title: AS2-Vec cells, deNG-IL6, 3h, replicate 3

city: Tainan

first: Chun-Hua

last: Hung

address: No. 138, Sheng-Li Rd., North Dist.

department: Department of Oncology

country: Taiwan

institute: National Cheng Kung University

description: Gene expression after 3h in deNG-IL6-treated AS2-Vec cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented  to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by nitrogen gun blowing.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) at 535 nm for Cy3 using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted (Saptial Detrend Surface Value) and spatially detrended Processed Signal intensities (Density-Mean background).  Number of rows:384; number of columns:164. Normalization by quantile. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: AS2-Vec cells, deNG-IL6, 3h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the examined cells and tissues with TRIzolTM Reagent (Invitrogen, 15596026) following the manufacturer’s protocol. The integrity of all the RNA samples was evaluated using a Bioanalyzer 2100 (Agilent Technologies) according to the manufacturer’s protocol.

treatment_protocol: AS2-Vec cells were treated with NG-IL6-containing or deNG-IL6-containing conditioned medium for 3 h.

value: lung adenocarcinoma cell

value: deNG-IL6, 3h


title: AS2-Vec cells, control medium, 3h, replicate 1

status: Public on Jul 16 2024

type: RNA

description: Gene expression after 3h in control medium-treated AS2-Vec cells

molecule: total RNA

organism: Homo sapiens

source_name: AS2-Vec cells, control medium, 3h

tag: cell line

tag: cell type

tag: treatment

value: control medium, 3h


title: AS2-Vec cells, control medium, 3h, replicate 3


title: AS2-Vec cells, NG-IL6, 3h, replicate 3

description: Gene expression after 3h in NG-IL6-treated AS2-Vec cells

source_name: AS2-Vec cells, NG-IL6, 3h

value: NG-IL6, 3h


title: AS2-Vec cells, deNG-IL6, 3h, replicate 1


title: AS2-Vec cells, NG-IL6, 3h, replicate 2


title: AS2-Vec cells, control medium, 3h, replicate 2


title: AS2-Vec cells, deNG-IL6, 3h, replicate 2


title: Tumor_resistant_1

city: Guangzhou

first: Rong

last: Luo

address: Yanjiangxi Road No.107

country: China

institute: Sun Yat-Sen University

description: The breast cancer biopsy tissue was collected before neoadjuvant chemotherapy.

hyb_protocol: he labeled cRNA samples were hybridized with Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the manufacturer's instructions.

scan_protocol: After washing the microarray with wash buffer, the slides were scanned immediately with Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (v11.0.1.1) extracted the data from the scanned images. The data were normalized and processed with the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: primary breast cancer

label_protocol: 1 μg of total RNA was amplified and labeled according to the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) protocols.

extract_protocol: Total RNA was extracted from breast cancer tissues stored in RNAlater with the TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

tag: disease state

value: primary breast cancer

tag: tissue

value: tumor

tag: chemotherapy efficacy

value: Resistant


title: AS2-Vec cells, NG-IL6, 3h, replicate 1


title: Tumor_resistant_3


title: Tumor_pre_NAC_1

tag: pre- or post-nac

value: pre-NAC


title: Tumor_sensitive_2

value: Sensitive


title: Tumor_post_NAC_2

description: The breast cancer tissue was collected after neoadjuvant chemotherapy during surgical resection.

value: post-NAC


title: Tumor_post_NAC_1


title: Tumor_pre_NAC_3


title: S9_biotinylated_cel-miR-67_replicate_2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description: S9 + Bi cel-miR-67 IP-M8

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's Sentrix Mouse Red-8 v3 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.53 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.The resulting dataset was analyzed with DIANE 6.0, a spreadsheet-based microarray analysis program. Using DIANE, the results were normalized by Z-Score transformation. Z-normalized data were then analyzed with principal component analysis (PCA). To determine the gene expression changes within each specific RNA comparison, Z-Scores for paired treatment groups were compared using the Z-Ratio statistic. Expression changes for individual genes were considered significant if they met four criteria: Z-Ratio above 1.5 or below -1.5; false detection rate (FDR) of less than 0.30; a P-value statistic for Z-Score replicability below 0.05; and mean background-corrected signal intensity greater than zero. Differentially expressed genes were identified as significant (p < 0.05) based on Z-scores.  Gene set analysis was performed using GO gene sets with the PAGE algorithm. All Venn diagrams of gene expression were generated using the online tool Venny.

source_name: CFTR-repaired IB3-1/S9 cells

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: CFTR-repaired IB3-1/S9 cells were maintained in LHC-8 serum-free medium (Invitrogen, 12678-017) in humidified 5% CO2. IB3-1/S9 cells (3.0x 10^6) were plated on one 100-mm dish and incubated in LHC-8 media for 24 hours, after which cells were transfected with 10 nM of 3'-biotinylated miR-155 (Dharmacon) or biotinylated cel-miR-67 control using siPORT-NeoFX (Invitrogen, AM4511). After a 24 hour incubation, cells were washed twice with PBS and lysed with 700 µl lysis buffer (20 mM Tris pH 7.5, 5 mM MgCl2, 100mM KCl, 0.3% NP40), including 50U RNaseOUT (Invitrogen, 10777-019) and proteinase inhibitor (Sigma-Aldrich, S8820).  Cells were collected by scraping the dish, and the collected cells were incubated on ice for 5 minutes before centrifugation at 10000×g for 5 min at 4°C, and collection of the supernatant for streptavidin purification. Streptavidin-coated magnetic beads (Invitrogen, 11205D) were incubated for 2 hours at 4°C with blocking buffer (20 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 0.3% NP40, 1 mg/ml yeast tRNA, 1 mg/ml BSA).  The cell lysate was then added to the magnetic beads, and incubated for 4 hours at 4°C, after which the beads were rinsed five times with lysis buffer, and RNA isolated from the beads.  For the second set of experiments, IB3-1/S9 cells (2.5x105) were plated on a 6-well plate in LHC-8 media for 24 hours, after which 10 nM miR-155 mimic or control mimic was transfected into cells with siPORT-NeoFX. RNA was isolated from these cells 48 hours after transfection.

extract_protocol: RNA was prepared using the miRVana kit (Thermo Fisher Scientific, Waltham, MA), according to the manufacturer's instructions.

treatment_protocol: A 3'-end-biotinylated miR-155 (10 nM, M5-M6, M9) or biotinylated cel-miR-67 control (M7-M8) was incubated with S9 lung epithelial cells for 24 hours, and cell lysates were enriched for mRNA:miR-155 and mRNA:cel-miR67 complexes, respectively, using streptavidin bead-based affinity purification.  S9 cells were treated with with miR-155-mimic (10 nM, M1-M2) or control mimic (M3-M4) for 48 hours

value: mRNA-cel-miR-67 pulldown

value: Lung

value: Epithelial cell


title: Tumor_pre_NAC_2


title: Tumor_sensitive_3


title: Tumor_post_NAC_3


title: Tumor_resistant_2


title: S9_biotinylated_miR-155_replicate_3

description: S9 + Bi MiR-155 IP-M9

value: mRNA-miR-155 pulldown


title: S9_biotinylated_cel-miR-67_replicate_1

description: S9 + Bi cel-miR-67 IP-M7


title: C636_Rep2_Modified

type: SRA

city: New Haven

first: Nicholas

last: Huston

state: Connecticut

address: 260 Whitney Avenue, YSB 308

institute: Yale University

library_source: transcriptomic

data_processing:
ShapeMapper
Library strategy: SHAPE-MaP

organism: Aedes albopictus

source_name: C6/36 Cells

growth_protocol: Vero and C6/36 cells were cultured in 10cm tissue culture plates

extract_protocol:
Trizol
cDNA was prepared from modified RNA using gene-specific RT primers, followed by generation of amplicons with gene-specific primers. Nextera-XT kit was used for library construction

treatment_protocol: At 4dpi, each sample was collected and treated with either 200mM NAI (final) or equivalent volume DMSO

tag: chemical modification

value: 2-methylnicotinic acid imidazolide


title: KO-M11

city: Brooklyn

first: Xian-Cheng

last: Jiang

state: New York

address: 450 Clarkson Ave

department: Cell Biology

institute: SUNY Downstate Medical Center

data_processing:
Raw sequence data (.bcl files) generated by the sequencer were converted into .fastq files and demultiplexed using Illumina’s bcl2fastq v.2.17 software.
The raw data of sequence reads that contained at least 29,800,000 total reads per sample were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were further mapped to the Mus musculus GRCm38 reference genome (Ensembl v.89) using the STAR aligner v.2.5.2b(59). Each sample had at least 28,300,000 unique mapped reads. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Only unique reads that fell within exon regions were counted. Gene hit counts were extracted and compared between each group using DESeq2 v.1.30.1(60). The Wald test was used to generate p values and log2 fold changes. P values were adjusted using the Benjamini–Hochberg method.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for all samples

organism: Musculus

source_name: sWAT

extract_protocol:
Total RNA was extracted from sWAT using an RNeasy Plus Micro Kit (Qiagen). RNA samples were quantified using a Qubit 4 fluorometer (Thermo Fisher Scientific), and RNA integrity was determined using a 4200 TapeStation System (Agilent Technologies).
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs) in accordance with the manufacturer’s instructions.

value: sWAT

value: adipose cells

tag: genotype


title: C636_Rep1_Modified


title: C636_Rep2_Unmodified

value: dimethyl sulfoxide


title: WT-M22

value: WT


title: WT-M24


title: WT-M25


title: LPCAT3-AKO

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw scRNA-seq data were processed using Cell Ranger v.6.1.2 (10x Genomics). Filtered feature-barcode matrix files were obtained from the Cell Ranger pipeline, which contained only barcodes associated with cells.
Further analyses were done using the R package Seurat v.4.10. Cells with number of genes < 300 and total number of molecules detected within a cell < 3 were removed from the data, and gene counts were normalized and scaled using sctransform. We integrated our data from two conditions into a single analysis using an algorithm implemented in Seurat(63).
We then applied a graph-based clustering algorithm to group cells into different clusters using the FindClusters function. We employed cluster tree analysis (clustree function) to assess relatedness between clusters and to annotate the clusters using known markers and data from relevant single-cell studies.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

extract_protocol: sWAT was collected from 5-week-old mice and stored in sterile PBS on ice. The tissues were minced in freshly made digestion medium containing 0.3% type I collagenase (Worthington Biochemical Corporation, LS004196) and 0.5% BSA (Sigma, A7906) in PBS and then shaken in a 37°C incubator shaker at 150 rpm for 40 min. After digestion, the suspensions were filtered through 100 μm filters and centrifuged at 500 × g for 5 min to remove mature primary adipocytes from the top. The SVF pellets were resuspended in ACK lysing buffer (Gibco, A1049201) for 5 min at room temperature and washed twice.

value: SVF

value: LPCAT3 knockout


title: KO-M15


title: C636_Rep1_Unmodified


title: KO-M5


title: WT-M21


title: KO-M3


title: Control

description: 10x Genomics


title: Tumor_sensitive_1

value: primary breast cancer


title: Term nasal cultured subject 24

city: Perth

first: Patricia

last: Agudelo-Romero

state: WA

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Ave, Nedlands

department: Chronic and Severe Diseases

country: Australia

institute: Telethon Kids Institute

data_processing:
Raw fastq files of the same sample were concatenated containing on average 28.1 million (M) reads. Next, these fastq files passed the quality-control steps (adapter removing, filtering and trimming) using FastQC .
High-quality reads were aligned to human reference genome (ENCODE; male hg19) using Spliced Transcripts Alignment to a Reference (STAR)
Human genome mapping percentage was evaluated with Samtools ranging between 95.22 and 99.87 %.
Gene-level quantification of raw counts was then performed using RNA-Seq by Expectation Maximization (RSEM)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Nasal epithelium

growth_protocol: Nasal airway epithelial cells were collected via brushing of the nasal turbinate and placed immediately into the transport medium and processed within 30 minutes after collection. The process was repeated for each nostril. Briefly, cells were vortexed and passed consecutively through a 27 g and 25 g needle to form a single cell suspension. A cell count was performed using Trypan Blue staining and, if cell number permitted, 1x10^6 cells fractioned and resuspended in 350 µL RLT lysis buffer containing 1% (v/v) ß-mercaptoethanol (Qiagen Hilden, Germany) for ex vivo RNA collection. Monolayer cell cultures were established by seeding 125,000 primary cells in a 1:1 ratio with irradiated NIH fibroblasts in fibronectin pre-coated tissue culture flasks and maintained in a modified F-medium. Once confluent, cells were trypsinised and 1x10^6 cells were re-suspended in 350 µL RLT lysis buffer containing 1% (v/v) ß-mercaptoethanol for in vitro RNA collection.

extract_protocol:
RNA was extracted from stored samples using the Ambion Purelink RNA mini kit (Thermo Scientific, Waltham, Mass) as per the manufacturer’s instructions. The integrity of the RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, California, United States).
High-quality RNAs were used to build TruSeq Illumina Stranded mRNA libraries (Illumina, California, United States)

value: Nasal epithelium

tag: Sex

value: Female

tag: age

tag: category

value: Cultured/ In vitro

tag: population

value: Term


title: Term nasal cultured subject 26


title: Term nasal cultured subject 25

value: Male


title: Term nasal cultured subject 23


title: S9_control-mimic_replicate_2

description: S9 + control mimic-M4

value: Control, miR-155 OE


title: S9_biotinylated_miR-155_replicate_1

description: S9 + Bi MiR-155 IP-M5

value: Lung


title: Smarcb1fl/fl_cd3_1

type: genomic

city: Ulm

first: Anja

last: Fischer

address: Albert-Einstein-Allee

department: Institute for Human Genetics

country: Germany

institute: University Medical Center Ulm

hyb_protocol: DNA methylation was interrogated by the Infinium MethylationEPIC BeadChips (Illumina) following the manufacturer's guidelines. Mouse samples were analyzed using a custom service for Infinium Mouse Methylation BeadChip

scan_protocol: Human samples were assessed using the Infinium MethylationEPIC BeadChip (Illumina) on a NextSeq550

data_processing: Raw IDAT files were imported into the R programming environment (v4.1.3) using the minfi package. Data was normalized to controls using the preprocess Illumina function without background correction. The methylation level at each CpG was calculated as beta value. CpGs on the gonosomes were excluded in downstream analyses. For the mouse samples, raw idat files were normalized with GenomeStudio (v2011.1; methylation module 1.9.0; Illumina Inc., San Diego, CA, USA) applying default settings and internal normalization controls.

label: Cy3, Cy5

molecule: genomic DNA

organism: Mus musculus

source_name: INI1 1346 TCells

label_protocol: 500 ng of genomic DNA was bisulfite-converted using the EZ DNA methylation kit (ZymoResearch).

growth_protocol: DNA was directly isolated from human and murine tissue.

extract_protocol: Mouse spleens were dissected and treated with StemPro Accutase (Gibco, #A1110501), Cd3+ T-cells isolated by FACS and genomic DNA extracted using Quick-DNA Microprep Kit (Zymo Research, #D3020). For human samples, DNA was isolated from FFPE tissue using the GeneRead DNA FFPE Kit (Qiagen, Hilden, Germany).

tag: smarcb1 aberration

value: Smarcb1 fl/fl


title: S9_miR-155-mimic_replicate_2

description: S9 + MiR-155 mimic-M2

value: miR-155 overexpression

value: Epithelial cell


title: Term nasal cultured subject 22


title: S9_control-mimic_replicate_1

description: S9 + control mimic-M3


title: S9_biotinylated_miR-155_replicate_2

description: S9 + Bi MiR-155 IP-M6

value: mRNA-miR-155 pulldown


title: Smarcb1fl/fl_spleen_2

source_name: INI1 1347 Milz


title: S9_miR-155-mimic_replicate_1

description: S9 + MiR-155 mimic-M1


title: Smarcb1fl/fl_spleen_3

source_name: INI1 1348 Milz


title: Term nasal cultured subject 21


title: Cd4-cre_Smarcb1fl/fl_lymphoma_4

description: PTCL-NOS

source_name: PTCL 23

value: CD4 :Smarcb1 fl/fl


title: Term nasal cultured subject 20


title: Term nasal cultured subject 19


title: Preterm nasal cultured subject 18

tag: gestation

value: Preterm


title: Smarcb1fl/fl_spleen_5

source_name: INI1 1362 Milz


title: Smarcb1fl/fl_spleen_1

source_name: INI1 1346 Milz


title: Cd4-cre_Smarcb1fl/fl_lymphoma_5

description: PTCL-NOS

source_name: PTCL 24


title: Preterm nasal cultured subject 16


title: Preterm nasal cultured subject 7


title: Smarcb1fl/fl_cd3_4

source_name: INI1 1349 TCells


title: Preterm nasal cultured subject 14


title: Preterm nasal cultured subject 13


title: Smarcb1fl/fl_spleen_4

source_name: INI1 1349 Milz


title: Preterm nasal cultured subject 12


title: Preterm nasal cultured subject 8


title: Cd4-cre_Smarcb1fl/fl_lymphoma_3

description: PTCL-NOS

source_name: PTCL 20


title: Preterm nasal cultured subject 15


title: Preterm nasal cultured subject 2


title: Preterm nasal cultured subject 17


title: Cd4-cre_Smarcb1fl/fl_lymphoma_2

description: PTCL-NOS

source_name: PTCL 10


title: Cd4-cre_Smarcb1fl/fl_lymphoma_1

description: PTCL-NOS

source_name: PTCL 9


title: Smarcb1fl/fl_cd3_5

source_name: INI1 1362 TCells


title: Smarcb1fl/fl_cd3_3

source_name: INI1 1348 TCells


title: Smarcb1fl/fl_cd3_2

source_name: INI1 1347 TCells


title: Preterm nasal cultured subject 11


title: Preterm nasal exvivo subject 6

value: Ex vivo


title: Preterm nasal exvivo subject 9


title: Preterm nasal exvivo subject 10


title: Preterm nasal exvivo subject 5


title: Preterm nasal exvivo subject 8


title: Preterm nasal exvivo subject 4


title: Preterm nasal exvivo subject 1


title: Preterm nasal exvivo subject 3


title: G_1

city: Wuhan

first: yue

last: chen

state: Hubei Province

address: no.1095 Jiefang Avenue

department: Tongji Hospital

institute: Huazhong University of Science and Technology

data_processing:
Quality control
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: gene_fpkm.xls file inclued fpkm data for each sample

molecule: polyA RNA

source_name: aortic smooth muscle cells

extract_protocol:
All samples were processed using an RNA-seq pipeline by Novogene Co., Ltd. (Beijing, China), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA samplepreparations.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering and sequencing (Novogene Experimental Department)
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: aortic smooth muscle cells

value: Cystine deprivation group


title: E_B_3

value: Imidazole ketone erastin + BRD4772 group


title: G_B_1

value: Cystine deprivation + BRD4770 group


title: G_3


title: G_2


title: E_3

value: Imidazole ketone erastin group


title: E_B_1

value: Imidazole ketone erastin + BRD4770 group


title: SMARCB1_deficient_PTCL_3

description: PTCL-NOS

value: loss protein expression


title: E_2


title: Preterm nasal exvivo subject 2

source_name: Nasal epithelium

value: Nasal epithelium

value: Male


title: SMARCB1_deficient_PTCL_4

description: PTCL-NOS


title: SMARCB1_deficient_PTCL_1

description: PTCL-NOS

value: mutation/deletion


title: E_1


title: D_3

value: DMSO control group


title: D_2


title: SMARCB1_deficient_PTCL_5

description: PTCL-NOS


title: SMARCB1_deficient_PTCL_2

description: PTCL-NOS


title: Strain CF13c1_rep 1

city: Madrid

first: Alvaro

last: San Millan

address: Darwin, 3

department: Biotecnología Microbiana

country: Spain

institute: Centro Nacional de Biotecnología-CSIC

description:
CF13c1.1
CF13_featureCounts.tsv
CF13_DE_results_raw.tsv

data_processing:
We trimmed and adapter-removed the reads with Trim Galore v0.6.4 (-q 20 --length 50 --illumina). We assessed the quality of the reads before and after trimming with FastQC v.0.11.9 and MultiQC v1.11.
After annotating the reference genomes with PGAP v2021-07-01.build5508, we mapped the trimmed reads to their corresponding reference genome with BWA-MEM v0.7.17.
We inspected the mappings to confirm the appropriate presence or absence of pOXA-48 in the replicates.
We obtained the raw counts of reads mapping to each genomic feature (including CDS, ncRNA, tRNA, tmRNA, antisense RNA, RNase P and SRP RNA) with featureCounts from the Rsubread v2.14.2 package.
We performed the DE analysis from raw counts using DESeq2 v1.40.1 by comparing the pOXA-48-carrying strain against the pOXA-48-free strain (first dataset) or the pOXA-48ΔlysR-carrying strain (second dataset).
Assembly: SAMN39826502, SAMN32542096, SAMN32542113, SAMN32542116, SAMN32542119, SAMN32542124, SAMN32542126, SAMN14640123, SAMN14640085, SAMN14640188, SAMN14640320, SAMN14640201
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (<strain>_featureCounts.tsv)
Supplementary files format and content: tab-delimited text files include log2FoldChanges, padj and other values for each differential expression analysis (<strain>_DE_results_raw.tsv or <strain>_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv)

organism: Citrobacter freundii

source_name: Enterobacteria

growth_protocol: We grew the cells in LB medium with continuous shaking. When cultures reached a turbidity of 0.5 (first dataset) or 0.2-0.3 (second dataset) at 600 nm, we collected the cells at 4ºC, pelleted them by centrifugation at 4ºC 12,000 g or 11,000 g for 1 min and immediately froze them at -70ºC.

extract_protocol:
We purified the total RNA from each sample using the NZY Total RNA Isolation kit (NZYTECH) (first dataset) or the Total RNA Mini Kit (BioRad’s Aurum) (second dataset). Then, we determined RNAs concentration using the Qubit RNA Broad-Range Assay following the manufacturer's instructions. Additionally, the quality of the RNA was examined using the Tape-Station system (Agilent).
We ribodepleted the RNA and sequenced it at the Wellcome Trust Centre for Human Genetics (WTCHG; Oxford, UK) using the Illumina's NovaSeq6000 platform, resulting in >8 million reads per sample (first dataset), or at SeqCoast Genomics (Portsmouth, NH, USA) with Illumina NextSeq2000, generating >6 million reads per sample (second dataset).

value: Enterobacteria

value: pOXA-48 cured

tag: dataset batch

value: First dataset


title: D_1


title: Strain CF13_rep 3

description:
CF13.3
CF13_featureCounts.tsv
CF13_DE_results_raw.tsv

value: WT


title: Strain CF13_rep 2

description:
CF13.2
CF13_featureCounts.tsv
CF13_DE_results_raw.tsv


title: E_B_2

value: Imidazole ketone erastin + BRD4771 group


title: 22 (Hepatic Endoderm)

city: Minato-ku

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

country: Japan

institute: The University of Tokyo

data_processing:
Raw data processing: Cell by gene count matrices were generated by processing FASTQ files using the Cell Ranger count (version 5.0.1, 10X Genomics) pipeline with the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference for each sample. Gene expression data were processed using the R package Seurat (version 4)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC-derived organoid

extract_protocol:
hiPSC-Hepatic Endoderm or Mesenchymal Cell were dissociated and collected in a tube.
Library construction was performed according to manufacturer’s instructions (10x genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: iPSC-derived organoid

value: hiPSC

value: Hepatic Endoderm


title: 23 (Mesenchymal Cell)

value: Mesenchymal Cell


title: Strain CF13_rep 1

description:
CF13.1
CF13_featureCounts.tsv
CF13_DE_results_raw.tsv


title: SUM159PT, YES1i, 48 hrs, rep 4

city: CLEVELAND

first: Ruth

last: Keri

state: OH

address: 10900 Euclid Ave

institute: Cleveland Clinic

data_processing:
Library preparations were sequenced on Illumina platform and paired-end reads were generated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene.
Assembly: hg38
Supplementary files format and content: read counts, txt

source_name: breast cancer

growth_protocol: Cells were seeded into 6 mm dishes at 3 x 10^6 cells/plate in 4 mL complete RMPI (231) or 2X10^6 Ham/F12 (SUM159) on day 0.

extract_protocol:
RNA was extracted using the RNAeasy Plus Minikit (Qiagen) per manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: On day 1, cells were treated with DMSO or 8uM YES1i. 48 hours post-treatment cells were collected.

value: breast cancer

value: triple negative breast cancer cells


title: SUM159PT, YES1i, 48 hrs, rep 3


title: Strain CF13c1_rep 2

description:
CF13c1.2
CF13_featureCounts.tsv
CF13_DE_results_raw.tsv


title: Strain CF13c1, rep 1

data_processing:
We trimmed and adapter-removed the reads with Trim Galore v0.6.4 (-q 20 --length 50 --illumina). We assessed the quality of the reads before and after trimming with FastQC v.0.11.9 and MultiQC v1.11.
We first identified in the genomes all copies of all IS families annotated by PGAP. Then, we masked the sequences of all but one copy of ISs per family (leaving the unmasked single copy preferentially in the chromosome or in the largest plasmid) from the reference genomes, using the bedtools maskfasta tool v2.27.1. This way, reads belonging to an IS family (like IS1) can map with low ambiguity to one region of the genome.
After re-annotating the masked genomes with PGAP v2021-07-01.build5508, we mapped the trimmed reads to their corresponding reference genome with BWA-MEM v0.7.17.
We inspected the mappings to confirm the appropriate presence or absence of pOXA-48 in the replicates. A replicate in K147c1 and in CF13c1 (cured from pOXA-48) actually carried the plasmid, so they were included as an additional replicate of the pOXA-48-carrying strains. The third replicate of C063p had a mutation in pOXA-48 (near the gene repA) that caused an increased plasmid copy number, unlike the other two replicates. Thus, we removed this replicate from the analysis.
We obtained the raw counts of reads mapping to each genomic feature (including CDS, ncRNA, tRNA, tmRNA, antisense RNA, RNase P and SRP RNA) with featureCounts from the Rsubread v2.14.2 package.
We performed the differential expression analysis from raw counts using DESeq2 v1.40.1 by comparing the pOXA-48-carrying strain against the pOXA-48-free strain.
Assembly: SAMN32542096, SAMN32542113, SAMN32542116, SAMN32542119, SAMN32542124, SAMN32542126, SAMN14640123, SAMN14640085, SAMN14640188, SAMN14640201
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (<strain>_featureCounts.tsv)
Supplementary files format and content: tab-delimited text files include log2FoldChanges, padj and other values for each differential expression analysis (<strain>_DE_results_raw.tsv)

growth_protocol: We grew the cells in LB medium with continuous shaking. When cultures reached a turbidity of 0.5 at 600 nm, we collected the cells at 4ºC, pelleted them by centrifugation at 4ºC 12,000 g for 1 min and immediately froze them at -70ºC.

extract_protocol:
We purified the total RNA from each sample using the NZY Total RNA Isolation kit (NZYTECH). Then, we determined RNAs concentration using the Qubit RNA Broad-Range Assay following the manufacturer's instructions. Additionally, the quality of the RNA was examined using the Tape-Station system (Agilent).
We ribodepleted the RNA and sequenced it at the Wellcome Trust Centre for Human Genetics (WTCHG; Oxford, UK) using the Illumina's NovaSeq6000 platform, resulting in >8 million reads per sample.

tag: strain


title: Strain CF13, rep 3


title: Strain CF13, rep 2


title: Strain CF13c1, rep 2


title: SUM159PT, DMSO, 48 hrs, rep 4

tag: cell line

value: DMSO


title: SUM159PT,  DMSO, 48 hrs, rep 2

tag: cell type


title: MDA-MB-231, YES1i, 48 hrs, rep 3

tag: treatment


title: SUM159PT, YES1i, 48 hrs, rep 2


title: BAP treated prime cells (CMO)

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

description:
sample.cmo.index.csv for demultiplexing
processed data linked to GEX sample

data_processing:
Demultiplexing, barcoded processing, gene counting were made using “cellranger multi” pipeline (v.6.1.1)  with default parameters
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primed hESCs

growth_protocol: Primed hPSC growing on hrLN-521 (10 μg/mL, Biolamina, LN521-02)  and NutriStem hPSC XF (Biological Industries, 05-100-1A) were enzymatically dissociated and seeded onto new plates also coated with hrLN-521 at a cell density of 1,84x104 cells/cm2.

extract_protocol:
Cells were dissociated with TrypLE Select (4min at 37°C; ThermoFisher Scientific, 12563011) and deactivated by adding 3 times more volume of NutriStem hPSC XF. Cells were collected in 0.04% BSA (Sigma-Aldrich, A7979) in PBS-/- and used following the Cell Multiplexing Oligo (CMO) Labeling for Single Cell RNA Sequencing Protocols with Feature Barcode technology protocol (10x Genomics, CG000391).
Following cell count and verification of live cells using the NC-200 Nucleocounter (Chemometec) of individual samples and the final pool  (4 CMO samples combined), we then used the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing (10x Genomics, CG000388) according to the recommended user guide. A 2000 target cell recovery was aimed for each individual sample. CMO libraries and transcriptome libraries were sequenced using Illumia NextSeq 2000.

treatment_protocol: 24h after seeding, hPSC were moved to a 5% CO2/5% O2 incubator and were differentiated into trophoblastic cells using NutriStem hPSC XF without bFGF and TGFb that was supplemented with 10ng/mL BMP4 (R&D Systems,  314-BP-050e), 1µM A83-01 (R&D Systems, 2939) and 0,1µM PD173074 (Sigma-Aldrich, P2499).The medium was changed daily during the 4 days of differentiation.

value: primed hESCs

value: BMP4, A83-01 and PD173074(BAP) treated primed cells

tag: library type

value: CMO


title: MDA-MB-231, YES1i, 48 hrs, rep 1

tag: tissue


title: MDA-MB-231, YES1i, 48 hrs, rep 4


title: CAR-NK cells, Donor 1, part 2 ADT

city: Frankfurt am Main

first: Katharina

last: Imkeller

address: Heinrich-Hoffmann-Str. 7

institute: University Hospital Frankfurt

description: read1 file contains cell barcode and UMI; read2 file contains transcript (amplicon), Antibody Derived Tag or Sample Tag

library_source: other

data_processing:
The generated FASTQ files were uploaded together with panel reference sequences for mRNAs and AbSeqs to the SevenBridges platform (Seven Bridges Genomics, https://www.sevenbridges.com) and processed using the BD Rhapsody analysis pipeline (BD Biosciences) with default settings. Thereby, low quality read pairs were ejected and remaining R1 reads were annotated for the detection of cell label and unique molecular identifier (UMI) sequences. The R2 reads were then mapped to the reference sequences and reads with identical cell label, UMI sequence and reference gene were collapsed into a single molecule. Afterwards, a recursive substitution error correction (RSEC) algorithm was used to adjust molecule counts for sequencing errors. Finally, cell counts were estimated and Sample Tags were assigned to cells in order to generate RSEC-adjusted molecule count matrices .
Assembly: Reference sequence file for amplicons (ImnRes_T_cell_mRNA_panel_ref_file.fasta) and antibody dependent tags (T_NK_NKT_47AbSeqPanel_ref_file.fasta).
Supplementary files format and content: BD Rhapsody pipeline output files: *_Sample_Tag_Calls.csv, *_RSEC_MolsPerCell.csv
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: peripheral blood

growth_protocol: For single cell sequencing analysis, the cryopreserved (genetically modified) NK cells from three different donors were thawed and seeded at 2x106 cells/ml in a 48-well plate in 750µl in NK-MACS® medium supplemented with 1% NK-MACS® Supplements, 5% human plasma, 1% Pen/Strep, 500 U/ml IL-2 (Miltenyi Biotec or Novartis) as well as 50 ng/ml IL-15 (CellGenix) per well.

extract_protocol:
NK cells were sorted as follows: NT-NK as CFSE-, KLRC1ko-NK as CFSE-/NKG2A-, CAR33-NK as CFSE-/CAR+ and CAR33-KLRC1ko-NK cells as CFSE-/NKG2A-/CAR+ cells. Afterwards, single cell sequencing was performed using a BD Rhapsody™ Single-cell analysis system (BD Biosciences).
After single-cell capture and cDNA synthesis, the predesigned human Immune Response Targeted Panel was used together with a custom-designed primer panel to amplify the cDNA of 434 different genes (ImnRes_T_cell_mRNA_panel_ref_file.fasta)  for eleven cycles according to the manufacturer´s protocol. Then, PCR1 products were purified using AMPureXP magnetic beads in a double sided size selection procedure. For purified mRNA and sample tag PCR1 products a second PCR with ten amplification cycles was performed. PCR2 products were purified by single sided size selection and their concentration and size were checked using the Qubit 4 Fluorometer (DNA HS Assay) and the Agilent 4150 Tapestation (DNA Screen Tape). Illumina Index PCR was performed with diluted samples (mRNA: 2.5 ng/µl, Sample Tag & AbSeq 1.1 ng/µl) for six cycles and the resulting final libraries were purified  by single sided size selection. Quality control of the final libraries was preformed via Qubit and Agilent 4150 Tapestation. Libraries were then pooled to a final concentration of 1 nM and sequenced together with 20 % PhiX DNA in multiple runs (75 bp paired-end) on a NextSeq2000 sequencer (Illumina) (further sequencing information needed or is this enough?).

treatment_protocol: Three days post thawing, cells were harvested and co-cultivated with OCI-AML2 cells in 6cm dishes at an E:T ratio of 1:1. OCI-AML2 cells were previously stained with Cell Trace CFSE proliferation kit (Invitrogen) according to manufacturer’s protocol. As a control, NK cells were cultured without contact to AML cells. After two hours the plated cells were harvested, and stained for sorting.

value: peripheral blood

value: NK cells (genetically modified)

value: mRNA amplicons + ADT + sample barcode

tag: antibodies/tags

value: Sample tags:1-NTbefore 2-KObefore 3-CARbefore 4-CARKObefore 5-NTafter 6-KOafter 7-CARafter 8-CARKOafter


title: CAR-NK cells, Donor 1, part 1 ADT


title: CAR-NK cells, Donor 2 RNA

value: Sample tags:5-Ntbefore, 6-Kobefore, 7-CARbefore, 8-CARKObefore, 9-Ntafter, 10-Koafter, 11-CARafter, 12-CARKOafter


title: SUM159PT, YES1i, 48 hrs, rep 1

value: WT


title: MDA-MB-231, DMSO, 48 hrs, rep 2


title: SUM159PT, DMSO, 48 hrs, rep 3


title: MDA-MB-231, DMSO, 48 hrs, rep 3


title: MDA-MB-231, YES1i, 48 hrs, rep 2


title: MDA-MB-231, DMSO, 48 hrs, rep 4


title: CAR-NK cells, Donor 1, part 2 RNA


title: BAP treated prime cells (GEX)

description: sample.cmo.index.csv for demultiplexing

value: GEX


title: Strain CF13, rep 1

value: Enterobacteria


title: CAR-NK cells, Donor 1, part 1 RNA


title: SUM159PT, DMSO, 48 hrs, rep 1


title: CAR-NK cells, Donor 2 ADT


title: Strain TC_KPN18_rep 3

description:
TC_KPN18.3
KPN18_featureCounts.tsv
KPN18_DE_results_raw.tsv

organism: Klebsiella pneumoniae

value: pOXA-48 transconjugant

value: First dataset


title: MDA-MB-231, DMSO, 48 hrs, rep 1


title: Strain TC_KPN18_rep 2

description:
TC_KPN18.2
KPN18_featureCounts.tsv
KPN18_DE_results_raw.tsv


title: Strain TC_KPN18_rep 1

description:
TC_KPN18.1
KPN18_featureCounts.tsv
KPN18_DE_results_raw.tsv


title: prlnc_veh3

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
STAR RSEM
Assembly: hg38
Supplementary files format and content: gene_count_taz_samples.txt

source_name: prostate

extract_protocol:
RNA was extracted using Qiagen column purification kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: prostate

value: LNCaP

value: cell line

value: vehicle

tag: group

value: PRAD


title: prlnc_veh2


title: Strain PF_KPN18_rep 3

description:
PF_KPN18.3
KPN18_featureCounts.tsv
KPN18_DE_results_raw.tsv


title: G_B_3

value: aortic smooth muscle cells

value: Cystine deprivation + BRD4772 group


title: G_B_2

value: Cystine deprivation + BRD4771 group


title: prlnc_veh1


title: Strain PF_KPN18_rep 2

description:
PF_KPN18.2
KPN18_featureCounts.tsv
KPN18_DE_results_raw.tsv


title: prlnc_taz3

value: 5 uM tazemetostat


title: Strain PF_KPN18_rep 1

description:
PF_KPN18.1
KPN18_featureCounts.tsv
KPN18_DE_results_raw.tsv


title: Strain TC_KPN15_rep 1

description:
TC_KPN15.1
KPN15_featureCounts.tsv
KPN15_DE_results_raw.tsv


title: Strain TC_KPN15_rep 2

description:
TC_KPN15.2
KPN15_featureCounts.tsv
KPN15_DE_results_raw.tsv


title: Strain PF_KPN15_rep 1

description:
PF_KPN15.1
KPN15_featureCounts.tsv
KPN15_DE_results_raw.tsv


title: prabl_veh2

value: LNCaP-abl


title: prabl_taz3


title: prabl_taz2


title: Strain TC_KPN10_rep 2

description:
TC_KPN10.2
KPN10_featureCounts.tsv
KPN10_DE_results_raw.tsv


title: Strain TC_KPN15_rep 3

description:
TC_KPN15.3
KPN15_featureCounts.tsv
KPN15_DE_results_raw.tsv


title: prlnc_taz2


title: prlnc_taz1


title: prabl_veh3


title: Strain PF_KPN10_rep 1

description:
PF_KPN10.1
KPN10_featureCounts.tsv
KPN10_DE_results_raw.tsv


title: ne155_veh2

value: patient-derived organoids

value: NEPC


title: Strain TC_KPN07_rep 3

description:
TC_KPN07.3
KPN07_featureCounts.tsv
KPN07_DE_results_raw.tsv


title: Strain TC_KPN07_rep 1

description:
TC_KPN07.1
KPN07_featureCounts.tsv
KPN07_DE_results_raw.tsv


title: ne155_veh1

value: WT


title: Strain PF_KPN15_rep 2

description:
PF_KPN15.2
KPN15_featureCounts.tsv
KPN15_DE_results_raw.tsv


title: ne155_taz1


title: Strain PF_KPN07_rep 2

description:
PF_KPN07.2
KPN07_featureCounts.tsv
KPN07_DE_results_raw.tsv


title: ne154_veh3


title: Strain TC_KPN04_rep 3

description:
TC_KPN04.3
KPN04_featureCounts.tsv
KPN04_DE_results_raw.tsv


title: ne154_veh2


title: prabl_veh1


title: ne154_taz3


title: Strain TC_KPN10_rep 1

description:
TC_KPN10.1
KPN10_featureCounts.tsv
KPN10_DE_results_raw.tsv


title: prabl_taz1


title: Strain TC_KPN04_rep 1

description:
TC_KPN04.1
KPN04_featureCounts.tsv
KPN04_DE_results_raw.tsv


title: ne155_veh3


title: ne154_taz2


title: Strain PF_KPN10_rep 2

description:
PF_KPN10.2
KPN10_featureCounts.tsv
KPN10_DE_results_raw.tsv


title: Strain PF_KPN04_rep 3

description:
PF_KPN04.3
KPN04_featureCounts.tsv
KPN04_DE_results_raw.tsv


title: Strain TC_KPN07_rep 2

description:
TC_KPN07.2
KPN07_featureCounts.tsv
KPN07_DE_results_raw.tsv


title: ne155_taz3


title: ne155_taz2


title: Strain PF_KPN07_rep 3

description:
PF_KPN07.3
KPN07_featureCounts.tsv
KPN07_DE_results_raw.tsv


title: ne1262_veh1


title: ne1262_taz3


title: ne1262_veh2


title: Strain PF_EC10_rep 3

description:
PF_EC10.3
EC10_featureCounts.tsv
EC10_DE_results_raw.tsv


title: ne1262_taz2


title: WCM154_sgEZH2_H3K27me3_rep2

library_source: genomic

data_processing:
bowtie2 followied by bamCompare (deepTools)
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN Epicypher kit was used.
CUT&RUN Epicypher kit was used.

value: pateint-dervied organoids

value: EZH2 knockout


title: Strain PF_KPN07_rep 1

description:
PF_KPN07.1
KPN07_featureCounts.tsv
KPN07_DE_results_raw.tsv

value: Enterobacteria


title: ne154_veh1


title: WCM154_sgEZH2_H3K27me3_rep1


title: WCM154_sgEZH2_H3K4me3_rep2


title: ne1262_veh3


title: Strain PF_KPN04_rep 2

description:
PF_KPN04.2
KPN04_featureCounts.tsv
KPN04_DE_results_raw.tsv

value: First dataset


title: Strain TC_EC10_rep 2

description:
TC_EC10.2
EC10_featureCounts.tsv
EC10_DE_results_raw.tsv

value: pOXA-48 transconjugant


title: Strain PF_KPN04_rep 1

description:
PF_KPN04.1
KPN04_featureCounts.tsv
KPN04_DE_results_raw.tsv


title: Strain TC_EC10_rep 1

description:
TC_EC10.1
EC10_featureCounts.tsv
EC10_DE_results_raw.tsv


title: Strain K147_rep 1

description:
K147.1
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: Strain TC_KPN04_rep 2

description:
TC_KPN04.2
KPN04_featureCounts.tsv
KPN04_DE_results_raw.tsv


title: Strain PF_EC10_rep 2

description:
PF_EC10.2
EC10_featureCounts.tsv
EC10_DE_results_raw.tsv


title: ne1262_taz1

value: prostate


title: Strain PF_EC10_rep 1

description:
PF_EC10.1
EC10_featureCounts.tsv
EC10_DE_results_raw.tsv


title: ne154_taz1


title: Strain H53c1_rep 2

description:
H53c1.2
H53_featureCounts.tsv
H53_DE_results_raw.tsv

value: pOXA-48 cured


title: Strain K147c1_rep 2

description:
K147c1.2
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: Strain K147c1_rep 1

description:
K147c1.1
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: WCM154_sgEZH2_IgG_rep1


title: Strain K147_rep 3

description:
K147.3
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: Strain K147_rep 2

description:
K147.2
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: Strain K147_rep 4

description:
K147.4
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: I.a. injected ATP-loaded OMV 2

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

description: OMV isolated from E. coli tolB mutant (Keio collection) growth culture after 24h. ATP-loading of OMV via electroporation, i.a. injection (25µg) into C57Bl6 mice and harvesting of lung, digestion and bead-sorting of neutrophils after 1h.

data_processing:
Debarcoding, fastp  -U --umi_loc=read1 --umi_len=12 (fastp)
Read alignment (STAR)
Counting Features (featureCounts)
Assembly: GRCm39 (Ensembl release 108)
Supplementary files format and content: data.csv (read count matrix)

source_name: bead-sorted neutrophils isolated from lungs of C57Bl6 mice

growth_protocol: 24h growth of E. coli tolB mutant in LB medium. Isolation of OMV via ultracentrifugation. Mock-electroporation or ATP-loading via electroporation.

extract_protocol:
Tissue digestion of lungs using a combination of collagenases (I, IV, D), bead-sorting of neutrophils (Miltenyi Biotec) and RNA extraction using Promega ReliaPrep RNA Cell Miniprep System from frozen neutrophil pellets.
Lexogen CORALL total RNA-seq library kit

treatment_protocol: I.a. injection of 25µg mock-electroporated or ATP-loaded OMV and harvesting of lungs after one hour.

value: I.a. injection of OMV, harvesting after one hour

value: ATP-loaded OMV 2


title: I.a. injected ATP-loaded OMV 6

value: bead-sorted neutrophils isolated from lungs of C57Bl6 mice

value: ATP-loaded OMV 6


title: Strain H53_rep 2

description:
H53.2
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: WCM154_sgINC_H3K27me3_rep2


title: I.a. injected ATP-loaded OMV 5

value: ATP-loaded OMV 5


title: Strain K275p, rep 3

description:
K275p.3
K275_featureCounts.tsv
K275_DE_results_raw.tsv


title: WCM154_sgEZH2_H3K4me3_rep1


title: I.a. injected mock-electroporated OMV 6

description: OMV isolated from E. coli tolB mutant (Keio collection) growth culture after 24h. Mock-electroporation of OMV, i.a. injection (25µg) into C57Bl6 mice and harvesting of lung, digestion and bead-sorting of neutrophils after 1h.

value: Mock-electroporated OMV 6


title: WCM154_sgEZH2_IgG_rep2


title: I.a. injected ATP-loaded OMV 4

value: ATP-loaded OMV 4


title: Strain H53c1_rep 3

description:
H53c1.3
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: I.a. injected mock-electroporated OMV 5

value: Mock-electroporated OMV 5


title: WCM154_sgINC_H3K4me3_rep2


title: Strain H53c1_rep 1

description:
H53c1.1
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: Strain K275, rep 2

description:
K275.2
K275_featureCounts.tsv
K275_DE_results_raw.tsv


title: Strain H53_rep 3

description:
H53.3
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: Strain K275, rep 1

description:
K275.1
K275_featureCounts.tsv
K275_DE_results_raw.tsv


title: I.a. injected ATP-loaded OMV 1

value: ATP-loaded OMV 1


title: Strain K249p, rep 2

description:
K249p.2
K249_featureCounts.tsv
K249_DE_results_raw.tsv


title: Strain K249p, rep 1

description:
K249p.1
K249_featureCounts.tsv
K249_DE_results_raw.tsv


title: Strain K275p, rep 2

description:
K275p.2
K275_featureCounts.tsv
K275_DE_results_raw.tsv


title: Strain H53_rep 1

description:
H53.1
H53_featureCounts.tsv
H53_DE_results_raw.tsv

value: WT


title: Strain K275p, rep 1

description:
K275p.1
K275_featureCounts.tsv
K275_DE_results_raw.tsv


title: Strain K249, rep 1

description:
K249.1
K249_featureCounts.tsv
K249_DE_results_raw.tsv


title: Strain K275, rep 3

description:
K275.3
K275_featureCounts.tsv
K275_DE_results_raw.tsv


title: I.a. injected mock-electroporated OMV 4

value: Mock-electroporated OMV 4


title: Strain K209p, rep 2

description:
K209p.2
K209_featureCounts.tsv
K209_DE_results_raw.tsv


title: WCM154_sgINC_H3K4me3_rep1

value: pateint-dervied organoids


title: I.a. injected mock-electroporated OMV 3

value: Mock-electroporated OMV 3


title: WCM154_sgINC_H3K27me3_rep1


title: Strain K249p, rep 3

description:
K249p.3
K249_featureCounts.tsv
K249_DE_results_raw.tsv

value: Enterobacteria


title: Strain K209, rep 2

description:
K209.2
K209_featureCounts.tsv
K209_DE_results_raw.tsv


title: LNCaPabl_taz_H3K27me3_rep1

value: LNCaPabl

value: cell line

value: 5uM tazemetostat


title: Strain K209, rep 1

description:
K209.1
K209_featureCounts.tsv
K209_DE_results_raw.tsv


title: WCM154_sgINC_IgG_rep2

value: prostate


title: LNCaPabl_taz_H3K4me3_rep2


title: WCM154_sgINC_IgG_rep1


title: I.a. injected mock-electroporated OMV 2

description: OMV isolated from E. coli tolB mutant (Keio collection) growth culture after 24h. Mock-electroporation of OMV, i.a. injection (25µg) into C57Bl6 mice and harvesting of lung, digestion and bead-sorting of neutrophils after 1h.

value: I.a. injection of OMV, harvesting after one hour

value: Mock-electroporated OMV 2


title: Strain K141p, rep 2

description:
K141p.2
K141_featureCounts.tsv
K141_DE_results_raw.tsv

value: pOXA-48 transconjugant


title: I.a. injected mock-electroporated OMV 1

value: bead-sorted neutrophils isolated from lungs of C57Bl6 mice

value: Mock-electroporated OMV 1


title: Strain K249, rep 2

description:
K249.2
K249_featureCounts.tsv
K249_DE_results_raw.tsv


title: Strain K141, rep 3

description:
K141.3
K141_featureCounts.tsv
K141_DE_results_raw.tsv


title: day 0 fresh sorted ATIIs from young and old mice_hto

city: South San Francisco

first: David

last: Garfield

state: CA

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

description:
Freshly sorted ATIIs from young and old mice
ngs4120_barcodes.tsv
ngs4120_genes.tsv
ngs4120_matrix.mtx

data_processing:
Fastq files were generated from the raw sequencing files using BCL2Fastq (Illumina, San Diego, CA) and then aligned using CellRanger (v6.0.1, 10x Genomics) against the mouse genome (GRCm38/mm10) with the “—include-introns” option set to ‘True’.
The resulting count matrices were then used to construct a SingleCellExperiment in R using DropletUtils package(v1.2.2)92.
Initial QC filtering was carried out using the ‘perCellQCFilters’ function from the scran.chan package93 as applied to individual samples using default settings with ‘nmads = 3’.
n/a
n/a
Assembly: GRCm38/mm10
Supplementary files format and content: Fastq files raw sequencing files are provided
Supplementary files format and content: Count matrix, gene expression and barcodes incformation are provided in .mtx and .tsv files accordingly.

source_name: lung

growth_protocol: See publication for details.

extract_protocol:
RNA was extracted using RNeasy kits (Qiagen, 74104). RNA quantity and quality was measured using a Nanodrop (Thermo Scientific). 100ng RNA per sample was used to make cDNA using the iScript™ cDNA Synthesis Kit (BioRad, 1708890)
We sorted Sytox blue negative, live cells for scRNA-seq using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (Dual Index, 10x Genomics, 1000269) with Feature Barcode technology for Cell Multiplexing (10x Genomics, 1000262). Libraries were prepared according to the manufacturer’s instructions. Prior to loading cells on the microfluidic chip, we performed quality control and cell counting. All cell suspensions were >75% viable and within the concentration range recommended by the manufacturer. Following GEM generation and barcoding via reverse transcription (RT), we performed post GEM-RT cleanup and cDNA amplification. Subsequently we proceeded with gene expression and cell multiplexing library construction, performed QC on the generated libraries and submitted them for sequencing.
Gene expression libraries were pooled with cell multiplexing libraries and sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) to generate a minimum 2,000 reads per cell for cell multiplexing libraries and 20,000 reads per cell for gene expression libraries in a 28/10/10/90 (R1/i7/i5/R2) bp configuration according to 10X Genomics guidelines.

treatment_protocol: See publication for details.

value: lung

value: Type 2 Peumocytes (ATII)

value: IL4Ra WT

value: mixed sample

value: hto


title: day 13 ATIIs from young mice_exp

description:
Multipled ATIIs from young mice from day 13 culture
ngs4120_barcodes.tsv
ngs4120_genes.tsv
ngs4120_matrix.mtx

value: expression


title: LNCaPabl_taz_IgG_rep2

value: WT


title: Strain K141p, rep 3

description:
K141p.3
K141_featureCounts.tsv
K141_DE_results_raw.tsv

value: Enterobacteria


title: Strain K209p, rep 1

description:
K209p.1
K209_featureCounts.tsv
K209_DE_results_raw.tsv


title: day 13 ATIIs from young mice_hto


title: LNCaPabl_taz_H3K4me3_rep1

value: LNCaPabl


title: day 13 ATIIs from young and old mice_exp

description:
Multiplexed ATIIs from young and old mice from day 13 culture
ngs4120_barcodes.tsv
ngs4120_genes.tsv
ngs4120_matrix.mtx


title: LNCaPabl_taz_H3K27me3_rep2

value: cell line


title: LNCaPabl_veh_H3K27me3_rep2

value: vehicle


title: Strain K141, rep 2

description:
K141.2
K141_featureCounts.tsv
K141_DE_results_raw.tsv


title: LNCaPabl_taz_IgG_rep1

value: prostate

value: 5uM tazemetostat


title: Strain K091p, rep 2

description:
K091p.2
K091_featureCounts.tsv
K091_DE_results_raw.tsv


title: Strain K091p, rep 3

description:
K091p.3
K091_featureCounts.tsv
K091_DE_results_raw.tsv


title: Strain K091, rep 1

description:
K091.1
K091_featureCounts.tsv
K091_DE_results_raw.tsv


title: day 13 ATIIs from young and old mice_hto


title: Strain K091p, rep 1

description:
K091p.1
K091_featureCounts.tsv
K091_DE_results_raw.tsv


title: LNCaPabl_veh_H3K27me3_rep1


title: Strain K141p, rep 1

description:
K141p.1
K141_featureCounts.tsv
K141_DE_results_raw.tsv


title: Strain K091, rep 2

description:
K091.2
K091_featureCounts.tsv
K091_DE_results_raw.tsv


title: Strain C063p, rep 1

description:
C063p.1
C063_featureCounts.tsv
C063_DE_results_raw.tsv


title: LNCaPabl_veh_H3K4me3_rep2


title: cre_exp_rep2

description:
ngs4956_barcodes_exp.tsv
ngs4956_genes_exp.tsv
ngs4956_matrix_exp.mtx

data_processing:
Feature count matrices for ATAC-seq and gene expression using Cell Ranger (v6.0.1, 10x Genomics) were constructed with reads aligned to the mouse genome (GRCm38/mm10).
Seurat (v4.3.0)94 and Signac (v1.10.0)95 packages were utilized to create a multimodal Seurat object with paired gene expression and chromatin accessibility.
Cells that had more than 20% of their reads aligned to the mitochondrial genome, more than 40% of their reads mapped to the ribosomal genome, or more than 6% of their reads in genomic blacklist regions were discarded.
n/a
n/a
Assembly: GRCm38/mm10
Supplementary files format and content: Fastq files raw sequencing files are provided
Supplementary files format and content: Count matrix, gene expression and barcodes incformation are provided in .mtx and .tsv files accordingly.

molecule: nuclear RNA

source_name: Lung

extract_protocol:
We extracted nuclei from live tdTomato+ cells sorted from spheres by FACS, using the nucleus extraction buffer (10mM Tris pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween 20, 0.1% NP40, 0.01% Digitonin and 1% BSA). Prior to nuclei loading on the microfluidic chip, we adjusted the nuclei concentration for each sample to fall within the recommended concentration range provided by the manufacturer. Using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, 1000285), Following transposition and GEM generation, we performed post GEM- cleanup and library pre-amplification PCR. Subsequently we proceeded with ATAC library and gene expression library construction, performed QC on the generated libraries and submitted them for sequencing.
Gene expression libraries were pooled with cell multiplexing libraries and sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) to generate a minimum 2,000 reads per cell for cell multiplexing libraries and 20,000 reads per cell for gene expression libraries in a 28/10/10/90 (R1/i7/i5/R2) bp configuration according to 10X Genomics guidelines. ATAC-seq libraries were pooled and sequenced on NovaSeq 6000 (Illumina, San Diego, CA) to generate 25,000 reads per cell for 10,000 targeting cells, equivalent to ~250 million paired-end reads per library in a 50/8/24/50 bp configuration according to 10X Genomics guidelines.

value: Lung

value: Cre

value: control


title: cre_exp_rep1


title: day 0 fresh sorted ATIIs from young and old mice_exp


title: Strain C063p, rep 2

description:
C063p.2
C063_featureCounts.tsv
C063_DE_results_raw.tsv

value: pOXA-48 transconjugant


title: Strain K141, rep 1

description:
K141.1
K141_featureCounts.tsv
K141_DE_results_raw.tsv


title: Strain C063, rep 3

description:
C063.3
C063_featureCounts.tsv
C063_DE_results_raw.tsv


title: sox9creOE_exp_rep1

value: Sox9 overexpression


title: LNCaPabl_veh_IgG_rep2


title: Strain C063, rep 2

description:
C063.2
C063_featureCounts.tsv
C063_DE_results_raw.tsv


title: LNCaPabl_veh_IgG_rep1


title: Strain C063, rep 1

description:
C063.1
C063_featureCounts.tsv
C063_DE_results_raw.tsv


title: cre_atac_rep2

description:
ngs4956_barcodes_atac.tsv
ngs4956_genes_atac.tsv
ngs4956_matrix_atac.mtx

library_source: genomic single cell

value: Type 2 Peumocytes (ATII)


title: Strain K091, rep 3

description:
K091.3
K091_featureCounts.tsv
K091_DE_results_raw.tsv


title: Strain K147c1, rep 1

description:
K147c1.1
K147_featureCounts.tsv
K147_DE_results_raw.tsv

value: pOXA-48 cured


title: cre_atac_rep1


title: Strain K147, rep 4

description:
K147.4
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: Strain K147, rep 3

description:
K147.3
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: WCM154_taz_H3K27me3_rep2

value: pateint-dervied organoids


title: sox9creOE_atac_rep2


title: sox9creOE_exp_rep2


title: Strain K147, rep 2

description:
K147.2
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: WCM154_taz_H3K27me3_rep1


title: Strain H53c1, rep 3

description:
H53c1.3
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: Strain H53c1, rep 2

description:
H53c1.2
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: WCM154_taz_H3K4me3_rep2


title: Bleomycin_IL4Ra KO_4

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10), using the GSNAP aligner as part of the HTSeqGenie R package (version 4.32.0)89.
Reads that uniquely aligned within exonic boundaries of genes were used to derive expression estimates.
For visualization and quality control, nRPKM (reads per kilobaseper normalized million mapped reads) were calculated per gene using the median ratio method described before90.
Differential gene expression analysis was performed using integer count values with limma-voom91 by a workflow implemented in Partek Flow (Partek Inc., St Louis, MO).
Gene ontology analysis was done by Enrichr (Mount Sinai, NY)
Assembly: GRCm38/mm10
Supplementary files format and content: Fastq files raw sequencing files are provided
Supplementary files format and content: Count matrix, gene expression and barcodes incformation are provided in .mtx and .tsv files accordingly.

extract_protocol:
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Q32852), and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies, 5067-5576).
cDNA library was generated from 2ng RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara, 634894).
150pg cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1024). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies, 5067-5582). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina, San Diego, CA) to generate an average of 30 million single-end 50-base pair reads for each sample.

value: IL4Ra KO

value: Bleomycin


title: LNCaPabl_veh_H3K4me3_rep1

value: WT


title: WCM154_taz_IgG_rep2


title: sox9creOE_atac_rep1


title: Strain H53c1, rep 1

description:
H53c1.1
H53_featureCounts.tsv
H53_DE_results_raw.tsv

value: Enterobacteria


title: Bleomycin_IL4Ra KO_2


title: Strain H53, rep 2

description:
H53.2
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: Strain H53, rep 3

description:
H53.3
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: Strain K147c1, rep 2

description:
K147c1.2
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: WCM154_veh_H3K27me3_rep2


title: WCM154_taz_IgG_rep1


title: Strain K147, rep 1

description:
K147.1
K147_featureCounts.tsv
K147_DE_results_raw.tsv


title: HBEC3-p53K

city: Maebashi

first: Noriaki

last: Sunaga

state: Gunma

address: 3-39-15 Showa-machi

department: Department of Respiratory Medicine

institute: Gunma University Graduate School of Medicine

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250

label: biotin

source_name: HBEC3 with mutant KRAS plus p53 shRNA

label_protocol: biotin

growth_protocol: Cells were cultured with RPMI 5% BFS (tumor lines) or K-SFM medium with 50 ug/mL bovine pituitary extract (HBEC3 lines)

extract_protocol: Qiagen RNeasy kit including DNase1 treatment

treatment_protocol: Mutant KRAS expressions in NSCLC cell lines were silenced with mutant KRAS-specific shRNA vectors. For HBEC samples, mutant KRAS-G12V transduction was mediated by the mutant KRAS-V12V expression vector, whereas p53 expression was silenced by the shRNA vector targeting the TP53 gene in the HBEC3 immortalized human bronchial epithelial cell line.

tag: histology

value: Bronchial epithelial cell line

tag: subtype

value: Bronchial epithelial cells


title: HBEC3-p53

source_name: HBEC3 with p53 shRNA


title: HBEC3-K

source_name: HBEC3 with mutant KRAS


title: Bleomycin_IL4Ra WT_2

tag: genotype

value: IL4Ra WT


title: Bleomycin_IL4Ra KO_1


title: Strain H53, rep 1

description:
H53.1
H53_featureCounts.tsv
H53_DE_results_raw.tsv


title: WCM154_taz_H3K4me3_rep1

value: prostate


title: WCM154_veh_IgG_rep2

value: vehicle


title: Bleomycin_IL4Ra WT_4

value: Lung


title: saline_IL4Ra WT_4

value: Saline


title: WCM154_veh_H3K27me3_rep1


title: H1299-Ctrl

source_name: H1299 with control shRNA

growth_protocol: RPMI 5% BFS

value: Lung cancer cell line

value: Adenocarcinoma


title: MB453_CRISPR lib_DOX_RGS-Res8

first: Guillermo

last: de Cárcer

state: Madrid

address: Arturo Duperier, 4

department: Cancer

institute: IIBM-CSIC

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's RTA (Real Time Analysis) integrated primary analysis software. Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Assembly: Human NCBI genome build GRCh38.p13
Supplementary files format and content: CSV excel file including raw counts for each sample

growth_protocol: MDA-MD-453 cells were grown in DMEM media supplemented with 10% FBS in a hunidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
RNA from control cells or the rigosertib-resistant colonies was extracted with the mirVana miRNA extraction kit (AM1571, Invitrogen) following the manual instructions
Total RNA samples (250 ng) with an average RIN=9.6 (range: 9.4-9.8) in a labchip analysis, were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) instrument by following manufacturer's protocols.

treatment_protocol: CRISPR-Cas9 library was activated using 1ug/ml of doxycycline for 3 days. Active Cas9 cells were treated with 100nM rigosertib for 3 days, and a 4 days drug holyday. This regime was done for 4 to 5 weeks until resistant colonies appeared.

value: Breast Cancer

value: DOX+rigosertib 100nM


title: H1299-KRAS-C12

source_name: H1299 with mutant KRAS-C12 shRNA

value: Large cell carcinoma


title: H1299-KRAS-V12

source_name: H1299 with mutant KRAS-V12 shRNA


title: Bleomycin_IL4Ra WT_3


title: HBEC3


title: Bleomycin_IL4Ra KO_3


title: H441-Ctrl

source_name: H441 with control shRNA


title: WCM154_veh_H3K4me3_rep2

value: pateint-dervied organoids


title: MB453_CRISPR lib_DOX_RGS-Res6


title: WCM154_sgEZH2#1_dTAGEZH2_dTAGv1_9days_rep2

data_processing:
STAR RSEM
Assembly: hg38
Supplementary files format and content: comma separated values

value: EZH2 rescue

value: 500 nM dTAGv1


title: saline_IL4Ra WT_1


title: MB453_CRISPR lib_DOX_RGS-Res4


title: WCM154_veh_H3K4me3_rep1

value: WT


title: WCM154_sgEZH2#1_dTAGEZH2_dTAGv1_9days_rep1


title: week5 WT rep3

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were mapped to the mouse reference genome sequences  (mm10) using STAR.
The aligned reads were quantitated by Htseq. The normalization and differentially expressed genes test were implemented by DESeq2.
Assembly: mm10
Supplementary files format and content: Excel file with all normalised counts for each sample

source_name: control

growth_protocol: Mice were hold in a SPF units. Doxcycline (1g/L) was added to the drining water for the duration of 1 or 2 or 5 weeks as described above.

extract_protocol:
Kidneys  were harvested from the mice and were subjected to RNA extraction using regular Trizol protocol
For library preparation NEBNext RNA ultra II RNA library preparation kit (NEB) was used. All RNA samples underwent PolyA selection following the manufacturers' protocols. Samples were multiplexed using suitable molecular barcodes and resulting cDNA pools were processed according to the NextSeq System Denature and Dilute Libraries guide. (Illumina). Quantification and quality control of the libraries were done using Qubit fluorimeter and Agilent 4200 TapeStation.

value: kidney

value: kidney cells

value: Doxcycyclin was added to the driniking water at a concentration of 1g/L for 5 W


title: H441-KRAS-V12

source_name: H441 with mutant KRAS-V12 shRNA


title: WCM154_veh_IgG_rep1


title: Bleomycin_IL4Ra WT_1

value: IL4Ra WT

value: Bleomycin


title: primary brain vessel endothelial cells, H3K4me3-2

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw CUT&Tag sequencing data were processed for quality control and adapter trimming using fastp (v.0.20). Paired-end reads (R1 and R2) were handled in this step, and potential contaminants in the sequencing data were detected using FastQ Screen (v.0.15.2)
Trimmed reads were then aligned to the mouse reference genome (mm10) using Bowtie2 (v.2.4.1).
The aligned BAM files were subsequently sorted using Sambamba (v.0.8.2), and duplicates were marked.
Peak calling on the processed data was performed using GoPeaks (v.1.0.0).
Coverage tracks in BigWig format were generated using the bamCoverage function of deepTools (v.3.5.1).
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&TAG

source_name: primary brain endothelial cells

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

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

value: primary brain endothelial cells

tag: chip antibody


title: MB453_CRISPR lib_DOX_ctrl

value: Doxycycline (DOX)


title: H1792-Ctrl

source_name: H1792 with control shRNA


title: week5 WT rep2


title: WCM154_sgEZH2#1_dTAGEZH2_veh_9days_rep2

value: prostate

value: vehicle


title: MB453_CRISPR lib_ctrl


title: WCM154_sgEZH2#1_dTAGEZH2_dTAGv1_9days_rep3


title: Breast mammary epithelial normal cell line cell line - MCF10A-SK-WA

city: Bathinda

first: Shashank

last: Kumar

state: Punjab

address: VPO Guddha

department: Biochemistry

country: India

institute: CENTRAL UNIVERSITY OF PUNJAB

description:
Breast normal epithelila cell line MCF10A WA treated
Sample names: MCF-10A-01, MCF-10A-02 and MCF-10A-03
The SRX contains data for three replicates within a single SRR.

data_processing:
Illumina genrated raw reads were filtered (Adaptor removal and length filtering) using trimgalore and cutadapt
High quality trimmed reads were alligned to human genome (GRCh38.p7) using miRDeep2 software
Raw count expression for each miRNA condidate and sample was calculated using edgeR software
Genome_build: Human genome (GRCh38.p7)
Supplementary_files_format_and_content: Microsoft office excel worksheet (.xlsx) table matrix having raw expression count for each miRNA condidate and each sample
Supplementary_files_format_and_content: Microsoft office excel worksheet (.xlsx) table matrix having normalized expression count for each miRNA condidate and each sample

source_name: Breast mammary gland

growth_protocol: MCF10A cells were grew in normal cell media at 5% CO2 level in CO2 incubator under the sterilized conditions

extract_protocol:
Small RNA was isolated from Withaferin non-treated and Withaferin A treated MCF10A samples
QIAseq® miRNA Library Kit (Cat: 331502) protocol (Qiagen, Maryland, U.S.A.) and NEBNext Multiplex Small RNA library prep kit (Catalog: E7330S, New England Biolabs) were used for Small RNA sequencing (smRNA) libraries of MCF10A-SK-repl1, MCF10A-SK-repl2, MCF10A-SK3-repl3 and MCF10A-SK-WA-repl1,  MCF10A-SK-WA-repl2,  MCF10A-SK-WA-repl3,  respectively.

treatment_protocol: MCF10A cells were treated with Withaferin A at 2 micro molar concentration for 24 h

value: Breast mammary gland

value: WA treated


title: saline_IL4Ra WT_2

value: Lung

value: Saline


title: primary brain vessel endothelial cells, HA-FOXQ1-1

value: HA


title: Breast mammary epithelial normal cell line cell line - MCF10A-SK

description:
Breast normal epithelila cell line MCF10A WA non-treated replicate 1
Sample names: AB-01, AB-02 and AB-03
The SRX contains data for three replicates within a single SRR.

value: non-treated


title: H1792-KRAS-C12

source_name: H1792 with mutant KRAS-C12 shRNA

value: Lung cancer cell line

value: Adenocarcinoma


title: WCM154_sgEZH2#1_dTAGEZH2_veh_9days_rep3

source_name: prostate

value: pateint-dervied organoids

value: EZH2 rescue


title: week2 WT rep3

value: kidney

value: kidney cells

value: Doxcycyclin was added to the driniking water at a concentration of 1g/L for 2 W


title: Brain, E18, KO-1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: FOXQ1_RNAseq_norm_data.csv

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent. 2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Brain

tag: developmental stage


title: WCM154_sgEZH2#1_dTAGEZH2_dTAGv1_8hr_rep1

value: 500 nM dTAGv1


title: saline_IL4Ra WT_3

value: IL4Ra WT


title: primary brain vessel endothelial cells, HA-FOXQ1-2

value: primary brain endothelial cells


title: primary brain vessel endothelial cells, H3K4me3-1


title: week5 WT rep1

value: Doxcycyclin was added to the driniking water at a concentration of 1g/L for 5 W


title: H358-KRAS-C12

source_name: H358 with mutant KRAS-C12 shRNA


title: WCM154_sgEZH2#1_dTAGEZH2_veh_8hr_rep2

value: prostate

value: vehicle


title: H358-Ctrl

source_name: H358 with control shRNA


title: week5 Transgen rep1

source_name: Specific Lin28A OE in the nephrons for 5W

value: Lox-stop-Lox-TetOn-Lin28A; Six2Cre


title: week2 WT rep1


title: WCM154_sgEZH2#1_dTAGEZH2_veh_9days_rep1


title: H23-KRAS-C12

source_name: H23 with mutant KRAS-C12 shRNA


title: week5 Transgen rep3


title: WCM154_sgEZH2#1_dTAGEZH2_dTAGv1_8hr_rep3


title: Butyrate4

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

description:
PS51BUT
Primary macrophages in culture treated with butyrate

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Assembly: GRCm38 - M. musculus
Supplementary files format and content: normalized TPMs

source_name: bone marrow

growth_protocol: alpha-MEM + 10% FBS + 1% PSQ + 10% L929-conditioned media

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform
RNA-seq, 75bp, paired-end sequencing

treatment_protocol: Cells were cultured in vehicle or butyrate for 7 days

value: bone marrow

value: macrophage

value: Wildtype mice

value: butyrate


title: WCM154_sgEZH2#1_dTAGEZH2_veh_8hr_rep3

value: pateint-dervied organoids


title: primary brain vessel endothelial cells, HA-IgG

value: HA


title: week5 Transgen rep2

value: kidney


title: PBS 21D rep 3

first: Kasia

last: Kready

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1.
UMI-based de-duplication was performed using fastp v.0.23.1 simultaneously.
Trimmed and de-duplicated reads were then mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: Trimmed and de-duplicated reads were then mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes TPM values for each Sample

source_name: mammary gland

growth_protocol: All animal work was approved by the Harvard Medical School IACUC under protocol IS00003310. C57bl/6j mice (Jackson; 000664) were mated at 8 weeks of age. On day 7 postpartum, litters were normalized to 5 pups per dam. Pups were weighed daily until they were weaned at day 21 postpartum or they reached endpoint (20% weight loss compared to positive controls).

extract_protocol:
Abdominal mammary glands were harvested and stored in RNAlater (Thermo Fisher Scientific, AM7020) overnight at 4C. Samples were then stored at -80C until submitted to Azenta/Genewiz for standard RNA sequencing. RNA extraction and PolyA selection was peformed by Azenta/Genewiz.
RNA library for RNA sequencing were constructed using the standard RNA sequencing package at Azenta/Genewiz

treatment_protocol: Beginning on day 7 postpartum, and every other day thereafter, dams were administered 5mg/kg dose of Prolactin-XL or a PBS control by subcutaneous. Dams were dosed until their pups were weaned at day 21 postpartum.

value: mammary gland

tag: age/sex

value: 6-20wk old, lactating  female with litter size n=5

value: WT

value: subcutaneous 100uL PBS every other day


title: PBS 21D rep 2


title: WCM154_sgEZH2#1_dTAGEZH2_dTAGv1_8hr_rep2

value: EZH2 rescue

value: 500 nM dTAGv1


title: Brain, E18, WT-2

value: Brain


title: H23-Ctrl

source_name: H23 with control shRNA

value: Lung cancer cell line

value: Adenocarcinoma


title: Brain, E18, KO-2


title: PBS 21D rep 1


title: PBS 18D rep 3


title: PBS 14D rep 2


title: week2 WT rep2

value: kidney cells

value: Doxcycyclin was added to the driniking water at a concentration of 1g/L for 2 W


title: PBS 18D rep 2


title: week1 WT rep3

value: Doxcycyclin was added to the driniking water at a concentration of 1g/L for 1 W


title: Brain, E18, WT-1


title: PBS 18D rep 1


title: WCM154_sgEZH2#1_dTAGEZH2_veh_8hr_rep1

value: prostate

value: vehicle


title: WCM154_sgEZH2#1_rep3

value: pateint-dervied organoids

value: EZH2 knockout


title: PBS 10D rep 2


title: week1 WT rep2

value: kidney


title: PBS 10D rep 3

value: mammary gland


title: week2 Transgen rep3

source_name: Specific Lin28A OE in the nephrons for 2W

value: Lox-stop-Lox-TetOn-Lin28A; Six2Cre


title: Butyrate1

description:
PS48BUT
Primary macrophages in culture treated with butyrate

value: bone marrow

value: macrophage

value: Wildtype mice

value: butyrate


title: WCM154_sgEZH2#1_rep2


title: PBS 14D rep 3

value: 6-20wk old, lactating  female with litter size n=5

value: WT

value: subcutaneous 100uL PBS every other day


title: Butyrate3

description:
PS50BUT
Primary macrophages in culture treated with butyrate


title: PBS 10D rep 1


title: week1 WT rep1

value: kidney cells


title: week2 Transgen rep2

value: Doxcycyclin was added to the driniking water at a concentration of 1g/L for 2 W


title: WCM154_sgEZH2#2_rep2


title: week2 Transgen rep1


title: Butyrate2

description:
PS49BUT
Primary macrophages in culture treated with butyrate


title: week1 Transgen rep3

source_name: Specific Lin28A OE in the nephrons for 1W

value: Doxcycyclin was added to the driniking water at a concentration of 1g/L for 1 W


title: WCM154_sgEZH2#2_rep1

value: prostate


title: PBS 14D rep 1


title: WCM154_sgEZH2#2_rep3


title: WCM154_sgINC_rep3


title: Vehicle4

description:
PS51CTRL
Primary macrophages in culture treated with vehicle

value: vehicle


title: week1 Transgen rep2


title: Vehicle1

description:
PS48CTRL
Primary macrophages in culture treated with vehicle


title: Vehicle3

description:
PS50CTRL
Primary macrophages in culture treated with vehicle


title: WCM154_sgINC_rep2

value: pateint-dervied organoids


title: Total peritoneal cells [pMac_scRNAseq]

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Assembly: GRCm38 - M. musculus
Supplementary files format and content: .tsv file with counts

source_name: Peritoneum

extract_protocol:
Single cells were loaded into droplets using 10X Chromium
mRNA library was prepared using the Illumina TruSeq platform

value: Peritoneum

value: Total peritoneal cells

value: total RNA


title: Vehicle2

description:
PS49CTRL
Primary macrophages in culture treated with vehicle


title: WCM154_sgEZH2#1_rep1

value: EZH2 knockout


title: PBS 9D rep 3

value: mammary gland


title: TEC organoids D7 biol rep1

city: Lausanne

first: Tania

last: Hübscher

address: Station 15

department: SV IBI

institute: EPFL

description: TEC organoids D7 biol rep1

data_processing:
Reads were aligned to the mouse genome (GRCm39) using star (version 2.7.0e).
R (version 4.1.2) was used to perform the differential expression analyses. Count values were imported and processed using edgeR.
Expression values were normalized using the trimmed mean of M values (TMM) method and lowly-expressed genes (< 1 counts per million) were filtered out.
Differentially expressed genes were identified using linear models (Limma-Voom), and P values were adjusted for multiple comparisons by applying the Benjamini-Hochberg correction method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include count values for each sample

source_name: Thymus

extract_protocol:
Sorted thymic epithelial cells were lysed in RLT buffer (QIAGEN, Catalog No. 74004) containing 40 mM DTT (ITW Reagents, Catalog No. A2948). Organoids were collected in cold PBS to dissolve Matrigel and then lysed in RLT buffer with DTT. Cells cultured in 2D were collected in RLT buffer with DTT. RNA was extracted using the QIAGEN RNeasy Micro Kit (QIAGEN, Catalog No. 74004) according to the manufacturer’s instructions.
Purified RNA was quality checked using a TapeStation 4200 (Agilent), and 88 ng were used for QuantSeq 3′ mRNA-Seq library construction according to the manufacturer’s instructions (Lexogen, Catalog No. 015.96).

value: Thymus

value: Organoids

value: No treatment


title: PBS 8D rep 2

value: 6-20wk old, lactating  female with litter size n=5


title: PBS 9D rep 2

value: WT


title: week1 Transgen rep1

value: kidney

value: Lox-stop-Lox-TetOn-Lin28A; Six2Cre


title: PBS 9D rep 1

value: subcutaneous 100uL PBS every other day


title: TEC organoids D7 biol rep2

description: TEC organoids D7 biol rep2


title: PBS 8D rep 3


title: PBS 8D rep 1


title: BMECs_b3KO_rep2

city: Heidelberg

first: Anouar

last: Belkacemi

address: Im Neuenheimer Feld 366

institute: Heidelberg University

data_processing:
Sequencing and data procession were performed by Novogene
Assembly: Hisat2 v2.0.5 software was used to map the paired-end clean reads to the reference genome
Supplementary files format and content: Excel files including FPKM

source_name: brain microvascular endothelial cells

growth_protocol: BMECs were maintained in DMEM medium containing 20% (v/v) fetal calf serum, 10 ng/mL Fibroblast Growth Factor, 100 ng/mL Heparin, 10,000 units/mL penicillin and 10 mg/mL streptomycin at 37°C and 5% CO2.

extract_protocol:
RNA was isolated from BMECs using the RNeasy Mini PLUS Kit following the manufacturer’s protocol
Sequencing libraries were generated via NEBNext® UltraTM RNA Library Prep Kit

value: brain microvascular endothelial cells

value: Cavb3 KO


title: Prolactin-XL 21D rep 3

value: subcutaneous 5mg/kg Prolactin-XL every other day


title: 2D cultured TECs biol rep2

description: 2D cultured TECs biol rep2


title: Bladder,  β‐Catenin negative 7

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
RNA sequencing reads were aligned to the human reference genome (GRCh38) by using the Subread (version 2.0.3) package
To quantify gene expression levels, we utilized the featureCounts function (Liao et al, 2014) within the Rsubread package.
Assembly: hg38
Supplementary files format and content: featureCounts(.csv)

source_name: Human urinary bladder tumor

extract_protocol:
RNA samples were isolated from FFPE samples
Libraries were prepared using an Illumina Truseq RNA Exome Kit (Illumina, San Diego, CA, United States), which is specific for RNA isolated from formalin-fixed paraffin-embedded tissues (FFPE), according to the manufacturer’s recommendations. Paired-end sequencing for total RNA was performed on Illumina NovaSeq 600 with 150 bp read lengths.
Truseq RNA Exome Kit

value: Human urinary bladder tumor


title: Bladder, SCCB 2


title: TEC organoids D3 biol rep2

description: TEC organoids D3 biol rep2


title: Bladder,  β‐Catenin negative 6


title: Bladder, SCCB 1


title: TEC organoids D3 biol rep1

description: TEC organoids D3 biol rep1


title: BMECs_b3KO_rep3


title: 2D cultured TECs biol rep1

description: 2D cultured TECs biol rep1


title: WCM154_sgINC_rep1

extract_protocol:
RNA was extracted using Qiagen column purification kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: prostate

value: pateint-dervied organoids


title: Prolactin-XL 21D rep 1


title: BMECs_WT_rep3

value: Wild-type


title: BMECs_b3KO_rep1


title: Bladder,  β‐Catenin negative 5


title: Bladder, SCCB 3


title: Prolactin-XL 21D rep 2


title: BMECs_b3KO_rep4


title: BMECs_WT_rep4


title: BMECs_WT_rep2


title: Prolactin-XL 18D rep 3


title: BMECs_WT_rep1


title: Bladder,  β‐Catenin negative 4


title: Prolactin-XL 18D rep 2


title: Bladder,  β‐Catenin negative 3


title: E13.5 Spinal cord, RNA, NFIA conditional knockout3

city: La Jolla

first: Stacey

middle: Marie

last: Glasgow

state: California

address: 9500 Gilman Dr, 3216 Pacific Hall

institute: University of California San Diego

data_processing:
Adaptor trimmed FASTQ paired- end reads were aligned using STAR (v.2.6.1a) to a mouse reference genome (mm10; --genome Dir /mouse/mm10/ --sjdbGTFfile gencode.vM10.primary_assembly.annotation.gtf).
Transcripts were quantified using HTSeq, data was normalized using RUV-seq and differential gene expression analysis was conducted using DESeq2.
Assembly: mm10
Supplementary files format and content: raw counts
Supplementary files format and content: bigWig

source_name: Spinal cord

growth_protocol: NFIA-ff (control) and NFIA-ff;Nestin-cre (NFIAcKO) embryos were harvested at E13.5 and whole spinal cords extracted.

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using the Illumina® Stranded mRNA Prep kit according to manufacturer protocols.

value: Spinal cord

value: NFIA-ff, Nestin-cre


title: BVLO #2

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

institute: The University of Tokyo

description:
IonXpress_008
20211222.rpm.bcmatrix.txt

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary files format and content: *.rpm.bcmatrix.txt: Tab-delimited text files include RPM values for each sample.

source_name: iPSC derived cells

growth_protocol: The human iPSC lines Ff-I01s04 were kindly provided by Kyoto University. All iPSC lines were maintained on dishes coated with the laminin 511E8 fragment (iMatrix-511TM, Nippi) in StemFit AK02N medium (Ajinomoto, Tokyo, Japan). The use of human iPSCs was approved by the ethics committee of University of Tokyo. Differentiation of hiPSC into Hepatic endoderm (HE), endothelial (EC), and mesenchymal cells (MC) were done as described previously (Takebe T et al. Cell reports 2017).

extract_protocol:
RNA was extracted with PureLink™ RNA Mini Kit (Invitrogen, Waltham, Massachusetts, USA) from planar-cultured cells according to the manufacturer’s instructions. PureLink™ RNA Micro Scale Kit (Invitrogen, Waltham, Massachusetts, USA) was used for RNA extraction from sorted cells.
RNA libraries were prepared using 30 ng of total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific).

treatment_protocol: Generation of hiPSC-derived liver bud was carried out as described previously (Takebe T et al. Cell reports 2017).

value: iPSC derived organoid


title: BVLO #3

description:
IonXpress_009
20211222.rpm.bcmatrix.txt


title: Bladder,  β‐Catenin negative 2


title: Freshly extracted TECs biol rep1

description: Freshly extracted TECs biol rep1

value: Thymus

value: In vivo


title: Freshly extracted TECs biol rep2

description: Freshly extracted TECs biol rep2

value: No treatment


title: Prolactin-XL 18D rep 1

value: mammary gland

value: 6-20wk old, lactating  female with litter size n=5

value: WT


title: E13.5 Spinal cord, RNA, NFIA conditional knockout2


title: Bladder,  β‐Catenin negative 1


title: Bladder,  β‐Catenin positive 21


title: E13.5 Spinal cord, RNA, Control3

value: NFIA-ff


title: LO #2

description:
IonXpress_006
20211222.rpm.bcmatrix.txt


title: E13.5 Spinal cord, RNA, Control2


title: LO #1

description:
IonXpress_005
20211222.rpm.bcmatrix.txt


title: Prolactin-XL 14D rep 2


title: Bladder,  β‐Catenin positive 19


title: Prolactin-XL 14D rep 3


title: Prolactin-XL 10D rep 3


title: Bladder,  β‐Catenin positive 22


title: E13.5 Spinal cord, RNA, NFIA conditional knockout1


title: Prolactin-XL 14D rep 1


title: IH (day12)

description:
IonXpress_026
20210121.rpm.bcmatrix.txt

value: iPSC derived hepatic cell lineage


title: Bladder,  β‐Catenin positive 20


title: MH (day21)

description:
IonXpress_029
20210121.rpm.bcmatrix.txt


title: E13.5 Spinal cord, RNA, Control1


title: IH (day14)

description:
IonXpress_028
20210121.rpm.bcmatrix.txt


title: Prolactin-XL 10D rep 2


title: E13.5 Spinal cord, Input

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (Q >= 25) were used for further  analysis.
Alignments were extended at their 3’-ends to 200 bp,  assigned to 32-nt bins along the genome, and formatted as bigWig files.
Peaks were called using MACS v2.1.0 with a cutoff p-value= 1e-7
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: Wildtype embryos were harvested at E13.5 and whole spinal cords extracted

extract_protocol:
Spinal cords were homogenized and fixed with 1% formaldehyde for 15 min. After quenching  and lysis, chromatin was sonicated and the DNA sheared to an average length of 300-500 bp using Active Motif’s EpiShear probe sonicator (cat# 53051).
Genomic DNA (Input) was prepared by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). 40 μg of DNA was used as a starting material for input and IP. Libraries were prepared using an automated system (Apollo 42, Wafergen Biosystems/Takara) and sequenced  on  Illumina NovaSeq 6000 sampes. Immunoprecipitation was performed with 30 μL of anti NFIA antibody (Atlas Antibodies, #HPA008884).

value: wildtype


title: Prolactin-XL 10D rep 1

value: subcutaneous 5mg/kg Prolactin-XL every other day


title: HE (day10)

description:
IonXpress_025
20210121.rpm.bcmatrix.txt