/mL streptomycin was used for both cell types.

extract_protocol: RNA was extracted from 6 well plates using the GeneEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) protocol including an on-column DNase digestion step. For cDNA synthesis, SuperScript II First-Strand Synthesis System for RT-PCR (Invitrogen) was used.

treatment_protocol: Conditioned medium (cell culture supernatant from naive or RD-prestimulated mouse muscle stromal cells in adherent culture) was applied on RD cells. Gene expression changes compared to control medium were analyzed 16 hours later.

value: Rhabdomyosarcoma cell line

value: control


title: SHARP_KO_36_Halo_only_2


title: CMprestimSKMS_rep4

description:
CM.prestim_SKMS_4
RD exposed to CM from prestimulated stromal cells, biological rep 4


title: control_rep3

description:
ctrl_3
RD control, biological rep 3


title: CM_rep3

description:
CM.SKMS_3
RD exposed to CM, biological rep 3

source_name: RD exposed to CM

value: exposed to CM


title: CM_rep2

description:
CM.SKMS_2
RD exposed to CM, biological rep 2


title: CMprestimSKMS_rep2

description:
CM.prestim_SKMS_2
RD exposed to CM from prestimulated stromal cells, biological rep 2


title: WT_H3K27me3_NeuN+_rep2

value: Striatum

value: female


title: CMprestimSKMS_rep3

description:
CM.prestim_SKMS_3
RD exposed to CM from prestimulated stromal cells, biological rep 3


title: CM_rep4

description:
CM.SKMS_4
RD exposed to CM, biological rep 4


title: Patient sample 61

description:
Library name: P_61
Targeted RNA-Seq


title: Patient sample 59

description:
Library name: P_59
Targeted RNA-Seq


title: R61_H3K27me3_NeuN-_rep2


title: SHARP_KO_30_1


title: SHARP_KO_30_HaloRBPJ_WT_1


title: R61_H3K27ac_NeuN+_rep1

value: H3K27ac: ab4729, Abcam


title: Patient sample 60

description:
Library name: P_60
Targeted RNA-Seq


title: R61_H3K27ac_NeuN-_rep1


title: 050C Normal tissue

city: Salaya

first: Sarin

last: Chimnaronk

state: Nakhon Pathom

address: 25/25 Phuttamonthon 4 Road

department: Institute of Molecular Biosciences

country: Thailand

institute: Mahidol University

description:
The miRNA counts (rows) of normal sample group containing 5 tissue samples (columns).
Normal_miRNA_counts.xlsx

data_processing:
The data processing for small RNA sequencing begins with the elimination of low-quality reads, adaptors, and other contaminants to get clean reads. The length distribution of the clean tags, common, and specific sequences between samples, are then summarized. Then the clean tags are annotated into different categories.
Assembly: miRBase 20.0
Supplementary files format and content: excel files containing miRNA counts (rows) and samples (columns)

source_name: Cervical

extract_protocol:
For tissue samples, the total RNA for each sample was extracted by BGI according to their manufacturing procedure. Whereas, the total RNA for each discharge sample was extracted by TRIzol reagent before sending to BGI for further processing of the samples according to their manufacturing procedure.
The small RNAs were filtered by separation on PAGE gel. Followed by 3’ adaptor ligation, reverse primer annealing, and 5’ adaptor ligation. Then the cDNA was synthesized and amplified. The library fragments were selected by separation of the amplified products of 100-120 bp by PAGE gel. The final step involved library quantitation and pooling cyclization.

value: Cervical

tag: disease

value: Normal


title: R61_H3K27me3_NeuN+_rep1


title: SHARP_KO_30_HaloRBPJ_WT_2


title: SHARP_KO_30_2


title: control_rep2

description:
ctrl_2
RD control, biological rep 2


title: CMprestimSKMS_rep1

description:
CM.prestimSKMS_1
RD exposed to CM from prestimulated stromal cells, biological rep 1


title: Patient sample 57

description:
Library name: P_57
Targeted RNA-Seq


title: WT_H3K27me3_NeuN-_rep1


title: SHARP_KO_30_Halo_only_1


title: WT_H3K27ac_NeuN-_rep1


title: 044C Normal tissue


title: WT_H3K27me3_NeuN+_rep1


title: 044A Normal tissue


title: 031A Normal tissue


title: RBPJ_KO_44_2


title: RBPJ_KO_eV_1


title: WT_H3K27ac_NeuN+_rep1


title: Patient sample 56

description:
Library name: P_56
Targeted RNA-Seq


title: Input_R61_NeuN-_rep1


title: Patient sample 58

description:
Library name: P_58
Targeted RNA-Seq


title: RBPJ_KO_42_HaloRBPJ_WT_2


title: RBPJ_KO_44_1


title: CM_rep1

description:
CM.SKMS_1
RD exposed to CM, biological rep 1


title: Patient sample 54

description:
Library name: P_54
Targeted RNA-Seq


title: 044B Normal tissue


title: control_rep1

description:
ctrl_1
RD control, biological rep 1


title: DC049V AIS discharge

description:
The miRNA counts (rows) of AIS sample group containing 4 tissue and 4 discharge samples (columns).
AIS_miRNA_counts.xlsx

tag: discharge

value: AIS


title: Input_R61_NeuN+_rep1


title: RBPJ_KO_eV_2


title: RBPJ_KO_42_HaloRBPJ_RFL_HAA_2


title: Input_WT_NeuN-_rep1


title: DC049E AIS discharge


title: Patient sample 55

description:
Library name: P_55
Targeted RNA-Seq

value: FFPE


title: Patient sample 51

description:
Library name: P_51
Targeted RNA-Seq


title: DC051E AIS discharge


title: RBPJ_KO_42_HaloRBPJ_WT_1

value: HeLa


title: Patient sample 53

description:
Library name: P_53
Targeted RNA-Seq


title: Patient sample 50

description:
Library name: P_50
Targeted RNA-Seq


title: RBPJ_KO_42_HaloRBPJ_RFL_HAA_1

value: RBPSUH (D10A4) XP Rabbit mAb (Cell Signaling #5313)


title: Input_WT_NeuN+_rep1


title: DC049C AIS discharge


title: Patient sample 49

description:
Library name: P_49
Targeted RNA-Seq


title: HELA_hnRNPC_MO_3_1

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

data_processing:
The raw sequenced reads were aligned to the human hg38 reference genome with STAR (v2.7.9a) default parameters in gene quantification mode. After this the software RSeQC v4.0.0 was used to check the stran used for sequencing. In this way only the 4th column of the star output was used to create the txt files.
Alternative splicing analysis was done with rMTAS turbo (v4.1.1), including variable-read-length criteria.
Assembly: hg38
Supplementary files format and content: contains STAR derived gene expression information in raw reads

molecule: polyA RNA

growth_protocol: HEK293 and HeLa cells were maintained in DMEM High Glucose (Biowest), supplemented with 10% fetal bovine serum (FBS; Biochrom) and 1%  penicillin/streptomycin (BioWest). Jurkat JSL1 cells were maintained in RPMI 1640 (Biowest) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Trizol (Bio&Sell) was used for RNA extraction as described in the user manual. Pure RNA was optained using DNAseI digestion and repurification. For the analysis of nascent transcripts, chromatin-associated RNA was isolated.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stimulated with 20ng/ml of phorbol myristate acetate (PMA, Sigma- Aldrich) or dimethyl sulfoxide (DMSO) as solvent control for different time points depending on the experiment setup. For morpholino experiments, heLa or HEK293 cells were seeded and transfected 1 day later using EndoPorter following the manufacturer’s manual.

value: HNRNPC-MO


title: 051B AIS tissue


title: Patient sample 52

description:
Library name: P_52
Targeted RNA-Seq


title: RBPJ_KO_42_HaloRBPJ_R218H_2


title: RBPJ_KO_42_HaloRBPJ_R218H_1


title: Patient sample 48

description:
Library name: P_48
Targeted RNA-Seq


title: RBPJ_KO_42_HaloRBPJ_KRS_2


title: HELA_hnRNPC_MO_2_1


title: 049C AIS tissue


title: RBPJ_KO_42_HaloRBPJ_KRS_1


title: 049B AIS tissue


title: HELA_hnRNPC_MO_1_1


title: Patient sample 47

description:
Library name: P_47
Targeted RNA-Seq


title: HELA_CTRL_MO_3_1

value: CTRL


title: 049A AIS tissue


title: Patient sample 46

description:
Library name: P_46
Targeted RNA-Seq


title: RBPJ_KO_42_HaloRBPJ_K195E_2


title: Patient sample 45

description:
Library name: P_45
Targeted RNA-Seq


title: DC055V HSIL discharge

description:
The miRNA counts (rows) of HSIL sample group containing 40 tissue and 19 discharge samples (columns).
HSIL_miRNA_counts.xlsx

value: HSIL


title: HELA_CTRL_MO_2_1


title: HELA_CTRL_MO_1_1


title: Patient sample 43

description:
Library name: P_43
Targeted RNA-Seq


title: RBPJ_KO_42_HaloRBPJ_FL_AA_2


title: HEK_hnRNPC_MO_3_1


title: HEK_hnRNPC_MO_2_1


title: RBPJ_KO_42_HaloRBPJ_K195E_1


title: RBPJ_KO_42_HaloRBPJ_FL_AA_1


title: Patient sample 42

description:
Library name: P_42
Targeted RNA-Seq


title: Patient sample 44

description:
Library name: P_44
Targeted RNA-Seq


title: RBPJ_KO_42_Halo_2


title: DC054V HSIL discharge


title: Patient sample 41

description:
Library name: P_41
Targeted RNA-Seq


title: HEK_hnRNPC_MO_1_1


title: DC054E HSIL discharge


title: DC055E HSIL discharge


title: DC055C HSIL discharge


title: DC054C HSIL discharge


title: HEK_CTRL_MO_3_1


title: Patient sample 40

description:
Library name: P_40
Targeted RNA-Seq


title: RBPJ_KO_42_Halo_1


title: RBPJ_KO_42_2


title: DC053V HSIL discharge


title: HEK_CTRL_MO_1_1


title: DC053E HSIL discharge


title: RBPJ_KO_42_1


title: Patient sample 38

description:
Library name: P_38
Targeted RNA-Seq


title: Input_SHARP_KO_eV


title: recurrent miscarriage 5 [T8]

city: Nanning

first: lihong

last: pang

state: Guangxi

address: NO.6 Shuangyong Road

department: Prenatal Diagnosis and Genetic Diseases

country: China

institute: Guangxi Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0) software.
The transcript abundances for each sample was estimated with StringTie（1.3.3）.
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.8.4)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: hg19
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

source_name: placental villus tissues

extract_protocol:
RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis. 1-2 µg of total RNA was used for the construction of sequencing libraries.
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: placental villus tissues

tag: subject status

value: recurrent miscarriage

tag: time point

value: 8.7 weeks


title: Patient sample 37

description:
Library name: P_37
Targeted RNA-Seq


title: DC053C HSIL discharge


title: Patient sample 36

description:
Library name: P_36
Targeted RNA-Seq


title: DC052V HSIL discharge


title: Patient sample 35

description:
Library name: P_35
Targeted RNA-Seq


title: Input_SHARP_KO_36_HaloRBPJ_WT_2


title: Input_SHARP_KO_36


title: Input_SHARP_KO_36_Halo_only_2


title: recurrent miscarriage 4 [T5]

value: 8.4 weeks


title: Patient sample 34

description:
Library name: P_34
Targeted RNA-Seq


title: recurrent miscarriage 1 [T11]

value: 6.5 weeks


title: Patient sample 33

description:
Library name: P_33
Targeted RNA-Seq


title: HEK_CTRL_MO_2_1


title: Input_SHARP_KO_30_HaloRBPJ_WT_1


title: DC052E HSIL discharge


title: DC051V HSIL discharge


title: DC052C HSIL discharge


title: recurrent miscarriage 2 [T19]

value: 7.5 weeks


title: Input_SHARP_KO_30_Halo_only_1


title: Patient sample 32

description:
Library name: P_32
Targeted RNA-Seq


title: normal pregnancy 5 [61]

value: normal pregnancy

value: 9.5 weeks


title: DC051C HSIL discharge

value: Cervical


title: Patient sample 39

description:
Library name: P_39
Targeted RNA-Seq


title: Input_SHARP_KO_30


title: normal pregnancy 4 [60]

value: 9.1 weeks


title: DC050V HSIL discharge


title: Patient sample 31

description:
Library name: P_31
Targeted RNA-Seq


title: Input_RBPJ_KO_eV


title: Patient sample 30

description:
Library name: P_30
Targeted RNA-Seq


title: normal pregnancy 3 [59]

value: 7.8 weeks


title: recurrent miscarriage 3 [T20]

value: 7.0 weeks


title: Input_RBPJ_KO_42_HaloRBPJ_WT

value: HeLa


title: Patient sample 29

description:
Library name: P_29
Targeted RNA-Seq

value: FFPE


title: DC048V HSIL discharge


title: Patient sample 28

description:
Library name: P_28
Targeted RNA-Seq


title: normal pregnancy 2 [58]

value: 7.9 weeks


title: Input_RBPJ_KO_42_HaloRBPJ_RFL_HAA


title: Input_RBPJ_KO_42_HaloRBPJ_R218H


title: Patient sample 27

description:
Library name: P_27
Targeted RNA-Seq


title: Input_RBPJ_KO_42_HaloRBPJ_KRS


title: normal pregnancy 1 [57]

value: 6.2 weeks


title: DC048E HSIL discharge

value: HSIL


title: DC048C HSIL discharge


title: Patient sample 26

description:
Library name: P_26
Targeted RNA-Seq


title: Human xenograft dorsal skin xenograft, wounded and treated with Verteporfin

description: host mouse strain: Black 6

value: dorsal skin wound

value: all cells (unsorted)


title: 055B HSIL tissue


title: 055C HSIL tissue


title: Human xenograft dorsal skin xenograft (unwounded)

description: host mouse strain: Black 6


title: Patient sample 25

description:
Library name: P_25
Targeted RNA-Seq


title: Input_RBPJ_KO_42_HaloRBPJ_FL_AA


title: Patient sample 24

description:
Library name: P_24
Targeted RNA-Seq


title: 055A HSIL tissue


title: Input_RBPJ_KO_42_Halo


title: DC050C HSIL discharge


title: Patient sample 23

description:
Library name: P_23
Targeted RNA-Seq


title: 054C HSIL tissue


title: Input_KO_44


title: Patient sample 22

description:
Library name: P_22
Targeted RNA-Seq


title: Input_KO_42


title: 054B HSIL tissue


title: Patient sample 21

description:
Library name: P_21
Targeted RNA-Seq


title: Patient sample 20

description:
Library name: P_20
Targeted RNA-Seq


title: Input_RBPJ_KO_42_HaloRBPJ_K195E


title: Spike 48, Rep 2

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

data_processing:
RNA-seq reads were mapped to GRCh38 (human) reference and SARS-CoV-2 (MN988713.1) genome using STAR aligner
Counts were tabulated for human protein coding genes, lncRNAs (ENSEMBL release 93 annotations) and viral genes (MN988713.1) using featureCounts.
Assembly: GRCh38, ENSEMBL release 93, GenBank MN988713.1
Supplementary files format and content: Raw feature counts per sample as tab delimited text.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Micro Kit
Libraries were prepared using the SMART-Seq  v4 low input RNA kit

value: Endothelial cell

value: SARS-CoV-2 spike protein

tag: treatment time

value: 48 hours


title: Human xenograft dorsal skin xenograft, wounded and treated with PBS

description: host mouse strain: Black 6


title: 054A HSIL tissue


title: 053A HSIL tissue


title: Spike 48, Rep 1


title: Patient sample 19

description:
Library name: P_19
Targeted RNA-Seq


title: CCLP1 transfected with GD3S rep2

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Hybridization was performed on Agilent Human Gene Expression v3 8x60K microarray.

scan_protocol: Slides were washed and scanned using the Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7.3.1 (Agilent Technologies). Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using The LIMMA (LInear Models for Microarray Analysis) R package. Background correction was performed with the normexp method with an offset of 50, and quantile was used for the between-array normalization. The empirical Bayes method was used to compute a moderated t-statistics for two-class comparison.

source_name: CCLP1 intrahepatic cholangiocarcinoma (iCCA) cell line

label_protocol: mRNA from 100 ng of totRNA was amplified and labeled with Cy3 fluorescent.

growth_protocol: CCLP1 and HUCCT1 cells, from intrahepatic bile duct cancer tissue, were kind gift from Dr. AJ Demetris, University of Pittsburgh. Cell lines were cultured as described [Gentilini A, Caligiuri A, Raggi C, Rombouts K, Pinzani M, Lori G, et al. CXCR7 contributes to the aggressive phenotype of cholangiocarcinoma cells. Biochim Biophys Acta Mol Basis Dis 2019;1865:2246-2256.]

extract_protocol: RNA was extracted following standard procedures (miRNeasy Kit, Qiagen).

treatment_protocol: For the transfection of GD3 Synthase in HUCCT1 and CCLP1 cells, ST8SIA1 Lentiviral Vector (Human) (CMV) (pLenti-GIII-CMV, LV701751) (#45655062, Applied Biological Materials Inc.) and pLenti-III-Blank Vector (LV587, as a blank control, Applied Biological Materials Inc). Transfection was performed according to Applied Biological Materials Inc. instructions, and after lentivirus infection, CCA infected cells were selected by puromycin (1ug/ml) at day 3 to day 5.

value: GD3S transfection


title: NC 48, Rep 2

value: SARS-CoV-2 Nucleocapsid protein


title: CCLP1 transfected with GD3S rep1


title: 052B HSIL tissue


title: Patient sample 18

description:
Library name: P_18
Targeted RNA-Seq


title: NC 48, Rep 1


title: 052A HSIL tissue


title: Patient sample 17

description:
Library name: P_17
Targeted RNA-Seq


title: Blank 48, Rep 2

value: No treatment


title: 0d-EVs-3

city: Shanghai

first: Yingyi

last: Shen

address: Shanghai Songjiang

institute: cloudseq

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
The trimmed reads were aligned to the merged pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNAmapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs.
Differentially expressed miRNA between two groups were filtered by Fold Change and P-value. miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNA target genes.
Assembly: rn6
Supplementary files format and content: miRNA_Expression.xlsx

organism: Rattus norvegicus

source_name: adipose tissue

extract_protocol:
Total RNA was extracted using Trizol reagent
GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.)

value: adipose tissue

value: DFAT cells

tag: sample type

value: 0d osteogenic induction medium

value: EVs


title: 0d-EVs-2


title: Blank 48, Rep 1


title: 051C HSIL tissue

value: Cervical


title: CCLP1 control rep1

value: not transfected


title: HUCCT1 control rep2

source_name: HUCCT1 intrahepatic cholangiocarcinoma (iCCA) cell line


title: Patient sample 15

description:
Library name: P_15
Targeted RNA-Seq

value: FFPE


title: CCLP1 control rep2


title: 050A HSIL tissue


title: 052C HSIL tissue


title: Spike 24, Rep 2

value: 24 hours


title: 0d-EVs-1


title: HUCCT1 control rep1


title: 051A HSIL tissue

value: HSIL


title: Patient sample 13

description:
Library name: P_13
Targeted RNA-Seq


title: 14d-EVs-3

value: 14d osteogenic induction medium


title: HUCCT1 transfected with GD3S rep2


title: Patient sample 14

description:
Library name: P_14
Targeted RNA-Seq


title: Patient sample 12

description:
Library name: P_12
Targeted RNA-Seq


title: 048D HSIL tissue


title: NC 24, Rep 2


title: 14d-EVs-2


title: 14d-EVs-1


title: Patient sample 11

description:
Library name: P_11
Targeted RNA-Seq


title: NC 24, Rep 1


title: Blank 24, Rep 2


title: 048C HSIL tissue


title: Root samples treated with mock (ethanol) for 24h- Biological replicate 3

city: Seoul

first: Souvik

last: Dhar

state: Gwanak gu

address: 1, Gwanak ro

country: South Korea

institute: Seoul National University

data_processing:
CLC Genomics Workbench v 22.0.1
Sequence reads were trimmed for adapter/low-quality sequence using CLC genomics workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Arabidopsis thaliana/TAIR10 using CLC genomic workbench (parameters- mismatch cost: 2, insertation cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: TAIR10
Supplementary files format and content: tab-delimited excel file includes raw counts for each library

organism: Arabidopsis thaliana

source_name: mock sample

growth_protocol: 4-5 days old p35S::XVE>>pLexA::STZ; Col-0 Arabidopsis seedlings were treated with estradiol (20µM) for 6h and 24h to understand transcriptional dynamics downstream of STZ.

extract_protocol:
The total RNA from Mock (M-1, M-2, M-3), 6h estradiol treated (6H-1, 6H-2, 6H-3) and 24h estradiol treated (24H-1, 24H-2, 24H-3) roots were isolated using RNeasy Plant Mini kit (Qiagen) by following manufacturer's instruction.
TruSeq Stranded mRNA Library Prep Kit was used by Macrogen (Korea) to prepare library by following TruSeq Stranded mRNA Reference Guide # 1000000040498 v00 protocol

treatment_protocol: Seedlings were treated on half-strength MS plates supplemented with either mock (ethanol) or estradiol (20µM)

value: root

value: cells from root tissue

value: p35S::XVE>>pLexA::STZ; Col-0

value: mock treatment (ethanol) for 24h


title: 048B HSIL tissue


title: Spike 24, Rep 1

value: Endothelial cell

value: SARS-CoV-2 spike protein


title: Patient sample 10

description:
Library name: P_10
Targeted RNA-Seq


title: 048A HSIL tissue


title: Root samples treated with mock (ethanol) for 24h- Biological replicate 2


title: 047C HSIL tissue


title: HUCCT1 transfected with GD3S rep1

value: GD3S transfection


title: Patient sample 9

description:
Library name: P_9
Targeted RNA-Seq


title: Patient sample 8

description:
Library name: P_8
Targeted RNA-Seq


title: Patient sample 7

description:
Library name: P_7
Targeted RNA-Seq


title: Root samples induced by estradiol for 6h- Biological replicate 3

source_name: 6h of STZ induced sample

value: 20 µM estradiol for 6h


title: B SMC Control, L2

value: Smooth muscle cell

value: Mock infection

value: 48 hours


title: B SMC Control, L1


title: A SMC Control, L2


title: 047B HSIL tissue

value: Cervical


title: Root samples induced by estradiol for 6h- Biological replicate 2


title: Patient sample 5

description:
Library name: P_5
Targeted RNA-Seq


title: A SMC Control, L1


title: 047A HSIL tissue


title: 046C HSIL tissue


title: Patient sample 6

description:
Library name: P_6
Targeted RNA-Seq


title: 046B HSIL tissue


title: Root samples treated with mock (ethanol) for 24h- Biological replicate 1


title: B EC Control, L2


title: 046A HSIL tissue


title: Root samples induced by estradiol for 6h- Biological replicate 1


title: Root samples induced by estradiol for 24h- Biological replicate 3

source_name: 24h of STZ induced sample

value: 20 µM estradiol for 24h


title: Patient sample 3

description:
Library name: P_3
Targeted RNA-Seq

value: FFPE


title: Root samples induced by estradiol for 24h- Biological replicate 2


title: B EC Control, L1


title: 045A HSIL tissue


title: Blank 24, Rep 1

value: No treatment

value: 24 hours


title: Root samples induced by estradiol for 24h- Biological replicate 1


title: 043D HSIL tissue

value: HSIL


title: Patient sample 2

description:
Library name: P_2
Targeted RNA-Seq


title: 6h PEP1 treated sample-Biological replicate 3

data_processing:
CLC Genomics Workbench v 22.0.1
Sequence reads were trimmed for adapter/low-quality sequence using CLC genomics workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Arabidopsis thaliana/TAIR10 using CLC genomic workbench (parameters- mismatch cost: 2, insertation cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: TAIR10
Supplementary files format and content: raw counts for each sample

source_name: root meristem

growth_protocol: 4-5 days old Arabidopsis seedlings were treated to mock or PEP1 (1µM) to understand transcriptomic cascades downstream of DAMP signals

extract_protocol:
We took 4-5 days old Arabidopsis seedling and treated them with 1µM PEP1 for 3h, 6h, 12h, and 24h. Following PEP1 treatment we dissected the root meristem from each mock or PEP1 treated samples. The RNA was isolated using RNeasy Micro kit (Qiagen). The purification of the samples and sequencing was done by Macrogen (Korea).
TruSeq Stranded mRNA Library Prep Kit was used by Macrogen (Korea) to prepare library by following TruSeq Stranded mRNA Reference Guide # 1000000040498 v00 protocol

treatment_protocol: Seedlings were treated on half-strength MS plates supplemented with either mock (distilled water) or PEP1 (1µM)

value: root meristem

value: meristematic cells

value: Columbia (Col-0)

value: 6 hours PEP1 (1µM) treatment


title: Patient sample 1

description:
Library name: P_1
Targeted RNA-Seq


title: A EC Control, L1

value: Endothelial cell


title: B EC HI 48 T, L2

value: Media from heat-inactivated SARS-CoV-2 treated SMCs


title: 042A HSIL tissue


title: 6h PEP1 treated sample-Biological replicate 2


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D30 rep3

city: San Francisco

first: Benoit

middle: G.

last: Bruneau

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: Ventricular_D30_rep3
vCM_d30.3

data_processing:
The .fastq files were analyzed using nf-core Nextflow RNA-seq pipeline aligning to hg38 reference genome and using STAR for alignment and Salmon quantification.
Assembly: hg38
Supplementary files format and content: .tsv format of gene counts and tpm values

growth_protocol: Cells were grown in 1 well of a 6- or 12-well dish per replicate.

extract_protocol:
Cells were dissociated in 0.25% Trypsin-EDTA for 10 mins, followed by quenching in 15%FBS in DPBS. Cells were lifted off the dish and resuspended to single cells by repeatedly using P1000 pipette and then transferred to a 1.5 ml tube and centrifuged at 300 x g for 5 min at room temperature. Pellets were snap frozen in dry ice. Total RNA was isolated using Qiagen RNeasy micro kit (Qiagen #74004) with QIAshredder (Qiagen #79656) and eluted in 25 µl water. RNA concentration was determined using Nanodrop and quality was checked using Agilent Bioanalyzer.
RNA-seq libraries were generated using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit were prepared as per manufacturer’s instructions using 400 ng of input RNA. Library concentration was quantified using Qubit Fluorometer and dsDNA HS Assay Kit and quality assessed on Agilent Bioanalyzer.

value: cardiomyocyte

value: WT


title: Patient sample 4

description:
Library name: P_4
Targeted RNA-Seq


title: 041B HSIL tissue


title: 6h PEP1 treated sample-Biological replicate 1


title: B EC HI 24 T, L2


title: Control sample for 6h PEP1 treatment

value: 6 hours mock treatment


title: 040A HSIL tissue


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D30 rep2

description:
Library name: Ventricular_D30_rep2
vCM_d30.2


title: B EC HI 48 T, L1


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D30 rep1

description:
Library name: Ventricular_D30_rep1
vCM_d30.1


title: B EC HI 24 T, L1


title: B EC 48 T, L2

value: Media from SARS-CoV-2 infected SMCs


title: 3h PEP1 treated sample-Biological replicate 3

value: 3 hours PEP1 (1µM) treatment


title: 039A HSIL tissue

value: Cervical


title: A EC Control, L2

value: Mock infection

value: 48 hours


title: 3h PEP1 treated sample-Biological replicate 2


title: 038A HSIL tissue


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D15 rep2

description:
Library name: Ventricular_D15_rep2
vCM_d15.2


title: 037A HSIL tissue


title: 3h PEP1 treated sample-Biological replicate 1


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D15 rep1

description:
Library name: Ventricular_D15_rep1
vCM_d15.1


title: Control sample for 3h PEP1 treatment

value: 3 hours mock treatment


title: B EC 24 T, L2

value: 24 hours


title: 036A HSIL tissue

value: HSIL


title: B EC 24 T, L1


title: 041A HSIL tissue


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D12 rep2

description:
Library name: Ventricular_D12_rep2
vCM_d12.2


title: 12h PEP1 treated sample-Biological replicate 3

value: root meristem

value: 12 hours PEP1 (1µM) treatment


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D12 rep3

description:
Library name: Ventricular_D12_rep3
vCM_d12.3


title: 035A HSIL tissue


title: 12h PEP1 treated sample-Biological replicate 2

value: meristematic cells

value: Columbia (Col-0)


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D15 rep3

description:
Library name: Ventricular_D15_rep3
vCM_d15.3


title: A EC HI 48 T, L1

value: Endothelial cell


title: 033A HSIL tissue


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D12 rep1

description:
Library name: Ventricular_D12_rep1
vCM_d12.1


title: Control sample for 12h PEP1 treatment

value: 12 hours mock treatment


title: B EC 48 T, L1


title: A EC HI 24 T, L1

value: Media from heat-inactivated SARS-CoV-2 treated SMCs


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D10 rep2

description:
Library name: Ventricular_D10_rep2
vCM_10.2

value: cardiomyocyte

value: WT


title: 24h PEP1 treated sample-Biological replicate 3

value: 24 hours PEP1 (1µM) treatment


title: 028B HSIL tissue


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D10 rep1

description:
Library name: Ventricular_D10_rep1
vCM_10.1


title: A EC 48 T, L2

value: Media from SARS-CoV-2 infected SMCs


title: 24h PEP1 treated sample-Biological replicate 2


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D6 rep3

description:
Library name: Ventricular_D6_rep3
vCM_d6.3

value: cardiac precursor


title: 028A HSIL tissue

value: Cervical


title: A EC HI 48 T, L2

value: 48 hours


title: 027A HSIL tissue


title: A EC 48 T, L1


title: 24h PEP1 treated sample-Biological replicate 1


title: 034A HSIL tissue


title: Control sample for 24h PEP1 treatment

value: 24 hours mock treatment


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D6 rep2

description:
Library name: Ventricular_D6_rep2
vCM_d6.2


title: shZMAT3_2

city: Changsha

first: Mian

last: Liu

address: Road Xiangya 87

institute: Xiangya hospital, Central South University

description: Library name: Sample 10

data_processing:
GCF_000001405.39_GRCh38.p13
Assembly: hg38
Supplementary files format and content: Excel files include raw counts for each Sample.
Supplementary files format and content: Excel files include TPM values for each Sample.

extract_protocol:
RNA was harvested using Trizol (ThermoFisher). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture's protocols.

value: papillary thyroid cancer

value: ZMAT3 knockdown

value: no


title: 12h PEP1 treated sample-Biological replicate 1

value: root meristem

value: 12 hours PEP1 (1µM) treatment


title: A EC HI 24 T, L2

value: 24 hours


title: A EC 24 T, L1

value: Endothelial cell


title: 029A HSIL tissue

value: HSIL


title: RNA-seq of Homo sapiens: ventricular  cardiomyocyte differentiation from WTC11 at D10 rep3

description:
Library name: Ventricular_D10_rep3
vCM_10.3


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D4 rep3

description:
Library name: Ventricular_D4_rep3
vCM_d4.3

value: cardiac mesoderm


title: TG CCI-ION sample 3

city: Suzhou

first: Jin

last: Tao

state: Jiangsu

address: 199 Ren-Ai Road

department: Physiology and Neurobiology

institute: Soochow University

data_processing:
Illumina HiseqX system software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using bowtie v1.1.1 with parameters -f -p 20
Use cutadapt (version 1.14) software to remove the connector sequence, fastx_ Toolkit (version 0.0.13) software for quality control of sequences, NGSQCToolkit (version 2.3.3) to filter out reads containing N bases, fastx_ The toolkit (version 0.0.13) to count the number of types of clean reads.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: Trigeminal ganglia

extract_protocol:
Trigeminal ganglia were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A trigeminal neuropathic pain model was produced by CCI-ION. After anesthetization, the left ION was dissected near the infraorbital foramen using glass rods. Two loose ligatures (4-0 silk) were placed around the ION using fine forceps. The sham-operated rats received only unilateral nerve exposure using the same procedure without ligation.

value: Sprague-Dawley

value: Trigeminal ganglia

tag: age

value: 8-10 weeks

value: CCI-ION


title: TG CCI-ION sample 2


title: OE-EDB(-)FN1_2

description: Library name: Sample 8

value: FN1 knockdown then EDB(-)FN1 overexpression


title: SMC B HI, L1

value: Smooth muscle cell

value: Heat-inactived SARS-CoV-2


title: TG CCI-ION sample 1


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D4 rep2

description:
Library name: Ventricular_D4_rep2
vCM_d4.2

value: WT


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D4 rep1

description:
Library name: Ventricular_D4_rep1
vCM_d4.1


title: A EC 24 T, L2

value: Media from SARS-CoV-2 infected SMCs


title: TG sham sample 2

value: sham-operation


title: SMC B, L1

value: 48 hours


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D2 rep3

description:
Library name: Ventricular_D2_rep3
vCM_d2.3


title: TG sham sample 3


title: OE-EDB(+)FN1_1

description: Library name: Sample 5

value: papillary thyroid cancer

value: FN1 knockdown then EDB(+)FN1 overexpression

value: no


title: SMC B, L2


title: OE-EDB(+)FN1_2

description: Library name: Sample 6


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D2 rep2

description:
Library name: Ventricular_D2_rep2
vCM_d2.2


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D2 rep1

description:
Library name: Ventricular_D2_rep1
vCM_d2.1


title: RNA-seq of Homo sapiens: ventricular cardiomyocyte differentiation from WTC11 at D6 rep1

description:
Library name: Ventricular_D6_rep1
vCM_d6.1

value: cardiac precursor


title: shZMAT3_1

description: Library name: Sample 9

value: ZMAT3 knockdown


title: SMC B HI, L2


title: shFN1_1

description: Library name: Sample 3

value: FN1 knockdown


title: M.m infection sample3

first: Dan

last: Chen

address: 2005, Songhu Road

department: Department of Microbiology

institute: Fudan University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files includes raw coutns for each Sample
Supplementary files format and content: Tab-delimited text files includes FPKM coutns for each Sample

organism: Danio rerio

source_name: kidneys

growth_protocol: The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co., Ltd. (Qingdao, China), and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish (water temperature ∼28°C, pH ∼7.4, and conductivity ∼1500μS).

extract_protocol:
After 7 days of the secondary immunization, kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed usingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: For determination of the host immune response induced by mRNA vaccine therapeutic,  adult zebrafish (AB strain, 3 to 4 months old) were infected with indicated M. marinum M strain (about 50-100 CFU per fish) for two weeks and were then injected twice with 3-day intervals (day 14 and 17) of the L3T mRNA (0.5μg) at the dorsal muscle using PV830 Pneumatic PicoPump microinjector, and negative control zebrafish were immunized with LPP-GFP mRNA or sterile PBS. After 7 days of  the final immunization, kidneys from 5 zebrafish were pooled as one sample and three samples (total 15 kidneys) collected for each group were subjected to RNA-seq analysis.  After 7 days of the secondary immunization, kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA-seq as mock (named as M.m infection group) and healthy kidneys as blank control (named as Blank group).

value: kidneys

value: whole cell (immune cell)

tag: group

value: 14 days of M.m infection  group

value: without treatment


title: TG sham sample 1

value: Sprague-Dawley

value: Trigeminal ganglia

value: 8-10 weeks


title: SMC A HI, L1

value: Smooth muscle cell

value: Heat-inactived SARS-CoV-2


title: M.m infection sample2


title: RNA-seq of Homo sapiens: WTC11 rep3

description:
Library name: D0_rep3
vCM_d0.3

value: iPSC

value: WT

value: atrial cardiomyocyte differentation


title: OE-EDB(-)FN1_1

description: Library name: Sample 7

value: papillary thyroid cancer

value: FN1 knockdown then EDB(-)FN1 overexpression


title: shControl_2

description: Library name: Sample 2

value: no


title: RNA-seq of Homo sapiens: WTC11 rep2

description:
Library name: D0_rep2
vCM_d0.2


title: shFN1_2

description: Library name: Sample 4


title: M.m infection sample1


title: SMC A, L1

value: 48 hours


title: SMC A, L2


title: shControl_1

description: Library name: Sample 1


title: RNA-seq of Homo sapiens: WTC11 rep1

description:
Library name: D0_rep1
vCM_d0.1


title: SMC A HI, L2


title: EC B HI, L2

value: Endothelial cell


title: EC B HI, L1


title: CT29_3D_5_TOM2

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
*library strategy: post-bisulphite adaptor tagging (PBAT) bisulphite-seq
Trimming using Trim Galore (v0.6.2) was performed to remove adaptors and poor quality bases from the 3' end. In addition 9bp were trimmed from the 5' end to remove PBAT biases
Bismark (v0.23.1) was then used to map to GRCh38, deduplicate and perform the methylation extraction following default parameters for PBAT processing
Assembly: GRCh38
Supplementary files format and content: DNA methylation values are provided for 100-CpG windows with at least 10 informative CpGs, spanning all autosomes.  Data is provided as a text file.

growth_protocol: Two cell lines of hTSCs (BTS11 and CT29) were obtained from the Arima lab upon written request (Okae et al., 2018). BTS refers to cell lines derived from a blastocyst stage embryo whilst CT originates from 1st trimester placental cytotrophoblast cells.  BTS11 and CT29 were initially cultured using the previously described protocol (Okae et al., 2018) with an updated concentration of CHIR99021 to 4µM (Sheridan et al., 2021). Samples were grown in Okae Media (OM) (Okae et al., 2018) or Trophoblast Organoid Media (TOM), detailed below, for 4 weeks. These cells were initially grown in standard 2D conditions until 80% confluent, then technical replicates of each cell line were either maintained in 2D culture conditions or moved into Matrigel for 3D culture. The conversion of 2D cultures into  3D trophoblast organoid was achieved by plating a single cell suspension onto 25µl Matrigel doplets in 48 well plates and culture followed the published protocol (Turco et al., 2018) for a total of 4 passages. During this time, cultures were overlaid with TOM media: Advanced DMEM/F12 (Thermo Fisher Scientific), N2 supplement (Thermo Fisher Scientific, 17502048, B27 supplement minus vitamin A (Thermo Fisher Scientific, 12587010; at manufacturer's recommended concentration), Primocin 100 μg/ml (InvivoGen, ant-pm),N-acetyl-L cysteine 1.25 mM (Sigma-Aldrich, A9165), L-glutamine 2 mM (Sigma-Aldrich, 25030024), recombinant human EGF 50 ng/ml (Peprotech, AF10015), CHIR99021 1.5 μM (Tocris, 4423), recombinant human R-spondin-1 80 ng/ml (R&D systems, 4645-RS-01M/CF), recombinant human FGF-2 100 ng/ml (Peprotech, 100-18B), recombinant human HGF 50 ng/ml (Peprotech, 100-39), A83-01 500 nM (Tocris, 2939), prostaglandin E2 2.5 μM (Sigma-Aldrich, P0409), and Y-27632 2 μM (Millipore, 688000).  After 4 weeks of culture, cells were dissociated at single cell suspension (Sheridan et al., 2020) and counted on a haemocytometer. Aliquots of 5000 cells were frozen in PBS at -80°C before proceeding to the bisulphite-sequencing.

extract_protocol:
Aliquots of 5000 cells suspended in PBS were thawed and then lysed in 10mM Tris buffer with 0.5% SDS and proteinase K at 37°C for 1 hour.
Bisulphite conversion was done using the EZ DNA Methylation Direct Kit (Zymo Research), as per the manufacturers protocol. First and then second strand synthesis was performed on eluted DNA using Klenow Fragment (3’->5’ exo-) enzyme (New England Biolabs) and customised 9bp random sequence containing biotin-conjugated adaptors. Using Phusion High-Fidelity DNA polymerase (New England Biolabs), libraries were amplified for 10 cycles in a 50uL reaction.

treatment_protocol: The BTS11 cell line was transduced with lentiviral particles of either pLV[Exp]-EGFP:T2A:Puro-EF1A>ORF_Stuffer (control) (VectorBuilder VB010000-9389rbj) or pLV[Exp]-EGFP:T2A:Puro-EF1A>hDNMT3L[NM_013369.3] (VectorBuilder VB900013-3690ksg) to overexpress DNMT3L. In both cases, the lentiviral particles were packaged by VectorBuilder. The BTS11 cells were transduced with the lentivirus supplemented with 8 μg/ml polybrene (Millipore, TR-1003-G) for 24 hours. After 48 hours, the cells were selected by adding 1 µg/ml puromycin to the medium for 7 days.

value: Trophoblast stem cells

value: male

value: Organoid culture in trophoblast organoid media in hypoxia


title: Blank sample2

value: kidneys

value: whole cell (immune cell)

value: Healthy group

value: without treatment


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 12

city: Ames

first: Melissa

last: Monson

state: Iowa

address: 1920 Dayton Ave

institute: USDA-ARS National Animal Disease Center

description: Library name: AMEoo/R_CT12

data_processing:
Trimmomatic v.0.39 was used to filter and trim raw reads (adapters removed with Illuminaclip, end trimmed if quality score < 20, and entire reads removed if average quality score < 30 or minimum length < 75 bp).
Filtered reads were mapped to the turkey reference genome using STAR v.2.7.10b with default parameters.
BAM files were sorted by name with samtools v.1.17.
Reads that uniquely mapped to genes (NCBI Annotation Release 103) in the turkey genome were counted using HTSeq v.2.0.2 with default parameters (except stranded = reverse).
Assembly: Meleagris gallopavo 5.1 (NCBI Genome Build GCF_000146605.3)
Supplementary files format and content: Tab delimited text file with the cumulative raw read counts (4 technical replicates combined) for each sample (columns) and each gene (rows).

organism: Meleagris gallopavo

source_name: cecal tonsil

growth_protocol: Turkey poults were randomly divided into six isolation rooms, each room housing one vaccination/challenge group. Poults were given ad libitum access to water and a game bird starter ration throughout the study.

extract_protocol:
Total RNA was extracted from cecal tonsil tissues using the RNAqueous Total RNA Isolation kit (Thermo Fisher Scientific Inc.) with manufacturer’s protocols modified to incorporate an on-column DNase treatment (RNase-free DNase Set; QIAgen Sciences).
Stranded mRNA-seq cDNA libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs) with the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) kit (New England Biolabs) for sample indexing.

treatment_protocol: Poults were mock-vaccinated (M/M and M/R) or vaccinated with BBS 866 (BBSoo/R) or AviPro Megan Egg (AME oo/R) at 1 day and 3 weeks of age. The M/R, BBSoo/R, and AMEoo/R groups were challenged with Salmonella enterica serovar Reading at 7 weeks of age, while the M/M group was mock-challenged.

value: cecal tonsil

value: AMEoo/R

tag: batch

tag: breed

value: Nicholas

value: 7 weeks

tag: days post_inoculation


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 11

description: Library name: AMEoo/R_CT11

tag: tissue


title: Blank sample1

tag: cell type

tag: treatment


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 10

description: Library name: AMEoo/R_CT10

tag: Sex


title: EC B, L2


title: BTS11_3D_5_TOM1


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 9

description: Library name: AMEoo/R_CT9


title: EC B, L1


title: BTS11_3D_5_TOM2


title: PBS treated sample3

value: PBS treated group

value: two dose of PBS immunized


title: PBS treated sample2


title: EC A HI, L2

value: Heat-inactived SARS-CoV-2


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 8

description: Library name: AMEoo/R_CT8


title: EC A HI, L1


title: PBS treated sample1


title: CT29_3D_21_TOM2

value: Organoid culture in trophoblast organoid media in normoxia


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 7

description: Library name: AMEoo/R_CT7


title: CT29_3D_21_TOM1


title: EC A, L2

value: 48 hours


title: LPP treated sample3

value: Vector control treated group

value: two dose of LPP-GFP mRNA immunized


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 6

description: Library name: AMEoo/R_CT6

value: male


title: BTS11_3D_21_TOM2

value: Trophoblast stem cells


title: LPP treated sample2

value: kidneys


title: Patient sample 16

description:
Library name: P_16
Targeted RNA-Seq

data_processing:
Raw read counts received from HTG Molecular Diagnostics, Inc. are first bach effect corrected using combat R package and subsequntly normalized using edgeR Bioconductor package.
Supplementary files format and content: Data matrix with sample ID in rows and log2 normalized expression values in columns in a comma separated text file.

extract_protocol: Patient tissue samples were obtained during standard of care treatment from various clinical timepoints and were sent to HTG Molecular Diagnostics, Inc. for targeted sequencing using their HTG EdgeSeq Oncology Biomarker Panel (OBP) consisting of 2549 cancer-associated genes. Raw data was assembled from five batches of separate HTG runs

value: FFPE


title: EC A, L1

value: Endothelial cell


title: CT29_3D_5_TOM1

value: Organoid culture in trophoblast organoid media in hypoxia


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 5

description: Library name: AMEoo/R_CT5

value: cecal tonsil


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 4

description: Library name: AMEoo/R_CT4

value: AMEoo/R


title: LPP treated sample1

value: whole cell (immune cell)


title: A549_2D_hypoxia

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 5000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: lung

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS and antibiotics; they were incubated at 37°C in a 5% carbon dioxide.

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro Kit (Qiagen) following the manufacturer’s instruction.
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

treatment_protocol: A549 cells were seeded on the solidified Matrigel for 3D or the usual culture dish for 2D and cultured for 5 days in DMEM supplemented with 5% FBS under normoxia or hypoxia (1% oxygen).

value: lung

value: adenocarcinoma

tag: genotype

value: WT

value: cultured in 2D under hypoxia (1% oxygen)


title: BTS11_3D_21_TOM1

tag: cell line

value: Organoid culture in trophoblast organoid media in normoxia


title: BTS11_2D_21_TOM

value: 2D culture in trophoblast organoid media in normoxia


title: Blank sample3

value: Healthy group

value: without treatment


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 3

description: Library name: AMEoo/R_CT3

value: Nicholas

value: male

value: 7 weeks


title: BTS11_2D_21_OM2

value: Trophoblast stem cells

value: 2D culture in okae media in normoxia


title: A549_3D_hypoxia

value: cultured in 3D under hypoxia (1% oxygen)


title: BTS11_2D_21_OM1


title: L3T treated sample2

value: kidneys

value: L3T treated group

value: two dose of L3T mRNA immunized


title: L3T treated sample3

value: whole cell (immune cell)


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 1

description: Library name: AMEoo/R_CT1

value: cecal tonsil

value: AMEoo/R


title: A549_2D_normoxia

value: lung

value: adenocarcinoma

value: WT

value: cultured in 2D under normoxia


title: kidneys, LPP immunized sample3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files includes FPKM counts for each Sample

extract_protocol:
After 12 days of the secondary immunization, kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed usingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: For determination of the host immune response induced by mRNA vaccine immunization, adult zebrafish (AB strain, 3 to 4 months old, 15 per group) were immunized twice with two-week intervals (week 0 and 2). Dose volumes were 2 μL for intramuscular (i.m) immunization. 1μg L3T mRNA vaccine or LPP-GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector (World Precision Instruments, Sarasota, FL). After 12 days of the secondary immunization, kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.

value: Vector control immunized group

value: two dose of LPP-GFP mRNA immunized


title: L3T treated sample1


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 12

description: Library name: BBSoo/R_CT12

value: BBSoo/R

value: Nicholas

value: male


title: CT29_2D_21_OM2

value: Trophoblast stem cells

value: 2D culture in okae media in normoxia


title: A549_3D_normoxia

value: cultured in 3D under normoxia


title: Lambda_d10

city: LYON cedex

first: Jenny

last: VALLADEAU-GUILEMOND

address: 28 rue Laennec

department: TERI

institute: CRCL

data_processing:
The primary base call files were converted into FASTQ sequence files using the bcl2fastq converter tool.
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.9a)
Gene expression was quantified using Salmon (v1.5) and the annotation of known genes from gencode v38
Gene expression was normalised with deseq2 (v1.30.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include deseq2 normalised counts values for each sample
Supplementary files format and content: tab-delimited text file include counts values for each sample
Supplementary files format and content: tab-delimited text files include samples annotations

source_name: Human plasmacytoid dendritic cell

growth_protocol: Plasmacytoid DC were purified from healthy donnor blood (Miltenyi ref:130-092-207)

extract_protocol:
Total RNAs were extracted from cultured cells using the single cell RNA purification kit (NORGEN, ref: 51800) according to the manufacturer’s instruction.
TruSeq stranded mRNA Library Prep

treatment_protocol: RNA sequencing was performed on untreated or pDCs treated 12h with IFN-a (1000 UI/mL), IFN-b (100ng/mL), IFN-g (100 ng/mL), IFN-L (100 ng/mL), or CpGB (4ug/mL)

value: Human plasmacytoid dendritic cell

value: lambda


title: Med_d10

value: medium


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 11

description: Library name: BBSoo/R_CT11

value: cecal tonsil

value: 7 weeks


title: Cecal tonsil, AMEoo/R, 2 dpi, biol rep 2

description: Library name: AMEoo/R_CT2

value: AMEoo/R


title: CT29_2D_21_OM1


title: Gamma_d10

value: gamma


title: kidneys, LPP immunized sample1

value: kidneys

value: whole cell (immune cell)


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 10

description: Library name: BBSoo/R_CT10


title: CT29_2_H3K9me3

data_processing:
adapter and quality trimming using Trim Galore (v0.6.6)
mapped to GRCh38 using Bowtie2 (v2.4.5)
Assembly: GRCh38
Supplementary files format and content: Histone enrichment was quantitated for 100-CpG windows as RPKM correcting for probe length, spanning all autosomes.  Data is provided as a text file.
Supplementary files format and content: Processed data file includes replicates from published datasets included as replicates in this study (as detailed in the're-analyzed_sample_details.txt').

growth_protocol: Two cell lines of hTSCs (BTS11 and CT29) were obtained from the Arima lab upon written request (Okae et al., 2018). BTS refers to cell lines derived from a blastocyst stage embryo whilst CT originates from 1st trimester placental cytotrophoblast cells.  BTS11 and CT29 were initially cultured using the previously described protocol (Okae et al., 2018) with an updated concentration of CHIR99021 to 4µM (Sheridan et al., 2021). Samples were grown in Okae Media (OM) (Okae et al., 2018). These cells were initially grown in standard 2D conditions until 80% confluent, then technical replicates of each cell line were maintained in 2D culture conditions.  Aliquots of  cells were processed immediately for ChIP-sequencing protocols.

extract_protocol:
Native chromatin immunoprecipitation-sequencing libraries were generated for BTS11 and CT29 cells grown in technical replicates using ULI-nChIP-seq method as previously described (Hanna et al., 2018). Briefly, cells were washed in PBS and 20,000 cells were resuspended in Nuclei isolation buffer (Sigma).  Cells were lysed in 0.1 % Triton X-100 and 0.1 % deoxycholate.
Chromatin was then digested to mononucleosomal fragments by MNase enzyme (NEB) at 21 °C for 7.5 minutes. Chromatin was then split into 4 reactions, immunoprecipitated overnight at 4 °C using antibodies for H3K4me3 (Diagenode, C15410003), H3K27me3 (Diagenode, C15410195), H3K36me3 (Diagenode, C15410192) or H3K9me3 (Diagenode, C15410056), with 10% taken for input controls. Following salt washes, DNA elution and purification with SPRI beads, sequencing libraries were generated using the MicroPlex Library Preparation kit by Diagenode (C05010001), as per the manufacturer’s instructions. Samples were then multiplexed and sequenced by 50 bp paired end on the Illumina NextSeq2000.  Three replicates of H3K36me3 were excluded due to poor enrichment. These data were analysed alongside published CUT&Tag, CUT&Run and ChIP-seq datasets, where available. In this study, we used H3K4me3, H3K27me3 and H3K9me3 ChIP-sequencing from naïve and primed hESCs (GSE75868) (Theunissen et al., 2016); H3K4me3, H3K27me3, and H3K9me3 CUT&RUN or CUT&TAG from hTSCs (CT27 and CT29) (GSE200763) (Frost et al., 2023); H3K4me3 and H3K36me3 CUT&RUN from hTSCs (GSE196221) (Zhou et al., 2023); H3K4me3 and H3K27me3 ChIP-sequencing from 2nd trimester cytotrophoblast (GSE127288) (Kwak et al., 2019).

tag: chip antibody


title: CT29_2D_21_TOM

value: 2D culture in trophoblast organoid media in normoxia


title: kidneys, L3T immunized sample3

value: L3T immunized group

value: two dose of L3T mRNA immunized


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 9

description: Library name: BBSoo/R_CT9

value: BBSoo/R

value: Nicholas


title: CT29_2_H3K27me3

value: Trophoblast stem cells

value: male


title: CpG-L_d10

value: CpG B + lambda


title: kidneys, L3T immunized sample2


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 8

description: Library name: BBSoo/R_CT8


title: Beta_d10

value: Human plasmacytoid dendritic cell

value: beta


title: CT29_2_H3K4me3

value: 2D culture in okae media in normoxia


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 7

description: Library name: BBSoo/R_CT7

value: cecal tonsil


title: CT29_1_H3K9me3


title: Alpha_d10

value: alpha


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 6

description: Library name: BBSoo/R_CT6

value: 7 weeks


title: CT29_1_H3K27me3


title: Med_d9

value: medium


title: kidneys, LPP immunized sample2

value: kidneys

value: Vector control immunized group

value: two dose of LPP-GFP mRNA immunized


title: Lambda_d9

value: lambda


title: Astrocytes, OGD/R+TGF-β1_group, biol rep 3

city: shenzhen

first: Qiang

last: Zhang

state: Guangdong

address: 628 Zhenyuaan Rd.

department: Emergency medicine

institute: The seventh Affiliated Hospital of Sun Yat sen University

data_processing:
The raw data was achieved by sequenceing of  Illumina hiseqtm 2000 and Soapnuke software （version 1.5.2）is used to obtain valid sequences
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Bowtie software (version: 2.3.3.1) is used to align effective sequences with the reference genome of corresponding species,Cufflinks software (version: 2.2.1) is used to assemble transcripts to obtain new transcripts，and Rsem (version: 1.3.1) is used to quantify gene expression
Assembly: reference sequence used for read alignment
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent according to the manufacturer’s protocol. 1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
After extracting total RNA from the sample and passing quality inspection, enrich the eukaryotic mRNA using magnetic beads with Oligo(dT) (if it is prokaryotic, use a kit to remove rRNA). Add fragmentation reagents and use a thermocycler to fragment the mRNA into short fragments. Synthesize first-strand cDNA using the fragmented mRNA as a template, and then prepare a reaction system for the synthesis of second-strand cDNA. Purify, repair sticky ends, and add a base "A" to the 3' end of the cDNA, followed by adapter ligation using a kit. Perform fragment size selection and PCR amplification to construct the library. After the constructed library passes quality inspection using the Agilent 2100 Bioanalyzer and Qubit, perform sequencing using the Illumina sequencer.

value: cell line

value: Rat Astrocytes

value: performed with OGD/R  +TGF-Beta1 treatment


title: CT29_1_H3K4me3

value: Trophoblast stem cells


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 5

description: Library name: BBSoo/R_CT5

value: BBSoo/R

value: Nicholas

value: male


title: Astrocytes, OGD/R+TGF-β1_group, biol rep 1


title: CpG_d10

value: Human plasmacytoid dendritic cell

value: CpG B


title: Gamma_d9

value: gamma


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 4

description: Library name: BBSoo/R_CT4

value: cecal tonsil


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 3

description: Library name: BBSoo/R_CT3

value: 7 weeks


title: BTS11_2_Input

value: 2D culture in okae media in normoxia


title: Astrocytes, OGD/R group, biol rep 3

value: performed with OGD/R treatment.


title: BTS11_2_H3K9me3


title: CpG_d9


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 2

description: Library name: BBSoo/R_CT2


title: Astrocytes, OGD/R group, biol rep 2


title: BTS11_2_H3K27me3


title: CpG-L_d9

value: CpG B + lambda


title: Astrocytes, OGD/R group, biol rep 1


title: kidneys, L3T immunized sample1

value: kidneys

value: whole cell (immune cell)

value: L3T immunized group

value: two dose of L3T mRNA immunized


title: Cecal tonsil, BBSoo/R, 2 dpi, biol rep 1

description: Library name: BBSoo/R_CT1


title: Beta_d9

value: beta


title: BTS11_2_H3K4me3

value: Trophoblast stem cells


title: MIRI+AICAR5

city: zunyi

first: Yang

last: Song

address: ddd

institute: dd

description: circRNA splicing count

data_processing:
First, we filter out low-quality, linker-contaminated, and unknown base N reads that are too high, and the filtered data is called clean reads. The clean reads were then aligned to the reference genome, and the circRNA was predicted by CIRI software.
Assembly: mm9
Supplementary files format and content: circRNA splicing count from ciri software with annotations

source_name: heart

extract_protocol:
1) DNaseI was used to digest the DNA fragments present in the total RNA sample and purify and recover them; 2) Ribosomal RNA removal from total RNA using the Ribo-off method;
3) Prepare the RNaseR reaction system, digest the linear RNA components, and purify the recovery reaction products; 4) RNA fragmentation at a certain temperature and ion environment; 5) Synthesis of one-strand cDNA using fragmented RNA as template; 6) synthesis of cDNA bistrands, in which dUTP is used instead of dTTP to synthesize bistranded cDNA; 7) Double-stranded cDNA is repaired at the end, with a "A" base added to the 3' end and linkers; 8) UDG enzyme digestion of U-stranded cDNA containing U-strand, and PCR amplification at the same time; 9) The quality of the constructed library was tested, the library products that passed the quality inspection were circularized, and the circular DNA molecules were replicated through rolling rings to form DNA nanospheres (DNBs);

value: heart

value: Cardiac muscle cell

value: MIRI+AICAR

value: Protective effect of myocardial cells


title: Astrocytes, OGD/R+TGF-β1_group, biol rep 2

value: cell line

value: Rat Astrocytes

value: performed with OGD/R  +TGF-Beta1 treatment


title: BTS11_1_Input

value: male


title: Cecal tonsil, M/R, 2 dpi, biol rep 11

description: Library name: M/R_CT11

value: cecal tonsil

value: M/R

value: Nicholas

value: 7 weeks


title: Cecal tonsil, M/R, 2 dpi, biol rep 12

description: Library name: M/R_CT12


title: Alpha_d9

value: Human plasmacytoid dendritic cell

value: alpha


title: Med_d8

value: medium


title: MIRI+AICAR3

description: circRNA splicing count


title: Cecal tonsil, M/R, 2 dpi, biol rep 10

description: Library name: M/R_CT10


title: BTS11_1_H3K27me3

value: 2D culture in okae media in normoxia


title: BTS11_1_H3K9me3

value: Trophoblast stem cells


title: Lambda_d8

value: lambda


title: BTS11_1_H3K4me3


title: MIRI+AICAR2

description: circRNA splicing count

value: heart

value: Cardiac muscle cell


title: Cecal tonsil, M/R, 2 dpi, biol rep 8

description: Library name: M/R_CT8


title: MIRI+AICAR1

description: circRNA splicing count

value: MIRI+AICAR

value: Protective effect of myocardial cells


title: Cecal tonsil, M/R, 2 dpi, biol rep 9

description: Library name: M/R_CT9


title: Gamma_d8

value: gamma


title: 3 KIJ 265 T; Cancer-2 CM

city: Warsaw

first: Agnieszka

last: Piekiełko-Witkowska

address: Marymoncka 99/103

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: Centre of Postgraduate Medical Education

data_processing:
exceRpt small RNA-seq Pipeline (v4.6.2)
Assembly: Sources of Small RNA Reference Sequences: miRNAs - miRBase version 21; tRNAs - gtRNAdb; piRNAs - RNAdb, Genome - Gencode version 21 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized quantifications - RPM values for each sample

source_name: kidney - tumor

growth_protocol: Caki-1 and RPTEC/TERT1 cells were cultured in accordance with manufacturer’s protocol (ATCC). KIJ265T were cultured as previously described (Boguslawska J, Piekielko-Witkowska A, Wojcicka A, Kedzierska H, Poplawski P, Nauman A. Regulatory feedback loop between T3 and microRNAs in renal cancer.

extract_protocol:
RNA isolation was done using Cell Culture Media Exosome Purification and RNA Isolation Mini Kit (Cat. 60700) (Norgen Biotek) elution was concentrated using RNA Clean-up and Concentration Micro-Elute Kit (Cat. 61000).
RNA libraries were performed by Noregene using Norgen Biotek Small RNA Library Prep Kit (Cat. 63600)

treatment_protocol: The cells were not treated.

value: kidney - tumor

value: renal cancer


title: CpG-L_d8

value: CpG B + lambda


title: MIRI+Compound C5

description: circRNA splicing count

value: MIRI+Compound C


title: Cecal tonsil, M/R, 2 dpi, biol rep 7

description: Library name: M/R_CT7

value: cecal tonsil

value: M/R

value: Nicholas

value: male


title: Cecal tonsil, M/R, 2 dpi, biol rep 6

description: Library name: M/R_CT6

value: 7 weeks


title: MIRI+Compound C4

description: circRNA splicing count


title: Beta_d8

value: Human plasmacytoid dendritic cell

value: beta


title: MIRI+Compound C3

description: circRNA splicing count


title: 1 KIJ 265 T; Cancer-2 CM


title: Alpha_d8

value: alpha


title: Cecal tonsil, M/R, 2 dpi, biol rep 4

description: Library name: M/R_CT4


title: Cecal tonsil, M/R, 2 dpi, biol rep 5

description: Library name: M/R_CT5


title: 3 Caki-1; Cancer-1 CM


title: MIRI+Compound C2

description: circRNA splicing count

value: heart


title: MIRI+Compound C1

description: circRNA splicing count

value: Cardiac muscle cell


title: 2 Caki-1; Cancer-1 CM


title: Med_d6

value: medium


title: Lambda_d6

value: lambda


title: MIRI3

description: circRNA splicing count

value: MIRI

value: Protective effect of myocardial cells


title: BTS11_1_H3K36me3

value: Trophoblast stem cells

value: 2D culture in okae media in normoxia


title: 1 Caki-1; Cancer-1 CM

value: kidney - tumor

value: renal cancer


title: Cecal tonsil, M/R, 2 dpi, biol rep 2

description: Library name: M/R_CT2

value: cecal tonsil

value: M/R


title: Gamma_d6

value: gamma


title: CpG_d8

value: CpG B


title: MIRI2

description: circRNA splicing count


title: 3 RPTEC; Control CM

source_name: kidney - normal

value: kidney - normal

value: RPTEC/TERT

value: proximal tubules


title: Cecal tonsil, M/R, 2 dpi, biol rep 1

description: Library name: M/R_CT1

value: Nicholas

value: male

value: 7 weeks


title: CpG_d6

value: Human plasmacytoid dendritic cell


title: MIRI1

description: circRNA splicing count

value: heart

value: Cardiac muscle cell

value: MIRI


title: 2 KIJ 265 T; Cancer-2 CM


title: CpG-L_d6

value: CpG B + lambda


title: Sham3

description: circRNA splicing count

value: nomal

value: Protective effect of myocardial cells


title: 2 RPTEC; Control CM


title: Cecal tonsil, M/M, 2 dpi, biol rep 11

description: Library name: M/M_CT11

value: cecal tonsil

value: M/M


title: 1 RPTEC; Control CM


title: Sham2

description: circRNA splicing count


title: Cecal tonsil, M/M, 2 dpi, biol rep 10

description: Library name: M/M_CT10


title: recurrent miscarriage 5 [T8; miRNA-seq]

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Assembly: miRBase Release 22
Supplementary files format and content: The xlsx format file contains the CPM value of gene in every sample

source_name: placental villus tissues

extract_protocol:
Total RNA was extracted from villus tissues using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135-155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: placental villus tissues

value: 8.7 weeks

value: recurrent miscarriage


title: Alpha_d6

value: alpha


title: MIRI+AICAR4

description: circRNA splicing count

value: MIRI+AICAR


title: Sham1

description: circRNA splicing count


title: Cecal tonsil, M/M, 2 dpi, biol rep 9

description: Library name: M/M_CT9

value: Nicholas


title: 4_aged_mitoDendra2_High_ATACseq

city: Singapore

first: Takayoshi

last: Matsumura

address: 14 Medical Drive #12-01

country: Singapore

institute: National University of Singapore

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw unique molecular identifier (UMI)-based data files were mapped against the mm10 reference genome, and mapped reads were counted using the Cell Ranger ARC package (10x Genomics) with default parameters.
The Seurat package in R was used to analyze the scRNA-seq data, and the Signac package was used to analyze the scATAC-seq data.
To mitigate the effects of cell cycle heterogeneity, cell-cycle scoring and regression were performed using vars.to.regress of SCTransform. scRNA-seq and scATAC-seq data were integrated by weighted-nearest neighbor (WNN) analysis using FindMultiModalNeighbors.
Clusters were detected using FindClusters, and annotated based on feature genes.
Differentially expressed genes were identified by running FindAllMarkers or FindMarkers.
Assembly: mm10
Supplementary files format and content: An HDF5 file continaing a feature barcode matrix of scRNA-seq.
Supplementary files format and content: atac_peaks.bed containing locations of open-chromatin regions,  atac_fragments.tsv.gz containing count and barcode information for every ATAC fragment, and per_barcode_metrics.csv containing ATAC and GEX read count summaries. These files can be loaded into R using Seurat and Signac.

source_name: bone marrow

extract_protocol:
Single nuclei of sorted HSCs were prepared according to the manufacturer's instruction.
Multiome single-cell/nuclei analysis was performed on the 10X Genomics platform using the Chromium Controller and the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics) following the manufacturer's instruction.
Single cell multiome analysis (single cell RNA-Seq and single cell ATAC-seq)

treatment_protocol: Slam HSCs (CD150+CD48- LSK cells) were sorted and then pooled from CD117+ cells-enriched bone marrow cells of 8 young (7 to 17 weeks old) and 2 aged (70 weeks old) male mito-Dendra2 mice.

value: bone marrow

value: Mitochondria high HSCs

value: mitoDendra2 mice

value: aged


title: N4BP1-2

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: primary human hepatocyte

extract_protocol:
Total RNA in PHHs was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: primary human hepatocyte

value: N4BP1-expressing adenovirus vectors and HBV infected


title: recurrent miscarriage 4 [T5; miRNA-seq]

first: lihong

last: pang

address: NO.6 Shuangyong Road

institute: Guangxi Medical University

value: 8.4 weeks


title: recurrent miscarriage 3 [T20; miRNA-seq]

value: 7.0 weeks


title: N4BP1-1


title: Cecal tonsil, M/M, 2 dpi, biol rep 12

description: Library name: M/M_CT12

value: male

value: 7 weeks


title: Cecal tonsil, M/M, 2 dpi, biol rep 6

description: Library name: M/M_CT6

value: cecal tonsil

value: M/M


title: 2_young_mitoDendra2_High_ATACseq

description: 10x Genomics

value: young


title: recurrent miscarriage 1 [T11; miRNA-seq]

value: placental villus tissues

value: 6.5 weeks

value: recurrent miscarriage


title: recurrent miscarriage 2 [T19; miRNA-seq]

value: 7.5 weeks


title: GFP-2

value: GFP-expressing adenovirus vectors and HBV infected


title: 3_aged_mitoDendra2_Low_ATACseq

description: 10x Genomics

value: bone marrow

value: Mitochondria low HSCs


title: Cecal tonsil, M/M, 2 dpi, biol rep 7

description: Library name: M/M_CT7

value: Nicholas


title: GFP-1

value: primary human hepatocyte


title: Cecal tonsil, M/R, 2 dpi, biol rep 3

description: Library name: M/R_CT3

value: M/R


title: normal pregnancy 5 [61; miRNA-seq]

value: 9.5 weeks

value: normal pregnancy


title: Cecal tonsil, M/M, 2 dpi, biol rep 5

description: Library name: M/M_CT5

value: male


title: HS578T siTLN1 rep2

city: Turku

first: Lea

last: Sistonen

address: Tykistökatu 6 A

department: Cell Biology

country: Finland

institute: Åbo Akademi University

data_processing:
Basecalling and adapter trimming was performed by bcl2fastq conversion software (NovaSeq 6000)
Reads were mapped to the human genome (GRCh38) using STAR v2.7.9a with the default parameters
Read pairs aligned to each genomic feature in the GENCODE annotation v33 (primary assembly) were counted with featureCounts from subread v2.0.0 with the parameter -isPairedEnd
The raw read counts were processed with edgeR v3.34.1 to filter out lowly expressed genes with filterByExpr() and were normalized using the TMM method.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing the raw read counts per feature for each sample
Supplementary files format and content: Tab-delimited text file containing the normalized logCPM values for each sample

source_name: breast cancer-derived epithelial cells

growth_protocol: HS578T cells were grown in DMEM supplemented with 10% FCS, 2 mM L-glutamine, 100 µg/mL penicillin-streptomycin and 10 µg/mL insulin, and maintained at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
48 h after transfection with siRNAs, the cells were collected and total RNA was purified with the AllPrep DNA/RNA/miRNA Universal Kit (80224, QIAGEN) according to manufacturer’s instructions.
RNA libraries were prepared according to the Illumina stranded mRNA preparation guide (1000000124518).

treatment_protocol: HS578T cells were transfected with 1.6 µM of the corresponding RNA (Scr or siTLN1) .

tag: sirna

tag: disease

value: Carcinoma


title: 1_young_mitoDendra2_Low_ATACseq

description: 10x Genomics

value: mitoDendra2 mice


title: Cecal tonsil, M/M, 2 dpi, biol rep 4

description: Library name: M/M_CT4

value: cecal tonsil

value: M/M

value: 7 weeks


title: 4_aged_mitoDendra2_High_RNAseq

description: 10x Genomics

value: Mitochondria high HSCs

value: aged


title: normal pregnancy 4 [60; miRNA-seq]

value: placental villus tissues

tag: time point

value: 9.1 weeks

tag: subject status


title: 3_aged_mitoDendra2_Low_RNAseq

description: 10x Genomics

value: bone marrow


title: HS578T siTLN1 rep1


title: normal pregnancy 3 [59; miRNA-seq]

value: 7.8 weeks


title: Cecal tonsil, M/M, 2 dpi, biol rep 3

description: Library name: M/M_CT3

value: Nicholas


title: Cecal tonsil, M/M, 2 dpi, biol rep 8

description: Library name: M/M_CT8


title: Cecal tonsil, M/M, 2 dpi, biol rep 2

description: Library name: M/M_CT2


title: 2_young_mitoDendra2_High_RNAseq

description: 10x Genomics

value: young


title: normal pregnancy 2 [58; miRNA-seq]

value: 7.9 weeks


title: HS578T SCR rep1

value: Scramble


title: 1_young_mitoDendra2_Low_RNAseq

description: 10x Genomics

value: Mitochondria low HSCs


title: Cecal tonsil, M/M, 2 dpi, biol rep 1

description: Library name: M/M_CT1

value: male


title: normal pregnancy 1 [57; miRNA-seq]

value: 6.2 weeks

value: normal pregnancy


title: YSX1

status: Public on Jan 07 2025

city: Yantai

first: Haifeng

last: Huang

state: Shandong

address: Middle Hongqi Road, Zhifu District

institute: Ludong University

description: Library name: YSX1

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: GIGA_Haliotis
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: Haliotis discus hannai

source_name: left epipodial tentacle

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: left epipodial tentacle

value: Aquaculture

value: Excision of left cephalic tentacle


title: ZX3

description: Library name: ZX3

source_name: left cephalic tentacle

value: left cephalic tentacle


title: YSX2

description: Library name: YSX2


title: ZSX3

description: Library name: ZSX3

source_name: right epipodial tentacle

value: right epipodial tentacle

value: Excision of right epipodial tentacle


title: ZX1

description: Library name: ZX1


title: YX4

description: Library name: YX4

source_name: right cephalic tentacle

value: right cephalic tentacle

value: Excision of right cephalic tentacle


title: ZX2

description: Library name: ZX2


title: ZSX1

description: Library name: ZSX1


title: YSX3

description: Library name: YSX3


title: ZSX2

description: Library name: ZSX2


title: YSX4

description: Library name: YSX4


title: YX1

description: Library name: YX1


title: YX2

description: Library name: YX2


title: YX3

description: Library name: YX3


title: ZY4

description: Library name: ZY4

source_name: left eyestalk

value: left eyestalk

value: Excision of left eyestalk


title: HS578T SCR rep2

value: Scamble

value: Carcinoma


title: ZY3

description: Library name: ZY3


title: ZY2

description: Library name: ZY2


title: YY4

description: Library name: YY4

source_name: right eyestalk

value: right eyestalk

value: Excision of right eyestalk


title: YY2

description: Library name: YY2


title: YY1

description: Library name: YY1


title: YY3

description: Library name: YY3


title: ZSX4

description: Library name: ZSX4


title: ZX4

description: Library name: ZX4


title: Beta_d6

value: Human plasmacytoid dendritic cell

value: beta


title: shXBP1.cl18.day72.rep2

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

description: Library name: SAM24405148

data_processing:
Bulk RNA-seq experiment was processed using the HTSeqGenie pipeline in BioConductor[85]. First, reads with low nucleotide qualities (70% of bases with quality<23) or matches to rRNA and adapter sequences were removed.
The remaining reads were aligned to the human reference genome GRCh37/hg19 using GSNAP (v.2013-10-10-v2)[86], allowing a maximum of two mismatches per 75 base-sequence (parameters: ‘-M2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 –pairmax-rna=200000 –clip-overlap’).
Transcript annotation was based on the Gencode genes database[87]. To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
The resulting count matrix was analysed in R (v.4.1.3; 03 November 2023) using the edgeR package (v.3.32.1)[88]. The count matrix was filtered to remove low expressed genes by keeping the features with at least 15 counts, considering library size differences, in more than the minimum number of samples of the experimental design. The resulting filtered count matrix was then log2-transformed and TMM-normalized with edgeR::cpm(log=T) and edgeR::calcNormFactors(method= “TMM”).
For exploratory data analysis, the matrix was further filtered to the most variable genes selected using projection score[89] to focus on the major contributors to the variance in transcriptional state. This matrix was then scaled using base:scale() for posterior exploration.
Differential expression analyses were conducted using limma (v.3.46.0)[90]. To identify significantly interacting genes between gene silencing backgrounds and time points, a polynomial spline model with three degrees of freedom was used for the design matrix. A large number of genes were significantly interacting and a more stringent false discovery rate adjusted p-value of 10−12 was used to perform exploratory data analysis.
Assembly: Human reference genome GRCh37/hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TMM normalized counts for each sample

source_name: Plasmacytoma

growth_protocol: AMO1 shIRE1 cl.1, cl.3 or shXBP1 cl.1, cl.18 cells grown in biological triplicates in T-75 flasks in RPMI 10% FBS

extract_protocol:
RNA from 1x106 cell was first extracted with RNeasy Plus kit (Qiagen), per manufacturer’s protocol. Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies).
Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: 0.2 ug/ml Doxycycline (Dox) for 0, 24, 48 or 72h

value: Plasmacytoma

value: Tumor Plasma cell

value: AMO-1 XBP1 sh4,6,7 Clone 18

value: 0.2 ug/ml Dox 72h


title: shXBP1.cl18.day48.rep3

description: Library name: SAM24405146

value: 0.2 ug/ml Dox 48h


title: shXBP1.cl18.day72.rep1

description: Library name: SAM24405147


title: shXBP1.cl18.day48.rep1

description: Library name: SAM24405144


title: ZY1

description: Library name: ZY1

value: Aquaculture


title: shXBP1.cl18.day0.rep2

description: Library name: SAM24405139

value: No treatment


title: shXBP1.cl18.day0.rep1

description: Library name: SAM24405138


title: shXBP1.cl1.day72.rep2

description: Library name: SAM24405136

value: AMO-1 XBP1 sh4,6,7 Clone 1


title: shXBP1.cl18.day48.rep2

description: Library name: SAM24405145


title: shXBP1.cl18.day24.rep3

description: Library name: SAM24405143

value: 0.2 ug/ml Dox 24h


title: shXBP1.cl1.day24.rep1

description: Library name: SAM24405129


title: shXBP1.cl1.day24.rep2

description: Library name: SAM24405130