title: HUVEC+H9 scONEseq 003

description:
RNA+DNA
Normal single cell 003

source_name: HUVEC+H9 cell line co-culture

value: Human umbilical vein endothelial cell and human embryonic stem cell


title: 8719R2_CIA9-52_IndexUDI0066_GTGTCGGA+GCTTGCGC_L004_001

status: Public on Dec 31 2022

type: SRA

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

country: Germany

institute: Sanofi-Aventis Deutschland GmbH

library_source: transcriptomic

data_processing:
Bioinformatics analyses of RNA-seq raw data were performed using the OmicSoft studio software package version 10.1.2.9 (Qiagen)
Mapping of RNA-seq reads (fastq files) to the mouse genome was done using OmicSoftGenCode V19 as gene model with B.38 as reference genome and OSA4 as aligner
Genes with FPKM <1 were filtered out according to a 50% fraction rule for each sample group to exclude minimally expressed genes. Differentially expressed genes were detected by applying the DESeq2 statistical test and P-values were adjusted by the Benjamini-Hochberg procedure to control FDR
Supplementary files format and content: Tab-delimited text file include FPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: front paws

extract_protocol:
Total RNA was isolated with the Qiagen RNeasy Mini Kit for animal tissues according to the manufacturer´s instructions
For RNA-seq library preparation the Illumina TruSeq Stranded mRNA Library Preparation Kit was used. RNA libraries were subjected to paired-end sequencing on a Novaseq 6000 system with a reading depth of 80 million raw reads per sample

treatment_protocol: Groups of  mice were treated with antibodies directed against murine TNF (clone XT3.11, BioXcell), murine IL-6 (clone MP5-20F3, BioXcell), or both twice per week by intraperitoneal injection of the indicated doses

tag: tissue

value: front paws

tag: strain

tag: Sex

value: male

tag: treatment

value: IgG1 isotype ctrl. 30 mg/kg

value: isotype


title: 8719R2_CIA9-51_IndexUDI0095_TCGATATC+ACACGAGT_L004_001


title: v-abl transformed B cells, ATRi AZD6738, run2, rep1

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

country: USA

institute: Columbia University

description:
20220118_AZD6738_1
gRNA PCR from genomic DNA
labeled: ATRiAZD6738-1

library_source: genomic

data_processing:
The results were analyzed via the MAGeCK FluteMLE pipeline as previously described (Wang B, et al., Nat Protoc, 2019) using the DMSO samples as the baseline.
Genes with positive z-score and FDR<0.2 identified in the CRISPR screen were analyzed for Gene Ontology (GO) using R studio.
Assembly: Mouse Improved Genome-wide Knockout CRISPR Library v2 developed by Kosuke Yusa was used. A list of gRNAs and genes included can be found on the Addgene listing (67988).
Supplementary files format and content: *.raw_count.xlsx: Processed data files are Excel files of raw gRNA counts generated by the MAGeCK software for all gRNAs represented in the gRNA library used. Each file contains treatments and replicates that were done together in the same experiment.

molecule: genomic DNA

source_name: bone marrow

growth_protocol: v-abl transformed B-cells were grown in DMEM media with 15% FBS.

extract_protocol:
At least 30 million cells were collected in triplicate for each treatment before dox-induction, after dox-induction but before drug treatment, and after 6 days of drug treatment. Cells were lysed and genomic DNA was extracted.
gRNA from extracted genomic DNA was amplified according to (Joung J, et al., Nat Protoc, 2017) using 2.5ug DNA x 96 reactions per treatment, NEBNext High Fidelity Master Mix (2x) (New England Biolabs) and NGS-Lib-Fwd and NGS-Lib-KO-Rev primers. PCR reactions were purified using Zymospin columns (Zymo Research) and cleaned up using AMPureXP beads (Beckman Coulter).
Amplicon-seq of gRNAs harvested from cells.

treatment_protocol: Cells were infected with a tetracycline inducible Cas9 (Addgene 50661), and a single clone was picked for high inducibility and low leakiness. Cells were then infected with a BFP-tagged whole genome mouse gRNA library (Addgene 67988) with an MOI ~1 and then FACS-sorted for BFP+ cells. At least 30 million cells were then treated with 3ug/ml doxycycline (Sigma-Aldrich) for 5 days, refreshing media every other day. Induced cells were then treated with the IC90 dose of drug (as measured by MTT assay (Roche) at 6 days) or DMSO for 6 days, with at least 30 million cells for each treatment to start, refreshing media as necessary. The IC90 doses used were VE821 (Selleckchem): 1.8uM, AZD6738 (Selleckchem): 0.4uM, LY2603618 (Selleckchem): 0.4uM, DMSO: 0.02%.

value: bone marrow

tag: cell type

value: v-abl transformed B cells

value: ATRi AZD6738


title: HCT116 scONEseq 097

city: Hong Kong

first: Angela

middle: Ruohao

last: WU

address: Clear water bay street

department: LIFS

country: China

institute: HKUST

description:
RNA+DNA
HCT116 single cell 193

data_processing:
Library strategy: scONE-Seq
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.

organism: Homo sapiens

source_name: HCT116 cell line

growth_protocol: HCT116 cells are cultured in DMEM; NPC43 cells are cultured in RPMI1640 with additional Rho-associated coiled-coil containing kinases inhibitor (Y-27632) at 4 μM; HUVEC are cultured in EGM BulletKit Medium (CC-3124) plus CC-4133 SingleQuots Kit (CC-4133);H9 cell line is purchased from WiCell. Cells are cultured in mTeSR™ Plus medium (Catalog #05825). Matrigel (Catalog #354230) coated 6-well plate (Catalog #140675) was used to culture stem cells.

extract_protocol:
Nuclei isolation was adapt from Omni-ATAC protocol. Single cells / nuclei were sorted with Aria III with propidium iodide or DAPI to remove dead cells or select nuclei.
scONE-seq; Smart-seq2; 10x Genomics

value: Colon

tag: method

value: scONE-seq


title: HUVEC+H9 scONEseq 001

description:
RNA+DNA
Normal single cell 001


title: v-abl transformed B cells, ATRi AZD6738, run2, rep2

description:
20220118_AZD6738_2
gRNA PCR from genomic DNA
labeled: ATRiAZD6738-2


title: 8719R2_CIA9-48_IndexUDI0094_CGTCTGCG+TTCACAAT_L004_001


title: v-abl transformed B cells, ATRi VE821, run2, rep3

description:
20220118_VE821_3
gRNA PCR from genomic DNA
labeled: ATRiVE821-1and2

value: ATRi VE821


title: 8719R2_CIA9-47_IndexUDI0069_GCCACAGG+CATGCCAT_L004_001


title: v-abl transformed B cells, ATRi VE821, run2, rep1

description:
20220118_VE821_1
gRNA PCR from genomic DNA
labeled: ATRiVE821-1


title: HCT116 scONEseq 095

description:
RNA+DNA
HCT116 single cell 191


title: 8719R2_CIA9-46_IndexUDI0039_TAAGTGGT+CTTAAGCC_L004_001


title: 8719R2_CIA9-50_IndexUDI0070_ATTGTGAA+TGCATTGC_L004_001


title: v-abl transformed B cells, ATRi VE821, run2, rep2

description:
20220118_VE821_2
gRNA PCR from genomic DNA
labeled: ATRiVE821-2


title: HCT116 scONEseq 096

description:
RNA+DNA
HCT116 single cell 192


title: WT_Rep1

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The processed reads were aligned to the tobacco (TN90) genome, GCF_000715135_TN90, using Hisat2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Supplementary_files_format_and_content: FPKM values of the genes obtained using Cuffdiff are provided as xlsx format

organism: Nicotiana tabacum

source_name: Transgenic plant leaves (2nd leaf from top)

growth_protocol: Rooted βC1 O.E lines were transferred to soil and kept for acclimatization for 3 days in plant growth chamber (12 hr light /Dark cycle, 70% RH, 24°C Temperature). The plants were then transferred to bigger pots in transgenic green house with the same condition.

extract_protocol:
Total RNA from seedlings were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected equally at 6 week post transfer to Green house.

tag: genotype

value: Tobacco, Wisconsin 38


title: v-abl transformed B cells, DMSO control, run2, rep3

description:
20220118_DMSO_3
gRNA PCR from genomic DNA
labeled: DMSO-1and2

value: DMSO


title: v-abl transformed B cells, DMSO control, run2, rep2

description:
20220118_DMSO_2
gRNA PCR from genomic DNA
labeled: DMSO-2


title: HCT116 scONEseq 094

description:
RNA+DNA
HCT116 single cell 190


title: WT_Rep2


title: Kidney at N2,biological rep 1

type: RNA

city: Guangzhou

first: Guanghai

last: Wang

address: Shatainan Road 1023

department: School of Public Health

institute: Southern Medical University

description: Gene expression data from kidney at 6 weeks treated with normal saline

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RTA 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Command Console Software 4.0(Affymetrix,Santa Clara,CA,US) using Affymetrix default analysis settings and gobal scaling as normalization method.The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Rattus norvegicus

source_name: Rattus norvegicus normal kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The rat kidney was harvested and stored at liquid nitrogen without delay with RNA inhibitor protection.

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

treatment_protocol: After grinding at the present of liquid nitrogen,kidney tissue was collected for futher total RNA extraction.

tag: time

value: 6 weeks

value: Normal saline


title: βC1OE_Rep2


title: v-abl transformed B cells, DMSO control, run2, rep1

description:
20220118_DMSO_1
gRNA PCR from genomic DNA
labeled: DMSO-1


title: HCT116 scONEseq 093

description:
RNA+DNA
HCT116 single cell 189


title: 8719R2_CIA9-44_IndexUDI0068_CCTTCACC+GACGCTCC_L004_001


title: v-abl transformed B cells, ATRi VE821, run1, rep3

description:
20201111_VE821_3
gRNA PCR from genomic DNA
labeled: VE821-D6-3


title: HCT116 scONEseq 092

description:
RNA+DNA
HCT116 single cell 188


title: Kidney at N3,biological rep 3

description: Gene expression data from kidney at 12 weeks treated with normal saline

value: 12 weeks


title: βC1OE_Rep1


title: Kidney at N2,biological rep 2


title: 8719R2_CIA9-43_IndexUDI0092_ACGCACCT+GGTGAAGG_L004_001


title: Kidney at N2,biological rep 3


title: Kidney at N1,biological rep 1

description: Gene expression data from kidney at 1 day treated with normal saline

value: 1 day


title: Kidney at N1,biological rep 2


title: v-abl transformed B cells, ATRi VE821, run1, rep2

description:
20201111_VE821_2
gRNA PCR from genomic DNA
labeled: VE821-D6-2-2


title: Kidney at N1,biological rep 3


title: 8719R2_CIA9-42_IndexUDI0067_TTCCTGTT+AGTATCTT_L004_001

value: combination


title: v-abl transformed B cells, ATRi VE821, run1, rep1

description:
20201111_VE821_1
gRNA PCR from genomic DNA
labeled: VE821-D6-1


title: v-abl transformed B cells, DMSO control, run1, rep3

description:
20201111_DMSO_3
gRNA PCR from genomic DNA
labeled: DMSO_D6_3


title: 8719R2_CIA9-45_IndexUDI0093_TACTCATA+CCTGTGGC_L004_001

value: front paws


title: HCT116 scONEseq 090

description:
RNA+DNA
HCT116 single cell 186


title: R0199 rep3

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

institute: Friedrich-Schiller-Universität Jena

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, munich, Blum group)
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4
The trimmed reads were checked for quality and mapped to the C. crescentus NA1000 reference genome; NCBI Acc.number: NC_011916 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1
Reads mapping in CDS were counted, and genes with a total count cutoff of >10 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 2.0 in either condition and a FDR adjusted p-value < = 0.05 were considered to be differentially expressed.
Genome_build: NC_011916
Supplementary_files_format_and_content: Read count table and edgeR (exact mode) analysis

organism: Caulobacter vibrioides

source_name: whole bacterial cells

growth_protocol: C. crescentus NA1000 carrying either pBVMCS-6 (empty vector control) or pKF482 (pBVMCS-6 with R0199) were grown in M2 medium (+ 0.2% glucose; supplemented with chloramphenicol) to OD660=0.8, when expression from the vanillate-inducible promoter was activated by addition of 0.5 mM vanillate. Cells were harvested 15 minutes post induction.

extract_protocol:
RNA was isolated using the HotPhenol method according to standard protocols. Prepared RNA was digested with DNaseI and cleaned up by phenol-chloroform extraction. Ribosomal RNA was depleted with the Ribo-Zero kit (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB E7760) according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: Cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethananol, 5% phenol) and snap frozen in liquid nitrogen until further processing.

tag: growth phase

value: 0.5 mM vanillate


title: v-abl transformed B cells, DMSO control, run1, rep2

description:
20201111_DMSO_2
gRNA PCR from genomic DNA
labeled: DMSO_D6_2


title: R0199 rep2


title: 8719R2_CIA9-41_IndexUDI0082_GGTCACGA+GTATTATG_L004_001

value: male


title: 8719R2_CIA9-38_IndexUDI0081_AACTGTAG+ACGCCGCA_L004_001


title: HCT116 scONEseq 089

description:
RNA+DNA
HCT116 single cell 185


title: HCT116 scONEseq 088

description:
RNA+DNA
HCT116 single cell 184


title: 8719R2_CIA9-37_IndexUDI0054_TGGTGGCA+TCCTGTAA_L004_001


title: v-abl transformed B cells, DMSO control, run1, rep1

description:
20201111_DMSO_1
gRNA PCR from genomic DNA
labeled: DMSO_D6_1


title: control rep2


title: HCT116 scONEseq 087

description:
RNA+DNA
HCT116 single cell 183


title: 8719R2_CIA9-36_IndexUDI0053_CAACAATG+CTTCACGG_L004_001


title: ApcMin/+ [scRNA-seq]

city: Philadelphia

first: Joshua

middle: .H

last: Rhoades

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Sequencing reads were first pre-processed with 10x Genomics Cell Ranger pipeline and aligned to the GRCm38 (mm10) reference genome. An initial filtering was performed on the raw gene-barcode matrix output by the Cell Ranger cellranger count function, removing barcodes that have less than 1000 transcripts (quantified by unique molecular identifier (UMI)) and 500 expressed genes (“expressed” means that there is at least 1 transcript from the gene in the cell).
Barcodes that pass this filter were considered as cells and were fed into downstream analysis. For samples multiplexed using the TotalSeq-B protocol, cells were demultiplexed by performing Louvain clustering on the umap generated with the hashtag count matrix.  Gene-barcode UMI count matrix combined from all datasets was size-factor corrected and log transformed to produce a normalized gene expression matrix.
Assembly: GRCm38
Supplementary files format and content: Cell ranger count output.

source_name: tumor

growth_protocol: Colon1/TumorAOM/ApcMin/APKS samples were harvested from C57BL/6 mice and C57BL/6J-ApcMin/J correspondingly. APKS organiod were generated with gRNA targeting Apc/Trp53/Smad4 and Kras(G12D) virus.

extract_protocol:
Cells were encapsulated using the Chromium Controller (10x Genomics) and the Chromium Single Cell 3′ Library & Gel Bead Kit (10x Genomics) following the standard manufacturer’s protocols.
All libraries were prepared for sequencing using standard 10x chromium protocols.

value: Colon tumor

value: Apc min

value: untreated


title: HCT116 scONEseq 091

description:
RNA+DNA
HCT116 single cell 187


title: control rep1


title: HCT116 scONEseq 086

description:
RNA+DNA
HCT116 single cell 182


title: 8719R2_CIA9-35_IndexUDI0052_GGTGAACC+GCGTTGGA_L004_001


title: AOM/DSS [scRNA-seq]

value: wild type

value: 10mg/kg AOM injected once, after one week treated with 2.5%DSS for 5 days and then change to H2O for 2 weeks(this is one cycle), totally 3 cycle.


title: 8719R2_CIA9-34_IndexUDI0091_GTATGTTC+AACAGGAA_L004_001


title: SW480 cells, NC_2

city: Qingdao

first: Xin

last: Yi

address: 758 Hefei Road

institute: Qilu hospital of Shandong University (Qingdao)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.91 whole genome using Hisat2.
Fragments Per kilobase Million of library size (FPKM) were calculated using Srtringtie. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: Csv file includes FPKM values and matrix table with raw gene counts for  all samples

organism: Homo

source_name: Colon cancer cell line

growth_protocol: SW480 cells were maintained in Leibovitz’s L-15 (Gibco) containing 10% fetal bovine serum (FBS; Gibco) and 100 U/ml penicillin and streptomycin (Gibco). The culture temperature was maintained at 37°C and 5% CO2.

extract_protocol:
24h after transfection,  RNA was harvested using Tianmo#TR205-200. SµreSelect Strand-Specific RNA Component kit (Agilent   Cat#G9691B) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina cBot protocols

treatment_protocol: In guo-1,2,3 groups, the SW480 colon cancer cells were transfected with pIRES2-ZsGreen1-KIAA1522 overexpression. In NC-1,2,3 groups, the SW480 colon cancer cells were transfected with control empty plasmid.

tag: cell line

value: control empty plasmid transfection


title: SW480 cells, NC_3


title: APKS [scRNA-seq]

value: Orthotopic injected Apc/Trp53/KrasG12D/Smad4 quadruple-mutant tumor organoids to C57BL/6 mice for 8 weeks


title: 8719R2_CIA9-33_IndexUDI0065_ACACTAAG+ATCCATAT_L004_001


title: HCT116 scONEseq 084

description:
RNA+DNA
HCT116 single cell 180

value: Colon

value: scONE-seq


title: R0199 rep1


title: control rep3


title: SW480 cells, NC_1


title: HCT116 scONEseq 083

description:
RNA+DNA
HCT116 single cell 179


title: Normal Colon [scRNA-seq]

source_name: epithelial


title: 8719R2_CIA9-31_IndexUDI0080_GTGAATAT+TCTCATTC_L004_001


title: AP_shCtl3

data_processing:
Adapters were trimmed using Trimmomatic v0.32 (Bolger, Lohse and Usadel 2014) and aligned to the mm10 genome using STAR v2.3.0e (Dobin et al.,2012). Samtools v0.1.19 (Li et al., 2009) was used to convert sam files to bam files, keep concordant primary alignments, sort and index. Rsubread’s (Liao et al., 2019) featureCounts command quantified reads per gene using Ensembl mm10 gene annotations.
We removed all lowly expressed genes that did not have CPM >1 in at least a quarter of the samples. Limma v3.48.3 (Ritchie et al., 2015) voom was used to log2 transform and normalize the dataset. Limma was again used to fit a linear model and find differential genes. Camera (Wu and Smyth 2012) was used with EnsDb.Mmusculus.v75 (Rainer 2017), as implemented with RNA-webInterface ( https://github.com/bapoorva/RNA-WebInterface ) to perform Gene Set Enrichment Analysis
Assembly: Mm10
Supplementary files format and content: expression matrix

source_name: Colon organoid

growth_protocol: Organoids were dissociated into single cells and seeded into 2D plates and infected with lentivirus plus 1 ug/ml polybrene.

extract_protocol:
Matrigel was 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: organoids were selected with the puromycin (10 µg/ml) for 3 days.

tag: strain background

value: Infected with shControl virus


title: HCT116 scONEseq 082

description:
RNA+DNA
HCT116 single cell 178


title: AP_shCtl2


title: 8719R2_CIA9-32_IndexUDI0064_CCATTCGA+GTTGTCCG_L004_001


title: SW480 cells, guo_2

value: pIRES2-ZsGreen1-KIAA1522 overexpression


title: AP_shCtl1


title: 8719R2_CIA9-30_IndexUDI0079_ACAGGCGC+CTCTGCCT_L004_001


title: SW480 cells, guo_1


title: 8719R2_CIA9-29_IndexUDI0063_TTGCCTAG+ACCACTTA_L004_001


title: AP_sh4

value: Infected with shNotum virus


title: HCT116 scONEseq 085

description:
RNA+DNA
HCT116 single cell 181


title: HCT116 scONEseq 080

description:
RNA+DNA
HCT116 single cell 176


title: HCT116 scONEseq 079

description:
RNA+DNA
HCT116 single cell 175


title: AP_sh3


title: HCT116 scONEseq 078

description:
RNA+DNA
HCT116 single cell 174


title: 8719R2_CIA9-27_IndexUDI0090_CGCTATGT+TCCGACAC_L004_001

value: anti TNFa mAb


title: SW480 cells, guo_3


title: AP_sh2


title: 8719R2_CIA9-26_IndexUDI0089_TATCGCAC+CTTAGTGT_L004_001


title: HCT116 scONEseq 077

description:
RNA+DNA
HCT116 single cell 173


title: LGCIN_Progressive_Case_32631

city: New Orleans

first: Jennifer

middle: E.

last: Cameron

state: LA

address: 1901 Perdido St.

department: Microbiology, Immunology & Parasitology

institute: LSU Health Sciences Center

hyb_protocol: Samples were hybridized overnight on µParaflo microfluidic chips (Atactic Technologies) per LC Sciences protocol. Each chip contains probes for all described human miRNAs annotated in miRBase v22, as well as technical and sample quality control probes. Probes are synthesized in situ and contain a polyethylene glycol spacer to extend the cognate binding sequence away from the substrate. Each experimental probe is a chemically modified oligonucleotide designed to enhance specificity of binding to a complementary target miRNA sequence in the sample.

scan_protocol: Fluorescent images were scanned and analysed using Array-Pro image analysis software (Media Cybernetics), per LC Sciences standard procedures.

data_processing: Data were background subtracted and normalized using cyclic LOWESS (locally weighted regression) method.

source_name: Low grade cervical dysplasia that progressed to high-grade dysplasia

label_protocol: Samples were labeled with Cy3 per LC Sciences protocol.

growth_protocol: Not applicable.

extract_protocol: Total cellular RNA was extracted from formalin fixed - paraffin embedded (FFPE) tissue biopsies using the Qiagen miRNeasy FFPE kit according to vendor protocol.

treatment_protocol: Not applicable.

tag: age

value: cervical tissue


title: HCT116 scONEseq 081

description:
RNA+DNA
HCT116 single cell 177


title: LGCIN_Resolving_Control_32799

source_name: Low grade cervical dysplasia that naturally resolved


title: HCT116 scONEseq 076

description:
RNA+DNA
HCT116 single cell 172


title: AP_sh1


title: A_shCtl3

value: Apc -/-


title: 8719R2_CIA9-24_IndexUDI0087_CTCACCAA+CTAGGCAA_L004_001

value: front paws


title: 8719R2_CIA9-25_IndexUDI0088_TCTGTTGG+TCGAATGG_L004_001

value: male


title: HCT116 scONEseq 075

description:
RNA+DNA
HCT116 single cell 171


title: HCT116 scONEseq 074

description:
RNA+DNA
HCT116 single cell 170


title: A_shCtl2


title: 8719R2_CIA9-28_IndexUDI0051_AACAGGTT+ATACCAAG_L004_001

value: combination


title: LGCIN_Progressive_Case_32161


title: LGCIN_Resolving_Control_32053


title: LGCIN_Resolving_Control_32051


title: 8719R2_CIA9-22_IndexUDI0050_GCGCTCTA+GCTCCGAC_L004_001


title: A_shCtl1


title: HCT116 scONEseq 073

description:
RNA+DNA
HCT116 single cell 169


title: HCT116 scONEseq 072

description:
RNA+DNA
HCT116 single cell 168


title: 8719R2_CIA9-21_IndexUDI0061_CGGAACTG+CACTACGA_L004_001


title: LGCIN_Progressive_Case_32156


title: LGCIN_Resolving_Control_32063


title: A_sh4


title: 8719R2_CIA9-2-1_IndexUDI0045_ATGGCATG+AAGGTACC_L004_001


title: 8719R2_CIA9-19_IndexUDI0060_AGCTCGCT+GCAGAATC_L004_001


title: HCT116 scONEseq 071

description:
RNA+DNA
HCT116 single cell 167


title: HCT116 scONEseq 070

description:
RNA+DNA
HCT116 single cell 166


title: A_sh2


title: A_shCtl4


title: HCT116 scONEseq 069

description:
RNA+DNA
HCT116 single cell 165


title: 8719R2_CIA9-23_IndexUDI0062_TAAGGTCA+TGTCGTAG_L004_001


title: LGCIN_Progressive_Case_32706


title: LGCIN_Progressive_Case_32839


title: A_sh3


title: HCT116 scONEseq 068

description:
RNA+DNA
HCT116 single cell 164


title: A_sh1


title: LGCIN_Resolving_Control_32045


title: LGCIN_Progressive_Case_32148


title: HCT116 scONEseq 066

description:
RNA+DNA
HCT116 single cell 162


title: 8719R2_CIA9-17-1_IndexUDI0058_CATAATAC+TTCTAACG_L004_001


title: 1090B-RNA

city: Helsinki

first: Piet

last: Finckenberg

address: Haartmaninkatu 8

department: Medicum

country: Finland

institute: University of Helsinki

data_processing:
Basecalls by Illumina NextSeq550 (3 days follow up samples) or Illumina HiSeq2000 (21 days follow up samples)
Sequence reads were aligned to the reference genome (GRCm38; Ensembl_81)  with Tophat (v2.0.11) and Bowtie2 (v. 2.2.2)
Cufflinks (v2.2.1) was used to assemble the transcriptome from the aligned  sequences followed by feature summation and normalization of expression estimates
Cuffdiff2 was used to calculate the FPKM (number of fragments per kilobase of transcript per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output.
The expression profiles of different treatment groups were compared and the transcript ratios between the average FPKMs were calculated. Transcripts showing a LogFC ≥1 and a False Discovery Rate (FDR) <0.05 were classified as differentially expressed.
Assembly: GRCm38; Ensembl_81
Supplementary files format and content: Animal number."gene.annotated.counts.txt" (Individual data containing gene locations, ensemble identifiers, gene names and counts) as TextEdit Documents

source_name: Cardiac muscle

growth_protocol: Neonatal mice were housed with their original litter and mother until sacrificed and cardiac samples were taken

extract_protocol:
Cardiac samples from the remote zone of the left ventricle for RNASeq and miRNASeq were collected, frozen in liquid nitrogen and stored at −80 °C. The samples were then homogenized and RNA was isolated with TRIzol reagent.
3 days follow up samples.  Library preparation was done using Illumina TruSeq stranded total RNA sample Library Prep Kit with the starting material of 500 ng total RNA. Library quality was inspected on Agilent Bioanalyzer 2100 or BioAnalyzer 4200 TapeStation. The library pool was quantified using qPCR and sequenced on Illumina NextSeq550 (2x75 cycles).
21 days follow up samples.  Library preparation was done using Illumina ScriptSeqV2 Library Prep Kit with the starting material of 500 ng total RNA. Library quality was inspected on Agilent Bioanalyzer 2100 or BioAnalyzer 4200 TapeStation. The library pool was quantified using qPCR and sequenced on Illumina HiSeq 2000 instrument (2x100 cycles).

treatment_protocol: Mice were subjected to LAD ligation or SHAM operation at the postnatal day 1 or 7. After the operation, the follow-up period lasted 3 or 21 days until the cardiac samples were collected

value: Left ventricular wall from the remote zone

tag: age (operation day + follow up time)

value: 7 + 3 days

value: MI at postnatal day 7


title: HCT116 scONEseq 067

description:
RNA+DNA
HCT116 single cell 163


title: 8719R2_CIA9-13_IndexUDI0077_TGCGAGAC+CATTGTTG_L004_001

value: anti IL-6 mAb


title: 1077B-RNA


title: HCT116 scONEseq 064

description:
RNA+DNA
HCT116 single cell 160


title: 1090A-RNA


title: 8719R2_CIA9-15_IndexUDI0085_AGGTTATA+CAGTTCCG_L004_001


title: 8719R2_CIA9-11_IndexUDI0076_GACGTCTT+GGTTCACC_L004_001


title: 8719R2_CIA9-10_IndexUDI0048_ACCTTGGC+GGCCTCAT_L004_001


title: 8719R2_CIA9-16_IndexUDI0086_GAACCGCG+TGACCTTA_L004_001


title: 1075F-RNA

value: SHAM at postnatal day 7


title: LGCIN_Resolving_Control_32004


title: LGCIN_Resolving_Control_32011


title: 8719R2_CIA9-18_IndexUDI0059_GATCTATC+ATGAGGCT_L004_001


title: LGCIN_Resolving_Control_32025


title: 8719R2_CIA9-14_IndexUDI0078_CATAGAGT+TGCCACCA_L004_001


title: HCT116 scONEseq 063

description:
RNA+DNA
HCT116 single cell 159


title: 1088D-RNA


title: 8719R2_CIA9-9_IndexUDI0047_GTTCCAAT+AATTCTGC_L004_001


title: 1075E-RNA


title: HCT116 scONEseq 062

description:
RNA+DNA
HCT116 single cell 158


title: LGCIN_Progressive_Case_32515


title: HCT116 scONEseq 061

description:
RNA+DNA
HCT116 single cell 157


title: 1075G-RNA


title: HCT116 scONEseq 065

description:
RNA+DNA
HCT116 single cell 161


title: 1086D-RNA

value: 1 + 3 days

value: MI at postnatal day 1


title: LGCIN_Progressive_Case_32214


title: 8719R2_CIA9-8-1_IndexUDI0084_TCATCCTT+AGCGAGCT_L004_001


title: LGCIN_Resolving_Control_32062B


title: 1075D-RNA


title: 1086C-RNA


title: LGCIN_Progressive_Case_32784


title: LGCIN_Progressive_Case_32838


title: HCT116 scONEseq 060

description:
RNA+DNA
HCT116 single cell 156

value: Colon

value: scONE-seq


title: HCT116 scONEseq 059

description:
RNA+DNA
HCT116 single cell 155


title: HCT116 scONEseq 056

description:
RNA+DNA
HCT116 single cell 152


title: LGCIN_Progressive_Case_32556


title: LGCIN_Resolving_Control_32092


title: 8719R2_CIA9-7_IndexUDI0075_AGTACTCC+AACCTGTT_L004_001


title: HCT116 scONEseq 058

description:
RNA+DNA
HCT116 single cell 154


title: 8719R2_CIA9-6_IndexUDI0074_TGGCCGGT+TAGAGCGC_L004_001


title: 1086A-RNA


title: LGCIN_Progressive_Case_32065


title: HCT116 scONEseq 054

description:
RNA+DNA
HCT116 single cell 150


title: HCT116 scONEseq 057

description:
RNA+DNA
HCT116 single cell 153


title: 8719R2_CIA9-5_IndexUDI0073_CAATTAAC+CGAGATAT_L004_001


title: 1059E-RNA


title: 1103E-RNA

value: SHAM at postnatal day 1


title: HCT116 scONEseq 055

description:
RNA+DNA
HCT116 single cell 151


title: LGCIN_Resolving_Control_32089


title: 8719R2_CIA9-4_IndexUDI0072_GTCTACAC+GCCAAGGT_L004_001


title: LGCIN_Progressive_Case_32731


title: LGCIN_Progressive_Case_32675


title: LGCIN_Resolving_Control_32094


title: LGCIN_Resolving_Control_32086


title: cdkd3-1/smg7-6 Rep3

city: Brno

first: Neha

last: Shukla

address: Kamenice 753

department: Plant Molecular Biology

country: Czech Republic

institute: CEITEC

description: rRNA removed

data_processing:
bcl2fastq v2.20.0.422 was used for base calling
Low-quality reads and adapters were trimmed using cutadapt v2.5.
Data was aligned on reference AtRTD2 transcript dataset (Zhang et al., 2017) and simultaneously quantified with quasi-mapping-based algorithm using Salmon software v1.5 (Patro et al., 2017).
Gene expression data normalization and differential expression analysis was done using 3D RNA-Seq tool (Guo et al., 2020; Calixto et al., 2018).
Assembly: Arabidopsis transcriptome reference dataset - AtRTD2 (Zhang et al., 2017)
Supplementary files format and content: comma-delimiled text file including TPM values for each gene in all samples and three replicates each

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Arabidopsis thaliana plants were grown in soil in phytotrons under controlled conditions of 20-21°C, 60% relative humidity and 16-h light/ 8-h photoperiod.

extract_protocol:
leaves from three weeks-old plants were pooled from five independent plants (technical replicate) grown at same time. Total RNA was extracted using RNA Blue (Top-Bio), following the manufacturer’s protocol.
Strand-specific libraries were prepared from ribosomal RNA-depleted total RNA using ScriptSeq complete kit for plant leaf (Epicentre; BPL1224) following manufacturer's protocol. The experiment was conducted in three biological replicates.

value: Leaves

value: 3-week old plants


title: 8719R2_CIA9-3_IndexUDI0046_GCAATGCA+GGAACGTT_L004_001


title: 8719R2_CIA9-20_IndexUDI0049_ATATCTCG+ATCTTAGT_L004_001


title: cdkd3-1/smg7-6 Rep2

description: rRNA removed


title: LGCIN_Resolving_Control_32067

value: cervical tissue


title: 1103D-RNA


title: 8719R2_CIA9-1_IndexUDI0071_ACTCGTGT+ATTGGAAC_L004_001


title: 1078F-RNA


title: TCR_YUMM-sgSCR TILs

city: San Diego

first: Yuqing

last: Hang

address: 10010 N Torrey Pines Rd

department: IGC Core

institute: Salk Institute for biological studies

description:
Platform: 10x Genomics
Sample id: YUMM-sgSCR
VSK1-TCR

data_processing:
Library strategy: TCR-seq
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 3.0.2) against the mm10 mouse reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied mouse VDJ reference genome.
Assembly: mm10
Supplementary files format and content: all contig annotation table, filtered contig annotation table, clonotypes table, filtered feature bc matrix, and a web summary generated by Cell Ranger

source_name: YUMM control

extract_protocol:
YUMM-sgSCR and MCJ KO were grown subcutaneosuly and at day 21 post implantation, tumour were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 2% fetal bovine serum (FBS, Gibco), and enzymatically digested with Collagenase IV (sigma) and DNase (Roche) for 20 min on a rotor at 37°C. The dissociated cells were subsequently passed through a 70 μm SmartStrainer and centrifuged at 400g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer and incubated at room temperature for 2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% FBS). Upon pooling samples (3 controls and 3 MCJ KO) single cell suspensions were stained and FACS sorted for CD3+ CD8+ T cells, CD3+ CD4+  T cells, CD3- CD45+ cells and CD45- cells using 100uM nozzle. A total of 10,000 cells from each sample were used for the 10x Chromium Single cell 5’ and VDJ library construction (10x Genomics), according to the manufacturer’s instructions.
10x Chromium Single cell 5’ + VDJ Library

value: YUMM-sgSCR


title: LGCIN_Resolving_Control_32088


title: HCT116 scONEseq 050

description:
RNA+DNA
HCT116 single cell 146


title: HCT116 scONEseq 052

description:
RNA+DNA
HCT116 single cell 148


title: cdkd3-1/smg7-6 Rep1

description: rRNA removed


title: LGCIN_Progressive_Case_32697


title: RNA_YUMM-sgSCR TILs

description:
Platform: 10x Genomics
Sample id: YUMM-sgSCR
VSK1-RNA

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 3.0.2) against the mm10 mouse reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied mouse VDJ reference genome.
Assembly: mm10
Supplementary files format and content: all contig annotation table, filtered contig annotation table, clonotypes table, filtered feature bc matrix, and a web summary generated by Cell Ranger


title: HCT116 scONEseq 053

description:
RNA+DNA
HCT116 single cell 149


title: cdkd3-1 Rep3

description: rRNA removed


title: TCR_YUMM-MCJ-KO TILs

description:
Platform: 10x Genomics
Sample id: YUMM-MCJKO
VSK3-TCR

source_name: YUMM MCJ KO

value: YUMM-MCJKO


title: HCT116 scONEseq 051

description:
RNA+DNA
HCT116 single cell 147


title: HCT116 scONEseq 048

description:
RNA+DNA
HCT116 single cell 144


title: HCT116 scONEseq 049

description:
RNA+DNA
HCT116 single cell 145


title: 1078G-RNA


title: RNA_YUMM-MCJ-KO TILs

description:
Platform: 10x Genomics
Sample id: YUMM-MCJKO
VSK3-RNA


title: cdkd3-1 Rep2

description: rRNA removed


title: HCT116 scONEseq 047

description:
RNA+DNA
HCT116 single cell 143


title: cdkd3-1 Rep1

description: rRNA removed


title: LGCIN_Resolving_Control_32042


title: brain cerebral cortex cells from three pooled WT mice, sample 2

city: Uppsala

first: Ying

last: Sun

address: Dag Hammarskjölds väg 20

country: Sweden

institute: Uppsala University

description: brain cerebral cortex from 9wk mice

data_processing:
The raw sequence reads were analyzed by Cell Ranger 3.0.1 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: brain cerebral cortex

extract_protocol:
Single cell sequencing was performed at the eukaryotic single cell genomics facility(ESCG) using the 10× Genomics Chromium method (Hochgerner et al., 2018).
Single cell sequencing was performed at the eukaryotic single cell genomics facility(ESCG) using the 10× Genomics Chromium  Single Cell 3' Solution V3 chemistry.

value: brain cerebral cortex

value: WT


title: brain cerebral cortex cells from three pooled WT mice, sample 3

description: brain cerebral cortex from 9wk mice


title: brain cerebral cortex cells from three pooled WT mice, sample 1

description: brain cerebral cortex from 9wk mice


title: LGCIN_Resolving_Control_32071


title: LGCIN_Progressive_Case_32101


title: LGCIN_Resolving_Control_32003


title: HCT116 scONEseq 046

description:
RNA+DNA
HCT116 single cell 142


title: S16

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to transcriptome of Ensembl OryCun2.0
DESeq2 for differential gene expression
Assembly: Ensembl OryCun2.0
Supplementary files format and content: A .csv file including TPM of each gene for all 8 samples

organism: Oryctolagus cuniculus

source_name: Premature rabbit pups treated with glycerol to induce intraventricular hemorrhage

extract_protocol:
Qiagen RNeasy micro kit was used for RNA extraction from dissected tissue samples collected using microscope from the SVZ region.
Illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: Premature rabbit pups were injected intraperitoneal glycerol (50%) to induce intraventricular hemorrhage and treated with unrestricted stem cells or deferoxamine

tag: disease state

value: intraventricular hemorrhage

value: Postnatal day 3

value: SVZ dissected tissue

value: Deferoxamine Treated (DFN)


title: HCT116 scONEseq 045

description:
RNA+DNA
HCT116 single cell 141


title: HCT116 scONEseq 044

description:
RNA+DNA
HCT116 single cell 140


title: S15


title: Vehicle Immune

city: St. Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue, Room 502

department: Internal Medicine/Oncology

institute: Washington University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the mouse Ensembl GRCh38.76 primary assembly with STAR aligner version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights
Genome_build: mouse Ensembl GRCh38.76 primary assembly
Supplementary_files_format_and_content: .tsv.gz, .mtx.gz

source_name: Pancreatic cancer

growth_protocol: KPC mice were genotyped and confirmed to have the correct transgenes.

extract_protocol:
Pancreas from mice were harvested, washed and digested sing a cocktail fo collagenase, hyaluronidase and DNAse into single cell suspension.Nuclei isolation was performed according to 10X genomics protocol-Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (CGOOO338 CA210181)
standard 10X Genomics  5′ GEX Single-Cell Library

treatment_protocol: 4 mice per group were treated with vehicle or CA-4948 100mg/kg daily for 14 days and taken down

value: Pancreatic cancer

value: Immune

tag: background strain

value: p48-Cre;TP53flox/flox; LSL-KRASG12D

value: Treated with Vehicle for 2 weeks


title: S14


title: Vehicle CAF

value: CAF


title: HCT116 scONEseq 043

description:
RNA+DNA
HCT116 single cell 139

source_name: HCT116 cell line

value: Colon

value: scONE-seq


title: IRAK4i Immune

value: Treated with CA-4948 for 2 weeks


title: LGCIN_Resolving_Control_32062A

value: cervical tissue


title: LGCIN_Resolving_Control_32097


title: HCT116 scONEseq 042

description:
RNA+DNA
HCT116 single cell 138


title: S12

value: Unrestricted Stem Cell Treated (USCT)


title: LGCIN_Progressive_Case_32785


title: IRAK4i CAF


title: LGCIN_Resolving_Control_32069


title: HCT116 scONEseq 041

description:
RNA+DNA
HCT116 single cell 137


title: S11


title: KO/ERRg-wt_14-11

city: Koto-ku

first: Tomoyoshi

last: Nakadai

state: Tokyo

country: Japan

institute: Cancer Institute of JFCR

data_processing:
Trimming of adaptor sequences by Skewer (v.0.2.2).
Mapping to mm10 genome by STAR (v.2.7.8a).
Counting mapped reads by featureCounts (v.2.0.10).
Genome_build: mm10
Supplementary_files_format_and_content: text file of expression count matrix

source_name: mouse ESC

growth_protocol: ESC clones (1600 cells) were seeded in a poly-L-ornithine- and laminin-coated 12-well plate in N2B27-LIF/PD/CH medium with 2 µg/ml doxycycline for 3 days.

extract_protocol:
All cells were harvested and total RNA was purified by RNAeasy (Qiagen) with Dnase-treatment step.
The library for RNA-seq was prepared from 400-500 ng of isolated RNA by using TruSeq Stranded Total RNA with Ribo-Zero kit (Illumina) according to the manufacturer’s instructions. The pooled libraries with unique index sequences were sequenced using NovaSeq SP (Illumina) with single-end 100 bp reads.

treatment_protocol: 2 µg/ml doxycycline for 3 days.

value: mouse ESC

value: ERR beta -/-

tag: ectopic expression

value: wild type ERR gamma


title: LGCIN_Resolving_Control_32087


title: S10

value: intraventricular hemorrhage


title: KO/ERRb-AF2M6_32-31, rep1

value: Coactivator-binding deficient ERR beta mutant (AF2M6)


title: HCT116 scONEseq 039

description:
RNA+DNA
HCT116 single cell 135


title: HCT116 scONEseq 038

description:
RNA+DNA
HCT116 single cell 134


title: HCT116 scONEseq 040

description:
RNA+DNA
HCT116 single cell 136


title: KO/ERRb-AF2M6_32-31, rep2


title: S9

value: Postnatal day 3

value: SVZ dissected tissue


title: S8

data_processing:
Kallisto for pseudo-alignment to transcriptome of Ensembl OryCun2.0
DESeq2 for differential gene expression
Genome_build: Ensembl OryCun2.0
Supplementary_files_format_and_content: A .csv file including TPM of each gene for all 8 samples

molecule: polyA RNA

source_name: SVZ dissected tissue

treatment_protocol: Premature rabbit pups were injected intraperitoneal glycerol (50%) to induce intraventricular hemorrhage and compared with healthy control no hemorrhage

tag: group

value: Premature rabbit pups treated with glycerol to induce intraventricular hemorrhage

value: Intraventricular Hemorrhage (GMH-IVH)

value: SVZ disected tissue


title: KO/ERRb-AF2M6_32-25, rep2


title: S13

tag: tissue

value: Deferoxamine Treated (DFN)


title: LGCIN_Resolving_Control_32091


title: LGCIN_Progressive_Case_32716


title: LGCIN_Progressive_Case_32545


title: HCT116 scONEseq 037

description:
RNA+DNA
HCT116 single cell 133

data_processing:
Library strategy: scONE-Seq
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.


title: S7


title: HCT116 scONEseq 036

description:
RNA+DNA
HCT116 single cell 132


title: S6


title: LGCIN_Progressive_Case_32014


title: S5


title: KO/ERRb-DBDm6_10-26, rep2

value: TFIIH-binding deficient ERR beta mutant (DBDm6)


title: KO/ERRb-AF2M6_32-25, rep1


title: LGCIN_Progressive_Case_32698


title: HCT116 scONEseq 035

description:
RNA+DNA
HCT116 single cell 131

value: Colon


title: KO/ERRg-wt_14-1-10


title: HCT116 scONEseq 034

description:
RNA+DNA
HCT116 single cell 130

value: scONE-seq


title: KO/ERRb-DBDm6_10-26, rep1


title: S4

value: Healthy premature rabbit pups

value: control


title: HCT116 scONEseq 033

description:
RNA+DNA
HCT116 single cell 129


title: LGCIN_Resolving_Control_32048

value: cervical tissue


title: S3


title: LGCIN_Resolving_Control_32084


title: KO/ERRb-DBDm6_10-24, rep2

value: mouse ESC


title: HCT116 scONEseq 032

description:
RNA+DNA
HCT116 single cell 128


title: KO/ERRb-DBDm6_10-24, rep1

value: ERR beta -/-


title: S2


title: LGCIN_Resolving_Control_32061


title: LGCIN_Resolving_Control_32083


title: HCT116 scONEseq 031

description:
RNA+DNA
HCT116 single cell 127


title: S1


title: HCT116 scONEseq 030

description:
RNA+DNA
HCT116 single cell 126


title: KO/ERRb-DBDm3_9-8, rep2

value: DNA-binding deficient ERR beta mutant (DBDm3)


title: KO/ERRb-DBDm3_9-8, rep1


title: LGCIN_Resolving_Control_32085


title: HCT116 scONEseq 029

description:
RNA+DNA
HCT116 single cell 125


title: LGCIN_Resolving_Control_32031


title: KO/ERRb-DBDm3_9-6, rep2


title: HCT116 scONEseq 028

description:
RNA+DNA
HCT116 single cell 124


title: osrdr2-3_pistil_mRNA_replicate3

city: Nanjing

first: Lili

address: Weigang No.1

institute: Nanjing Agricultural University

description: fem1-3_pistil_rep3 mRNA-seq

data_processing:
Low-quality reads had been eliminated.
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Tophat.
Expression level were normalized through fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: MSU 7.0

organism: Oryza sativa

source_name: pistil

growth_protocol: Rice plants grown in soil in Jiangsu province

extract_protocol:
RNA was extrated using TRIzol method.
1.Total RNA used DNaseI to digest DNA, and enriched mRNA using magnetic beads with Oligo(dT).  2.Adding reagent in Thermomixer to interrupt mRNA into short fragments.  3.The fragmented mRNA was used as template to synthesize the first strand of cDNA, and then synthesized the second strand.  4.Purified by using the kit, and repaired the adhesive termination, added the base "A" and adapter in the CDNA 3'end, then selected 200-300bp fragments and performed PCR amplification.   5.The libraries were checked with Agilent 2100 Bioanalyzer and ABI Real-Time PCR System, the qualified libraries were sequenced using sequencing platform.
mRNA Illumina sequencing

tag: cultivar

value: Japponica


title: KO/ERRb-DBDm3_9-6, rep1


title: WT, scRNAseq

city: Nagoya

first: Takenori

last: Yoshikawa

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole skin

extract_protocol:
The full-thickness skins of the back from one WT and one Card14KI mice at one year after birth were excised surgically. The two samples digestion was performed using the whole skin dissociation kit for human (Miltenyi Biotec, Germany). Enzymatic digestion was completed in 73 min, followed by mechanical dissociation using gentleMacs Octo Dissociator with heaters (Miltenyi Biotec), running the gentle MACS mice program 37C_m_Bo_WSDK_2. Next, dead cells and debris were removed, using the dead cell removal kit (Miltenyi Biotec).
Preparation of the scRNAseq library, sequencing and data preprocessing were outsourced to AZENTAⓇ corporation Japan branch office. Single cell cDNA libraries were prepared by using 3’ Gene expression v 3.1(10X Genomics), and the constructed libraries were sequenced on DNBSEQ-G400 (MGI-Tech, China) with paired end 150 bp. Raw sequencing data were processed via Cell Ranger (10X Genomics)

value: Epidermal cells, Mesenchymal cells, Endothelial  cells, Immune cells,   erythrocytes, cells derived from the neural crest, death cells

value: Whole skin

tag: strain

value: 12 months old

value: wild type


title: LGCIN_Progressive_Case_32240


title: HCT116 scONEseq 026

description:
RNA+DNA
HCT116 single cell 122

extract_protocol:
Nuclei isolation was adapt from Omni-ATAC protocol. Single cells / nuclei were sorted with Aria III with propidium iodide or DAPI to remove dead cells or select nuclei.
scONE-seq; Smart-seq2; 10x Genomics


title: osrdr2-3_pistil_mRNA_replicate2

description: fem1-3_pistil_rep2 mRNA-seq


title: Placenta_LGA_No_Sample59 [HF2_1048]

type: genomic

city: Toronto

first: Zhong-Cheng

last: Luo

state: Ontario

address: 60 Murray, L5-240, LTRI

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital, University of Toronto

description: There are a total of 96 samples in 12 slides in the experiments (36 samples are not a part of the present study)

hyb_protocol: standard illumina protocol

scan_protocol: standard illumina protocol

data_processing:
normalized (functional normalization, BMIQ, slide adjustment using "ComBat" function in "sva" package
the 'signal_intensities.txt' contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Placenta tissue from the fetal side

label_protocol: standard illumina protocol

extract_protocol: DNA was extracted from fetal-side placental samples using Dneasy Blood & Tissue Kit (Qiagen, Cat No. 69504)

tag: Sex

value: Male

tag: lga status

value: No

tag: gestational diabetes

tag: maternal age

tag: pre-pregnancy body mass index

tag: primiparity

value: Yes

tag: gestational age at birth

tag: cesarean section

tag: slide


title: Placenta_LGA_No_Sample60 [HF2_909]

value: Female


title: osrdr2-3_pistil_mRNA_replicate1

description: fem1-3_pistil_rep1 mRNA-seq


title: HCT116 scONEseq 025

city: Hong Kong

first: Angela

institute: HKUST

description:
RNA+DNA
HCT116 single cell 121

value: Colon

tag: method


title: KO/ERRb-wt_8-4, rep1

tag: cell type

tag: genotype

value: wild type ERR beta


title: KO/ERRb-wt_8-3, rep2

tag: ectopic expression


title: Placenta_LGA_No_Sample58 [HF2_414]


title: Nip_pistil_mRNA_replicate3

description: Nip_pistil_rep3 mRNA-seq


title: Card14KI, scRNAseq

description: 10x Genomics

tag: age

value: Card14 KI +/+


title: HCT116 scONEseq 024

description:
RNA+DNA
HCT116 single cell 120

tag: tissue

value: scONE-seq


title: Placenta_LGA_No_Sample57 [HF2_317]


title: KO/ERRb-wt_8-3, rep1


title: Nip_pistil_mRNA_replicate2

description: Nip_pistil_rep2 mRNA-seq

tag: cultivar


title: HCT116 scONEseq 023

description:
RNA+DNA
HCT116 single cell 119


title: KO/Mock_12-3, rep2


title: Placenta_LGA_No_Sample56 [GF4_756]


title: Nip_pistil_mRNA_replicate1

description: Nip_pistil_rep1 mRNA-seq


title: KO/ERRb-wt_8-4, rep2


title: osrdr2-3_stamen_mRNA_replicate3

description: fem1-3_stamen_rep3 mRNA-seq

source_name: stamen


title: Placenta_LGA_No_Sample55 [GF4_842]


title: Rpb1 E1126G shTHOC5 total RNAs / Rpb1 E1126G shCr  total RNAs

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 1000 ng of each labelled cRNA population (Alexa Fluor 555 and 647) were combined and cohybridized onto one Microarray.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE2_107_Sep09.xml’, except that ‘Multiplicative detrending’ algorithm was inactivated.

source_name: Rpb1 E1126G shCr  total RNAs

label_protocol: Synthesis of labeled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies), except that NTP-mix and fluorescently-labeled CTP (to be used in the T7 reaction) were exchanged by a mix containing 15 mM of each ATP, CTP, GTP, 13.75 mM of UTP, and 1.25 mM of aaUTP (final concentration of each nucleotide was 1.875 mM). The labeling of aaUTP-cRNA was performed by use of the Amino Allyl MessageAmp™ II Kit (#AM1753; Life Technologies) and Alexa Fluor 555 and 647 Reactive Dyes (#A32756, #A32757; LifeTechnologies).

growth_protocol: The cells were maintained in DMEM supplemented with 10% FBS, 200 μg/mL hygromycin B, 6.5 μg/mL blasticidin, and penicillin/streptomycin.

extract_protocol: Total RNAs were isolated using High Pure RNA isolation kit (Roche)

treatment_protocol: Cells were infected with shControl and shTHOC5 virus in growth medium contaning 2.0 μg/mL doxycycline for 12–16 h and treatment with 2.5 μg/mL α-amanitin for a further 42 h

value: embryonic kidney cells (293 cells)

source_name: Rpb1 E1126G shTHOC5 total RNAs


title: HCT116 scONEseq 021

last: WU

address: Clear water bay street

description:
RNA+DNA
HCT116 single cell 117


title: KO/Mock_12-1, rep2

value: mouse ESC


title: Placenta_LGA_No_Sample54 [XH2_389]


title: HCT116 scONEseq 027

description:
RNA+DNA
HCT116 single cell 123


title: HCT116 scONEseq 020

description:
RNA+DNA
HCT116 single cell 116


title: Placenta_LGA_No_Sample53 [HF2_675]


title: KO/Mock_12-1, rep1

value: ERR beta -/-


title: osrdr2-3_stamen_mRNA_replicate1

description: fem1-3_stamen_rep1 mRNA-seq


title: WT/Mock_5-5, rep2


title: HCT116 scONEseq 019

description:
RNA+DNA
HCT116 single cell 115


title: Rpb1 R749H shTHOC5 total RNAs / Rpb1 R749H shCr  total RNAs

source_name: Rpb1 R749H shCr  total RNAs

source_name: Rpb1 R749H shTHOC5 total RNAs


title: Nip_stamen_mRNA_repplicate3

description: Nip_stamen_rep3 mRNA-seq


title: HCT116 scONEseq 022

description:
RNA+DNA
HCT116 single cell 118


title: Placenta_LGA_No_Sample52 [XH2_363]


title: HCT116 scONEseq 018

description:
RNA+DNA
HCT116 single cell 114


title: Nip_stamen_mRNA_repplicate2

description: Nip_stamen_rep2 mRNA-seq


title: Placenta_LGA_No_Sample51 [GF4_912]


title: Placenta_LGA_No_Sample50 [HF2_637]


title: Nip_stamen_mRNA_replicate1

description: Nip_stamen_rep1 mRNA-seq


title: WT/Mock_5-2, rep2


title: KO/Mock_12-3, rep1


title: Placenta_LGA_No_Sample49 [HF2_33]


title: WT/Mock_5-2_rep1


title: osrdr2-6_pistil_Bs

description: fem1-6_pistil Bs-seq

data_processing:
Low-quality sequences(q<20) and adapters were trimmed using trimmomatic.
Reads were mapped to MSU7.0 using bismark with default parameters
Genome_build: MSU 7.0

extract_protocol:
genomic DNA was extrated using CTAB method.
Genomic DNA was sonicated and then end-repaired with End repair Enzyme Mix. The blunt-ended DNA were treated with Klenow fragment and dATP to yield a proruding3-"A" and cytosine-methylated adaptors from Illumina were ligated according to manufacture's instructions.
Bisulfite treated Illumina sequencing


title: HCT116 scONEseq 015

description:
RNA+DNA
HCT116 single cell 111


title: Placenta_LGA_No_Sample48 [HF2_1029]


title: HCT116 scONEseq 014

description:
RNA+DNA
HCT116 single cell 110


title: H3K27ac_Il4_day6

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
Library strategy: CUT&Tag
All sequence reads were Quality control by FastQC v0.11.9.
Sequence reads were aligned to the mouse genome assembly (mm10) using bowtie2 (2.2.1) paras as default.
Bigwig file were created by bamCoverage with Effective genome size 2652783500.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

source_name: Bone marrow

growth_protocol: BMDMs were differentiated from bone marrow, treated with 40ng/ml MCSF.

extract_protocol:
All procedures were carried out by following the manufacturer’s instructions described in NovoNGSR CUT&Tag 3.0 (Novoprotein, N259-YH01).
Chromatin immunoprecipitation fragments were prepared for sequencing using standard Illumina protocols.

treatment_protocol: BMDMs treated with 20 ng/ml IL4.

tag: strain

value: Bone marrow-derived macrophages

tag: treatment

value: 20 ng/ml IL4, day6

tag: antibody


title: Placenta_LGA_No_Sample47 [HF2_671]

tag: Sex

tag: lga status

tag: gestational diabetes


title: H3K27ac_NS_day6

value: Untreated, day6


title: HCT116 scONEseq 013

description:
RNA+DNA
HCT116 single cell 109


title: Placenta_LGA_No_Sample46 [HF2_573]

tag: maternal age

tag: pre-pregnancy body mass index

tag: primiparity


title: HCT116 scONEseq 012

description:
RNA+DNA
HCT116 single cell 108


title: osrdr2-6_stamen_Bs

last: Wang

description: fem1-6_stamen Bs-seq

value: Japponica


title: Nip_pistil_Bs

description: Nip_pistil Bs-seq


title: osrdr2-3_stamen_Bs

description: fem1-3_stamen Bs-seq


title: H3K4me1_NS_day6


title: HCT116 scONEseq 017

description:
RNA+DNA
HCT116 single cell 113


title: HCT116 scONEseq 010

description:
RNA+DNA
HCT116 single cell 106


title: HCT116 scONEseq 011

description:
RNA+DNA
HCT116 single cell 107


title: HCT116 scONEseq 016

description:
RNA+DNA
HCT116 single cell 112


title: H3K27ac_Il4_24h

value: 20 ng/ml IL4, 24h


title: Placenta_LGA_No_Sample44 [HF2_980]

tag: gestational age at birth

tag: cesarean section

tag: slide


title: H3K27ac_NS_24h

tag: cell type

value: Untreated, 24h


title: Placenta_LGA_No_Sample45 [HF2_774]

value: Male


title: Round 3 Selected Library on Bl6 T-cells

city: durham

first: Jonathan

last: Ark

address: 3 genome ct

institute: Duke University

data_processing:
Find sequences
Translate Sequences
Enumerate Sequencing %
Assembly: NA
Supplementary files format and content: list of sequence representation csv
Library strategy: Amplicon-seq

organism: Dependoparvovirus

source_name: Virus

extract_protocol:
IBI gDNA extraction kit (IB47200)
Custom

value: Virus

tag: infected cell_type

value: T-cell

tag: genotype

value: Evolved


title: Nip_stamen_Bs

description: Nip_stamen Bs-seq


title: Placenta_LGA_No_Sample43 [HF2_969]

value: No

value: Yes


title: H3K4me1_Il4_24h


title: Placenta_LGA_No_Sample42 [HF2_354]

value: Female


title: HCT116 scONEseq 008

description:
RNA+DNA
HCT116 single cell 104

tag: tissue

value: Colon

tag: method

value: scONE-seq


title: osrdr2-3_pistil_Bs

description: fem1-3_pistil Bs-seq

tag: cultivar


title: H3K4me1_Il4_day6

tag: strain

tag: treatment


title: Marburg, H2/CO2, biol rep 3

city: Tübingen

first: Bastian

last: Molitor

state: Baden Württemberg

address: Schnarrenbergstr. 94-96

department: Center for Applied Geosciences

institute: University of Tübingen

data_processing:
Sequencing reads were quality filtered and trimmed with BBMap version 38.93 and FastX Toolkit version 0.0.14 with specific parameters for paired-end reads.
Reads from each bioreactor culture were mapped to the reference genomes of M. thermautotrophicus ΔH (CP064324), M. thermautotrophicus Z-245 (CP064336 and CP064337) and M. marburgensis Marburg (CP069376 and CP069377) using BWA-MEM version 0.7.17.
Mapped reads were assigned to genomic features using the FeatureCounts program from the Subread package version 2.0.1. Additionally, an alignment-free quantification of gene features was performed using Salmon version 1.5.2.
Pairwise differential expression analysis was performed on the Salmon counts using DESeq2 version 1.32.0 with the homologous genes present in the pan-genome database (see manuscript) and ConsensusDE version 1.10.0.
The adjusted P-value cut-off threshold was set to 0.05
Assembly: Reference genomes of M. thermautotrophicus ΔH (CP064324), M. thermautotrophicus Z-245 (CP064336 and CP064337) and M. marburgensis Marburg (CP069376 and CP069377)
Supplementary files format and content: quant.sf = Salmon's quantification file, plain-text, tab-separated file, with the headers: Name, Length, EffectiveLength, TPM, NumReads

organism: Methanothermobacter marburgensis

source_name: prokaryotic

growth_protocol: Briefly: The three microbes were culivated continuously in bioreactors with minimal salts media and fed and 80/20 v/v % gas mixture of H2/CO2. Details on cultivation can be found in manuscript.

extract_protocol:
A hot phenol method was used for RNA extraction. The samples were thawed on ice and centrifuged at 4°C and 4100 × g for 10 min, the supernatant discarded, and the samples resuspended in 800 µL of RNase free water.
The 800 µL were mixed with 950 µL of saturated phenol (Sigma-Aldrich, Merck, Germany) and 115 μL of a lysis solution in Lysing Matrix B (MP Biomedicals Germany GmbH, Eschwege, Germany). The lysis solution contained sodium acetate (20 mM pH 5.2), sodium dodecyl sulfate (SDS; 0.5 % v/v), ethylenediaminetetraacetic acid (EDTA; 1 mM), and DNase/RNase-free distilled water (DI; Invitrogen, Thermo Fischer Scientific, Germany).
The cells were homogenized for one cycle (5 x 40 s at 6 m/s and 20 s off) in a FastPrep-24TM 5G bead-beater (MP Biomedicals Germany GmbH, Eschwege, Germany) and then centrifuged at room temperature and 21130 × g for 10 min (5424 Eppendorf, Hamburg, Germany). The top layer was placed into 600 µL of phenol-chloroform-isoamyl alcohol (ROTI® Aqua-P/C/I, Carl Roth, Karlsruhe, Germany) and centrifuged as in the previous step. This step was repeated twice.
The top layer was added to 1.2 mL of ethanol (undenatured absolute, SERVA Electrophoresis GmbH, Heidelberg, Germany) and left overnight at -80 °C to precipitate the RNA. The following day, the tubes were centrifuged at 4°C and 21130 × g for 10 min, and then the supernatant was removed. The RNA pellet was washed with 1 mL of 75% v/v ethanol solution and centrifuged as in the previous step. The supernatant was pipetted off, and the pellet was resuspended with 53 µL of DNase/RNase-free distilled water.
The RNA was cleaned (which included DNA depletion) and concentrated using the RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, United States), according to the manufacturer’s instructions. The cleaning and concentrating protocols were repeated four times.
RNA libraries for RNA-seq were prepared using 100 ng of RNA and the TruSeq™ Stranded Total RNA Kit with Ribo-Zero™ Plus following manufacturer's protocols.

treatment_protocol: After 7 days of which 2.7 days were at steady state, four-times 9 ml of bioreactor sample was placed in 5 mL of prechilled RNAlater (overnight at 4°C). The samples were stored overnight at 4°C and then frozen at -20°C until RNA isolation.

value: prokaryotic

value: Marburg

value: WT

tag: developmental stage

value: exponential growth (continous bioreactors) day 7

tag: reactor id


title: Marburg, H2/CO2, biol rep 4


title: Placenta_LGA_No_Sample41 [XH2_173]

tag: Sex

tag: lga status

tag: gestational diabetes


title: H3K4me1_NS_24h

value: Bone marrow-derived macrophages

tag: antibody


title: HCT116 scONEseq 007

description:
RNA+DNA
HCT116 single cell 103


title: scRNA_MEF_Ola_IFNb_6h_Rep1_merged

city: Heidelberg

first: Markus

last: Muckenhuber

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing:
scRNA-seq: Raw reads were applied to CellRanger (v1.3.1), a full automatic pipeline especially for scRNA-seq data done by the 10x Chromium.
scRNA-seq counttable: The default output folders with the counttable for downstream analysis.
supplementary file format and content: scRNA-seq: The folder contains the deault output of Cellranger. A list of detected barcodes in the sample. A List of identified genes in the sample as ENSEMBL ID and gene symbole. And a matix which is the counttable.
Genome_build: mm10

source_name: Mouse embryonic fibroblasts

growth_protocol:
Embryonic stem cells: Cultured on 0.1 % gelatinized tissue flasks in ESC media. Cells were incubated at 37 °C and 5 % CO2. Media was PowerStem ESPro1 (PAN-Biotech; P04-77510K) with self-made LIF (1:1000).
Mouse embryonic fibroblasts: Cells were incubated at 37 °C and 5 % CO2. Media was DMEM (Gibco, 11880-28), 10% FCS (PAN-Biotech; P30-3602), 1x L-Glutamine (PAN-Biotech, P04-80050), 1x PenStrep (PAN-Biotech, P06-07050).
Neural progenitor cells: ESCs were differentiated into NPCs based on the Bible-protocol Bibel et al. 2007. 4-5*10^6 cultured ESCs were split onto a T75 UltraLow-BindingPlates (Corning, 3814) in 15 ml StemPAN media (PAN-biotech, P08-50500). After 4 days 5µM retinoic acid (Sigma-Aldrich, R2625) was added. On day 8, cells were platted on plates coated with 1% Matrigel (Corning, 356230) in neuronal base medium (Gibco, 211103049), G5 supplements (Gibco, 17503012), NSC supplements (Gibco, 17502048). Experiments were performed five days after neuronal plating.

extract_protocol:
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).

treatment_protocol: All cells were treated with 500U/ml of self-made interferon beta (16.6U/µl) for 1 hour or 6 hours

value: Mouse embryonic fibroblasts


title: HCT116 scONEseq 006

description:
RNA+DNA
HCT116 single cell 102

growth_protocol: HCT116 cells are cultured in DMEM; NPC43 cells are cultured in RPMI1640 with additional Rho-associated coiled-coil containing kinases inhibitor (Y-27632) at 4 μM; HUVEC are cultured in EGM BulletKit Medium (CC-3124) plus CC-4133 SingleQuots Kit (CC-4133);H9 cell line is purchased from WiCell. Cells are cultured in mTeSR™ Plus medium (Catalog #05825). Matrigel (Catalog #354230) coated 6-well plate (Catalog #140675) was used to culture stem cells.


title: Marburg, H2/CO2, biol rep 2


title: Placenta_LGA_No_Sample39 [HF2_385]

tag: maternal age

tag: pre-pregnancy body mass index

tag: primiparity

tag: gestational age at birth


title: scRNA_MEF_Ola_IFNb_1h_Rep1_merged

tag: cell type


title: Placenta_LGA_No_Sample40 [XH2_97]

tag: cesarean section

tag: slide


title: HCT116 scONEseq 005

description:
RNA+DNA
HCT116 single cell 101

tag: tissue

tag: method


title: scRNA_MEF_Ola_IFNb_0h_Rep1_merged

tag: strain


title: Placenta_LGA_No_Sample38 [HF2_709]


title: Placenta_LGA_No_Sample37 [XH2_74]


title: HCT116 scONEseq 003

description:
RNA+DNA
HCT116 single cell 099


title: scATAC_MEF_Ola_IFNb_6h_Rep1_merged

data_processing:
scATAC-seq: Raw reads were applied to CellRanger (v1.1.0), a full automatic pipeline especially for scATAC-seq data done by the 10x Chromium.
scATAC-seq: The default output counttable for downstream analysis.
supplementary file format and content: scATAC: Counttable with a the coordinates of mapped fragments, the barcode of the fragment and the counts.
Genome_build: mm10

extract_protocol:
scATAC-seq: The experiment was performed based on the standard manufacturer’s protocol Chromium Single Cell ATAC Reagent Kits (PN-1000110).
scATAC-seq: The experiment was performed based on the standard manufacturer’s protocol Chromium Single Cell ATAC Reagent Kits (PN-1000110).

tag: treatment


title: monkey_oocyte_IVM_rep3

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

data_processing:
Raw reads of the RNA-seq data were trimmed using trim_galore (version 0.6.7) with the parameters: --phred33 --length 36 -e 0.1 --stringency 4 --paired.
Then the clean reads were aligned to Macaca fascicularis genome (macFas5) using bowtie2 (version 2.4.5) with default parameters.
The resulted SAM files were converted to BAM files and indexed using samtools (version 1.15.1).
The raw counts of each sample were obtained using featureCounts (version 2.0.1) with default parameters.
The differentially expressed genes were identified using DESeq2.
The heatmap illustration showing DEGs between GV, IVM oocytes and IVO oocytes were performed using ComplexHeatmap in R.
The Pearson’s correlation between biological replications was calculated using the FPKM by the cor function in R.
Assembly: macFas5
Supplementary files format and content: a txt file containing the total raw counts of each sample

organism: Macaca fascicularis

source_name: Oocyte

extract_protocol:
The oocytes were lysed in 72℃ and then put back on ice. Then the samples were spined down and reverse transcribed to cDNA based on polyA tail.  Switch the template at 5’ end of the RNA and amplify the full-length cDNA by PCR. Quality control of the amplification products were performed using Agilent 2100 bioanalyzer instrument.
The library was constructed following the Tagmentation-based library construction protocol. The double stranded PCR products were purified using the Agencourt AMPure XP-Medium kit and quantified by Agilent 2100 bioanalyzer. Next, the DNA were heat denatured and circularized by the split oligo sequence. The qualified single strand circle DNA were formatted as the final library. Finally, the library was amplified to make DNA nanoballs (DNB) which were loaded into the patterned nanoarray and the reads of paired-end 100 bases were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS).

value: Oocyte

tag: cell line

value: MII

value: IVM-MII oocyte

tag: genotype

value: wild type

value: treated


title: HCT116 scONEseq 009

description:
RNA+DNA
HCT116 single cell 105


title: monkey_oocyte_IVM_rep2


title: scATAC_MEF_Ola_IFNb_1h_Rep1_merged


title: Placenta_LGA_No_Sample36 [XH2_2]

tag: Sex

value: Male


title: WT/Mock_5-5, rep1

value: mouse ESC

tag: ectopic expression


title: monkey_oocyte_IVM_rep1


title: HCT116 scONEseq 002

description:
RNA+DNA
HCT116 single cell 098


title: scATAC_MEF_Ola_IFNb_0h_Rep1_merged


title: monkey_oocyte_MII_rep2

value: IVO-MII oocyte

value: control


title: monocyte_IFN-treated_24h_rep3

first: Limin

last: Yang

state: jiangsu

address: pukou 11

institute: Nanjing university

data_processing:
The illumina high-throughput sequencing results initially existed as original image data files and were converted into original sequencing sequence (raw read) by BCL2FastQ2
The raw read were filtrated through removing adaptor, low-quality and N ratio greater than 3% sequence.
The filtrated read was mapped to mouse reference transcripts  using softwave Hisat2 (version2.2.1)
Gene expression value was quantitatively estimated through Fragments per Kilobase per Million Mapped Fragments (FPKM)
Gene differential expression between the for groups was analyzed by edgeR (version3.3.3).
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse bone marrow

growth_protocol: MACS-purified mouse BM monocytes were cultured in the presence of 20ng/ml M-CSF

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

treatment_protocol: BM monocytes were treated with IFNβ for 12h or 24h

value: monocyte

value: IFN-treated

tag: time


title: monkey_oocyte_MII_rep1


title: Marburg, H2/CO2, biol rep 1

value: prokaryotic

tag: developmental stage

tag: reactor id


title: monocyte_IFN-treated_24h_rep2


title: HCT116 scONEseq 004

description:
RNA+DNA
HCT116 single cell 100

source_name: HCT116 cell line

value: Colon

value: scONE-seq


title: monkey_oocyte_GV_rep2

value: GV

value: GV oocyte


title: Smart-HCT-95

description: HCT116 single cell 095

data_processing:
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.


title: monocyte_IFN-treated_24h_rep1


title: Placenta_LGA_No_Sample32 [HF2_636]

value: Female

tag: lga status

value: No

tag: gestational diabetes

tag: maternal age

tag: pre-pregnancy body mass index

value: Yes


title: Smart-HCT-96

description: HCT116 single cell 096


title: monkey_oocyte_GV_rep1

value: Oocyte

tag: cell type


title: monocyte_control_24h_rep3


title: Placenta_LGA_No_Sample33 [HF2_693]

tag: primiparity

tag: gestational age at birth

tag: cesarean section

tag: slide


title: Smart-HCT-94

description: HCT116 single cell 094

tag: tissue

tag: method


title: Placenta_LGA_No_Sample31 [HF2_455]


title: monocyte_control_24h_rep2

tag: treatment


title: Smart-HCT-93

description: HCT116 single cell 093


title: Smart-HCT-92

description: HCT116 single cell 092


title: JK6_rep3

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

institute: University of British Columbia

data_processing:
illumina hiseq was used for basecalling
Sequenced reads were trimmed for adapter content using BBDuk and parameters ktrim=r k=23 mink=11
Trimmed sequences were then aligned (and genes counted) to the  Ustilago_maydis genome Umaydis521_2.0  via STAR version 2.7.6a with parameters   --runMode alignReads --twopassMode Basic --quantMode GeneCounts --outSAMtype BAM Unsorted --outSAMunmapped Within
Counts were normalized during differential expression analysis via DESeq2’s median of ratios from Anders, S., & Huber, W. (2010).
Genome_build: Umaydis521_2.0
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 normalized expression (DESeq2) information for each gene and every sample

organism: Mycosarcoma maydis

source_name: Ustilago Maydis 521

growth_protocol: Ustilago Maydis 521 was grown in ustilago minimal media at 28 degrees in glass tubes shaking at 220rpm overnight prior to conducting treatment.

extract_protocol:
RNA was extracted immediately after treatment using the Qiagen Rneasy protocol for yeast (mechanical disruption)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ustilago Maydis 521 was grown in either 1% glucose, 1% glucose + 0.5% malate, or 1% glucose + 0.5% malate + aeration for up to 72 hours. Samples were taken at 24 hours and 72 hours for all conditions for total RNA

tag: strain

value: 521 mating type a1b1

value: 1% glucose + 0.5% malate + aeration at 72hours


title: Placenta_LGA_Yes_Sample30 [YF4_838]

tag: Sex


title: monocyte_control_24h_rep1

tag: time


title: JK6_rep1


title: HCT116 scONEseq 001

description:
RNA+DNA
HCT116 single cell 097


title: Placenta_LGA_No_Sample35 [XH2_7]

value: Male


title: monocyte_IFN-treated_12h_rep3


title: Placenta_LGA_Yes_Sample29 [YF4_850]


title: Placenta_LGA_Yes_Sample28 [YF4_679]


title: Smart-HCT-91

description: HCT116 single cell 091


title: Placenta_LGA_No_Sample34 [HF2_504]


title: Smart-HCT-90

description: HCT116 single cell 090


title: JK5_rep3

value: 1% glucose + 0.5% malate at 72hours


title: JK5_rep2


title: Smart-HCT-89

description: HCT116 single cell 089


title: Smart-HCT-88

description: HCT116 single cell 088


title: Placenta_LGA_Yes_Sample27 [YF4_282]


title: Placenta_LGA_Yes_Sample26 [XH2_4562]


title: monocyte_control_12h_rep3


title: JK4_rep3

value: 1% glucose at 72hours


title: monocyte_IFN-treated_12h_rep2


title: monocyte_IFN-treated_12h_rep1


title: Placenta_LGA_Yes_Sample25 [XH2_2960]


title: monocyte_control_12h_rep2

value: control


title: JK6_rep2


title: JK4_rep1


title: Placenta_LGA_Yes_Sample23 [XH2_2067]


title: JK4_rep2


title: monocyte_control_12h_rep1

value: monocyte


title: Placenta_LGA_Yes_Sample22 [XH2_2046]


title: Smart-HCT-85

description: HCT116 single cell 085


title: JK3_rep3

value: 1% glucose + 0.5% malate + aeration at 24hours


title: Smart-HCT-84

description: HCT116 single cell 084


title: BMDMs, IL-6+IL-13, 24h, rep3

first: Yuyan

last: Zhang

data_processing:
Illumina Casava software used for basecalling
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.05 and |log2_Foldchange|≥1 are identified as differentially expressed genes
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BMDMs, IL-6+IL-13, 24h

growth_protocol: Bone marrow was harvested and cultured with DMEM media containing 10% FBS and 20 ng/ml recombinant M-CSF. BM-derived cells were cultured for 7 days to generate mature macrophages

treatment_protocol: BMDMs were treated with the individual or combianed cytokine for 24h

value: bone marrow

value: Bone marrow derived macrophages (BMDMs)


title: BMDMs, IL-6+IL-13, 24h, rep2


title: JK3_rep2


title: Placenta_LGA_Yes_Sample21 [XH2_1953]


title: Smart-HCT-83

description: HCT116 single cell 083

value: Colon


title: BMDMs, IL-6+IL-13, 24h, rep1


title: JK5_rep1


title: Placenta_LGA_Yes_Sample20 [XH2_508]


title: Smart-HCT-82

description: HCT116 single cell 082


title: Placenta_LGA_Yes_Sample19 [XH2_412]


title: Smart-HCT-87

description: HCT116 single cell 087


title: JK2_rep3

value: 1% glucose + 0.5% malate at 24hours


title: Placenta_LGA_Yes_Sample24 [XH2_2223]


title: Smart-HCT-86

description: HCT116 single cell 086


title: Smart-HCT-80

description: HCT116 single cell 080


title: Placenta_LGA_Yes_Sample18 [XH2_99]


title: JK2_rep2


title: Placenta_LGA_Yes_Sample17 [XH2_4602]


title: Placenta_LGA_Yes_Sample16 [HF2_668]


title: JK1_rep3

value: 1% glucose at 24hours


title: BMDMs, IL-13, 24h, rep1

source_name: BMDMs, IL-13, 24h


title: JK2_rep1


title: Smart-HCT-78

description: HCT116 single cell 078


title: Placenta_LGA_Yes_Sample15 [HF2_181]


title: BMDMs, IL-4+IL-6, 24h, rep2

source_name: BMDMs, IL-4+IL-6, 24h


title: JK1_rep2


title: BMDMs, IL-4+IL-6, 24h, rep1


title: Smart-HCT-77

description: HCT116 single cell 077


title: JK1_rep1


title: JK3_rep1


title: Placenta_LGA_Yes_Sample14 [HF2_39]

source_name: Placenta tissue from the fetal side


title: BMDMs, IL-13, 24h, rep3


title: Placenta_LGA_Yes_Sample13 [GF4_711]


title: IC463254_low_nit

city: Hyderabad

first: C

middle: N

last: Neeraja

state: Telangana

address: Principal Scientist, ICAR-IIRR, Rajendranagar, Hyderabad 500030

department: Crop improvement

institute: ICAR-Indian Institute of Rice Research

description: small RNA sequencing

data_processing:
reads were trimmed using fastp, the bases were trimmed with a quality threshold of Q20. Adapters were identified using dnapi at default parameters
reads were aligned to ncRNA from Oryza sativa japonica with bowtie 1 using RNACentral , barring miRNA mature and precursor sequences
unaligned sequences from above were aligned to the genome, and mature mirna were identifed using the gff from RNACentral
mirdeep was used to predict novel miRNA, which were aggregated from all the samples using bedtools
subread feature counts was used to predict the differential features for novel and known miRNA. targets were predicted for mirnas using psRNATarget2
Assembly: IRGSP-1
Supplementary files format and content: Tab delimited files specifying the mature mirna counts and novel mirna counts. Novel mirna file has the first column specifying the coordinates in chr:start..end

organism: Oryza sativa Indica Group

source_name: ICAR – IIRR

extract_protocol:
Trizol extraction using standard protocol
Used TruSeq smallRNA library kits
Library was sequenced on the Illumina Hiseq 1000

tag: genotype

value: Panicle


title: BMDMs, IL-13, 24h, rep2


title: Smart-HCT-76

description: HCT116 single cell 076


title: Smart-HCT-81

description: HCT116 single cell 081


title: BMDMs, IL-4, 24h, rep2

source_name: BMDMs, IL-4, 24h


title: Placenta_LGA_Yes_Sample12 [GF4_539]

value: Female

value: No


title: BMDMs, IL-4, 24h, rep3


title: Smart-HCT-75

description: HCT116 single cell 075


title: IC463254_rec_nit

description: small RNA sequencing


title: Smart-HCT-74

description: HCT116 single cell 074


title: BMDMs, IL-4, 24h, rep1


title: Smart-HCT-79

description: HCT116 single cell 079


title: BMDMs, IL-4+IL-6, 24h, rep3


title: Placenta_LGA_Yes_Sample11 [GF4_74]

value: Yes


title: Smart-HCT-73

description: HCT116 single cell 073


title: ThururBhog_low_nit

description: small RNA sequencing

value: ThururBhog


title: BMDMs, control, 24h, rep3

source_name: BMDMs, control, 24h


title: Smart-HCT-72

description: HCT116 single cell 072


title: KolaJoha_low_nit

description: small RNA sequencing

value: KolaJoha


title: Placenta_LGA_Yes_Sample9 [CM5_710]


title: Smart-HCT-71

description: HCT116 single cell 071


title: ThururBhog_rec_nit

description: small RNA sequencing


title: BMDMs, control, 24h, rep2


title: osrdr2-3_stamen_mRNA_replicate2

description: fem1-3_stamen_rep2 mRNA-seq

source_name: stamen

tag: cultivar

value: Japponica


title: Placenta_LGA_Yes_Sample8 [CM5_696]

value: Male

tag: lga status


title: KolaJoha_rec_nit

description: small RNA sequencing


title: BMDMs, control, 24h, rep1


title: Placenta_LGA_Yes_Sample7 [CM5_690]

tag: gestational diabetes


title: Basmati370_low_nit

description: small RNA sequencing


title: Basmati370_rec_nit

description: small RNA sequencing


title: Smart-HCT-69

description: HCT116 single cell 069


title: Placenta_LGA_Yes_Sample5 [CM5_294]

tag: maternal age


title: Smart-HCT-70

description: HCT116 single cell 070


title: Placenta_LGA_Yes_Sample6 [CM5_302]

tag: pre-pregnancy body mass index


title: smg7-6 Rep3

city: Brno

first: Neha

last: Shukla

address: Kamenice 753

institute: CEITEC

description: rRNA removed

data_processing:
bcl2fastq v2.20.0.422 was used for base calling
Low-quality reads and adapters were trimmed using cutadapt v2.5.
Data was aligned on reference AtRTD2 transcript dataset (Zhang et al., 2017) and simultaneously quantified with quasi-mapping-based algorithm using Salmon software v1.5 (Patro et al., 2017).
Gene expression data normalization and differential expression analysis was done using 3D RNA-Seq tool (Guo et al., 2020; Calixto et al., 2018).
Assembly: Arabidopsis transcriptome reference dataset - AtRTD2 (Zhang et al., 2017)
Supplementary files format and content: comma-delimiled text file including TPM values for each gene in all samples and three replicates each

source_name: Leaves

extract_protocol:
leaves from three weeks-old plants were pooled from five independent plants (technical replicate) grown at same time. Total RNA was extracted using RNA Blue (Top-Bio), following the manufacturer’s protocol.
Strand-specific libraries were prepared from ribosomal RNA-depleted total RNA using ScriptSeq complete kit for plant leaf (Epicentre; BPL1224) following manufacturer's protocol. The experiment was conducted in three biological replicates.

value: Leaves

tag: age

value: 3-week old plants


title: smg7-6 Rep2

description: rRNA removed


title: A5_ko_3 - Myα5KO 7d #3

city: Bronx

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

data_processing:
Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis. Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (mm10; GRCm38.p6) using TopHat2 algorithm alignment program v.2.0.9.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm.
HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene.
Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length.
Genome_build: mm10
Supplementary_files_format_and_content: File including raw readcounts for every gene and every sample
Supplementary_files_format_and_content: File including FPKM values for every gene and every sample

source_name: Cardiac Macrophages

extract_protocol:
Macrophage and neutrophil cell suspensions were obtained from 12-week-old infarcted ITGA5fl/fl and Myα5 ITG KO hearts after 7 days of coronary occlusion. Macrophages were magnetically sorted with a MACS separator (Miltenyi Biotec), obtaining first a Ly6G- cell suspension (No Neutrophils) and second selecting from this suspension de CD11b+ cells. RNA was isolated from Ly6G-CD11b+ cells (Macrophages) using TRIzol reagent (Qiagen, #79306) according to manufacterer's instructions.
RNA samples were sent to Novogene (Sacramento, California) to construct a total of eight cDNA libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). Briefly, libraries were prepared using at least 1ug high quality total RNA input per sample. mRNA purification and enrichmes was preformed using oligo(dt)-attached magnetic beads. After fragmentation, double stranded cDNA synthesis was preformed. Sequencing adaptors were ligated and cDNA fragmets were selected (150-200bp), amplified and purified. Library concentration and quality were assessed using a Bioanalyzer 2100 system (Agilent). These librarys were sequenced on Illumina NovaSeq 6000 devices, generating 150 bp paired-end reads.

value: ITGA5 fl/fl + LyzM-Cre (My{alpha}5KO)

tag: cell type

value: Cardiac Macrophages

tag: cell subset

value: Ly6G- CD11b+


title: Placenta_LGA_Yes_Sample4 [CM5_181]

tag: primiparity

tag: gestational age at birth

tag: cesarean section


title: A5_fl_3 - ITGA5 fl/fl 7d #3

value: ITGA5 fl/fl


title: A5_fl_2 - ITGA5 fl/fl 7d #2


title: A5_ko_1 - Myα5KO 7d #1


title: Smart-HCT-66

description: HCT116 single cell 066

tag: tissue

value: Colon

tag: method


title: A5_ko_2 - Myα5KO 7d #2

tag: strain


title: Placenta_LGA_Yes_Sample10 [GF4_15]

tag: Sex

tag: slide


title: Smart-HCT-68

description: HCT116 single cell 068


title: smg7-6 Rep1

description: rRNA removed

tag: genotype


title: Placenta_LGA_Yes_Sample3 [CM5_167]


title: Smart-HCT-65

description: HCT116 single cell 065


title: A5_fl_1 - ITGA5 fl/fl 7d #1


title: Smart-HCT-64

description: HCT116 single cell 064


title: Placenta_LGA_Yes_Sample2 [CM5_161]


title: Col WT Rep3

description: rRNA removed

value: Wild type


title: Placenta_LGA_Yes_Sample1 [CM5_200]


title: Smart-HCT-63

description: HCT116 single cell 063


title: Col WT Rep2

description: rRNA removed


title: FN_a5_2 - FN coated dishes + BMM + Anti-ITGA5 #2

source_name: Bone Marrow Macrophages (BMMs)

growth_protocol: Tibial Bone Marrow derived Macrophages (BMMs) were obtained from 2- to 3-month-old Wild-type C57BL/6J mice as previously described. Briefly, bone marrow cells were incubated for 24 h in DMEM/F-12 medium supplemented with 15% fetal calf serum (GIBCO) and 12 ng/ml CSF-1 (R&D systems). Non-adherent primitive mononuclear phagocytes were reseeded in media containing 15% fetal calf serum and CSF-1 (120 ng/ml) for 48 hours, in order to allow their differentiation to adherent mononuclear phagocytes. The resulting adherent macrophages were passaged once into 10 µm/ml fibronectin (Sigma, F1141) pre-coated plates (overnight) or normal cell culture plates. Cells used for experiments were cultured until confluent, and then treated.

extract_protocol:
RNA was isolated using TRIzol reagent (Qiagen, #79306) according to manufacterer's instructions.
RNA samples were sent to Novogene (Sacramento, California) to construct a total of eight cDNA libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). Briefly, libraries were prepared using at least 1ug high quality total RNA input per sample. mRNA purification and enrichmes was preformed using oligo(dt)-attached magnetic beads. After fragmentation, double stranded cDNA synthesis was preformed. Sequencing adaptors were ligated and cDNA fragmets were selected (150-200bp), amplified and purified. Library concentration and quality were assessed using a Bioanalyzer 2100 system (Agilent). These librarys were sequenced on Illumina NovaSeq 6000 devices, generating 150 bp paired-end reads.

treatment_protocol: A group of samples (n=3) from each group, coated vs no coated, was incubated with IgG antibody (10 µg/ml, Biolegend, 400902) or anti-ITGA5 neutralizing antibody (10 µg/ml, Biolegend, 103910) for 24 hours. After this incubation time samples were collected for RNA isolation.

value: Bone Marrow Macrophages (BMMs)

tag: dish coating

value: Fibronectin 10 µg/ml

tag: treatment

value: anti-ITGA5 neutralizing antibody


title: FN_a5_3 - FN coated dishes + BMM + Anti-ITGA5 #3


title: Col WT Rep1

description: rRNA removed


title: FN_a5_1 - FN coated dishes + BMM + Anti-ITGA5 #1


title: Smart-HCT-67

description: HCT116 single cell 067


title: Smart-HCT-61

description: HCT116 single cell 061


title: FN_3 - FN coated dishes + BMM + IgG_H #3

value: IgG antibody


title: Smart-HCT-60

description: HCT116 single cell 060


title: Smart-HCT-59

description: HCT116 single cell 059


title: FN_1 - FN coated dishes + BMM + IgG_H #1


title: FN_2 - FN coated dishes + BMM + IgG_H #2


title: Smart-HCT-58

description: HCT116 single cell 058


title: itga5_3 - BMM + Anti-ITGA5 #3


title: Smart-HCT-57

description: HCT116 single cell 057


title: itga5_2 - BMM + Anti-ITGA5 #2


title: Smart-HCT-56

description: HCT116 single cell 056


title: itga5_1 - BMM + Anti-ITGA5 #1


title: Ctrl_3 - BMM + IgG_H #3


title: Smart-HCT-62

description: HCT116 single cell 062


title: Smart-HCT-55

description: HCT116 single cell 055


title: Smart-HCT-54

description: HCT116 single cell 054


title: Ctrl_2 - BMM + IgG_H #2


title: Smart-HCT-53

description: HCT116 single cell 053


title: Ctrl_1 - BMM + IgG_H #1


title: NCI-H2023-Parental_CTRL_REP2

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

description: NCI-H2023-Parental cells subjected to treatment cycles (n=11) of vehicle solution (NaCl 0.9%) and then transfected with a negative control mimic

hyb_protocol: Samples were then hybridized ON, washed, stained, and scanned using the GeneChip Hybridization Oven 640, Fluidic Station 450.

scan_protocol: Scanner 3000 7G (Thermo Fisher Scientific) were used to generate the raw data files (.CEL files) according to the manufacturer's instruction.

data_processing: Quality control and normalization of CEL files were performed using Transcriptome Analysis Console (TAC) software v4.0 (Thermo Fisher Scientific) by performing “Gene level SST-RMA” summarization method with human genome version hg38. The analyses were performed in two independent biological experiments and gene expression data were Log2 transformed before analyses.

label: biotin

source_name: cell line, overexpressing a negative control mimic

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (GeneChip® Human Clarion S Array; ThermoFisher Scientific).

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 5% FBS and 1% penicillin/streptomycin (Gibco). Cells were maintained at 37°C and 5% CO2 in a humidified incubator. Cells were routinely verified as free of mycoplasma contamination.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Hilden, Germany), treated with DNase-RNase free (Qiagen, Hilden, Germany) and quantified by Nanodrop (Thermo Fisher Scientific).

treatment_protocol: Negative control mimic (Qiagen, cat. 1027281) and miR-455-5p mimic (Qiagen, cat. 219600) were transiently transfected at a concentration of 5nM using Lipofectamine RNAiMAX (Invitrogen). To obtain NCI-H2023-Parental and NCI-H2023-CDDP-R cells,  NCI-H2023 cells were subjected prior transfection to treatment cycles (n=11) consisting of 3-4 days of either NaCl 0.9% vehicle solution or cisplatin (sigma) treatment and 1-2 weeks of culture in RPMI 5% FBS 1% penicillin/streptomycin .

tag: cell line id

value: Lung adenocarcinoma cell line from lymph node of stage IIIA NSCLC


title: NCI-H2023-CDDP-R_CTRL_REP1

description: NCI-H2023-CDDP-R cells subjected to treatment cycles (n=11) of Cisplatin and then transfected with a negative control mimic


title: NCI-H2023-CDDP-R_CTRL_REP2


title: NCI-H2023-Parental_CTRL_REP1