title: CN5 - Control Normoxia

description:
Library name: CN5
Column name in raw counts all_sample_deseq.csv: CN5

value: Control Normoxia


title: CN4 - Control Normoxia

status: Public on Jun 16 2025

type: SRA

city: Oxford

first: Ryan

middle: Daniel

last: Carter

address: Sherrington Building, Sherrington Rd

department: DPAG

country: United Kingdom

institute: University of Oxford

description:
Library name: CN4
Column name in raw counts all_sample_deseq.csv: CN4

library_source: transcriptomic

data_processing:
Quality control was performed with FastQC, trimming with cutadapt to remove adaptors and low-quality sequences
Transcript quantification for hiPSC-CM was executed with Salmon using decoys and a gentrome indexed from the gencode v44 GRCh38
Gene level counts were summarised using tximport
Assembly: gencode v44 GRCh38
Supplementary files format and content: raw gene counts in csv format

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: IMR90 human induced pluripotent stem cells (hiPSCs) were differentiated into hiPSC-derived cardiomyocytes (hiPSC-CMs) using a Wnt signaling modulation protocol. Cells were grown to confluency in TeSR-E8 media on Matrigel-coated plates, then differentiated over 15 days. Key steps included treatment with CHIR99021 (days 0-1), Wnt-C59 (day 3), and glucose-free media (days 11-13) for metabolic selection. From day 15, cells were maintained in RB+ media (RPMI with B27 complete).

extract_protocol:
Cells were washed in PBS, lysed using the RNAeasy kit QIAzol lysis agent, scraped, and homogenised using needles before being flash-frozen in liquid nitrogen. RNA was extracted from the lysates using the Qiagen RNeasy Mini kit following the manufacturer’s protocol.
Stranded paired 150-bp poly-A enrichment protocol by Novogene

treatment_protocol: Insulin resistance (IR) was induced in hiPSC-CMs or EHTs using a six-day protocol with two media types: glucose-free IR media (3 days) and glucose-enriched IR media (3 days), both containing palmitic acid, insulin, and supplements. Controls were cultured in maturation media. For some experiments, hiPSC-CMs were exposed to high palmitate media (0.4 mM palmitate) or hypoxia (2% O2 for 16 hours), with controls in normoxia (21% O2).

tag: cell line

tag: cell type

value: hiPSC cardiomyocytes

tag: treatment


title: CN3 - Control Normoxia

description:
Library name: CN3
Column name in raw counts all_sample_deseq.csv: CN3


title: IRH4 - Insulin Resistant Hypoxia

description:
Library name: IRH4
Column name in raw counts all_sample_deseq.csv: IRH4

value: Insulin Resistant Hypoxia


title: IRN4 - Insulin Resistant Normoxia

description:
Library name: IRN4
Column name in raw counts all_sample_deseq.csv: IRN4

value: Insulin Resistant Normoxia


title: IRH3 - Insulin Resistant Hypoxia

description:
Library name: IRH3
Column name in raw counts all_sample_deseq.csv: IRH3


title: IRH2 - Insulin Resistant Hypoxia

description:
Library name: IRH2
Column name in raw counts all_sample_deseq.csv: IRH2


title: CN1 - Control Normoxia

description:
Library name: CN1
Column name in raw counts all_sample_deseq.csv: CN1


title: IL1B_rep3

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

country: USA

institute: UCSD

description: Library name: IL1B_rep3

library_source: genomic

data_processing:
ATAC-seq FASTQ files  were trimmed to 30 bp. ATAC-seq and ChIP-seq FASTQ were mapped to mm10 or hg38 using Bowtie 2 with default parameters.
After mapping, tag directories were created using the HOMER (Heinz et al., Mol Cell 2010) command 'makeTagDirectory'.
ATAC-seq experiments were performed in replicates with corresponding input experiments. Peaks were called with HOMER 's 'findPeaks'for each tag directory with relaxed peak finding parameters “-L 0 -C 0 -fdr 0.9”.
IDR was used to test for reproducibility between replicates, only peaks with an IDR < 0.05 were used for downstream analyses. Peak sets from all pairwise IDR comparisons were merged into a final set of peaks for further analysis.
To quantify the chromatin accessibility between conditions, raw and normalized tag counts at merged IDR peaks called by HOMER’s 'mergePeaks' were identified using HOMER’s 'annotatePeaks' with “-noadj,”  “-size 200". DESeq2 was used to identify differentially differential distal chromatin accessibility (p-adj. < 0.05 and FC >2 or <-2).
Assembly: hg38
Supplementary files format and content: annotated peaks with raw and normalzied counts

molecule: genomic DNA

source_name: brain

extract_protocol:
Cells were lysed in 50 µl lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 in water). Resulting nuclei were centrifuged at 500xg for 10 min.
Pelleted nuclei were resuspended in 50 μL transposase reaction mix (47.5 μL ATAC lysis bufferand 2.5 μL Tagment DNA TDE1 enzyme I (Illumina, 20034197)) and incubated at 37°C for 30 min. DNA was purified with Zymo ChIP DNA concentrator columns (Zymo Research, D5205), eluted with 11 µL of elution buffer, and amplified using NEBNext High-Fidelity 2x PCR Master Mix (New England BioLabs, M0541) with the Nextera primer Ad1 (1.25 µM) and a unique barcoding primer Ad2 (1.25 µM) for 8-12 cycles. Resulting libraries were size selected by gel excision to 155–250 bp

tag: tissue

value: brain

value: primary

value: primary astrocytes

tag: genotype

value: control


title: Vehicle_rep3

description: Library name: Vehicle_rep3


title: IgG

city: Nanjing

first: Cong

last: Wang

address: 639, Longmi Avenue

country: China

institute: China Pharmaceutical University

description:
Library name: IgG_CHIP
The raw data are being made available for controlled access in dbDaP

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018)software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content ofthe clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to thereference genome using BWA mem (v 0.7.12).
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and presentsignificant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al.,2008) predicted method with default parameters. MACS2 scan all the genome with a specific windowsize and calculate the reads enrichment level. A particular number of windows were used as samples tobuild enrichment model and to predict fragment size. The following peak calling analysis was based onthis predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak callingsoftware to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for alldata sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment,significant level and peak summit number per peak were all displayed.
The interaction between transcript factor or chromatin histone modification and DNA were not random,while they show some specific sequence preference. Homer (Heinz et al., 2010) was used to detect thedenovo sequence motif and the matched known motifs.
Assembly: hg18
Supplementary files format and content: bigWig

growth_protocol: DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin.

extract_protocol:
cells were firstly crosslinked with 1% paraformaldehyde. After addtion of glycine solution , cells were lysed with cell lysis buffer and nuclear lysis buffer.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by NovogeneCorporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illuminaplatform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: ovarian cancer

value: wt


title: CH4 - Control Hypoxia

description:
Library name: CH4
Column name in raw counts all_sample_deseq.csv: CH4

value: Control Hypoxia


title: CH5 - Control Hypoxia

description:
Library name: CH5
Column name in raw counts all_sample_deseq.csv: CH5


title: CH3 - Control Hypoxia

description:
Library name: CH3
Column name in raw counts all_sample_deseq.csv: CH3


title: CH1 - Control Hypoxia

description:
Library name: CH1
Column name in raw counts all_sample_deseq.csv: CH1


title: CH2 - Control Hypoxia

description:
Library name: CH2
Column name in raw counts all_sample_deseq.csv: CH2


title: IRH1 - Insulin Resistant Hypoxia

description:
Library name: IRH1
Column name in raw counts all_sample_deseq.csv: IRH1


title: T-PLL patient sample P16, 8h, JPX

city: Leipzig

first: Marco

last: Herling

address: Johannisallee 32a

department: Department for Hematology, Cell Therapy, Hemostaseology, and Infectious Diseases

country: Germany

institute: University Clinic Leipzig

description: Library name: 82

data_processing:
RNA sequencing reads were aligned to the hg38 reference genome using Bowtie2 (version 2.3.5.1) with default settings. Quality control was performed using FastQC and MultiQC. Samtools 1.10 was utilized post-alignment for sorting and indexing the aligned reads
Gene-level counts were quantified using the Rsubread package (version 2.14.2) with the featureCounts function.
Assembly: hg38
Supplementary files format and content: Text file includes raw counts for each sample

molecule: total RNA

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was isolated using the Qiagen RNeasy Plus Mini Kit (#74134) according to the manufacturer’s instructions. RNA quality and concentration were assessed using the 4150 TapeStation (Agilent, Santa Clara, USA).
Library preparation was conducted with the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (rRNA-depleted total mRNA, #20020599). The samples were processed without ERCC RNA Spike-In controls. Paired-end sequencing (2x100bp) was performed with 50 million reads per sample.

tag: diagnosis

value: T-PLL

value: Peripheral blood mononuclear cells


title: T-PLL patient sample P16, 24h, JPX

description: Library name: 86


title: T-PLL patient sample P16, 8h, control

description: Library name: 81


title: T-PLL patient sample P26, 24h, JPX

description: Library name: 78


title: T-PLL patient sample P16, 24h, control

description: Library name: 85


title: T-PLL patient sample P16, 8h, control + IL6

description: Library name: 83


title: T-PLL patient sample P26, 8h, JPX

description: Library name: 74


title: CN2 - Control Normoxia

description:
Library name: CN2
Column name in raw counts all_sample_deseq.csv: CN2


title: T-PLL patient sample P26, 24h, JPX + IL6

description: Library name: 80


title: T-PLL patient sample P16, 8h, JPX + IL6

description: Library name: 84


title: T-PLL patient sample P26, 24h, control

description: Library name: 77


title: T-PLL patient sample P26, 24h, control + IL6

description: Library name: 79


title: T-PLL patient sample P26, 8h, control

description: Library name: 73


title: T-PLL patient sample P19, 24h, JPX + IL6

description: Library name: 72


title: T-PLL patient sample P16, 24h, control + IL6

description: Library name: 87


title: T-PLL patient sample P16, 24h, JPX + IL6

description: Library name: 88


title: T-PLL patient sample P26, 8h, JPX + IL6

description: Library name: 76


title: T-PLL patient sample P19, 24h, control

description: Library name: 69


title: T-PLL patient sample P26, 8h, control + IL6

description: Library name: 75


title: T-PLL patient sample P19, 24h, JPX

description: Library name: 70


title: T-PLL patient sample P19, 24h, control + IL6

description: Library name: 71


title: T-PLL patient sample P19, 8h, JPX + IL6

description: Library name: 68


title: T-PLL patient sample P19, 8h, control + IL6

description: Library name: 67


title: T-PLL patient sample P19, 8h, JPX

description: Library name: 66


title: T-PLL patient sample P14, 24h, JPX + IL6

description: Library name: 64


title: T-PLL patient sample P19, 8h, control

description: Library name: 65


title: T-PLL patient sample P14, 24h, control + IL6

description: Library name: 63


title: T-PLL patient sample P14, 24h, JPX

description: Library name: 62


title: T-PLL patient sample P14, 24h, control

description: Library name: 61


title: T-PLL patient sample P14, 8h, JPX + IL6

description: Library name: 60


title: T-PLL patient sample P14, 8h, control + IL6

description: Library name: 59


title: T-PLL patient sample P21, 8h, JPX + IL6

description: Library name: 52


title: T-PLL patient sample P14, 8h, control

description: Library name: 57


title: T-PLL patient sample P21, 24h, JPX + IL6

description: Library name: 56


title: T-PLL patient sample P21, 8h, JPX

description: Library name: 50


title: T-PLL patient sample P21, 8h, control

description: Library name: 49


title: T-PLL patient sample P21, 24h, control + IL6

description: Library name: 55


title: T-PLL patient sample P21, 24h, JPX

description: Library name: 54


title: H3K4me3_co-culture_ESCs

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Library name: Sample12

data_processing:
Aligned using bowtie2 with paramters --local --very-sensitive --no-mixed --no-discordant
Assembly: mm10
Supplementary files format and content: bigWig: normalized read coverage
Library strategy: CUT&Tag

organism: Mus musculus

source_name: cell line

growth_protocol: The ESCs were cultured on 0.1% gelatin-coated dishes at 37°C in a 5% CO2 atmosphere. The DMEM/10% FBS medium was prepared by supplementing DMEM (Gibco) with 10% FBS (Gibco), 0.1 mM β-mercaptoethanol (Sigma), 1% MEM Non-Essential Amino Acids Solution (Gibco), and 2 mM L-glutamine (Gibco). To expand naive-state ESC, 3 µM CHIR-99021 (Selleckchem), 1 µM PD03 (Selleckchem), and 20 ng/ml LIF (Peprotech) (2iL) were added to the DMEM/FBS  medium. E14TG2a ESC cultured under 2iL conditions in DMEM/FBS medium. For  Primed PSCs' condition, 20 ng/ml Activin A (PeproTech), 20 ng/ml bFGF (PeproTech), and 2 µM XAV-939 (Sigma) were added to  the DMEM/FBS  medium. The co-cultureed ESCs/EpiSCs were cultured on 0.1% gelatin-coated dishes at 37°C in a 5% CO2 atmosphere in BRD0705/IWR1 medium, on feeders. For BRD0705/IWR conditions, 8 µM BRD0705 (Cayman Chemical) and 2.5 µM IWR-1 (Selleckchem) were added to the N2B27. DMEM/F12-N2 medium was prepared by adding 1 ml of N2 (Gibco) 100× stock solution to 100 ml of DMEM/F12. For Neurobasal/B27 medium, 2 ml of B27 (Gibco) and 2 mM L-glutamine were added to 100 ml of Neurobasal medium. N2B27 medium was prepared by mixing DMEM/F12-N2 medium with Neurobasal/B27 medium at a 1:1 ratio, followed by the addition of 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Co-cultured cells and sepreated cultured naive/primed ESCs were trypsinized and dissociated for CUT&TAG against H3K37me3, H3K27ac and H3K4me3 following the mannual protocol,  Epicypher CUTANA CUT&Tag Kit.
We used Cleavage under targets and Tagmentation (Cut-and-Tag) against H3K37me3, H3K27ac and H3K4me3 in co-cultured ESCs/EpiSCs and sepreated cultured naive/primed ESCs, using the Epicypher CUTANA CUT&Tag Kit. Sequencing was carried out on Illumina sequencers.

value: ESCs

value: WT


title: T-PLL patient sample P21, 8h, control + IL6

description: Library name: 51


title: T-PLL patient sample P06, 8h, control + IL6

description: Library name: 43


title: T-PLL patient sample P06, 8h, control

description: Library name: 41


title: H3K4me3_primed EpiSCs

description: Library name: Sample10


title: T-PLL patient sample P06, 24h, JPX

description: Library name: 46


title: T-PLL patient sample P36, 24h, JPX + IL6

description: Library name: 40


title: T-PLL patient sample P06, 8h, JPX + IL6

description: Library name: 44


title: T-PLL patient sample P06, 24h, control

description: Library name: 45


title: T-PLL patient sample P06, 24h, control + IL6

description: Library name: 47


title: H3K4me3_co-culture_EpiSCs

description: Library name: Sample11


title: H3K4me3_naive ESCs

description: Library name: Sample09


title: H3K27me3_primed EpiSCs

description: Library name: Sample06


title: H3K27me3_co-culture_EpiSCs

description: Library name: Sample07


title: H3K27me3_co-culture_ESCs

description: Library name: Sample08


title: H3K27me3_naive ESCs

description: Library name: Sample05


title: T-PLL patient sample P06, 8h, JPX

description: Library name: 42


title: T-PLL patient sample P36, 24h, control + IL6

description: Library name: 39


title: T-PLL patient sample P36, 24h, JPX

description: Library name: 38


title: T-PLL patient sample P36, 24h, control

description: Library name: 37


title: T-PLL patient sample P14, 8h, JPX

description: Library name: 58


title: T-PLL patient sample P21, 24h, control

description: Library name: 53


title: T-PLL patient sample P36, 8h, JPX + IL6

description: Library name: 36


title: H3K27ac_co-culture_ESCs

description: Library name: Sample04


title: H3K27ac_co-culture_EpiSCs

description: Library name: Sample03


title: T-PLL patient sample P06, 24h, JPX + IL6

description: Library name: 48


title: H3K27ac_primed EpiSCs

description: Library name: Sample02


title: H3K27ac_naive ESCs

description: Library name: Sample01


title: T-PLL patient sample P36, 8h, control

description: Library name: 33


title: CD11b+, Mandible, rep2

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

description: Library name: Mandible_rep2

data_processing:
ATAC-Seq fastq files were checked for quality with fastqc and metrics were aggregated with multiQC.Trimmomatic was used to trim low quality sequence and adapters.
Trimmed reads were aligned to the GRCm39 Mus musculus genome using Bowtie2. 21 Mapped reads with MAPQ < 20 were removed using samtools22 and then picard was used to mark and remove duplicates.
Peak calling was performed with Genrich in ATAC mode for each pair of sample duplicates.
Femur and mandible peaks were merged with bedtools merge and then a GTF file was created using a custom python script.
featureCounts was used to quantify peaks for each of the 4 sample bam files and to calculate the Fraction of Reads in Peaks (FRIP) QC metric. All samples passed the ENCODE recommended FRIP score threshold of 30%, the average FRIP score was 37.9%.
Normalized bigWig files were created with deeptools.
Assembly: GRCm39
Supplementary files format and content: bigWig and count txt files for peak signals

source_name: mandible

extract_protocol:
Monocytes were selected following the protocol of the mouse monocyte isolation kit (Miltenyi Biotec, catalog #130-100-629). Briefly, flushed cells were pelleted and resuspended in MACS buffer (phosphate–buffered saline (PBS), pH 7.2, 0.5% bovine serum albumin, 2 mM EDTA). The cells then were incubated with FCR Blocking Reagent and Monocyte Biotin–Antibody Cocktail. After five minutes the cells were rinsed with MACS buffer, pelleted, and resuspended in MACS buffer. The cells were incubated with Anti–Biotin Microbeads for 10 min. After this incubation period the cells were applied to the MACS column in a magnetic field. Flow through was collected as isolated monocytes. The columns were rinsed three times to collect unbound monocyte cells. Collected monocyte cells were counted and volume required for 20,000 cells was calculated. Volumes were pelleted and washed with 50 μl of PBS. After wash cells were pelleted and resuspended in 50 μl of ATAC-Seq Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and spun for 10 minutes. Cells were pelleted and resuspended in transposition mixture consisting of 25 μl TD (Illumina catalog #121-1030), 2.5 μl TDE1 (Nextera Tn5 Transposase, Illumina Cat #FC-121-1030) and 22.5 μl nuclease free water and incubated in mixture for 30 minutes.
Nextera Tn5 Transposase, Illumina Cat #FC-121-1030 was used for ATAC-library generation

value: mandible

tag: Sex

value: male

tag: age

value: 2 months

tag: batch

value: B


title: T-PLL patient sample P07, 24h, JPX + IL6

description: Library name: 32


title: CD11b+, Femur, rep2

description: Library name: Femur_rep2

source_name: femur

value: femur


title: T-PLL patient sample P07, 24h, control + IL6

description: Library name: 31


title: T-PLL patient sample P07, 24h, control

description: Library name: 29


title: CD11b+, Femur, rep1

description: Library name: Femur_rep1

value: A


title: T-PLL patient sample P07, 8h, JPX + IL6

description: Library name: 28


title: T-PLL patient sample P07, 24h, JPX

description: Library name: 30


title: T-PLL patient sample P36, 8h, control + IL6

description: Library name: 35


title: Zygote_P2_070723_gDNA_C12_S65

first: Micah

last: Gearhart

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

description: Library name: Zygote_P2_070723_gDNA_C12_S65

data_processing:
gDNA was processed using the Kronos scRT computational pipeline. cDNA samples were processed using Seurat pipeline.
Assembly: GRCm39
Supplementary files format and content: cDNA samples were processed using Seurat pipeline and the counts matrix of genes expressed per cell was generated. gDNA coverage plots were processed and present as bigWig files.

source_name: Zygote

extract_protocol:
Mouse zygotes at E0.5 were extracted from super ovulated C57/Bl6 mice. Zygotes were cultured in vitro until 2-cell and 4-cell stages. Zygotes/1-cell embryos were directly transferred into RLT buffer in 96-well plates with 1 zygote/ well. Single cells from 2-cell embryos were extracted 26-28 hours after zygote extraction. Single cells from 4-cell embryos were extracted 38-40 hours after zygote extraction. For 2-cell and 4-cell stages, first the zona pellucida was removed using the Tyrode Acid Solution, then the embryos were incubated in TrypLE: Accutase (1:3) solution for ~10 minutes until the embryos dissociated into single cells. Single cells were then mouth pipetted into individual wells of a 96-well plate containing RLT buffer. The wells were spun down and stored at -20C until further processing.
Nextera XT DNA Library Prep Kit was used for for each sample. Nextera XT 96-index kit was used to barcode each sample. All samples were pooled together before sequencing on the same chip.

value: Zygote


title: Zygote_P2_070723_gDNA_C7_S60

description: Library name: Zygote_P2_070723_gDNA_C7_S60


title: Zygote_P2_070723_gDNA_C11_S64

description: Library name: Zygote_P2_070723_gDNA_C11_S64


title: T-PLL patient sample P11, 24h, JPX + IL6

description: Library name: 24


title: Zygote_P2_070723_gDNA_C10_S63

description: Library name: Zygote_P2_070723_gDNA_C10_S63


title: Zygote_P2_070723_gDNA_C9_S62

description: Library name: Zygote_P2_070723_gDNA_C9_S62


title: T-PLL patient sample P07, 8h, JPX

description: Library name: 26


title: Zygote_P2_070723_gDNA_C8_S61

description: Library name: Zygote_P2_070723_gDNA_C8_S61


title: T-PLL patient sample P11, 24h, control + IL6

description: Library name: 23


title: T-PLL patient sample P07, 8h, control

description: Library name: 25


title: Zygote_P2_070723_gDNA_C5_S58

description: Library name: Zygote_P2_070723_gDNA_C5_S58


title: Zygote_P2_070723_gDNA_C4_S57

description: Library name: Zygote_P2_070723_gDNA_C4_S57


title: Zygote_P2_070723_gDNA_C6_S59

description: Library name: Zygote_P2_070723_gDNA_C6_S59


title: CD11b+, Mandible, rep1

description: Library name: Mandible_rep1


title: T-PLL patient sample P11, 8h, control + IL6

description: Library name: 19


title: T-PLL patient sample P36, 8h, JPX

description: Library name: 34


title: T-PLL patient sample P11, 24h, control

description: Library name: 21


title: T-PLL patient sample P11, 8h, JPX + IL6

description: Library name: 20


title: Zygote_P2_070723_gDNA_C2_S55

description: Library name: Zygote_P2_070723_gDNA_C2_S55


title: T-PLL patient sample P15, 24h, control + IL6

description: Library name: 15


title: T-PLL patient sample P11, 8h, JPX

description: Library name: 18


title: T-PLL patient sample P15, 24h, control

description: Library name: 13


title: T-PLL patient sample P07, 8h, control + IL6

description: Library name: 27


title: Zygote_P2_070723_gDNA_C1_S54

description: Library name: Zygote_P2_070723_gDNA_C1_S54


title: Zygote_P2_070723_gDNA_B8_S49

description: Library name: Zygote_P2_070723_gDNA_B8_S49


title: Zygote_P2_070723_gDNA_B6_S47

description: Library name: Zygote_P2_070723_gDNA_B6_S47


title: T-PLL patient sample P11, 24h, JPX

description: Library name: 22


title: T-PLL patient sample P15, 8h, control

description: Library name: 9


title: Zygote_P2_070723_gDNA_B4_S45

description: Library name: Zygote_P2_070723_gDNA_B4_S45


title: T-PLL patient sample P15, 8h, JPX

description: Library name: 10


title: T-PLL patient sample P11, 8h, control

description: Library name: 17


title: Zygote_P2_070723_gDNA_B12_S53

description: Library name: Zygote_P2_070723_gDNA_B12_S53


title: Zygote_P2_070723_gDNA_B2_S43

description: Library name: Zygote_P2_070723_gDNA_B2_S43


title: T-PLL patient sample P15, 24h, JPX + IL6

description: Library name: 16


title: T-PLL patient sample P15, 24h, JPX

description: Library name: 14


title: Zygote_P2_070723_gDNA_B10_S51

description: Library name: Zygote_P2_070723_gDNA_B10_S51


title: Zygote_P2_070723_gDNA_B1_S42

description: Library name: Zygote_P2_070723_gDNA_B1_S42


title: Zygote_P2_070723_gDNA_B9_S50

description: Library name: Zygote_P2_070723_gDNA_B9_S50


title: T-PLL patient sample P15, 8h, JPX + IL6

description: Library name: 12


title: Zygote_P2_070723_gDNA_B11_S52

description: Library name: Zygote_P2_070723_gDNA_B11_S52


title: Zygote_P2_070723_gDNA_B7_S48

description: Library name: Zygote_P2_070723_gDNA_B7_S48


title: T-PLL patient sample P01, 8h, JPX

description: Library name: 2


title: Zygote_P2_070723_gDNA_C3_S56

description: Library name: Zygote_P2_070723_gDNA_C3_S56


title: Zygote_P2_070723_gDNA_B5_S46

description: Library name: Zygote_P2_070723_gDNA_B5_S46


title: Zygote_P2_070723_gDNA_A11_S40

description: Library name: Zygote_P2_070723_gDNA_A11_S40


title: T-PLL patient sample P15, 8h, control + IL6

description: Library name: 11


title: T-PLL patient sample P01, 24h, control + IL6

description: Library name: 7


title: Zygote_P2_070723_gDNA_B3_S44

description: Library name: Zygote_P2_070723_gDNA_B3_S44


title: T-PLL patient sample P30, untouched

description: Library name: P30


title: T-PLL patient sample P01, 24h, control

description: Library name: 5


title: T-PLL patient sample P01, 8h, control

description: Library name: 1


title: Zygote_P2_070723_gDNA_A7_S36

description: Library name: Zygote_P2_070723_gDNA_A7_S36


title: T-PLL patient sample P29, untouched

description: Library name: P29


title: Zygote_P2_070723_gDNA_A8_S37

description: Library name: Zygote_P2_070723_gDNA_A8_S37


title: Zygote_P2_070723_gDNA_A10_S39

description: Library name: Zygote_P2_070723_gDNA_A10_S39


title: Zygote_P2_070723_gDNA_A9_S38

description: Library name: Zygote_P2_070723_gDNA_A9_S38


title: Zygote_P2_070723_gDNA_A6_S35

description: Library name: Zygote_P2_070723_gDNA_A6_S35


title: T-PLL patient sample P31, untouched

description: Library name: P31


title: T-PLL patient sample P32, untouched

description: Library name: P32


title: T-PLL patient sample P01, 8h, control + IL6

description: Library name: 3


title: T-PLL patient sample P28, untouched

description: Library name: P28


title: Zygote_P2_070723_gDNA_A5_S34

description: Library name: Zygote_P2_070723_gDNA_A5_S34


title: T-PLL patient sample P01, 8h, JPX + IL6

description: Library name: 4


title: Zygote_P2_070723_gDNA_A12_S41

description: Library name: Zygote_P2_070723_gDNA_A12_S41


title: T-PLL patient sample P24, untouched

description: Library name: P24


title: T-PLL patient sample P27, untouched

description: Library name: P27


title: T-PLL patient sample P25, untouched

description: Library name: P25


title: Zygote_P2_070723_gDNA_A3_S32

description: Library name: Zygote_P2_070723_gDNA_A3_S32


title: Zygote_P2_070723_gDNA_A2_S31

description: Library name: Zygote_P2_070723_gDNA_A2_S31


title: Zygote_P2_070723_gDNA_A1_S30

description: Library name: Zygote_P2_070723_gDNA_A1_S30


title: T-PLL patient sample P23, untouched

description: Library name: P23


title: T-PLL patient sample P22, untouched

description: Library name: P22


title: Zygote_P2_070723_cDNA_C10_S28

description: Library name: Zygote_P2_070723_cDNA_C10_S28

library_source: transcriptomic single cell


title: Zygote_P2_070723_cDNA_C11_S29

description: Library name: Zygote_P2_070723_cDNA_C11_S29


title: T-PLL patient sample P21, untouched

description: Library name: P21


title: Zygote_P2_070723_cDNA_C9_S27

description: Library name: Zygote_P2_070723_cDNA_C9_S27


title: T-PLL patient sample P19, untouched

description: Library name: P19


title: Zygote_P2_070723_cDNA_C8_S26

description: Library name: Zygote_P2_070723_cDNA_C8_S26


title: T-PLL patient sample P18, untouched

description: Library name: P18


title: T-PLL patient sample P17, untouched

description: Library name: P17


title: Zygote_P2_070723_cDNA_C6_S24

description: Library name: Zygote_P2_070723_cDNA_C6_S24


title: Zygote_P2_070723_cDNA_C5_S23

description: Library name: Zygote_P2_070723_cDNA_C5_S23


title: T-PLL patient sample P20, untouched

description: Library name: P20


title: Zygote_P2_070723_cDNA_C7_S25

description: Library name: Zygote_P2_070723_cDNA_C7_S25


title: T-PLL patient sample P26, untouched

description: Library name: P26


title: T-PLL patient sample P16, untouched

description: Library name: P16


title: Zygote_P2_070723_cDNA_C3_S21

description: Library name: Zygote_P2_070723_cDNA_C3_S21


title: Zygote_P2_070723_gDNA_A4_S33

description: Library name: Zygote_P2_070723_gDNA_A4_S33


title: T-PLL patient sample P14, untouched

description: Library name: P14


title: T-PLL patient sample P13, untouched

description: Library name: P13


title: Zygote_P2_070723_cDNA_C4_S22

description: Library name: Zygote_P2_070723_cDNA_C4_S22


title: Zygote_P2_070723_cDNA_C2_S20

description: Library name: Zygote_P2_070723_cDNA_C2_S20


title: Zygote_P2_070723_cDNA_C1_S19

description: Library name: Zygote_P2_070723_cDNA_C1_S19


title: Zygote_P2_070723_cDNA_B11_S17

description: Library name: Zygote_P2_070723_cDNA_B11_S17


title: T-PLL patient sample P12, untouched

description: Library name: P12


title: T-PLL patient sample P10, untouched

description: Library name: P10


title: Zygote_P2_070723_cDNA_B10_S16

description: Library name: Zygote_P2_070723_cDNA_B10_S16


title: T-PLL patient sample P09, untouched

description: Library name: P09


title: Zygote_P2_070723_cDNA_B9_S15

description: Library name: Zygote_P2_070723_cDNA_B9_S15


title: T-PLL patient sample P08, untouched

description: Library name: P08


title: Zygote_P2_070723_cDNA_B8_S14

description: Library name: Zygote_P2_070723_cDNA_B8_S14


title: T-PLL patient sample P07, untouched

description: Library name: P07


title: Zygote_P2_070723_cDNA_B4_S13

description: Library name: Zygote_P2_070723_cDNA_B4_S13


title: T-PLL patient sample P06, untouched

description: Library name: P06


title: Zygote_P2_070723_cDNA_A12_S11

description: Library name: Zygote_P2_070723_cDNA_A12_S11


title: T-PLL patient sample P15, untouched

description: Library name: P15


title: Zygote_P2_070723_cDNA_B1_S12

description: Library name: Zygote_P2_070723_cDNA_B1_S12


title: T-PLL patient sample P03, untouched

description: Library name: P03


title: T-PLL patient sample P05, untouched

description: Library name: P05


title: T-PLL patient sample P04, untouched

description: Library name: P04


title: Zygote_P2_070723_cDNA_A11_S10

description: Library name: Zygote_P2_070723_cDNA_A11_S10


title: T-PLL patient sample P02, untouched

description: Library name: P02


title: T-PLL patient sample P01, untouched

description: Library name: P01


title: Zygote_P2_070723_cDNA_A10_S9

description: Library name: Zygote_P2_070723_cDNA_A10_S9


title: Zygote_P2_070723_cDNA_A8_S7

description: Library name: Zygote_P2_070723_cDNA_A8_S7


title: Zygote_P2_070723_cDNA_B12_S18

description: Library name: Zygote_P2_070723_cDNA_B12_S18


title: Zygote_P2_070723_cDNA_A6_S5

description: Library name: Zygote_P2_070723_cDNA_A6_S5


title: BT549, siPAFAH1B1, 72 hrs, rep 4

city: Cleveland

first: Ruth

middle: A

last: Keri

state: Ohio

address: 9500 Euclid Ave, ND4-52

department: Cancer Biology

institute: Cleveland Clinic

description:
Library name: BT549_PAF_4
Column name in BT549_raw_counts.txt: BT549_PAF_4

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads mapped to each gene.
Assembly: hg38
Supplementary files format and content: raw read counts as tab-delimited txt files

source_name: breast cancer

growth_protocol: Cells were seeded into 6 cm dishes at 3 x 10^6 cells/plate in 5 mL complete RPMI on day 0.

extract_protocol:
RNA was extracted using the RNeasy Plus Minikit (Qiagen) per the 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 dTTP.

treatment_protocol: On day 1, cells were transfected using Lipofectamine 2000 in OptiMEM with siRNA that was non-specific (siNS) or targeted to PAFAH1B1 (siPAFAH1B1). After 6 hrs, transfection media was removed and replaced with complete media. After 72 hours, RNA was collected from cells.

value: breast cancer

value: TNBC


title: BT549, siPAFAH1B1, 72 hrs, rep 3

description:
Library name: BT549_PAF_3
Column name in BT549_raw_counts.txt: BT549_PAF_3


title: Zygote_P2_070723_cDNA_A9_S8

description: Library name: Zygote_P2_070723_cDNA_A9_S8


title: BT549, siPAFAH1B1, 72 hrs, rep 2

description:
Library name: BT549_PAF_2
Column name in BT549_raw_counts.txt: BT549_PAF_2


title: Zygote_P2_070723_cDNA_A4_S4

description: Library name: Zygote_P2_070723_cDNA_A4_S4


title: Zygote_P2_070723_cDNA_A7_S6

description: Library name: Zygote_P2_070723_cDNA_A7_S6


title: Zygote_P2_070723_cDNA_A3_S3

description: Library name: Zygote_P2_070723_cDNA_A3_S3


title: BT549, siPAFAH1B1, 72 hrs, rep 1

description:
Library name: BT549_PAF_1
Column name in BT549_raw_counts.txt: BT549_PAF_1


title: T-PLL patient sample P11, untouched

description: Library name: P11


title: BT549, siNS, 72 hrs, rep 4

description:
Library name: BT549_NS_4
Column name in BT549_raw_counts.txt: BT549_NS_4

value: siNS


title: Zygote_P2_070723_cDNA_A2_S2

description: Library name: Zygote_P2_070723_cDNA_A2_S2


title: Zygote_P2_070723_cDNA_A1_S1

description: Library name: Zygote_P2_070723_cDNA_A1_S1


title: BT549, siNS, 72 hrs, rep 2

description:
Library name: BT549_NS_2
Column name in BT549_raw_counts.txt: BT549_NS_2


title: BT549, siNS, 72 hrs, rep 3

description:
Library name: BT549_NS_3
Column name in BT549_raw_counts.txt: BT549_NS_3


title: BT549, siNS, 72 hrs, rep 1

description:
Library name: BT549_NS_1
Column name in BT549_raw_counts.txt: BT549_NS_1


title: 4cell_P1_111323_gDNA_E2_S246

description: Library name: 4cell_P1_111323_gDNA_E2_S246

source_name: 4 cell embryo

value: 4 cell embryo


title: HCC38, siPAFAH1B1, 72 hrs, rep 2

description:
Library name: HCC38_PAF_2
Column name in HCC38_raw_counts.txt: HCC38_PAF_2


title: HCC38, siPAFAH1B1, 72 hrs, rep 4

description:
Library name: HCC38_PAF_4
Column name in HCC38_raw_counts.txt: HCC38_PAF_4


title: 4cell_P1_111323_gDNA_E1_S245

description: Library name: 4cell_P1_111323_gDNA_E1_S245


title: 4cell_P1_111323_gDNA_E5_S248

description: Library name: 4cell_P1_111323_gDNA_E5_S248


title: HCC38, siPAFAH1B1, 72 hrs, rep 1

description:
Library name: HCC38_PAF_1
Column name in HCC38_raw_counts.txt: HCC38_PAF_1


title: 4cell_P1_111323_gDNA_D10_S243

description: Library name: 4cell_P1_111323_gDNA_D10_S243


title: 4cell_P1_111323_gDNA_E3_S247

description: Library name: 4cell_P1_111323_gDNA_E3_S247


title: HCC38, siNS, 72 hrs, rep 4

description:
Library name: HCC38_NS_4
Column name in HCC38_raw_counts.txt: HCC38_NS_4


title: 4cell_P1_111323_gDNA_D9_S242

description: Library name: 4cell_P1_111323_gDNA_D9_S242


title: 4cell_P1_111323_gDNA_D8_S241

description: Library name: 4cell_P1_111323_gDNA_D8_S241


title: HCC38, siNS, 72 hrs, rep 3

description:
Library name: HCC38_NS_3
Column name in HCC38_raw_counts.txt: HCC38_NS_3


title: 4cell_P1_111323_gDNA_D12_S244

description: Library name: 4cell_P1_111323_gDNA_D12_S244


title: 4cell_P1_111323_gDNA_D7_S240

description: Library name: 4cell_P1_111323_gDNA_D7_S240


title: HCC38, siNS, 72 hrs, rep 1

description:
Library name: HCC38_NS_1
Column name in HCC38_raw_counts.txt: HCC38_NS_1


title: MDA-MB-231, siPAFAH1B1, 72 hrs, rep 3

description:
Library name: MB231_PAF_3
Column name in MB231_raw_counts.txt: MB231_PAF_3


title: MDA-MB-231, siPAFAH1B1, 72 hrs, rep 4

description:
Library name: MB231_PAF_4
Column name in MB231_raw_counts.txt: MB231_PAF_4


title: MDA-MB-231, siPAFAH1B1, 72 hrs, rep 1

description:
Library name: MB231_PAF_1
Column name in MB231_raw_counts.txt: MB231_PAF_1


title: 4cell_P1_111323_gDNA_D3_S237

description: Library name: 4cell_P1_111323_gDNA_D3_S237


title: MDA-MB-231, siPAFAH1B1, 72 hrs, rep 2

description:
Library name: MB231_PAF_2
Column name in MB231_raw_counts.txt: MB231_PAF_2


title: 4cell_P1_111323_gDNA_D4_S238

description: Library name: 4cell_P1_111323_gDNA_D4_S238


title: 4cell_P1_111323_gDNA_D2_S236

description: Library name: 4cell_P1_111323_gDNA_D2_S236


title: 4cell_P1_111323_gDNA_D1_S235

description: Library name: 4cell_P1_111323_gDNA_D1_S235


title: HCC38, siPAFAH1B1, 72 hrs, rep 3

description:
Library name: HCC38_PAF_3
Column name in HCC38_raw_counts.txt: HCC38_PAF_3


title: MDA-MB-231, siNS, 72 hrs, rep 4

description:
Library name: MB231_NS_4
Column name in MB231_raw_counts.txt: MB231_NS_4


title: MDA-MB-231, siNS, 72 hrs, rep 3

description:
Library name: MB231_NS_3
Column name in MB231_raw_counts.txt: MB231_NS_3


title: 4cell_P1_111323_gDNA_C12_S234

description: Library name: 4cell_P1_111323_gDNA_C12_S234


title: 4cell_P1_111323_gDNA_C11_S233

description: Library name: 4cell_P1_111323_gDNA_C11_S233


title: MDA-MB-231, siNS, 72 hrs, rep 2

description:
Library name: MB231_NS_2
Column name in MB231_raw_counts.txt: MB231_NS_2


title: MDA-MB-231, siNS, 72 hrs, rep 1

description:
Library name: MB231_NS_1
Column name in MB231_raw_counts.txt: MB231_NS_1


title: 4cell_P1_111323_gDNA_C10_S232

description: Library name: 4cell_P1_111323_gDNA_C10_S232


title: 4cell_P1_111323_gDNA_C9_S231

description: Library name: 4cell_P1_111323_gDNA_C9_S231


city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description: Library name: MN07_LacZ_Rep3_snRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch2

data_processing:
For the snRNAseq analysis, raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters (--include-introns was used for nuclei mapping)
Assembly: GRCh38
Supplementary files format and content: Cellranger filtered_feature_bc_matrix

extract_protocol:
The nuclei isolation from theday 15 cerebral organoids was performed according to Jönsson et al., 2021. In brief, 5 organoids per replicate were dissociated in ice-cold lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before being resuspended in 300 𝝻l of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 𝝻m). Nuclei were run through the FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 𝝻m nozzle (reanalysis showed >95% purity).
For the snRNAseq libraries, 8500-10000 nuclei were directly loaded onto the Chromium Next GEM Chip G  Single Cell Kit along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Next GEM Single Cell 3’ Kit (10x Genomics, PN-1000268) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics using 13 cycles of amplification. Sequencing libraries were generated with unique dual indices (TT set A).
The generated libraries for snRNA sequencing were sequenced on a Novaseq6000 or Novaseq X plus (paired end, ~ 150 bp) using a 100-cycle kit and 28-10-10-90 reads.

tag: lentivirus

tag: type

value: organoid

tag: target gene

value: LacZ


description: Library name: MN07_LacZ_Rep3_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_gDNA_C7_S229

description: Library name: 4cell_P1_111323_gDNA_C7_S229


description: Library name: MN07_LacZ_Rep2_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch3


title: HCC38, siNS, 72 hrs, rep 2

description:
Library name: HCC38_NS_2
Column name in HCC38_raw_counts.txt: HCC38_NS_2


title: 4cell_P1_111323_gDNA_D6_S239

description: Library name: 4cell_P1_111323_gDNA_D6_S239


title: 4cell_P1_111323_gDNA_C4_S227

description: Library name: 4cell_P1_111323_gDNA_C4_S227


description: Library name: MN07_LacZ_Rep2_snRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch2


description: Library name: MN07_LacZ_Rep2_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_gDNA_C5_S228

description: Library name: 4cell_P1_111323_gDNA_C5_S228


description: Library name: MN07_LacZ_Rep1_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch2


title: 4cell_P1_111323_gDNA_C3_S226

description: Library name: 4cell_P1_111323_gDNA_C3_S226


description: Library name: MN07_LacZ_Rep1_snRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch1


title: 4cell_P1_111323_gDNA_B12_S223

description: Library name: 4cell_P1_111323_gDNA_B12_S223


title: 4cell_P1_111323_gDNA_C2_S225

description: Library name: 4cell_P1_111323_gDNA_C2_S225


title: 4cell_P1_111323_gDNA_B11_S222

description: Library name: 4cell_P1_111323_gDNA_B11_S222


description: Library name: MN07_LacZ_Rep1_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch1


description: Library name: MN07_gRNA2_Rep2_snRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_gDNA_B10_S221

description: Library name: 4cell_P1_111323_gDNA_B10_S221


description: Library name: MN07_gRNA2_Rep1_snRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch2


title: 4cell_P1_111323_gDNA_B9_S220

description: Library name: 4cell_P1_111323_gDNA_B9_S220


description: Library name: MN07_gRNA1_Rep3_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_gDNA_C8_S230

description: Library name: 4cell_P1_111323_gDNA_C8_S230


title: 4cell_P1_111323_gDNA_B8_S219

description: Library name: 4cell_P1_111323_gDNA_B8_S219


title: 4cell_P1_111323_gDNA_B7_S218

description: Library name: 4cell_P1_111323_gDNA_B7_S218


description: Library name: MN07_gRNA1_Rep3_snRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch2


title: 4cell_P1_111323_gDNA_B6_S217

description: Library name: 4cell_P1_111323_gDNA_B6_S217


description: Library name: MN07_gRNA1_Rep2_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch3


title: 4cell_P1_111323_gDNA_B5_S216

description: Library name: 4cell_P1_111323_gDNA_B5_S216


title: 4cell_P1_111323_gDNA_B4_S215

description: Library name: 4cell_P1_111323_gDNA_B4_S215


title: 4cell_P1_111323_gDNA_B3_S214

description: Library name: 4cell_P1_111323_gDNA_B3_S214


description: Library name: MN07_gRNA1_Rep1_snRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch1


title: 4cell_P1_111323_gDNA_B2_S213

description: Library name: 4cell_P1_111323_gDNA_B2_S213


description: Library name: MN07_gRNA1_Rep1_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch1


description: Library name: MN07_gRNA1_Rep1_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch2


title: 4cell_P1_111323_gDNA_C1_S224

description: Library name: 4cell_P1_111323_gDNA_C1_S224


title: 4cell_P1_111323_gDNA_A12_S212

description: Library name: 4cell_P1_111323_gDNA_A12_S212


title: 4cell_P1_111323_gDNA_A10_S210

description: Library name: 4cell_P1_111323_gDNA_A10_S210


description: Library name: MN07_gRNA2_Rep3_snRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_gDNA_A9_S209

description: Library name: 4cell_P1_111323_gDNA_A9_S209


title: 4cell_P1_111323_gDNA_A11_S211

description: Library name: 4cell_P1_111323_gDNA_A11_S211


description: Library name: MN07_gRNA1_Rep1_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch7

data_processing:
RNAseq Unique mapping (L1 loci mapping): STAR aligner (version 2.7.8a; --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.03).
RNAseq Genes were quantified using featureCounts (Subread version 1.6.3), forcing matching strandness of the reads to the features being quantified (-s 2).
RNAseq BAM files were indexed using samtools (version 1.16.1) and converted to bigwig files using deeptools bamCoverage (version 2.5.4) (--normalizeUsingRPKM)
Assembly: GRCh38
Supplementary files format and content: Bigwigs for genome browser visualization
Supplementary files format and content: Bulk RNAseq read count matrix for genes

extract_protocol:
Total RNA for bulkRNAseq was isolated using the RNeasy Mini Kit (Quiagen) with on column DNAse treatment following the manufacturer’s instructions. RNA sequencing was performed using 3 biological replicates.
Libraries for RNA sequencing were generated using Illumina TruSeq Stranded mRNA library prep kit (with poly-A selection).
The generated libraries for RNA sequencing were optimized for long fragments, and sequenced on a Novaseq6000 (paired end, ~ 150 bp) yielding an average of 46M reads.

tag: crispr guide_rna


description: Library name: MN07_gRNA1_Rep3_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch7


description: Library name: MN07_gRNA2_Rep3_bulkRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch7


description: Library name: MN07_gRNA2_Rep2_bulkRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch7


title: 4cell_P1_111323_gDNA_A7_S208

description: Library name: 4cell_P1_111323_gDNA_A7_S208


title: 4cell_P1_111323_gDNA_A6_S207

description: Library name: 4cell_P1_111323_gDNA_A6_S207


description: Library name: MN07_gRNA1_Rep2_snRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch2


title: 4cell_P1_111323_gDNA_A4_S205

description: Library name: 4cell_P1_111323_gDNA_A4_S205


description: Library name: MN07_gRNA1_Rep2_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch4


description: Library name: MN07_LacZ_Rep3_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch7


description: Library name: MN07_LacZ_Rep1_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch7


title: 4cell_P1_111323_gDNA_A3_S204

description: Library name: 4cell_P1_111323_gDNA_A3_S204


title: 4cell_P1_111323_gDNA_A2_S203

description: Library name: 4cell_P1_111323_gDNA_A2_S203


title: 4cell_P1_111323_gDNA_A1_S202

description: Library name: 4cell_P1_111323_gDNA_A1_S202


description: Library name: MN07_LacZ_Rep3_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch6


title: 4cell_P1_111323_cDNA_E4_S200

description: Library name: 4cell_P1_111323_cDNA_E4_S200


title: 4cell_P1_111323_cDNA_E5_S201

description: Library name: 4cell_P1_111323_cDNA_E5_S201


description: Library name: MN07_LacZ_Rep2_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch6


description: Library name: MN07_gRNA1_Rep3_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch6


title: 4cell_P1_111323_cDNA_E3_S199

description: Library name: 4cell_P1_111323_cDNA_E3_S199


description: Library name: MN07_gRNA1_Rep2_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch7


description: Library name: MN07_gRNA1_Rep2_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch6


title: 4cell_P1_111323_cDNA_D12_S197

description: Library name: 4cell_P1_111323_cDNA_D12_S197


title: MN07_WT_Rep3_bulkRNA_hiPS48_batch5

description: Library name: MN07_WT_Rep3_bulkRNA_hiPS48_batch5

value: hiPSC


title: 4cell_P1_111323_gDNA_A5_S206

description: Library name: 4cell_P1_111323_gDNA_A5_S206


description: Library name: MN07_gRNA1_Rep1_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch6


title: 4cell_P1_111323_cDNA_D10_S195

description: Library name: 4cell_P1_111323_cDNA_D10_S195


title: 4cell_P1_111323_cDNA_D11_S196

description: Library name: 4cell_P1_111323_cDNA_D11_S196


title: MN07_WT_Rep2_bulkRNA_hiPS48_batch5

description: Library name: MN07_WT_Rep2_bulkRNA_hiPS48_batch5


description: Library name: MN07_gRNA2_Rep1_bulkRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch7


description: Library name: MN07_LacZ_Rep2_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch7


title: MN07_WT_Rep3_bulkRNA_hiPS6_batch5

description: Library name: MN07_WT_Rep3_bulkRNA_hiPS6_batch5


title: 4cell_P1_111323_cDNA_D9_S194

description: Library name: 4cell_P1_111323_cDNA_D9_S194


title: 4cell_P1_111323_cDNA_D8_S193

description: Library name: 4cell_P1_111323_cDNA_D8_S193


title: MN07_WT_Rep1_bulkRNA_hiPS6_batch5

description: Library name: MN07_WT_Rep1_bulkRNA_hiPS6_batch5


title: 4cell_P1_111323_cDNA_D6_S191

description: Library name: 4cell_P1_111323_cDNA_D6_S191


title: 4cell_P1_111323_cDNA_D7_S192

description: Library name: 4cell_P1_111323_cDNA_D7_S192


title: MN07_WT_Rep1_bulkRNA_hiPS48_batch5

description: Library name: MN07_WT_Rep1_bulkRNA_hiPS48_batch5


description: Library name: MN07_gRNA1_Rep3_bulkRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_cDNA_D5_S190

description: Library name: 4cell_P1_111323_cDNA_D5_S190


title: 4cell_P1_111323_cDNA_D4_S189

description: Library name: 4cell_P1_111323_cDNA_D4_S189


title: 4cell_P1_111323_cDNA_D2_S187

description: Library name: 4cell_P1_111323_cDNA_D2_S187


title: 4cell_P1_111323_cDNA_D3_S188

description: Library name: 4cell_P1_111323_cDNA_D3_S188


description: Library name: MN07_gRNA1_Rep2_bulkRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_cDNA_E2_S198

description: Library name: 4cell_P1_111323_cDNA_E2_S198


description: Library name: MN07_LacZ_Rep3_bulkRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch4


description: Library name: MN07_gRNA1_Rep1_bulkRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch4


description: Library name: MN07_LacZ_Rep1_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch6


description: Library name: MN07_LacZ_Rep1_bulkRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch4


title: 4cell_P1_111323_cDNA_D1_S186

description: Library name: 4cell_P1_111323_cDNA_D1_S186


description: Library name: MN07_LacZ_Rep2_bulkRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch4


description: Library name: MN07_LacZ_Rep3_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch3


title: 4cell_P1_111323_cDNA_C11_S184

description: Library name: 4cell_P1_111323_cDNA_C11_S184


title: MN07_WT_Rep2_bulkRNA_hiPS6_batch5

description: Library name: MN07_WT_Rep2_bulkRNA_hiPS6_batch5


title: 4cell_P1_111323_cDNA_C9_S182

description: Library name: 4cell_P1_111323_cDNA_C9_S182


title: 4cell_P1_111323_cDNA_C10_S183

description: Library name: 4cell_P1_111323_cDNA_C10_S183


title: 4cell_P1_111323_cDNA_C12_S185

description: Library name: 4cell_P1_111323_cDNA_C12_S185


description: Library name: MN07_gRNA2_Rep3_bulkRNA_hiPS6_LV3822_L1_CRISPRi_batch3


title: 4cell_P1_111323_cDNA_C8_S181

description: Library name: 4cell_P1_111323_cDNA_C8_S181


description: Library name: MN07_LacZ_Rep2_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch3


description: Library name: MN07_gRNA2_Rep2_bulkRNA_hiPS6_LV3822_L1_CRISPRi_batch3


title: 4cell_P1_111323_cDNA_C7_S180

description: Library name: 4cell_P1_111323_cDNA_C7_S180


description: Library name: MN07_LacZ_Rep1_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch3


title: 4cell_P1_111323_cDNA_C6_S179

description: Library name: 4cell_P1_111323_cDNA_C6_S179


description: Library name: MN07_gRNA2_Rep1_bulkRNA_hiPS6_LV3822_L1_CRISPRi_batch3


title: 4cell_P1_111323_cDNA_C5_S178

description: Library name: 4cell_P1_111323_cDNA_C5_S178


title: 4cell_P1_111323_cDNA_C4_S177

description: Library name: 4cell_P1_111323_cDNA_C4_S177


description: Library name: MN07_LacZ_Rep2_bulkRNA_hiPS48_LV3599_L1_CRISPRi_batch2


title: 4cell_P1_111323_cDNA_C3_S176

description: Library name: 4cell_P1_111323_cDNA_C3_S176


description: Library name: MN07_LacZ_Rep1_bulkRNA_hiPS48_LV3599_L1_CRISPRi_batch2


title: 4cell_P1_111323_cDNA_C1_S174

description: Library name: 4cell_P1_111323_cDNA_C1_S174


description: Library name: MN07_gRNA1_Rep1_bulkRNA_hiPS48_LV3824_L1_CRISPRi_batch2


description: Library name: MN07_gRNA1_Rep3_bulkRNA_hiPS48_LV3824_L1_CRISPRi_batch2


description: Library name: MN07_gRNA1_Rep2_bulkRNA_hiPS48_LV3824_L1_CRISPRi_batch2


description: Library name: MN07_gRNA1_Rep3_bulkRNA_hiPS6_LV3824_L1_CRISPRi_batch1


title: 4cell_P1_111323_cDNA_C2_S175

description: Library name: 4cell_P1_111323_cDNA_C2_S175


title: 4cell_P1_111323_cDNA_B10_S171

description: Library name: 4cell_P1_111323_cDNA_B10_S171


title: 4cell_P1_111323_cDNA_B12_S173

description: Library name: 4cell_P1_111323_cDNA_B12_S173


title: 4cell_P1_111323_cDNA_B9_S170

description: Library name: 4cell_P1_111323_cDNA_B9_S170


title: 4cell_P1_111323_cDNA_B8_S169

description: Library name: 4cell_P1_111323_cDNA_B8_S169


description: Library name: MN07_LacZ_Rep1_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch1


description: Library name: MN07_LacZ_Rep3_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch1


title: 4cell_P1_111323_cDNA_B7_S168

description: Library name: 4cell_P1_111323_cDNA_B7_S168


title: 4cell_P1_111323_cDNA_B6_S167

description: Library name: 4cell_P1_111323_cDNA_B6_S167


description: Library name: MN07_gRNA1_Rep1_bulkRNA_hiPS6_LV3824_L1_CRISPRi_batch1


description: Library name: MN07_gRNA1_Rep2_bulkRNA_hiPS6_LV3824_L1_CRISPRi_batch1


description: Library name: MN07_LacZ_Rep2_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch1


title: CAS9 (Perturb-seq)

city: South San Francisco

first: Ittai

middle: Ethan

last: Eres

state: CA

address: 750 Gateway Boulevard

department: CRADI

institute: Amgen

description: Files labeled S# are transcriptome runs, others labeled gRNA are gRNA runs

data_processing:
After demultiplexing raw BCL sequencing files of GEX and gRNA libraries to generate per-library FASTQs, libraries were aligned to GRCh38-3.0.0 and a custom feature reference table, respectively, using CellRanger v6.0.0 (10X Genomics).
gRNA species were assigned to respective cells by merging count matrices from different library samples, and cell barcodes expressing less than 100 gRNA UMIs were removed. gRNA expression was then normalized across cells using centered log-ratio transformation and scaling. Perturbation class assignment was then performed per-cell based on gRNA expression.
Cell barcodes containing less than 2000 features, greater than 6500 features, or greater than 10% fraction mitochondrial reads were filtered out. Seurat version 3.9.9 was used to analyze the data further, transforming raw UMI counts with log-normalization and quantifying cell cycle with the CellCycleScoring() function. PCA and clustering were used to interrogate cell cycle as a confounder on the impact of perturbation upon the transcriptome.
The top 5000 features were selected using FindVariableFeatures(), their expression values were scaled, and cell cycle effects regressed out. Top 40 PCs were used for shared nearest neighbor (SNN) assignment of cell neighborhoods, and clustering done with Louvain algorithm at a resolution of 0.6. We further used Mixscape to separate perturbed from non-perturbed cells and filtered out the latter (representing 5% of our cells).
Differential expression was carried out with MAST and clusterProfiler version 4.12.0 was used to run enrichment analyses for KEGG pathways. Visualization was performed using linear discriminant analysis (LDA) to maximize variance between gRNA classes. gRNA class differentiated cell populations & top 20 components were used to calculate a UMAP projection.
Assembly: hg38
Supplementary files format and content: Seurat object with processed data across cells
Library strategy: Perturb-seq

source_name: Heart

growth_protocol: Immortalized human cardiac fibroblasts were generated from adult heart ventricle primary cells (Applied Biological Materials).

extract_protocol:
Each cell pool (containing at least 100k cells) was harvested by trypsinization, 1x wash in culture media, and 1x wash and resuspension into PBS + 0.04% BSA at concentration of 300-500 cells/microliter for droplet encapsulation.
Single-cell perturb-seq (transcriptome and gRNA sequencing at single-cell resolution) was performed with the Chromium 3' V3.1 method with Feature Barcoding to allow for CRISPR screening, following manufacturer's guidelines (10X Genomics, User Guide CG000205 Rev D). For more details, please see the paper methods.

treatment_protocol: Cells were treated with serial dilutions of lentivirus gRNA libraries targeting putative enhancers appearing in open chromatin and with transcription factor binding sites. Triple antibiotic selection was employed to ensure only infected cells containing the targeting gRNAs were used. For more details please see the publication methods.

value: Heart

value: Immortalized human cardiac fibroblast

value: Perturb-seq Cas9


title: 4cell_P1_111323_cDNA_B4_S165

description: Library name: 4cell_P1_111323_cDNA_B4_S165


title: 4cell_P1_111323_cDNA_B5_S166

description: Library name: 4cell_P1_111323_cDNA_B5_S166


title: NonTargeting_Control (Perturb-seq)

value: Perturb-seq non-targeting gRNA


title: 4cell_P1_111323_cDNA_B3_S164

description: Library name: 4cell_P1_111323_cDNA_B3_S164


title: FURIN (Perturb-seq)

value: Perturb-seq of enhancer region


title: ACTA2 (Perturb-seq)


description: Library name: MN07_LacZ_Rep3_bulkRNA_hiPS48_LV3599_L1_CRISPRi_batch2


title: CXCL12 (Perturb-seq)


title: GJA1 (Perturb-seq)


title: 4cell_P1_111323_cDNA_B2_S163

description: Library name: 4cell_P1_111323_cDNA_B2_S163


title: 4cell_P1_111323_cDNA_A12_S161

description: Library name: 4cell_P1_111323_cDNA_A12_S161


title: 4cell_P1_111323_cDNA_A11_S160

description: Library name: 4cell_P1_111323_cDNA_A11_S160


title: atac.wt.treatment_dmso.dox.rep3

city: Research Triangle Park

first: Paul

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

data_processing:
Adapters were clipped from raw read pairs with TrimGalore v0.6.6.
Read pairs were mapped to the hg38 reference assembly with bowtie2 v2.4.5 using default settings, then filtered with samtools v1.19.2 for minimum MAPQ of 30.
Duplicate mapped fragments were then removed by MarkDuplicate from the Picard tool suite v.2.27.1 with parameter REMOVE_DUPLICATES=TRUE.
For treated samples (BRM14, DMSO, or lentivirus AFOS or empty), replicates were merged prior to calling peaks with macs2 v2.2.9.1 (parameters: --nomodel -q 0.0001 -f BAMPE).  For untreated samples, peaks calls with macs2 were made for individual samples, then filtered to retain only those with intersecting peak calls in all three biological replicates.
Final peaks for analysis were established by concatenating within a given experimental subset, merging with bedtools v2.30.0, and filtering to remove exclusion list regions (ENCODE) and non-canonical chromosomes.
Fragments at peaks were counted by the featureCounts function of subread v2.0.3 with parameters "-p -countReadPairs".
Genomic coverage tracks were generated by deeptools bamCoverage v3.5.3 with parameters "--normalizeUsing RPGC --binSize 10 --ignoreDuplicates --effectiveGenomeSize 2913022398".
Assembly: hg38
Supplementary files format and content: Fragment counts per peak in tab-delimited text format.
Supplementary files format and content: Normalized genomic coverage tracks in bigWig format; *merged files are linked to the corresponding rep1 sample records

growth_protocol: Doxycycline (dox) inducible wildtype (wt) and TA1del (ta1) GATA3 cell lines were generated in SUM159PT basal breast cancer cell line.

extract_protocol:
ATAC-seq samples were generated as previously described (Orlando et al. 2020) with the following modifications: 50,000 cells per reaction, omni-ATAC was performed for cell lysis steps (Corces et al. 2017, Grandi et al. 2022) and Tn5 to volume ratio was 1:10.
ATAC-seq libraries were generated by PCR amplification for 5 cycles followed by qPCR for determining remaining cycle numbers (~1/3 curve). Following DNA purification with Qiagen MinElute kit, final libraries were double-sided size selected (0.5X and 1.8X) with AMPure beads.

treatment_protocol: To investigate changes in chromatin accesibility by ATAC-seq following WT or TA1del-GATA3 expression, cells were induced with +/- DOX (1 ug/mL) for 24 hr.To determine the effect of AP-1 binding on chromatin accesibilty changes by WT GATA3, cells were transduced with lentivirus containing empty vector or AFOS (dominant negative AP-1 that inhibits binding) for 48 hrs prior to DOX induction for 24 hrs. To determine the effect of ATPase function by SWI/SNF on WT GATA3 dependent chromatin accesibility, cells were treated concurrently +/- DOX (1 ug/ml) and either DMSO (8 uL) or BRM014 (8 uM) for 24 hrs.

value: basal breast cancer line

value: WT GATA3 (1-444aa)

tag: induced

value: DOX

value: DMSO (8ul)


title: 4cell_P1_111323_cDNA_A10_S159

description: Library name: 4cell_P1_111323_cDNA_A10_S159


title: atac.wt.treatment_dmso.dox.rep2


title: 4cell_P1_111323_cDNA_A9_S158

description: Library name: 4cell_P1_111323_cDNA_A9_S158


title: 4cell_P1_111323_cDNA_B11_S172

description: Library name: 4cell_P1_111323_cDNA_B11_S172


title: atac.wt.treatment_dmso.dox.rep1


title: IL6R (Perturb-seq)


title: 4cell_P1_111323_cDNA_A7_S156

description: Library name: 4cell_P1_111323_cDNA_A7_S156


title: atac.wt.treatment_dmso.ctrl.rep2

value: Control/Uninduced


title: 4cell_P1_111323_cDNA_A6_S155

description: Library name: 4cell_P1_111323_cDNA_A6_S155


title: atac.wt.treatment_dmso.ctrl.rep3


title: atac.wt.treatment_dmso.ctrl.rep1


title: 4cell_P1_111323_cDNA_A8_S157

description: Library name: 4cell_P1_111323_cDNA_A8_S157


title: atac.wt.treatment_brm014.dox.rep3


title: 4cell_P1_111323_cDNA_A4_S153

description: Library name: 4cell_P1_111323_cDNA_A4_S153


title: 4cell_P1_111323_cDNA_A2_S151

description: Library name: 4cell_P1_111323_cDNA_A2_S151


title: 4cell_P1_111323_cDNA_B1_S162

description: Library name: 4cell_P1_111323_cDNA_B1_S162


title: atac.wt.treatment_brm014.ctrl.rep3


title: atac.wt.treatment_brm014.dox.rep1


title: 4cell_P1_111323_cDNA_A1_S150

description: Library name: 4cell_P1_111323_cDNA_A1_S150


title: atac.wt.treatment_brm014.dox.rep2


title: 4cell_P1_111323_cDNA_A3_S152

description: Library name: 4cell_P1_111323_cDNA_A3_S152


title: 2cell_P2_110723_gDNA_D10_S149

description: Library name: 2cell_P2_110723_gDNA_D10_S149

source_name: 2 cell embryo

value: 2 cell embryo


title: atac.wt.treatment_brm014.ctrl.rep1


title: 2cell_P2_110723_gDNA_D9_S148

description: Library name: 2cell_P2_110723_gDNA_D9_S148


title: atac.wt.lenti_empty.dox.rep3


title: atac.wt.lenti_empty.dox.rep2


title: 2cell_P2_110723_gDNA_D8_S147

description: Library name: 2cell_P2_110723_gDNA_D8_S147


title: 2cell_P2_110723_gDNA_D7_S146

description: Library name: 2cell_P2_110723_gDNA_D7_S146


title: atac.wt.lenti_empty.dox.rep1


title: 2cell_P2_110723_gDNA_D6_S145

description: Library name: 2cell_P2_110723_gDNA_D6_S145


title: atac.wt.lenti_empty.ctrl.rep3


title: 2cell_P2_110723_gDNA_D5_S144

description: Library name: 2cell_P2_110723_gDNA_D5_S144


title: 4cell_P1_111323_cDNA_A5_S154

description: Library name: 4cell_P1_111323_cDNA_A5_S154


title: atac.wt.lenti_empty.ctrl.rep2


title: 2cell_P2_110723_gDNA_D4_S143

description: Library name: 2cell_P2_110723_gDNA_D4_S143


title: 2cell_P2_110723_gDNA_D3_S142

description: Library name: 2cell_P2_110723_gDNA_D3_S142


title: 2cell_P2_110723_gDNA_C12_S140

description: Library name: 2cell_P2_110723_gDNA_C12_S140


title: atac.wt.lenti_afos.dox.rep3


title: atac.wt.lenti_empty.ctrl.rep1


title: atac.wt.treatment_brm014.ctrl.rep2


title: atac.wt.lenti_afos.dox.rep2


title: 2cell_P2_110723_gDNA_C10_S139

description: Library name: 2cell_P2_110723_gDNA_C10_S139


title: atac.wt.lenti_afos.dox.rep1


title: atac.wt.lenti_afos.ctrl.rep3


title: 2cell_P2_110723_gDNA_C8_S137

description: Library name: 2cell_P2_110723_gDNA_C8_S137


title: atac.wt.dox.rep3


title: atac.wt.lenti_afos.ctrl.rep1


title: 2cell_P2_110723_gDNA_C9_S138

description: Library name: 2cell_P2_110723_gDNA_C9_S138


title: atac.wt.dox.rep2


title: 2cell_P2_110723_gDNA_C6_S135

description: Library name: 2cell_P2_110723_gDNA_C6_S135


title: 2cell_P2_110723_gDNA_C5_S134

description: Library name: 2cell_P2_110723_gDNA_C5_S134


title: atac.wt.dox.rep1


title: atac.wt.ctrl.rep3


title: 2cell_P2_110723_gDNA_C4_S133

description: Library name: 2cell_P2_110723_gDNA_C4_S133


title: atac.wt.ctrl.rep2


title: 2cell_P2_110723_gDNA_C3_S132

description: Library name: 2cell_P2_110723_gDNA_C3_S132


title: 2cell_P2_110723_gDNA_C1_S130

description: Library name: 2cell_P2_110723_gDNA_C1_S130


title: atac.wt.ctrl.rep1


title: 2cell_P2_110723_gDNA_D2_S141

description: Library name: 2cell_P2_110723_gDNA_D2_S141


title: 2cell_P2_110723_gDNA_B12_S129

description: Library name: 2cell_P2_110723_gDNA_B12_S129


title: atac.ta1.dox.rep2

value: TA1del GATA3 (126-444aa)


title: 2cell_P2_110723_gDNA_B10_S128

description: Library name: 2cell_P2_110723_gDNA_B10_S128


title: atac.ta1.dox.rep3


title: 2cell_P2_110723_gDNA_C7_S136

description: Library name: 2cell_P2_110723_gDNA_C7_S136


title: atac.ta1.ctrl.rep3


title: atac.wt.lenti_afos.ctrl.rep2


title: atac.ta1.ctrl.rep2


title: atac.ta1.dox.rep1


title: atac.ta1.ctrl.rep1


title: 2cell_P2_110723_gDNA_B9_S127

description: Library name: 2cell_P2_110723_gDNA_B9_S127


title: 2cell_P2_110723_gDNA_B6_S124

description: Library name: 2cell_P2_110723_gDNA_B6_S124


title: 2cell_P2_110723_gDNA_B8_S126

description: Library name: 2cell_P2_110723_gDNA_B8_S126


title: BT20 cells, PAI1_3

city: Kanazawa

first: Tsunaki

last: Hongu

address: Kakuma-machi

department: Cancer Research Institute

country: Japan

institute: Kanazawa University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore (length20 and phred33).
Trimmed sequence reads were mapped to hg38 using STAR 2.7.10a.
Read count extraction and normalization were performed using RSEM 1.3.3.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts, TPM and FPKM for each sample.

source_name: BT20 cells

growth_protocol: BT20 breast cancer cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was harvested using RNeay Mini kit (Qiagen), and mRNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™II Directional RNA Library Prep Kit (NEB) following manufacture's protocols.

treatment_protocol: BT20 cells suspended in DMEM/F12 medium containing 1x B27 (Gibco) were seeded on ultra-low attachment plate (Corning) and stimulated with 200 ng/ml recombinant PAI1 (Peprotech) for 24 hours

value: BT20 cells

value: Breast cancer cells

value: WT

value: Treated with PAI1


title: 2cell_P2_110723_gDNA_B3_S121

description: Library name: 2cell_P2_110723_gDNA_B3_S121


title: BT20 cells, PAI1_1


title: BT20 cells, PAI1_2


title: 2cell_P2_110723_gDNA_B4_S122

description: Library name: 2cell_P2_110723_gDNA_B4_S122


title: 2cell_P2_110723_gDNA_B2_S120

description: Library name: 2cell_P2_110723_gDNA_B2_S120


title: BT20 cells, Veh_2

value: Untreated


title: 2cell_P2_110723_gDNA_C2_S131

description: Library name: 2cell_P2_110723_gDNA_C2_S131


title: BT20 cells, Veh_1


title: 2cell_P2_110723_gDNA_A12_S118

description: Library name: 2cell_P2_110723_gDNA_A12_S118


title: Patient_17_premalignant_SMA

city: Asan

first: Jeong-An

last: Gim

address: 22 Suncheonhyang-ro

country: South Korea

institute: Soonchunhyang University

description: FFPE

data_processing:
Raw sequencing data were processed using the Nanostring GeoMX pipleline to generate FASTQ files
Assembly: hg19
Supplementary files format and content: AK_WTA.xlsx
Library strategy: Spatial Transcriptomics

molecule: nuclear RNA

source_name: Cutaneous squamous cell carcinoma

extract_protocol:
TMA FFPE slide was sectioned at a thickness of 5 µm.
Spatial transcriptome sequencing libraries were prepared with Nanostring GeoMX

value: Cutaneous squamous cell carcinoma

tag: tissue portion

tag: individual


title: 2cell_P2_110723_gDNA_A11_S117

description: Library name: 2cell_P2_110723_gDNA_A11_S117


title: Patient_17_premalignant_PanCK

description: FFPE


title: 2cell_P2_110723_gDNA_B7_S125

description: Library name: 2cell_P2_110723_gDNA_B7_S125


title: Patient_17_invasive_CD45

description: FFPE


title: 2cell_P2_110723_gDNA_A9_S115

description: Library name: 2cell_P2_110723_gDNA_A9_S115


title: 2cell_P2_110723_gDNA_B5_S123

description: Library name: 2cell_P2_110723_gDNA_B5_S123


title: Patient_17_invasive_PanCK

description: FFPE


title: 2cell_P2_110723_gDNA_A7_S113

description: Library name: 2cell_P2_110723_gDNA_A7_S113


title: 2cell_P2_110723_gDNA_B1_S119

description: Library name: 2cell_P2_110723_gDNA_B1_S119


title: Patient_16_premalignant_CD45

description: FFPE


title: 2cell_P2_110723_gDNA_A5_S111

description: Library name: 2cell_P2_110723_gDNA_A5_S111


title: 2cell_P2_110723_gDNA_A8_S114

description: Library name: 2cell_P2_110723_gDNA_A8_S114


title: Patient_16_premalignant_PanCK

description: FFPE


title: BT20 cells, Veh_3


title: Patient_16_premalignant_SMA

description: FFPE


title: 2cell_P2_110723_gDNA_A4_S110

description: Library name: 2cell_P2_110723_gDNA_A4_S110


title: 2cell_P2_110723_gDNA_A3_S109

description: Library name: 2cell_P2_110723_gDNA_A3_S109


title: 2cell_P2_110723_gDNA_A6_S112

description: Library name: 2cell_P2_110723_gDNA_A6_S112


title: Patient_16_invasive_CD45

description: FFPE


title: Patient_17_premalignant_CD45

description: FFPE


title: 2cell_P2_110723_gDNA_A2_S108

description: Library name: 2cell_P2_110723_gDNA_A2_S108


title: Patient_17_invasive_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_D9_S106

description: Library name: 2cell_P2_110723_cDNA_D9_S106


title: Patient_16_invasive_SMA

description: FFPE


title: Patient_16_invasive_PanCK

description: FFPE


title: Patient_15_premalignant_CD45

description: FFPE


title: 2cell_P2_110723_gDNA_A10_S116

description: Library name: 2cell_P2_110723_gDNA_A10_S116


title: Patient_15_premalignant_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_D7_S104

description: Library name: 2cell_P2_110723_cDNA_D7_S104


title: Patient_15_premalignant_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_D6_S103

description: Library name: 2cell_P2_110723_cDNA_D6_S103


title: Patient_15_invasive_CD45

description: FFPE


title: Patient_15_invasive_PanCK

description: FFPE


title: Patient_15_invasive_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_D3_S100

description: Library name: 2cell_P2_110723_cDNA_D3_S100


title: 2cell_P2_110723_cDNA_D5_S102

description: Library name: 2cell_P2_110723_cDNA_D5_S102


title: 2cell_P2_110723_cDNA_D4_S101

description: Library name: 2cell_P2_110723_cDNA_D4_S101


title: Patient_14_premalignant_SMA

description: FFPE


title: Patient_14_premalignant_CD45

description: FFPE


title: Patient_14_premalignant_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_C9_S96

description: Library name: 2cell_P2_110723_cDNA_C9_S96


title: 2cell_P2_110723_cDNA_C10_S97

description: Library name: 2cell_P2_110723_cDNA_C10_S97


title: 2cell_P2_110723_cDNA_C12_S98

description: Library name: 2cell_P2_110723_cDNA_C12_S98


title: 2cell_P2_110723_cDNA_C8_S95

description: Library name: 2cell_P2_110723_cDNA_C8_S95


title: Patient_14_invasive_CD45

description: FFPE


title: 2cell_P2_110723_cDNA_D10_S107

description: Library name: 2cell_P2_110723_cDNA_D10_S107


title: Patient_14_invasive_SMA

description: FFPE


title: Patient_14_invasive_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_C7_S94

description: Library name: 2cell_P2_110723_cDNA_C7_S94


title: Patient_13_premalignant_CD45

description: FFPE


title: 2cell_P2_110723_cDNA_C6_S93

description: Library name: 2cell_P2_110723_cDNA_C6_S93


title: 2cell_P2_110723_cDNA_D8_S105

description: Library name: 2cell_P2_110723_cDNA_D8_S105


title: Patient_13_premalignant_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_C4_S91

description: Library name: 2cell_P2_110723_cDNA_C4_S91


title: 2cell_P2_110723_cDNA_C5_S92

description: Library name: 2cell_P2_110723_cDNA_C5_S92


title: Patient_13_premalignant_PanCK

description: FFPE


title: Patient_13_invasive_CD45

description: FFPE


title: 2cell_P2_110723_cDNA_C3_S90

description: Library name: 2cell_P2_110723_cDNA_C3_S90


title: Patient_13_invasive_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_C2_S89

description: Library name: 2cell_P2_110723_cDNA_C2_S89


title: Patient_13_invasive_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_D2_S99

description: Library name: 2cell_P2_110723_cDNA_D2_S99


title: Patient_12_premalignant_CD45

description: FFPE


title: 2cell_P2_110723_cDNA_B12_S87

description: Library name: 2cell_P2_110723_cDNA_B12_S87


title: 2cell_P2_110723_cDNA_C1_S88

description: Library name: 2cell_P2_110723_cDNA_C1_S88


title: 2cell_P2_110723_cDNA_B10_S86

description: Library name: 2cell_P2_110723_cDNA_B10_S86


title: Patient_12_premalignant_PanCK

description: FFPE


title: Patient_12_premalignant_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_B9_S85

description: Library name: 2cell_P2_110723_cDNA_B9_S85


title: Patient_12_invasive_CD45

description: FFPE


title: Patient_12_invasive_SMA

description: FFPE


title: Patient_12_invasive_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_B5_S82

description: Library name: 2cell_P2_110723_cDNA_B5_S82


title: Patient_11_premalignant_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_B4_S81

description: Library name: 2cell_P2_110723_cDNA_B4_S81


title: Patient_11_premalignant_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_B7_S84

description: Library name: 2cell_P2_110723_cDNA_B7_S84


title: 2cell_P2_110723_cDNA_B3_S80

description: Library name: 2cell_P2_110723_cDNA_B3_S80


title: 2cell_P2_110723_cDNA_B2_S79

description: Library name: 2cell_P2_110723_cDNA_B2_S79


title: Patient_11_invasive_CD45

description: FFPE


title: 2cell_P2_110723_cDNA_B1_S78

description: Library name: 2cell_P2_110723_cDNA_B1_S78


title: 2cell_P2_110723_cDNA_A12_S77

description: Library name: 2cell_P2_110723_cDNA_A12_S77


title: Patient_11_invasive_PanCK

description: FFPE


title: Patient_11_invasive_SMA

description: FFPE


title: Patient_11_premalignant_CD45

description: FFPE


title: 2cell_P2_110723_cDNA_A11_S76

description: Library name: 2cell_P2_110723_cDNA_A11_S76


title: Patient_10_premalignant_CD45

description: FFPE


title: Patient_10_premalignant_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_A9_S74

description: Library name: 2cell_P2_110723_cDNA_A9_S74


title: Patient_10_premalignant_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_A8_S73

description: Library name: 2cell_P2_110723_cDNA_A8_S73


title: 2cell_P2_110723_cDNA_A7_S72

description: Library name: 2cell_P2_110723_cDNA_A7_S72


title: 2cell_P2_110723_cDNA_A6_S71

description: Library name: 2cell_P2_110723_cDNA_A6_S71


title: Patient_10_invasive_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_A5_S70

description: Library name: 2cell_P2_110723_cDNA_A5_S70


title: Patient_10_invasive_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_B6_S83

description: Library name: 2cell_P2_110723_cDNA_B6_S83


title: Patient_09_premalignant_CD45

description: FFPE


title: Patient_09_invasive_CD45

description: FFPE


title: 2cell_P2_110723_cDNA_A4_S69

description: Library name: 2cell_P2_110723_cDNA_A4_S69


title: 2cell_P2_110723_cDNA_A3_S68

description: Library name: 2cell_P2_110723_cDNA_A3_S68


title: 2cell_P2_110723_cDNA_A1_S66

description: Library name: 2cell_P2_110723_cDNA_A1_S66


title: Patient_09_premalignant_PanCK

description: FFPE


title: Patient_09_invasive_SMA

description: FFPE


title: Patient_08_premalignant_CD45

description: FFPE


title: 0 % methylation control

city: Wuerzburg

first: Jana

last: Durackova

address: Am Hubland

department: Institute of Human Genetics

institute: Julius Maximilians University

description: Library name: zeropercent

data_processing:
Illumina'´s BCL Convert software version 4.2.7 was used to process the 150 bp paired end reads to FASTQ files
Amplikzyer 2 software was used for read alignment and calculation of methylation rates on a single nucleotide and regional level (https://bitbucket.org/svenrahmann/amplikyzer/src/master/, accessed on 18.10.2024), generating .txt files used for further processing.
Assembly: GRCh37; CATCCGGAGGCCCAACCTCTCCAG,CGACAGGTCGCCAGAGGACAGCGTGTCAGCAATAACCCGGCGGCCCAAAATGCCGACTCGGAGCGAAAGATATACCTCCCCCGGGGCCGGGAGGTCGCGTCACCGACCACGCCGCCGGCCCAGGCNACGCGCGACACGGACACCTGTCCCCAAAAACGCCACCATCGCAGCCACACACGGAGCGCCC,GGGGCCCTCTGGTCAACCCCAGGACACA
Supplementary files format and content: Processed data file in the .txt format generated by Amplikyzer2 includes name of the assay, sample name and detected SNP in a specified position in the header, followed by the number of detected reads, number of CpGs, average methylation rate of the sample, average methylation rate of each CpG and average rate methylation of each read

source_name: Methylated control

extract_protocol:
DNA extraction using the QIAmp DNA mini kit (Qiagen, Hilden, Germany) according to manufacturers instructions
300 ng of genomic DNA were bisulfite converted using the EpiTect Fast Bisulfite conversion kit (Qiagen, Hilden, Germany) according to manufacturers instructions. 3 µl of Bisulfite coverted DNA was subsequently used in first round of PCRs in 50 µl volume reactions for target enrichment. 0 % and 100 % methylation controls served as controls for assessing the reliability of methylation measurements. The samples were quantified using the Qubit fluorometer and diluted to a concentration of 0.2 ng/µl. In the subsequent PCRs, samples were barcoded using NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 2). The purified and quantified PCR pools were diluted to a concentration of 4 nM, and 3 µl of this dilution from each of the MIDs were combined into a single final pool for next-generation sequencing, using the NextSeq 2000 platform (Illumina, California, USA) and Reagent Kit P1 (300 cycles) cartridge (Illumina) according to the manufacturer’s instructions.

value: Methylated control


title: Patient_09_invasive_PanCK

description: FFPE


title: P13, 79 years, Liver

description: Library name: 13_L

source_name: Liver

value: Liver

value: Female


title: Patient_08_premalignant_SMA

description: FFPE


title: 2cell_P2_110723_cDNA_A10_S75

description: Library name: 2cell_P2_110723_cDNA_A10_S75


title: 100 % methylation control

description: Library name: hundredpercent

source_name: Unmethylated control

value: Unmethylated control


title: Patient_08_invasive_CD45

description: FFPE


title: Patient_08_premalignant_PanCK

description: FFPE


title: P13, 79 years, Kidney

description: Library name: 13_K

source_name: Kidney

value: Kidney


title: Patient_08_invasive_SMA

description: FFPE


title: P13, 79 years, Heart

description: Library name: 13_H

value: Heart


title: Patient_08_invasive_PanCK

description: FFPE


title: Patient_07_premalignant_SMA

description: FFPE


title: P13, 79 years, Cerebrum

description: Library name: 13_B

source_name: Cerebrum

value: Cerebrum


title: P12, 77 years, Kidney

description: Library name: 12_K


title: Patient_07_premalignant_CD45

description: FFPE


title: P13, 79 years, Cerebellum

description: Library name: 13_Cer

source_name: Cerebellum

value: Cerebellum


title: Patient_09_premalignant_SMA

description: FFPE


title: P12, 77 years, Colon

description: Library name: 12_Col

source_name: Colon

value: Colon


title: Patient_10_invasive_CD45

description: FFPE


title: Patient_07_premalignant_PanCK

description: FFPE


title: P11, 73 years, Liver

description: Library name: 11_L


title: P11, 73 years, Heart

description: Library name: 11_H


title: P11, 73 years, Kidney

description: Library name: 11_K


title: Patient_07_invasive_SMA

description: FFPE


title: P11, 73 years, Colon

description: Library name: 11_Col


title: Patient_06_premalignant_CD45

description: FFPE


title: P10, 67 years, Spleen

description: Library name: 10_S

source_name: Spleen

value: Spleen

value: Male


title: Patient_06_premalignant_SMA

description: FFPE


title: P11, 73 years, Cereberum

description: Library name: 11_B


title: P13, 79 years, Intestines

description: Library name: 13_I

source_name: Intestines

value: Intestines


title: P10, 67 years, Liver

description: Library name: 10_L


title: Patient_06_premalignant_PanCK

description: FFPE


title: Patient_06_invasive_CD45

description: FFPE


title: P10, 67 years, Kidney

description: Library name: 10_K


title: Patient_06_invasive_SMA

description: FFPE


title: P10, 67 years, Heart

description: Library name: 10_H


title: Patient_06_invasive_PanCK

description: FFPE


title: P10, 67 years, Cerebrum

description: Library name: 10_B


title: P9, 66 years, Colon

description: Library name: 9_Col


title: Patient_05_premalignant_PanCK

description: FFPE


title: P8, 64 years, Liver

description: Library name: 8_L


title: P9, 66 years, Cerebrum

description: Library name: 9_B


title: Patient_07_invasive_CD45

description: FFPE


title: Patient_05_invasive_CD45

description: FFPE


title: Patient_07_invasive_PanCK

description: FFPE


title: 2cell_P2_110723_cDNA_A2_S67

description: Library name: 2cell_P2_110723_cDNA_A2_S67

value: 2 cell embryo


title: P8, 64 years, Heart

description: Library name: 8_H


title: P10, 67 years, Cerebellum

description: Library name: 10_Cer


title: Patient_04_premalignant_CD45

description: FFPE


title: Patient_05_invasive_PanCK

description: FFPE


title: Patient_04_premalignant_SMA

description: FFPE


title: Patient_05_invasive_SMA

description: FFPE


title: P7, 64 years, Kidney

description: Library name: 7_K


title: P7, 64 years, Liver

description: Library name: 7_L


title: Patient_04_invasive_CD45

description: FFPE


title: Patient_04_invasive_SMA

description: FFPE


title: P7, 64 years, Intestines

description: Library name: 7_I


title: P7, 64 years, Heart

description: Library name: 7_H


title: Patient_05_premalignant_CD45

description: FFPE


title: Patient_03_premalignant_CD45

description: FFPE


title: Patient_04_invasive_PanCK

description: FFPE


title: Patient_05_premalignant_SMA

description: FFPE


title: P7, 64 years, Cerebrum

description: Library name: 7_B


title: P7, 64 years, Cerebellum

description: Library name: 7_Cer


title: Patient_03_premalignant_SMA

description: FFPE


title: Patient_03_premalignant_PanCK

description: FFPE


title: P6, 64 years, Kidney

description: Library name: 6_K


title: Patient_03_invasive_CD45

description: FFPE


title: P6, 64 years, Heart

description: Library name: 6_H


title: P8, 64 years, Kidney

description: Library name: 8_K


title: Patient_03_invasive_SMA

description: FFPE


title: P6, 64 years, Colon

description: Library name: 6_Col


title: Patient_03_invasive_PanCK

description: FFPE


title: P8, 64 years, Colon

description: Library name: 8_Col


title: P6, 64 years, Cerebellum

description: Library name: 6_Cer


title: Patient_04_premalignant_PanCK

description: FFPE


title: Patient_02_premalignant_SMA

description: FFPE


title: P6, 64 years, Cerebrum

description: Library name: 6_B


title: Patient_02_premalignant_CD45

description: FFPE


title: Patient_02_premalignant_PanCK

description: FFPE


title: P5, 60 years. Female, Liver

description: Library name: 5_L


title: P5, 60 years. Female, Kidney

description: Library name: 5_K


title: P5, 60 years. Female, Colon

description: Library name: 5_Col


title: Patient_02_invasive_SMA

description: FFPE


title: Patient_02_invasive_CD45

description: FFPE


title: Patient_02_invasive_PanCK

description: FFPE


title: P4, 59 years, Liver

description: Library name: 4_L


title: Patient_01_premalignant_CD45

description: FFPE


title: P4, 59 years, Kidney

description: Library name: 4_K


title: P4, 59 years, Heart

description: Library name: 4_H


title: P4, 59 years, Colon

description: Library name: 4_Col


title: Patient_01_premalignant_SMA

description: FFPE


title: Patient_01_premalignant_PanCK

description: FFPE


title: P6, 64 years, Liver

description: Library name: 6_L


title: P4, 59 years, Cerebellum

description: Library name: 4_Cer


title: Patient_01_invasive_CD45

description: FFPE


title: Patient_01_invasive_SMA

description: FFPE


title: P4, 59 years, Cerebrum

description: Library name: 4_B


title: P3, 59 years, Liver

description: Library name: 3_L


title: P3, 59 years, Kidney

description: Library name: 3_K


title: Patient_01_invasive_PanCK

description: FFPE


title: BT16 cells treated with DMSO (Vehichle control)

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
The reads were aligned to the human reference genome (GRCh38 V3.0.0).
Differentially expressed genes were identified using the “FindAllMarkers” function in Seurat (v 4.0.4).
Genes with a fold change of more than 1.5 and an adjusted p value less than 0.05 were considered as differentially expressed genes.
Cell clustering was performed using the “RunUMAP” and “FindClusters” function in Seurat with setting parameters dims=1:10 and resolution= 0.6 and visualized using Uniform Manifold Approximation and Projection (UMAP).
Assembly: GrCh38 V3.0.0
Supplementary files format and content: Tab-delimited text

source_name: cerebellum

growth_protocol: BT16 ATRT cells were cultured in RPMI medium (Life Technologies, Gibco #11875-093) supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals, Inc. #S11550) and 1% penicillin/streptomycin (Life Technologies, Gibco #15140-122).  Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
Tumors were collected from mice cerebellum, disaggregated with razor, filtered using 100um cell strainer, centrifugated and resuspended with 2%FBS in PBS. Cells were sorted for GFP color, nucleus were isolated (10x genomic kit#cG000366) and cells were processed for single RNA sequencing.
ScRNA sequencing was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit (v3.1 10x Genomics, Pleasanton, CA) and the Chromium X.

treatment_protocol: Female athymic nude (Foxn1 nu) mice (6 weeks old; weight, 18 20 g) from Harlan Laboratories were used. Luciferase-expressing  BT16  ATRT cells were obtained by transfection with the pLV[Exp]-Bsd-EFS>Luc2(ns):T2A:TurboGFP vector (VectorBuilder, Inc.). 300,000 luciferase-expressing  BT16  ATRT cells were injected into mice cerebellum.For bioluminescence analysis, mice were imaged using the Xenogen IVIS 200 in Vivo Imaging System (PerkinElmer, Waltham, MA, USA). Tumor bioluminescence was analyzed using Living Image 2.60.1 software (Caliper Life Sciences, PerkinElmer, Waltham, MA, USA).. Treatmet started when tumors were established. Mice were treated with either TM (50 mg/kg IP 3/week for 4 weeks) or Vehichle control. All Animal procedures were approved by the University of Colorado Anschutz Campus Institutional Animal Care and Use Committee (protocol number:00052)

value: cerebellum

value: Atypical teratoid rhabdoid tumor

value: DMSO


title: BT16 cells treated with TM

value: TM


title: HCT116 cell,FTOKO,bio rep 3

city: XIAN

first: xu

middle: chang

last: wei

address: 169 Changle West Road, Xincheng District

institute: AIR FORCE MEDICAL UNIVERSITY

data_processing:
2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Assembly: mm10
Supplementary files format and content: gene counts and FPKM values

source_name: cell line

extract_protocol:
RNA was harvested usingTRIzol reagent (Invitrogen, Carlsbad, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: cell line

value: colon carcinoma cells

value: FTO knockout


title: P3, 59 years, Cerebrum

description: Library name: 3_B

value: Female


title: P2, 47 years, Liver

description: Library name: 2_L

value: Liver


title: HCT116 cell,FTOKO,bio rep 1


title: HCT116 cell,WT,bio rep 3

value: Wildtype


title: P2, 47 years, Heart

description: Library name: 2_H

value: Heart


title: P2, 47 years, Cerebellum

description: Library name: 2_Cer

value: Cerebellum


title: HCT116 cell,WT,bio rep 2


title: P2, 47 years, Cerebrum

description: Library name: 2_B

value: Cerebrum


title: HCT116 cell,WT,bio rep 1


title: P1, 44 years, Liver

description: Library name: 1_L


title: P1, 44 years, Kidney

description: Library name: 1_K

value: Kidney


title: HT29 cell,FTOKO,bio rep 2


title: 29H_Pa+let7

city: Hanover

first: Sharanya

last: Sarkar

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

description:
Library name: 190276_15
Donor 29H

data_processing:
Prepared libraries were pooled and sequenced on a NextSeq2000 platform, aiming at 10 million single-end 100 bp reads per sample.
Paired-end reads were processed by trimming with Cutadapt v4.056 followed by alignment to the GRCh38 human genome reference using Hisat2 v2.2.1 (RRID:SCR_015530)57.
Gene expression levels were quantified with FeatureCounts v2.0.158, using Human Ensembl v97 as the reference annotation.
Alignment and quantification metrics were assessed with Samtools v1.15.1 (RRID:SCR_001105)59 and Picard v2.27.160.
Assembly: hg38 (GRCh38)
Supplementary files format and content: tsv file containing raw counts alinged to hg38 genome

source_name: lung

growth_protocol: pHBEC were maintained in BronchiaLife basal medium (Lifeline Cell Technology, Frederick, MD, Cat. No. LM-0007) at 37°C with 5% CO₂. The medium was supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline Cell Technology, Cat. No. LS-1047) and antibiotics (penicillin, 10,000 U/mL; streptomycin, 10,000 μg/mL; Sigma-Aldrich, Cat. No. P4333). Cells were used for experiments between passages 4 and 9, and the data was not dependent on the passage number. Samples were seeded on 24-mm permeable supports (Corning, Catalog #3407) pre-coated with type IV collagen (Sigma-Aldrich, Catalog #C-7521). The cells were cultured in air-liquid interface media (University of North Caroline, Chapel Hill) of  at 37°C for 3 - 4 weeks to establish polarized monolayer.

extract_protocol:
RNA was isolated from HBECs using the miRNeasy Kit (Qiagen, Germantown, MD, Catalog #217004). cDNA synthesis was performed with 1 µg of RNA as input, using SuperScript IV (Invitrogen, Grand Island, NY, Catalog #18090050).
A total of 100 ng of RNA was used as input for library preparation following the QuantSeq FWD workflow (Lexogen) according to the manufacturer’s protocol.

treatment_protocol: P. aeruginosa PA14 (3 × 10⁸/mL) was introduced to the apical side of the monolayers for 1 hour. Subsequently, either PC, NC MSC EVs, or let-7b MSC EVs (2 × 10⁹/mL) were added for an additional 5 hours, completing a 6-hour treatment period. One monolayer of pHBEC served as a second control, receiving neither P. aeruginosa nor EVs, while another monolayer was treated only with P. aeruginosa with no EVs.

value: lung

value: primary bronchial epithelial cells

value: homozygous delta-F508

value: PA and let-7b-5p-loaded MSC EV


title: HT29 cell,WT,bio rep 3


title: HT29 cell,FTOKO,bio rep 1


title: P1, 44 years, Intestines

description: Library name: 1_I

value: Intestines

value: Male


title: P1, 44 years, Heart

description: Library name: 1_H


title: HT29 cell,WT,bio rep 2


title: 29H_Pa+PC

description:
Library name: 190276_13
Donor 29H

value: PA and process control


title: HT29 cell,FTOKO,bio rep 3

value: cell line


title: P3, 59 years, Intestines

description: Library name: 3_I


title: 29H_Pa

description:
Library name: 190276_12
Donor 29H

value: PA


title: 29H_Pa+NC

description:
Library name: 190276_14
Donor 29H

value: PA and negative control MSC EV


title: HCT116 cell,FTOKO,bio rep 2

value: colon carcinoma cells

value: FTO knockout


title: HT29 cell,WT,bio rep 1

value: Wildtype


title: GBC-6

city: taiyuan

first: ming

last: gao

state: Shanxi

address: NO.56 Xinjian South Road

institute: Shanxi Medical University

data_processing:
Illumina Casava 1.8 software was used for basecalling
Raw data (raw reads) in fastp 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 reads with low quality. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were conducted using the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Differential expression analysis of two groups (five biological replicates per group) was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values and read count numbers for each sample

source_name: adjacent tumor tissue

extract_protocol:
The total RNA samples for RNA-seq were extracted using TRIzol reagent and then treated with DNaseⅠ in order to eliminate the DNA contamination. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used to prepared the RNA-seq libraries according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adjacent tumor tissue


title: GBC-7


title: 29H_UT

description:
Library name: 190276_11
Donor 29H

value: Untreated


title: 32G_Pa+let7

description:
Library name: 190276_10
Donor 32G


title: 32G_Pa+NC

description:
Library name: 190276_09
Donor 32G


title: 32G_Pa+PC

description:
Library name: 190276_08
Donor 32G


title: GBC-5


title: GBC-2


title: GBC-3


title: 32G_Pa

description:
Library name: 190276_07
Donor 32G


title: 32G_UT

description:
Library name: 190276_06
Donor 32G


title: 22F_Pa+let7

description:
Library name: 190276_05
Donor 22F


title: GBC-1


title: AT-7

source_name: gallbladder cancer tissue

value: gallbladder cancer tissue


title: AT-6


title: AT-4


title: 22F_Pa+PC

description:
Library name: 190276_03
Donor 22F


title: 22F_Pa

description:
Library name: 190276_02
Donor 22F


title: AT-1


title: AT-3