title: FIX00145-2616BW NK none

description:
Library name: FIX00145
10x Genomics Flex


title: FIX00146-2616BW NK IFNa

status: Public on Jun 30 2026

type: SRA

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

description:
Library name: FIX00146
10x Genomics Flex

library_source: transcriptomic single cell

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the  Fixed RNA Profiling capability (version 7.0.0, released May 17, 2022), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Cells mapping to dendritic cell populations were removed. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

molecule: total RNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Frozen Ficoll purified PBMC from healthy subjects were acquired from Bloodworks Northwest (#4570). T cells, B cells, NK cells or CD14 monocytes in each donor from freshly thawed frozen PBMC were enriched by magnetic negative selection kits (STEMCELL technologies) for human T cells (#19051), human pan B  cells (#19554), human NK cells (#19055) or human CD14 monocytes (#19059), respectively. To ensure high purity in enriched B, NK, and CD14 monocytes, contaminated T cells were further depleted by using CD3 kit (STEMCELL technologies #17851). Three to eight hundred thousand of enriched cells from each immune cell subset or total PBMC were seeded in 200 uL of 10 % human AB serum (Millipore Sigma #H3667-20ML) containing RPMI-1640 media (ThermoScientific #11875093) per well.

extract_protocol:
After 21 hour stimulation with various IFNs, cells were washed, counted, and fixed in 4% Paraformaldehyde for 1 hour (25°C). Fixed samples were quenched and subsequently washed with an additional 200 uL of PBS + 0.02% BSA (Costar). Samples were barcoded for multiplexing using 10X Genomics Fixed RNA Feature Barcode Multiplexing Kit (#PN-1000628). Probe hybridization was completed according to the 10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673,  Rev A). Up to 2 million fixed cells were hybridized per sample. After 16-24 hours of probe hybridization incubation (42°C), samples were diluted in Post-Hyb Wash buffer and 11 µL was removed for counting. The counting fraction was stained 1:5 with 44 uL of PI solution and counted on a Nexcelom Cellaca MX cell counter.
Samples were then pooled at equivalent cell concentrations at a minimum of 50,000 cells/sample, incubated for 3 rounds of 10 minutes at 42°C, washed in Post-Hyb wash buffer, and strained using 30 uM strainers (Miltenyi). The single cell suspension pool was loaded onto Chip Q for GEM generation at an overloaded concentration of 400,000 cells. Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300, Novaseq S2 PE200, or a NovaSeq S4 PE100 flow cell, targeting a minimum read depth of 10,000 reads per cell.

treatment_protocol: Each enriced immune cells were stimulated with IFN-a2A (1000 units/mL, PBL Assay Science #11101-2) or IFN-b (100 units/mL, R&D #8499-IF-010/CF) or IFN-g (25 ng/mL, Biolegend #570206) or IFN-L1 (100 ng/mL, R&D #1598-IL-025/CF) or no stimulation for 21 hours in 37°C.

tag: tissue

value: Blood

tag: cell type

value: NK

tag: treatment

value: IFNa

tag: subject id

tag: age at_blood_drawn

tag: Sex

value: male

tag: ethnics/race

value: Caucasian/Non-hisp

tag: cmv stats

value: Negative

tag: treatment time

value: 21 hours

tag: batch id

tag: pool id

value: PB

tag: batch pool

tag: probe barcode_id


title: FIX00125-2616BW Monocyte IFN-L1

description:
Library name: FIX00125
10x Genomics Flex

value: Monocyte

value: PA


title: FIX00124-2616BW Monocyte IFNg

description:
Library name: FIX00124
10x Genomics Flex

value: IFNg


title: FIX00123-2616BW Monocyte IFNb

description:
Library name: FIX00123
10x Genomics Flex

value: IFNb


title: FIX00122-2616BW Monocyte IFNa

description:
Library name: FIX00122
10x Genomics Flex


title: FIX00144-2616BW Bcell IFN-L1

description:
Library name: FIX00144
10x Genomics Flex

value: Bcell


title: FIX00121-2616BW Monocyte none

description:
Library name: FIX00121
10x Genomics Flex


title: FIX00143-2616BW Bcell IFNg

description:
Library name: FIX00143
10x Genomics Flex


title: FIX00142-2616BW Bcell IFNb

description:
Library name: FIX00142
10x Genomics Flex


title: FIX00141-2616BW Bcell IFNa

description:
Library name: FIX00141
10x Genomics Flex


title: FIX00140-2616BW Bcell none

description:
Library name: FIX00140
10x Genomics Flex


title: FIX04861-003-6811BW Tcell IFN-L1

description:
Library name: FIX04861-003
10x Genomics Flex

value: Tcell

value: Positive

value: PC


title: FIX04861-002-6811BW Tcell IFNg

description:
Library name: FIX04861-002
10x Genomics Flex


title: FIX00105-3955BW Tcell IFN-L1

description:
Library name: FIX00105
10x Genomics Flex

value: female


title: FIX04861-001-6811BW Tcell none

description:
Library name: FIX04861-001
10x Genomics Flex

value: Blood


title: FIX00103-3955BW Tcell none

description:
Library name: FIX00103
10x Genomics Flex


title: FIX00104-3955BW Tcell IFNg

description:
Library name: FIX00104
10x Genomics Flex


title: FIX00108-3491BW Tcell IFN-L1

description:
Library name: FIX00108
10x Genomics Flex


title: FIX00107-3491BW Tcell IFNg

description:
Library name: FIX00107
10x Genomics Flex


title: FIX04862-018-3283BW Tcell IFN-L1

description:
Library name: FIX04862-018
10x Genomics Flex

value: Asian/Non-hisp


title: FIX00106-3491BW Tcell none

description:
Library name: FIX00106
10x Genomics Flex


title: FIX04862-017-3283BW Tcell IFNg

description:
Library name: FIX04862-017
10x Genomics Flex


title: FIX04862-016-3283BW Tcell none

description:
Library name: FIX04862-016
10x Genomics Flex


title: VZ_1757

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description: Library name: FETHB2_0004_01_LB01-01

library_source: genomic

data_processing:
A standard bioinformatics pipeline was used to process the EMseq data; processing statistics are reported in Supplementary Table 2.  Fastp 0.23.213 was used to ascertain read quality and perform adapter trimming. Reads were aligned to the hg38 genome using bwa-meth 0.2.514. Duplicates were filtered using Picard MarkDuplicates (https://broadinstitute.github.io/picard/). MethylDackel (https://github.com/dpryan79/MethylDackel) was used to compute Mbias plots. MethylDackel extract --maxVariantFrac 0.2 --minOppositeDepth 5 --cytosine_report --OT 0,0,0,147 --OB: 3,0,5,0 was used to compute cytosine-level methylation reports while removing potential C > T variants. Methylation non-conversion rate was measured using the methylation level of the lambda phage genome. Samples had a mean non-conversion rate of 0.34% (range 0.21 - 0.64) and all samples were retained. All samples showed consistent patterns of genome-wide methylation with over 50% of CpGs having 90% methylation and 10% CpGs with <10% methylation. Hierarchical clustering of CpG methylation in the region of SOX2 and EOMES largely separated the rhombic lip ventricular zone and subventricular zone samples, and no samples were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Cytosine report files generated by MethylDackel
Library strategy: EM-seq

molecule: genomic DNA

source_name: Cerebellar rhombic lip

growth_protocol: These data were generated from primary human tissue; therefore, this column is not applicable.

extract_protocol:
DNA was extracted using a protocol based on Qiagen Puregene.
The NEBNext Enzymatic Methyl-seq Kit was used.

treatment_protocol: This project was approved by the Research Ethic Board at the University of Toronto (RIS Human Protocol #42524). We received frozen mid-gestation human hindbrains from the University of Maryland Brain and Tissue Bank. Tissue cryosectioning and immunohistochemistry was performed by the University Health Network Pathology Research Program Laboratory. Brain tissue was cryosectioned on the mid-sagittal plane and stained for cresyl violet, SOX2 (CST Sox2 (D6D9) XP Rabbit mAb #3579) and KI67 (Dako #M7240 Mouse monoclonal antibody). The rhombic lip was identified at the edge of the fourth ventricle by its size and prominent KI67+ staining.  Selected sections were stained with CD34 (Dako #M7165 Monoclonal Mouse Anti-Human) and GFAP (Dako #Z334) to identify the vascular bed that separates the rhombic lip ventricular zone and subventricular zone (Supplementary Figure 1). Using immunohistochemistry, we identified the rhombic lip ventricular (SOX2+ KI67+) and subventricular (SOX2- KI67+) zone in each sample. We used laser capture microdissection (LCM) to isolate tissue separately from the rhombic lip ventricular zone and subventricular zone. LCM was performed by the Ontario Institute for Cancer Research Tissue Portal using the Leica LMD6 instrument; cresyl violet was used to visualize the tissue.

value: Cerebellar rhombic lip

tag: cell compartment

value: VZ

tag: gestation weeks

tag: ethnicity

value: Black or African-American

value: Male

tag: batch

tag: pmi hours


title: VZ_1644

description: Library name: FETHB2_0003_01_LB02-01

tag: tissue

value: White


title: FIX00110-2616BW Tcell IFNg

description:
Library name: FIX00110
10x Genomics Flex

tag: cell type

tag: treatment

value: male

value: Caucasian/Non-hisp

value: Negative

value: 21 hours


title: FIX00111-2616BW Tcell IFN-L1

description:
Library name: FIX00111
10x Genomics Flex

tag: subject id

tag: age at_blood_drawn


title: FIX00109-2616BW Tcell none

description:
Library name: FIX00109
10x Genomics Flex

tag: Sex

tag: ethnics/race


title: FIX04862-003-3283BW Tcell IFNb

description:
Library name: FIX04862-003
10x Genomics Flex

value: IFNb

tag: cmv stats

tag: treatment time

value: PB


title: FIX04862-002-3283BW Tcell IFNa

description:
Library name: FIX04862-002
10x Genomics Flex

value: Tcell

value: IFNa

tag: batch id

tag: pool id


title: FIX04862-001-3283BW Tcell none

description:
Library name: FIX04862-001
10x Genomics Flex

value: Positive

tag: batch pool

tag: probe barcode_id


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1126]

type: genomic

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Hyderabad

address: Jawahar nagar

department: Biological Sciences

country: India

institute: Birla Institute of Technology and Science

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina HumanMethylation 450K Bead Chip

scan_protocol: Arrays were imaged using BeadArray Reader and standard recommended illumina scanner setting

data_processing: Methylation Module in GenomeStudio

label: Cy3 and Cy5

source_name: Cortex

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from cortex samples were extracted using Proteinase K Phenol-chloroform method

value: Cortex

value: F

tag: subject status

value: schizophrenia patient


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1082]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1106]

value: M


title: FIX04862-013-3283BW NK IFN-L1

description:
Library name: FIX04862-013
10x Genomics Flex

value: Blood

value: NK

value: female

value: Asian/Non-hisp


title: FIX04862-012-3283BW NK IFNg

description:
Library name: FIX04862-012
10x Genomics Flex

value: IFNg


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1133]


title: FIX04862-011-3283BW NK IFNb

description:
Library name: FIX04862-011
10x Genomics Flex


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1081]


title: FIX04862-010-3283BW NK IFNa

description:
Library name: FIX04862-010
10x Genomics Flex


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1102]


title: FIX04862-009-3283BW NK none

description:
Library name: FIX04862-009
10x Genomics Flex


title: FIX04862-026-3283BW Monocyte IFN-L1

description:
Library name: FIX04862-026
10x Genomics Flex

value: Monocyte

value: PA


title: FIX04862-025-3283BW Monocyte IFNg

description:
Library name: FIX04862-025
10x Genomics Flex

value: 21 hours


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1077]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1098]


title: FIX04862-024-3283BW Monocyte IFNb

description:
Library name: FIX04862-024
10x Genomics Flex

value: IFNb


title: FIX04862-023-3283BW Monocyte IFNa

description:
Library name: FIX04862-023
10x Genomics Flex


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1094]


title: FIX04862-022-3283BW Monocyte none

description:
Library name: FIX04862-022
10x Genomics Flex


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1115]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1089]


title: FIX04862-008-3283BW Bcell IFN-L1

description:
Library name: FIX04862-008
10x Genomics Flex

value: Bcell

value: PB


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1100]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1104]


title: FIX04862-007-3283BW Bcell IFNg

description:
Library name: FIX04862-007
10x Genomics Flex


title: FIX04862-006-3283BW Bcell IFNb

description:
Library name: FIX04862-006
10x Genomics Flex


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1096]


title: FIX04862-005-3283BW Bcell IFNa

description:
Library name: FIX04862-005
10x Genomics Flex

value: IFNa


title: FIX04862-004-3283BW Bcell none

description:
Library name: FIX04862-004
10x Genomics Flex

value: Positive


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1073]

value: Cortex


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1095]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1097]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1120]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1140]


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1113]

value: F


title: FIX00072-3955BW Tcell IFNa

description:
Library name: FIX00072
10x Genomics Flex

value: Tcell

value: Caucasian/Non-hisp

value: Negative


title: FIX00071-3955BW Tcell none

description:
Library name: FIX00071
10x Genomics Flex

value: Blood


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1076]

value: M

value: schizophrenia patient


title: FIX00082-3955BW NK IFNg

description:
Library name: FIX00082
10x Genomics Flex

value: NK

value: IFNg

value: female


title: Genomic DNA isolated from cortex of a healthy individual  [1141]

value: healthy individual


title: FIX00083-3955BW NK IFN-L1

description:
Library name: FIX00083
10x Genomics Flex

value: 21 hours


title: FIX00081-3955BW NK IFNb

description:
Library name: FIX00081
10x Genomics Flex

value: IFNb


title: Genomic DNA isolated from cortex of a healthy individual  [1071]


title: Genomic DNA isolated from cortex of a healthy individual  [1139]


title: FIX00080-3955BW NK IFNa

description:
Library name: FIX00080
10x Genomics Flex

value: PB


title: Genomic DNA isolated from cortex of a healthy individual  [1107]


title: FIX00079-3955BW NK none

description:
Library name: FIX00079
10x Genomics Flex


title: FIX00073-3955BW Tcell IFNb

description:
Library name: FIX00073
10x Genomics Flex


title: Genomic DNA isolated from cortex of a schizophrenia patient  [1069]


title: Genomic DNA isolated from cortex of a healthy individual  [1137]


title: Genomic DNA isolated from cortex of a healthy individual  [1110]


title: Genomic DNA isolated from cortex of a healthy individual  [1135]


title: FIX00059-3955BW Monocyte IFN-L1

description:
Library name: FIX00059
10x Genomics Flex

value: Monocyte

value: PA


title: FIX00057-3955BW Monocyte IFNb

description:
Library name: FIX00057
10x Genomics Flex


title: Genomic DNA isolated from cortex of a healthy individual  [1123]

value: Cortex


title: FIX00056-3955BW Monocyte IFNa

description:
Library name: FIX00056
10x Genomics Flex

value: IFNa


title: FIX00055-3955BW Monocyte none

description:
Library name: FIX00055
10x Genomics Flex


title: Genomic DNA isolated from cortex of a healthy individual  [1132]

value: F


title: FIX00058-3955BW Monocyte IFNg

description:
Library name: FIX00058
10x Genomics Flex

value: Caucasian/Non-hisp


title: FIX00078-3955BW Bcell IFN-L1

description:
Library name: FIX00078
10x Genomics Flex

value: Bcell

value: Negative


title: Genomic DNA isolated from cortex of a healthy individual  [1125]

value: M


title: Genomic DNA isolated from cortex of a healthy individual  [1129]


title: FIX00077-3955BW Bcell IFNg

description:
Library name: FIX00077
10x Genomics Flex

value: Blood


title: Genomic DNA isolated from cortex of a healthy individual  [1128]


title: Genomic DNA isolated from cortex of a healthy individual  [1138]


title: FIX00076-3955BW Bcell IFNb

description:
Library name: FIX00076
10x Genomics Flex


title: FIX00075-3955BW Bcell IFNa

description:
Library name: FIX00075
10x Genomics Flex


title: FIX00074-3955BW Bcell none

description:
Library name: FIX00074
10x Genomics Flex


title: HBMECOGD3

city: Wuhan

first: Haipeng

last: Wang

address: Shizishan Rd, Wuhan, Hubei

country: China

institute: Huazhong Agriculture Unversity

description: Library name: Sample6

library_source: transcriptomic

data_processing:
1 Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic with default parameters. 2 Mapping by HISAT2. 3 Sorting and indexing comparison results using Samtools. 4 Gene Expression Quantification with featureCounts. 5 Finally,using edgeR to Differential Expression Analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Brain

extract_protocol:
RNA was harvested using Triquick Reagent (Solarbio). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

value: Brain

tag: cell line

value: HBMEC

value: Endothelial cell


title: HBMECOGD2

description: Library name: Sample5


title: Genomic DNA isolated from cortex of a healthy individual  [1118]

value: healthy individual


title: Genomic DNA isolated from cortex of a healthy individual  [1099]


title: HBMECOGD1

description: Library name: Sample4


title: Genomic DNA isolated from cortex of a healthy individual  [1117]


title: HBMECCON3

description: Library name: Sample3


title: Genomic DNA isolated from cortex of a healthy individual  [1111]


title: Genomic DNA isolated from cortex of a healthy individual  [1070]


title: HBMECCON2

description: Library name: Sample2


title: Genomic DNA isolated from cortex of a healthy individual  [1074]


title: HBMECCON1

description: Library name: Sample1


title: miRNA-seq of Hs578T cells cultured in 3D (replicate 3)

city: Mexico City

first: Yarely M.

last: Salinas-Vera

address: Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360 Mexico City, CDMX

department: Biochemistry

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del IPN

description:
Library name: Hs578T_miR_3D_3
Column name in raw_counts_All_Samples.csv

data_processing:
Raw reads were quality filtered using Trimmomatic (mRNA/lncRNA) and Cutadapt (miRNA) to remove adapter sequences and low-quality bases. Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 for mRNA/lncRNA and Bowtie for miRNA. Transcript assembly and quantification of mRNA/lncRNA were performed with StringTie and expression levels reported as FPKM. For miRNA, identification and quantification of known and novel miRNAs were carried out using miRDeep2, and expression was reported as TPM.
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: The Hs578T breast cancer cell line was maintained with DMEM medium supplemented with 10% fetal bovine serum and penicillin-streptomycin (50 units/mL; Invitrogen, Waltham, MA, USA).

extract_protocol:
RNA extraction was performed according to the manufacturer´s protocol for the 2D cultures RNeasy plus mini kit (Qiagen, Hilden, Germany). For 3D culture assays, total RNA was collected 6 days after seeding using the RNeasy Plus Mini Kit (Qiagen) with minor modifications.
Three micrograms of RNA from each sample were used as input for RNA-seq library preparation. First, ribosomal RNA (rRNA) was removed with the Epicenter Ribo-Zero rRNA Removal Kit (Illumina, USA), and small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample. Meanwhile, mRNA and lncRNA sequencing libraries were generated using  NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, USA).

treatment_protocol: To establish organotypic 3D cell cultures, we followed the methodology previously described by Salinas-Vera and coworkers (4). Briefly, 3.2 × 104 cells/well were seeded in a 24-well plate previously coated with 120 μL of matrigel (Geltrex; Thermo Fisher Scientific, Waltham, MA, USA). The 3D cell cultures were maintained for 6 days using DMEM and 5% Matrigel with medium changes every 2 days.

value: breast cancer cells

tag: genotype

value: WT

value: 3D culture

tag: time

value: Day 6


title: Genomic DNA isolated from cortex of a healthy individual  [1088]

tag: tissue


title: RNA-seq of Hs578T 3D culture (mRNA/lncRNA) rep3_1

description:
Library name: Hs578T_3D_3_1
Column name in raw_counts_All_Samples.csv

tag: cell type


title: miRNA-seq of Hs578T cells cultured in 3D (replicate 2)

description:
Library name: Hs578T_miR_3D_2
Column name in raw_counts_All_Samples.csv

tag: treatment


title: Genomic DNA isolated from cortex of a healthy individual  [1075]


title: RNA-seq of Hs578T 3D culture (mRNA/lncRNA) rep2_1

description:
Library name: Hs578T_3D_2_1
Column name in raw_counts_All_Samples.csv


title: miRNA-seq of Hs578T cells cultured in 3D (replicate 1)

description:
Library name: Hs578T_miR_3D_1
Column name in raw_counts_All_Samples.csv


title: Genomic DNA isolated from cortex of a healthy individual  [1127]


title: RNA-seq of Hs578T 3D culture (mRNA/lncRNA) rep1_1

description:
Library name: Hs578T_3D_1_1
Column name in raw_counts_All_Samples.csv


title: Genomic DNA isolated from cortex of a healthy individual  [1078]


title: miRNA-seq of Hs578T cells cultured in 2D (replicate 3)

description:
Library name: Hs578T_miR_2D_3
Column name in raw_counts_All_Samples.csv

value: 2D culture

value: Day 0


title: RNA-seq of Hs578T 2D culture (mRNA/lncRNA) rep3_1

description:
Library name: Hs578T_2D_3_1
Column name in raw_counts_All_Samples.csv


title: PNC018_B1

type: RNA

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G. GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing:
The data were analyzed using the “limma”package and R studio version 4.2.2.
The data were analyzed using the “limma”package and R studio version 4.2.2.

label: biotin

source_name: pancreas transplant biopsy

label_protocol:
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA

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

tag: age at biopsy

tag: histology cathegory

value: ACR


title: Genomic DNA isolated from cortex of a healthy individual  [1087]

value: Cortex

tag: Sex

value: F


title: PNC017_B4


title: PNC017_B2

value: Indeterminate


title: PNC017_B1

value: Marginal


title: Genomic DNA isolated from cortex of a healthy individual  [1108]

value: M


title: Genomic DNA isolated from cortex of a healthy individual  [1124]


title: PNC017_B3


title: miRNA-seq of Hs578T cells cultured in 2D (replicate 2)

description:
Library name: Hs578T_miR_2D_2
Column name in raw_counts_All_Samples.csv


title: PNC016_B1


title: RNA-seq of Hs578T 2D culture (mRNA/lncRNA) rep2_1

description:
Library name: Hs578T_2D_2_1
Column name in raw_counts_All_Samples.csv


title: Genomic DNA isolated from cortex of a healthy individual  [1091]


title: Genomic DNA isolated from cortex of a healthy individual  [1079]


title: Genomic DNA isolated from cortex of a healthy individual  [1093]


title: miRNA-seq of Hs578T cells cultured in 2D (replicate 1)

description:
Library name: Hs578T_miR_2D_1
Column name in raw_counts_All_Samples.csv


title: RNA-seq of Hs578T 2D culture (mRNA/lncRNA) rep1_1

description:
Library name: Hs578T_2D_1_1
Column name in raw_counts_All_Samples.csv


title: PNC015_B2


title: CAL-27 cell, shYTHDC2,bio rep 3

city: xi'an

first: Liangliang

last: Shen

address: West changle road 169

institute: The fourth military medical university

description: Library name: Sample 6

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions)    exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: FPKM values

extract_protocol: Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1  g total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then 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. At last, we performed the 2  150bp paired-end sequencing (PE150) on an illumina Novaseq  6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Oral squamous cell carcinoma


title: PNC015_B1


title: PNC014_B1


title: CAL-27 cell, shYTHDC2,bio rep 2

description: Library name: Sample 5


title: CAL-27 cell, shYTHDC2,bio rep 1

description: Library name: Sample 4


title: CAL-27 cell, NC,bio rep 2

description: Library name: Sample 2

value: NC


title: PNC012_B1

value: No-rejection


title: CAL-27 cell, NC,bio rep 3

description: Library name: Sample 3


title: PNC013_B1


title: PNC011_B2


title: PNC011_B1


title: CAL-27 cell, NC,bio rep 1

description: Library name: Sample 1


title: HK-2-GDF5-3

city: Chongqing

first: linqiang

last: ma

address: Medical University, No. 1 Youyi St

institute: The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

description:
Library name: sample6
GDF3

data_processing:
HISAT2 DESeq2
Assembly: GRCh38
Supplementary files format and content: processed data.xls FPKM

extract_protocol:
Total RNA was extracted from samples using TRIzol reagent
RNA Libraries for RNA-seq were prepared using the Illumina Strand-Specific RNA-Seq Library Construction Protocol


title: PNC009_B1_2D


title: PNC009_B2


title: HK-2-GDF5-2

description:
Library name: sample5
GDF2


title: PNC008_B1


title: HK-2-GDF5-1

description:
Library name: sample4
GDF1


title: HK-2-CON-3

description:
Library name: sample3
C3


title: HK-2-CON-2

description:
Library name: sample2
C2


title: PNC006_B1


title: PNC007_B1


title: PNC005_B1


title: Genomic DNA isolated from cortex of a healthy individual  [1086]


title: AIS-064

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description:
Library name: V1202
FFPE spatial transcriptome sequencing

data_processing:
Raw reads were processed using SpaceRanger version 2.0.0.
Assembly: GRCh38
Supplementary files format and content: HDF5 file containing per-molecule information for all molecules.
Library strategy: Spatial Transcriptomics

source_name: Pre-invasive lung adenocarcinoma

extract_protocol:
FFPE slides were mounted onto Visium slides using CytAssist
Libraries were constructed using the 10x Visium from FFPE supplied reagents

value: Pre-invasive lung adenocarcinoma

tag: pathologic stage

value: AIS


title: PNC003_B1


title: AIS-029

description:
Library name: V1201
FFPE spatial transcriptome sequencing


title: HK-2-CON-1

description:
Library name: sample1
C1


title: PNC004_B1


title: PNC002_B1_2D


title: MIA-148

description:
Library name: V1104
FFPE spatial transcriptome sequencing

value: MIA


title: PNC109_B1


title: MIA-089

description:
Library name: V1103
FFPE spatial transcriptome sequencing


title: MIA-019

description:
Library name: V1102
FFPE spatial transcriptome sequencing


title: PNC108_B1


title: MIA-010

description:
Library name: V1101
FFPE spatial transcriptome sequencing


title: PNC107_B1

value: x


title: PNC106_B1


title: X197

city: seoul

first: Dakyung

last: Lee

address: 101 Daehakro

country: South Korea

institute: University

description: Library name: X197

data_processing:
WES reads were aligned to the GRCh38 human reference genome using the Burrows–Wheeler Aligner. Subsequently, we used GATK best practices, followed by Markduplicates and BaseRecalibrator analyses. Quality metrics were examined employing GATK DepthofCoverage and Flagstat. Somatic mutation calling was conducted using Mutect2 according to GATK best practices.  For xenograft samples, reads were aligned separately to the GRCh38 human reference genome and the mm10 mouse reference genome. To remove murine contamination, we applied XenofilteR, which takes the bam files aligned to both references as input and filter out mouse-derived reads from the human aligned bam file. Subsequent preprocessing and variant calling were performed using the same GATK-based pipeline as described above. The blood samples were matched controls.
Assembly: GRCh38
Supplementary files format and content: WES reads were aligned to the GRCh38 human reference genome using the Burrows–Wheeler Aligner. Subsequently, we used GATK best practices, followed by Markduplicates and BaseRecalibrator analyses. Quality metrics were examined employing GATK DepthofCoverage and Flagstat.

source_name: xenograft tumor

extract_protocol:
For genomic DNA extraction, we used the Dneasy Blood & Tissue Kit (Qiagen, Cat# 69504, Germany) and followed the manufacturer’s protocol.
SureSelect SureSelect All Exon V5

value: xenograft tumor


title: MIA-131

description:
Library name: V1004
FFPE spatial transcriptome sequencing


title: X196

description: Library name: X196


title: PNC104_B2


title: PNC105_B1


title: X193

description: Library name: X193


title: MIA-033

description:
Library name: V1003
FFPE spatial transcriptome sequencing


title: MIA-005

description:
Library name: V1002
FFPE spatial transcriptome sequencing


title: X148

description: Library name: X148


title: X142

description: Library name: X142


title: X141

description: Library name: X141


title: PNC104_B1


title: PNC001_B1


title: X135

description: Library name: X135


title: MIA-014

description:
Library name: V1001
FFPE spatial transcriptome sequencing


title: PNC102_B1


title: PNC101_B1


title: X134

description: Library name: X134


title: X61

description: Library name: X61


title: X27

description: Library name: X27


title: MIA-069

description:
Library name: V0902
FFPE spatial transcriptome sequencing


title: X12

description: Library name: X12


title: MIA-075

description:
Library name: V0804
FFPE spatial transcriptome sequencing


title: T197

description: Library name: T197

source_name: primary tumor

value: primary tumor


title: T196

description: Library name: T196


title: MIA-068

description:
Library name: V0803
FFPE spatial transcriptome sequencing


title: PNC099_B1


title: PNC098_B1


title: T193

description: Library name: T193


title: MIA-076

description:
Library name: V0802
FFPE spatial transcriptome sequencing


title: T142

description: Library name: T142


title: T141

description: Library name: T141


title: MIA-065

description:
Library name: V0704
FFPE spatial transcriptome sequencing


title: T135

description: Library name: T135


title: T134

description: Library name: T134


title: PNC097_B1


title: MIA-083

description:
Library name: V0703
FFPE spatial transcriptome sequencing


title: PNC097_B2


title: PNC096_B1


title: T61

description: Library name: T61


title: PNC095_B1


title: MIA-136

description:
Library name: V0702
FFPE spatial transcriptome sequencing


title: T27

description: Library name: T27


title: T12

description: Library name: T12


title: MX1_434

description: Library name: MX1_434


title: MX_430

description: Library name: MX_430


title: PNC094_B1


title: MX_429

description: Library name: MX_429


title: MIA-170

description:
Library name: V06B170
FFPE spatial transcriptome sequencing


title: MX_426

description: Library name: MX_426


title: PNC092_B2


title: MX_411

description: Library name: MX_411


title: MIA-164

description:
Library name: V06A164
FFPE spatial transcriptome sequencing


title: PNC093_B1


title: T148

description: Library name: T148


title: MX_409

description: Library name: MX_409


title: PNC092_B1


title: MX_408

description: Library name: MX_408


title: MX_407

description: Library name: MX_407


title: 5mC mapping in HepG2 cells with DEHP exposure

city: wuhan

first: neng

middle: bin

last: xie

address: 115 donghu road

institute: wuhan university

description: Library name: BS-seq sequencing data for HepG2 cells with DEHP exposure

data_processing:
To ensure the initial quality control of the raw sequencing data in FASTQ format, we utilized FastQC software (version 0.11.8). Following this, we employed Cutadapt (version 3.5) and Trimmomatic (version 0.39) to trim low-quality bases and remove adaptor sequences. Next, we utilized Bismark (version 0.24.0) to align the bisulfite-treated reads to the human reference genome (GRCh38.p13), with the indexing process facilitated by Bowtie.2 For methylation quantification at each cytosine site, we calculated the number of 'C' bases representing 5mC sites (denoted as NC) and the number of 'T' bases indicating unmodified cytosines (denoted as NT). Sequencing depth was defined as N = NC + NT, and we computed the sample coverage using both Bismark and Samtools (version 1.9). Methylated sites were statistically identified through a binomial test that considered the counts of methylated cytosines (mC), the total count of cytosines (mC + C), and the non-conversion rate of the bisulfite treatment. A site was classified as methylated when it had an FDR-corrected P-value of less than 0.05. To calculate methylation levels across the genome, we partitioned the sequenced data into 10 kb bins. The methylation level (ML) for each bin or individual cytosine site was determined as the proportion of methylated 'C' reads, calculated using the formula: ML(C) = reads(mC) / (reads(mC) + reads(C)).
Assembly: GRCh38.p13
Supplementary files format and content: C1.mC_level_Identification_stat.txt.gz: identified 5mC sites in HepG2 cells without DEHP exposure
Supplementary files format and content: H1.mC_level_Identification_stat.txt.gz: identified 5mC sites in HepG2 cells with DEHP exposure

extract_protocol:
Genomic DNA of HepG2 cells was extracted using Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA)
Briefly, the isolated genomic DNA from theHepG2 cells with or without DEHP exposure was fragmented into 200-400 bp using a Covaris S220 Focused-ultrasonicator (Covaris, USA). The Accel-NGS Methyl-Seq DNA Library kit (Swift, USA) was utilized to construct the sequencing library. Library quality was assessed using the Agilent 5400 system (Agilent, USA). Paired-end sequencing of sample was performed on Illumina platform (Illumina, USA).

value: Human Hepatocarcinoma Cells


title: PNC091_B1


title: MX_404

description: Library name: MX_404


title: 5mC mapping in HepG2 cells without DEHP exposure

description: Library name: BS-seq sequencing data for HepG2 cells without DEHP exposure


title: MX_373

description: Library name: MX_373


title: PANC1_nc_Input

city: Guangzhou

first: Tianhao

last: Huang

state: Guangdong

address: No.106 Zhong Shan Er Road

institute: Southern Medical University

description: Library name: Sample4

data_processing:
Raw reads were processed using fastp v0.20.1 to trim adapters and filter low-quality reads.
Reads aligned to rRNA were removed using SortMeRNA v2.1.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 v2.1.0.
Peaks were called using MACS2 v2.2.7.1 with input as control. Peaks were annotated with BEDTools v2.29.2. Motif analysis was performed with HOMER v4.11.1.
Assembly: GRCh38 / Ensembl release 107
Supplementary files format and content: Processed files include BED files of peaks, bigWig tracks for visualization, and count matrices of RIP signal intensity and gene-level expression.
Supplementary files format and content: Additional files include differential peak analysis results (MAnorm or DiffBind), annotated peaks, and GO/KEGG enrichment result tables.

source_name: pancreas

growth_protocol: PANC-1 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a 5% CO₂ humidified incubator.

extract_protocol:
RIP was performed using anti-NSUN2 antibody bound to Protein A/G magnetic beads. Cell lysates were prepared in polysome lysis buffer (PLB), immunoprecipitated for 4 hours at 4°C, washed, and RNA was extracted using TRIzol reagent. Input samples were collected before immunoprecipitation.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, Cat# 634888), following the manufacturer’s protocol.

treatment_protocol: Cells were treated with 30 mM sodium lactate or ddH₂O (vehicle control) for 24 hours before RNA immunoprecipitation.

value: pancreas

value: pancreatic ductal adenocarcinoma cell

value: wild-type


title: PNC089_B1


title: MX_363

description: Library name: MX_363


title: MX_354

description: Library name: MX_354


title: PNC088_B1


title: PANC1_lac_Input

description: Library name: Sample2


title: MX_327

description: Library name: MX_327


title: MX_347

description: Library name: MX_347


title: PANC1_lac_IP

description: Library name: Sample1


title: MX_292

description: Library name: MX_292


title: Homo sapiens, human ishikawa cell, PGCL experiment group, biol repl3

city: Shanghai

first: Yan

last: Zhou

address: 197 Ruijin 2nd Road

department: Department of Reproductive Medical Center

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

description:
Library name: PGCL3
Column name in gene_count.xls: LNG3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.22.0 (the default parameters) Trimmed sequence reads were mapped to hg38  using hisat2 v2.2.0 (the default parameters). Read count was calculated and normalized by featurecount v2.0.6 (-p)
Assembly: hg38
Supplementary files format and content: Excel reads count values of genes for each sample

molecule: polyA RNA

source_name: human ishikawa cell

growth_protocol: The human endometrial cancer cell line Ishikawa were routinely cultured in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) medium (Thermo Fisher Scientific, Waltham, MA, USA) at 37 °C and 5% CO2. The media contained 10% fetal bovine serum (FBS; Gibco, Grand Island, NY, USA), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (Thermo Fisher Scientific). Ishikawa incubated with the PGC or PGCL scaffold extract for 4 days were collected using the Trizol reagent (Thermo Fisher Scientific).

extract_protocol:
Ishikawa incubated with the PGC or PGCL scaffold extract for 4 days were collected using the Trizol reagent (Thermo Fisher Scientific).
The sequencing library was then sequenced on the NovaSeq6000 platform (Illumina) with the assistance of Gene-Kinder Co., Ltd. (Shanghai, China).

value: human ishikawa cell


title: MX_285

description: Library name: MX_285


title: PNC087_B1

value: Indeterminate


title: PNC086_B1


title: MX_276

description: Library name: MX_276


title: PNC085_B1


title: MX_265

description: Library name: MX_265


title: MX_261

description: Library name: MX_261


title: MX_247

description: Library name: MX_247


title: Homo sapiens, human ishikawa cell, PGCL experiment group, biol repl1

description:
Library name: PGCL1
Column name in gene_count.xls: LNG1


title: MX_246

description: Library name: MX_246


title: Homo sapiens, human ishikawa cell, PGC1 control group, biol repl3

description:
Library name: PGC3
Column name in gene_count.xls: Control3


title: MX_231

description: Library name: MX_231


title: PNC082_B1

value: Mixed


title: PNC083_B1


title: Homo sapiens, human ishikawa cell, PGC1 control group, biol repl2

description:
Library name: PGC2
Column name in gene_count.xls: Control2


title: PNC081_B1


title: MX_217

description: Library name: MX_217


title: MX_215

description: Library name: MX_215


title: Homo sapiens, human ishikawa cell, PGC1 control group, biol repl1

description:
Library name: PGC1
Column name in gene_count.xls: Control1


title: MX_214

description: Library name: MX_214


title: PNC080_B1

value: ACR


title: Nit+sor rep3

first: Xiaoxia

last: Liu

address: 26 Yuancun Erheng Road

department: The Sixth Affiliated Hospital

institute: Sun Yat-sen University

description:
Library name: ST3
Column name in SC NS_TreatVS SC_Ctrl_Gene_differential_expression.xlsx:FPKM.ST3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCh38
Supplementary files format and content: Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human colon cancer

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (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 was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were 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 were 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 librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: human colon cancer

value: Primary cells

value: Colon cancer cells

value: MSS


title: MX_195

description: Library name: MX_195


title: MX_192

description: Library name: MX_192


title: MX_179

description: Library name: MX_179


title: Nit+sor rep2

description:
Library name: ST2
Column name in SC NS_TreatVS SC_Ctrl_Gene_differential_expression.xlsx:FPKM.ST2


title: PNC078_B1


title: Nit+sor rep1

description:
Library name: ST1
Column name in SC NS_TreatVS SC_Ctrl_Gene_differential_expression.xlsx:FPKM.ST1


title: MX_173

description: Library name: MX_173


title: MX_158

description: Library name: MX_158


title: PNC077_B1


title: MX_99

description: Library name: MX_99


title: PNC076_B1

value: Marginal


title: DMSO rep3

description:
Library name: SC3
Column name in SC NS_TreatVS SC_Ctrl_Gene_differential_expression.xlsx:FPKM.SC3


title: MT1_285

description: Library name: MT1_285


title: PNC075_B1


title: MT_430

description: Library name: MT_430


title: DMSO rep2

description:
Library name: SC2
Column name in SC NS_TreatVS SC_Ctrl_Gene_differential_expression.xlsx:FPKM.SC2


title: MT_429

description: Library name: MT_429


title: DMSO rep1

description:
Library name: SC1
Column name in SC NS_TreatVS SC_Ctrl_Gene_differential_expression.xlsx:FPKM.SC1


title: MT_426

description: Library name: MT_426


title: PNC074_B2


title: MT_411

description: Library name: MT_411


title: SLE6, Urinary eoxsome

city: Jinan

first: Shule

last: Zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

description:
Library name: SLE_6
SLE_6

data_processing:
Read sequence include the following sequences: miRNA sequence, a 19 base Qiagen adapter sequence, a 12 base uniquemolecular index (UMI), a 34 base Illumina adapter sequence. Adapter sequences need to be trimmed prior to alignment.
The clean reads were mapped to reference genome.
Map reads to mature miRNA and hairping which recorded in miRBase(release 21) to identiy known-miRNA.
DEGseq was used for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: csv files include count values for each sample

source_name: urine

extract_protocol:
Extract total RNA using miRNeasy Mini kit (Qiagen, 217004).
The libraries were constructed using QIAseq® miRNA Library Kit (Qiagen, 331505) according to the manufacturer's instructions.

value: urine

tag: disease

value: pSLE


title: PNC073_B2


title: MT_409

description: Library name: MT_409


title: MT_408

description: Library name: MT_408


title: PNC073_B1


title: SLE5, Urinary eoxsome

description:
Library name: SLE_5
SLE_5


title: MT_407

description: Library name: MT_407


title: PNC072_B1


title: MT_404

description: Library name: MT_404


title: MT_381

description: Library name: MT_381


title: SLE3, Urinary eoxsome

description:
Library name: SLE_3
SLE_3


title: MT_370

description: Library name: MT_370


title: MT_373

description: Library name: MT_373


title: PNC071_B1


title: MT_363

description: Library name: MT_363


title: SLE2, Urinary eoxsome

description:
Library name: SLE_2
SLE_2


title: MT_354

description: Library name: MT_354


title: PNC070_B1


title: MX_197

description: Library name: MX_197

value: xenograft tumor


title: MT_347

description: Library name: MT_347

value: primary tumor


title: MT_327

description: Library name: MT_327


title: PNC069_B1_opak


title: Normal Control5, Urinary exosome

description:
Library name: Control_5
Control_5

value: control


title: MT_292

description: Library name: MT_292


title: PNC068_B1

value: No-rejection


title: MT_276

description: Library name: MT_276


title: MT_265

description: Library name: MT_265


title: PNC067_B2


title: Normal Control3, Urinary exosome

description:
Library name: Control_3
Control_3


title: MT_246

description: Library name: MT_246


title: PNC067_B1


title: Normal Control2, Urinary exosome

description:
Library name: Control_2
Control_2


title: PNC066_B1_opak


title: MT_231

description: Library name: MT_231


title: Normal Control1, Urinary exosome

description:
Library name: Control_1
Control_1


title: SLE4, Urinary eoxsome

description:
Library name: SLE_4
SLE_4


title: PNC065_B2


title: MT_217

description: Library name: MT_217


title: MT_215

description: Library name: MT_215


title: IP_P8_VDJ

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description: Library name: IP_P8_VDJ

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
genome build/assembly: GRCh38
processed data files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
processed data files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
processed data files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples

source_name: CAR T cells

extract_protocol:
Tumors (single-nucleus): Single cell supsensions produced by tumor sample dissociation with gentleMACS Octo Dissociator and filtered through 75 uM strainer before single nucleus prep with CHAPS; Cerebrospinal and infusion product: Cells or nucei input directly into 10x genomics single cell library preparation protocol. Tumors (Bulk RNAseq from FFPE). Malignant cell-enriched regions were extracted from slides using laser-capture microdissection. RNA was extracted using a Qiagen RNA FFPE kit.
Chromium GEM-X Single Cell 5' Kit v3 with Chromium Single Cell Human TCR Amplification kit (single-cell, single-nucleus). SMART-Seq® Total RNA Pico Input with UMIs (ZapR™ Mammalian) (Bulk RNA sequencing)

treatment_protocol: 5e6, 1e7 or 2.5e7 bivalent CAR T cells targeting EGFR and IL13RA2 administered intracerebroventricularly

value: CAR T cells

value: Normal

value: Pre-treatment

tag: batch


title: PNC065_B1_opak_04_09_24


title: MT_214

description: Library name: MT_214


title: MT_227

description: Library name: MT_227


title: SLE1, Urinary eoxsome

description:
Library name: SLE_1
SLE_1


title: MT_197

description: Library name: MT_197


title: Normal Control4, Urinary exosome

description:
Library name: Control_4
Control_4


title: MIA-105

description:
Library name: V0701
FFPE spatial transcriptome sequencing

value: Pre-invasive lung adenocarcinoma

value: MIA


title: IP_P8_GEX

description: Library name: IP_P8_GEX


title: PNC064_B1_opak_04_09_24

value: ACR


title: MT_195

description: Library name: MT_195


title: MT_192

description: Library name: MT_192


title: MT_258

description: Library name: MT_258


title: MT_261

description: Library name: MT_261


title: PNC062_B1


title: MT_247

description: Library name: MT_247


title: CSF_P8D21_VDJ

description: Library name: CSF_P8D21_VDJ

source_name: Cerebrospinal Fluid

value: Cerebrospinal Fluid

value: Immune cells

value: Bivalent CAR T cells (EGFR, IL13RA2)


title: PNC090_B1

value: Mixed


title: MX_381

description: Library name: MX_381


title: MT_179

description: Library name: MT_179


title: MT_173

description: Library name: MT_173


title: MT_158

description: Library name: MT_158


title: CSF_P8D7_VDJ

description: Library name: CSF_P8D7_VDJ

value: Primary cells


title: PANC1_nc_IP

description: Library name: Sample3

value: pancreas

value: pancreatic ductal adenocarcinoma cell

value: wild-type


title: MT_99

description: Library name: MT_99

value: primary tumor


title: CSF_P8D0_VDJ

description: Library name: CSF_P8D0_VDJ


title: MLN_359

description: Library name: MLN_359


title: MX_370

description: Library name: MX_370

value: xenograft tumor


title: MX_359

description: Library name: MX_359


title: PNC060_B2

value: No-rejection


title: PNC059_B1


title: PNC061_B1


title: MB_430

description: Library name: MB_430

source_name: blood

value: blood


title: CSF_P8D21_GEX

description: Library name: CSF_P8D21_GEX

value: Normal


title: MB_434

description: Library name: MB_434


title: MB_429

description: Library name: MB_429


title: FUS_GFP_WT_ACMS_Rep3

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

country: Germany

institute: University Medical Center Rostock

description:
Library name: L155963
N/A

data_processing:
Libraries from above were sequenced on an Illumina® NovaSeq 6000 in 100 bp paired-end mode to a depth 40 million fragments (short reads) per library. Short reads were aligned to the human reference genome hg38 with support of the Ensembl 104 splice sites using the aligner STAR (v2.7.10b) (associated manuscript: Dobin et al., 2013), and the custom settings “--outSAMmultNmax 1 --sjdbOverhang 100”. Counts per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1) (associated manuscript: Liao et al., 2014), and the settings “-s 2 -t ‘exon’ -p -Q 1”. Normalization of raw fragments based on library size and testing for differential expression between the different conditions was done with the DESeq2 R package (v1.38.3, R v4.2.2) (associated manuscript: Love et al., 2014). Principal Component Analysis (PCA) based on the 500 most variable genes was performed to explore the relationship between biological replicates and different libraries. DEGs were determined using the Wald test of DESeq2. Resulting p-values of DEGs were calculated from the variance across the four biological replicas of each condition (see above) and corrected for multiple testing with the Independent Hypothesis Weighting package (IHW 1.26.0) (associated manuscript: Ignatiadis et al., 2016). Genes with a maximum of 5% false discovery rate (adjusted p-value ≤ 0.05) and |log2FoldChange| ≥ ± 1.5 were considered significantly differentially expressed. DEGs were calculated for each cell line for ACMS versus UT, respectively, as well as for FUS-GFP P525L UT versus isogenic FUS-GFP WT UT.
Assembly: hg38
Supplementary files format and content: tab-separated excel file includes the output of gene counts. Each columns is either describing characteristics of a gene (gene name, ensembl_id, strand, position, chromosom) or a sample. Each row list genes with the details of the gene and the TPM counts per gene per sample.

source_name: Skin

growth_protocol: Spinal MNs were differentiated from cryoconserved neuronal progenitor cells (NPCs) derived from iPSCs as illustrated in Fig. 1H of the associated manuscript. The coating and assembly of MFCs (Xona Microfluidics RD900) to prepare for the seeding of MNs was performed as described (refer to associated manuscript: Naumann et al., 2018; Pal et al., 2018, 2021). MNs were seeded for maturation into one site of a MFC to obtain a fully compartmentalized culture with proximal somata and their dendrites being physically separated from their distal axons as only the latter type of neurite was capable to grow from the proximal seeding site through a microgroove barrier of 900 µm-long microchannels to the distal site where they sprouted out from the distal channel exits to the open space. ACMS sessions were performed at 30, 35, 40 and 45 DIV of axon growth and MN maturation as shown in Fig. 1H, J of the associated manuscript. All subsequent total RNA extractions for RNA-seq were performed at 48 DIV.

extract_protocol:
Total RNA from entire MFC MN cultures was extracted and purified at 48 DIV as illustrated in associated manuscript: Fig. 1J either after ACMS (at 25 Hz, perpendicular field orientation and 10 mT) or from untreated controls (UT). The preparation was performed with the Qiagen RNeasy® Plus kit (Cat no. 74134) according to the manufacture’s manual and typically resulting in 5-10 µg of total RNA dissolved in a total volume of 80 µl of DNAse/RNAse-free water. Concentration and integrity of each RNA sample was analyzed on an Agilent® 2100 Bioanalyzer (assay class: eukaryote total RNA nano, version 2.6), all resultant RNA integrity numbers (RIN) were in the range of 8.7 - 9.7, indicating high purity and integrity of all samples.
Messenger RNA was isolated from 500 ng of each total RNA sample (see above) by poly-dT enrichment using the New England Biolabs® (NEB) Next Poly-A mRNA Magnetic Isolation Module according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation, Next Adapters for Illumina of the NEB Next Multiplex Oligos for Illumina kit were used. After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 0.9:1 to the samples. Unique dual indexing was performed during the following PCR enrichment (12 cycles) using amplification primers carrying the same sequence for i7 and i5 index (i5: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, i7: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (0.9:1), libraries were quantified using the Fragment Analyzer (Agilent®).

treatment_protocol: We designed and fabricated electromagnetic coils (solenoids) with cylindrical geometry for operation inside standard cell culture incubators. To compensate for heating beyond 37 °C due to ohmic losses, we equipped the coils with a water-cooling system. The solenoids with an open central bore of 50 mm diameter and a height of 100 mm could harbor up to six cell culture dishes (35 mm diameter and 12 mm height) within their central bore in custom-tailored sample holders to expose them to a homogeneous magnetic field. For field generation, we applied alternating currents (AC) by using a function generator connected to an amplifier. The entire ACMS protocol comprised four consecutive treatment sessions as illustrated in Fig. 1J of the associated manuscript and was performed with a biphasic sine waveform at a field strength of 10 mT (time-averaged mean) at 25 Hz. The first ACMS session was performed at 30, the second at 35, the third at 40 and the fourth at 45 DIV with field-less resting intervals for the cells of four days each between. After the fourth and final ACMS treatment session, the cells were maintained in culture for two more resting days before the sustained impact of the ACMS was assessed at 48 DIV by RNA-seq.

value: Skin

value: Fibroblast (iPSC source)

value: iPSC-derived spinal motor neurons

value: isogenic control

tag: mutation/tag

value: FUS WT with carboxyterminal eGFP

tag: biological replica_(rep)_#

value: ACMS


title: FUS_GFP_WT_ACMS_Rep1

description:
Library name: L155961
N/A


title: MX_258

description: Library name: MX_258


title: Homo sapiens, human ishikawa cell, PGCL experiment group, biol repl2

description:
Library name: PGCL2
Column name in gene_count.xls: LNG2

value: human ishikawa cell


title: CSF_P8D7_GEX

description: Library name: CSF_P8D7_GEX

value: Cerebrospinal Fluid

value: Immune cells

value: Bivalent CAR T cells (EGFR, IL13RA2)


title: MB_411

description: Library name: MB_411


title: MB_426

description: Library name: MB_426


title: MB_408

description: Library name: MB_408


title: CSF_P7D21_VDJ

description: Library name: CSF_P7D21_VDJ

value: Primary cells


title: PNC058_B1


title: MB_407

description: Library name: MB_407


title: PNC084_B1

value: Marginal


title: CSF_P8D0_GEX

description: Library name: CSF_P8D0_GEX

value: Pre-treatment


title: MB_409

description: Library name: MB_409


title: MB_404

description: Library name: MB_404


title: CSF_P7D7_VDJ

description: Library name: CSF_P7D7_VDJ


title: PNC055_B3

value: ACR


title: PNC057_B1


title: MB_370

description: Library name: MB_370


title: CSF_P7D0_VDJ

description: Library name: CSF_P7D0_VDJ


title: MB_363

description: Library name: MB_363


title: PNC055_B2

value: Mixed


title: CSF_P7D21_GEX

description: Library name: CSF_P7D21_GEX


title: MB_354

description: Library name: MB_354

value: blood


title: PNC055_B1


title: MB_347

description: Library name: MB_347


title: PNC054_B1

value: Indeterminate


title: CSF_P7D7_GEX

description: Library name: CSF_P7D7_GEX

value: Normal


title: MB_292

description: Library name: MB_292


title: MB_327

description: Library name: MB_327


title: CSF_P7D0_GEX

description: Library name: CSF_P7D0_GEX


title: MB_285

description: Library name: MB_285


title: PNC052_B2_opak


title: MB_276

description: Library name: MB_276


title: MB_265

description: Library name: MB_265


title: CSF_P6D7_VDJ

description: Library name: CSF_P6D7_VDJ


title: MB_261

description: Library name: MB_261


title: MB_258

description: Library name: MB_258


title: CSF_P6D0_VDJ

description: Library name: CSF_P6D0_VDJ


title: MB_247

description: Library name: MB_247


title: MB_246

description: Library name: MB_246


title: CSF_P6D21_GEX

description: Library name: CSF_P6D21_GEX


title: MB_231

description: Library name: MB_231


title: PNC051_B1


title: MB_227

description: Library name: MB_227


title: CSF_P6D7_GEX

description: Library name: CSF_P6D7_GEX


title: MB_217

description: Library name: MB_217


title: MB_215

description: Library name: MB_215


title: MB_214

description: Library name: MB_214


title: CSF_P6D0_GEX

description: Library name: CSF_P6D0_GEX


title: MB_197

description: Library name: MB_197


title: CSF_P5D21_VDJ

description: Library name: CSF_P5D21_VDJ


title: MB_195

description: Library name: MB_195


title: PNC049_B1

value: No-rejection


title: PNC056_B1


title: MB_192

description: Library name: MB_192


title: PNC048_B2


title: PNC048_B3


title: CSF_P5D7_VDJ

description: Library name: CSF_P5D7_VDJ


title: MB_179

description: Library name: MB_179


title: MB_173

description: Library name: MB_173


title: CSF_P5D0_VDJ_run2

description:
Library name: CSF_P5D0_VDJ_run2
P5D0 run 1 and run 2 are made from two different CSF samples from P5, Day 0.


title: MB_158

description: Library name: MB_158


title: MB_99

description: Library name: MB_99


title: PNC047_B1


title: B197

description: Library name: B197


title: CSF_P5D0_VDJ_run1

description:
Library name: CSF_P5D0_VDJ_run1
P5D0 run 1 and run 2 are made from two different CSF samples from P5, Day 0.


title: B196

description: Library name: B196


title: PNC046_B1


title: CSF_P5D21_GEX

description: Library name: CSF_P5D21_GEX


title: B193

description: Library name: B193


title: PNC045_B1


title: B148

description: Library name: B148


title: PNC045_B2


title: B142

description: Library name: B142


title: CSF_P5D7_GEX

description: Library name: CSF_P5D7_GEX


title: MB_381

description: Library name: MB_381


title: B135

description: Library name: B135


title: CSF_P5D0_GEX_run2

description:
Library name: CSF_P5D0_GEX_run2
P5D0 run 1 and run 2 are made from two different CSF samples from P5, Day 0.


title: B134

description: Library name: B134


title: MB_359

description: Library name: MB_359


title: MB_373

description: Library name: MB_373


title: CSF_P5D0_GEX_run1

description:
Library name: CSF_P5D0_GEX_run1
P5D0 run 1 and run 2 are made from two different CSF samples from P5, Day 0.


title: B61

description: Library name: B61


title: PNC044_B1


title: PNC044_B2


title: B27

description: Library name: B27


title: B12

description: Library name: B12


title: CSF_P4D21_VDJ

description: Library name: CSF_P4D21_VDJ


title: PNC043_B2


title: PNC053_B1


title: PNC043_B1


title: X268

description: Library name: X268

data_processing:
RNA sequencing data were processed using RSEM, which employs the STAR aligner to map reads to the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
To isolate RNA from tumor tissues of patients and PDX models, approximately 5 mm³ of tumor tissue was snap-frozen in liquid nitrogen and homogenized in 1 ml of Tri-RNA Reagent (Favorgen, Cat# FATRR001, Taiwan) using a Biomasher (Takara, Cat# 9791A, Japan). Subsequently, 200 µl of chloroform was added for phase separation, followed by isopropanol precipitation to extract total RNA from the homogenized tissue.
TruSeq RNA

value: xenograft tumor


title: CSF_P6D21_VDJ

description: Library name: CSF_P6D21_VDJ


title: CSF_P4D7_VDJ

description: Library name: CSF_P4D7_VDJ


title: X197

description: Library name: X197


title: PNC042_B1


title: X192

description: Library name: X192


title: PNC041_B1


title: CSF_P4D21_GEX

description: Library name: CSF_P4D21_GEX


title: X141

description: Library name: X141


title: PNC052_B1


title: X139

description: Library name: X139


title: CSF_P4D7_GEX

description: Library name: CSF_P4D7_GEX


title: PNC040_B1


title: PNC039_B1


title: X135

description: Library name: X135


title: PNC050_B1


title: CSF_P4D0_GEX

description: Library name: CSF_P4D0_GEX


title: CSF_P3D21_VDJ

description: Library name: CSF_P3D21_VDJ


title: X125

description: Library name: X125


title: X61

description: Library name: X61


title: X27

description: Library name: X27


title: CSF_P3D7_VDJ

description: Library name: CSF_P3D7_VDJ


title: X12

description: Library name: X12


title: PNC038_B1


title: T268

description: Library name: T268

value: primary tumor


title: T197

description: Library name: T197


title: CSF_P3D0_VDJ

description: Library name: CSF_P3D0_VDJ


title: PNC037_B1


title: PNC036_B2


title: T192

description: Library name: T192


title: PNC036_B1


title: CSF_P3D21_GEX

description: Library name: CSF_P3D21_GEX


title: T139

description: Library name: T139


title: T141

description: Library name: T141


title: T135

description: Library name: T135


title: T125

description: Library name: T125


title: PNC035_B1


title: PNC048_B1


title: CSF_P3D7_GEX

description: Library name: CSF_P3D7_GEX


title: T61

description: Library name: T61


title: CSF_P3D0_GEX

description: Library name: CSF_P3D0_GEX


title: T27

description: Library name: T27


title: PNC034_B1


title: T12

description: Library name: T12


title: PNC033_B1


title: CSF_P2D21_VDJ

description: Library name: CSF_P2D21_VDJ


title: NT268

description: Library name: NT268

source_name: normal

value: normal


title: NT197

description: Library name: NT197


title: PNC032_B1


title: NT192

description: Library name: NT192


title: NT141

description: Library name: NT141


title: CSF_P2D7_VDJ

description: Library name: CSF_P2D7_VDJ


title: NT139

description: Library name: NT139


title: NT135

description: Library name: NT135


title: CSF_P2D21_GEX

description: Library name: CSF_P2D21_GEX


title: PNC031_B1


title: NT125

description: Library name: NT125


title: PNC030_B1


title: NT12

description: Library name: NT12


title: CSF_P2D0_GEX

description: Library name: CSF_P2D0_GEX


title: PNC029_B2


title: MX2-215

description: Library name: MX2-215


title: MX1_434

description: Library name: MX1_434


title: CSF_P1D21_VDJ

description: Library name: CSF_P1D21_VDJ


title: PNC029_B1


title: MX-265

description: Library name: MX-265


title: MX-261

description: Library name: MX-261


title: PNC028_B1


title: MX-214

description: Library name: MX-214


title: PNC025_B1


title: CSF_P1D0_VDJ

description: Library name: CSF_P1D0_VDJ


title: MX_404

description: Library name: MX_404


title: PNC027_B1


title: MX_381

description: Library name: MX_381


title: CSF_P4D0_VDJ

description: Library name: CSF_P4D0_VDJ


title: CSF_P1D21_GEX

description: Library name: CSF_P1D21_GEX


title: MX_370

description: Library name: MX_370


title: PNC024_B1


title: MX_347

description: Library name: MX_347


title: CSF_P1D7_GEX

description: Library name: CSF_P1D7_GEX


title: PNC023_B1


title: MX_327

description: Library name: MX_327


title: CSF_P1D0_GEX

description: Library name: CSF_P1D0_GEX


title: MX_317

description: Library name: MX_317


title: CRC357ORG

city: Tampere

first: Toni

middle: T

last: Seppälä

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description:
Library name: CRC357ORG
Column name in raw_counts_pdtos.txt: CRC357ORG

data_processing:
kallisto v.0.50.1 was used to extract transcript-level counts from fastq files. The human transcriptome index constructed from the Ensembl reference transcriptome version 108 was downloaded (https://github.com/pachterlab/kallisto-transcriptome-indices/releases) and the tximport R package v.1.32.0 was used to summarize transcript-level counts to gene-level and create a count matrix.
Assembly: Ensembl human reference transcriptome version 108
Supplementary files format and content: Tab-delimited text file contains estimated raw counts for each sample

source_name: rectum

growth_protocol: Patient-derived tumor organoids were maintained in Organoid Culture Medium supplemented with growth factors in a humidified atmosphere with 5% CO2 at 37 C

extract_protocol:
Total RNA was extracted by using NucleoSpin RNA Plus Isolation Kit
Total RNA (100 ng) was ribo-depleted using Illumina's Stranded Total RNA Prep with Ribo-Zero Plus (20040529) and library preparation was completed using standard Illumina protocols.

treatment_protocol: Patient-derived tumor organoids were not treated prior to RNA isolation

value: rectum

value: Patient-derived tumor organoids

tag: passage

tag: sequencing batch


title: MX_309

description: Library name: MX_309


title: MX_246

description: Library name: MX_246


title: AML12 cells, SMF3

city: Xi'an

first: Xuan

last: Han

state: ShaanXi

address: Medical department of Xi'an JiaoTong University

institute: Xi'an Jiaotong University

description: Library name: Sample6

data_processing:
Filter In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads); Alignment The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Assembly: GRCm39
Supplementary files format and content: txt files include FPKM values for each Sample

organism: Mus musculus

extract_protocol:
Invitrogen TRIZOL Reagent were used for RNA extraction; VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina were used for library construction (1) The Nanodrop2000 microspectrophotometer detects sample purity and concentration; (2) The Labchip GX touch microfluidic capillary system detects the integrity of RNA samples.
(1) The library was constructed starting with Total RNA and mRNA with ployA tails was enriched by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries; (6) Double-stranded cDNA is denatured at high temperature into single-stranded DNA, and cyclisation primers are added to form a single stranded Circular DNA library (single stranded Circular DNA).

value: SMF


title: PNC020_B1


title: CRC491ORG

description:
Library name: CRC491ORG
Column name in raw_counts_pdtos.txt: CRC491ORG


title: MX_179

description: Library name: MX_179


title: MX_192

description: Library name: MX_192


title: AML12 cells, SMF1

description: Library name: Sample4


title: MX_173

description: Library name: MX_173


title: CRC076ORG

description:
Library name: CRC076ORG
Column name in raw_counts_pdtos.txt: CRC076ORG


title: MX_158

description: Library name: MX_158


title: AML12 cells, Control4

description: Library name: Sample3


title: CRC669ORG

description:
Library name: CRC669ORG
Column name in raw_counts_pdtos.txt: CRC669ORG


title: MT-265

description: Library name: MT-265


title: MT-246

description: Library name: MT-246


title: AML12 cells, Control3

description: Library name: Sample2


title: MT-234

description: Library name: MT-234


title: AML12 cells, Control2

description: Library name: Sample1


title: NT61

description: Library name: NT61


title: MT-215

description: Library name: MT-215


title: CRC103ORG_2

description:
Library name: CRC103ORG_2
Column name in raw_counts_pdtos.txt: CRC103ORG_2


title: MT-214

description: Library name: MT-214


title: MT-192

description: Library name: MT-192


title: CRC033ORG

description:
Library name: CRC033ORG
Column name in raw_counts_pdtos.txt: CRC033ORG

source_name: colon

value: colon


title: MT-197

description: Library name: MT-197


title: Preterm infant blood miRNA - H12 (Control)

city: Almaty

first: Iskander

last: Isgandarov

address: Timiryazev 45

country: Kazakhstan

institute: Institute of plant biology and biotechnology

hyb_protocol: Labeled samples hybridized to Affymetrix GeneChip miRNA 4.1 Array using GeneTitan Multi-Channel (MC) instrument, 96-well plate format, per Affymetrix miRNA Assay protocol.

scan_protocol: Arrays scanned using Affymetrix GeneTitan MC instrument.

data_processing: Raw CEL files imported in R using oligo package (v1.62). RMA normalization applied (background=FALSE). All 36,353 probe set intensity values (RMA log2 scale) provided in Matrix table. Probe set names correspond to Affymetrix miRNA-4_1-st-v1 annotation (20160922). For differential expression: human miRNA probes (n=2,578) with mean log2 intensity >5 were retained (n=233); limma (v3.54) with empirical Bayes, adjusted for gestational age and birth weight.

source_name: Peripheral blood

label_protocol: RNA (100 ng) labeled with Affymetrix FlashTag Biotin HSR RNA Labeling Kit per manufacturer protocol.

growth_protocol: N/A - clinical study; preterm newborns managed per standard NICU protocols.

extract_protocol: Peripheral blood (1 ml) collected from each infant on days 10-14 of life. Total RNA including miRNA extracted using miRNeasy Mini Kit (Qiagen) per manufacturer instructions. Quality assessed by Agilent Bioanalyzer (RIN >7) and NanoDrop.

treatment_protocol: N/A - no experimental treatment applied.

tag: disease status

value: Control

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

tag: rds

value: grade 1

tag: surfactant administration

value: yes

tag: mechanical ventilation from birth

value: no

tag: ivh

value: grade 2


title: MT-179

description: Library name: MT-179

tag: tissue


title: CRC973ORG

description:
Library name: CRC973ORG
Column name in raw_counts_pdtos.txt: CRC973ORG

tag: cell line

tag: cell type


title: Preterm infant blood miRNA - D04 (Control)


title: MT-158

description: Library name: MT-158


title: CRC040ORG

description:
Library name: CRC040ORG
Column name in raw_counts_pdtos.txt: CRC040ORG


title: MT-130

description: Library name: MT-130


title: Preterm infant blood miRNA - D02 (Control)


title: MT_434

description: Library name: MT_434


title: CRC650ORG

description:
Library name: CRC650ORG
Column name in raw_counts_pdtos.txt: CRC650ORG


title: MT_404

description: Library name: MT_404


title: MT_381

description: Library name: MT_381


title: Preterm infant blood miRNA - D01 (BPD)

value: BPD


title: MT_347

description: Library name: MT_347


title: Preterm infant blood miRNA - C12 (Control)


title: CRC870ORG

description:
Library name: CRC870ORG
Column name in raw_counts_pdtos.txt: CRC870ORG


title: MT_317

description: Library name: MT_317


title: Preterm infant blood miRNA - C11 (Control)


title: CRC770ORG

description:
Library name: CRC770ORG
Column name in raw_counts_pdtos.txt: CRC770ORG


title: Preterm infant blood miRNA - C10 (BPD)


title: CRC698ORG

description:
Library name: CRC698ORG
Column name in raw_counts_pdtos.txt: CRC698ORG


title: MT_370

description: Library name: MT_370


title: MT_261

description: Library name: MT_261


title: CSF_P2D0_VDJ

description: Library name: CSF_P2D0_VDJ

value: Cerebrospinal Fluid

value: Primary cells

value: Immune cells

tag: genotype

tag: treatment

value: Pre-treatment


title: CRC405ORG

description:
Library name: CRC405ORG
Column name in raw_counts_pdtos.txt: CRC405ORG


title: NT27

description: Library name: NT27


title: CSF_P2D7_GEX

description: Library name: CSF_P2D7_GEX

value: Normal

value: Bivalent CAR T cells (EGFR, IL13RA2)

tag: batch


title: MX-217

description: Library name: MX-217

value: xenograft tumor


title: MT_327

description: Library name: MT_327

value: primary tumor


title: CRC374ORG

description:
Library name: CRC374ORG
Column name in raw_counts_pdtos.txt: CRC374ORG

value: Patient-derived tumor organoids


title: MNT-265

description: Library name: MNT-265

value: normal


title: CSF_P1D7_VDJ

description: Library name: CSF_P1D7_VDJ


title: Preterm infant blood miRNA - C09 (Control)


title: MNT-246

description: Library name: MNT-246


title: MX_359

description: Library name: MX_359


title: CRC003ORG

description:
Library name: CRC003ORG
Column name in raw_counts_pdtos.txt: CRC003ORG

value: colon


title: MNT-215

description: Library name: MNT-215


title: MNT-234

description: Library name: MNT-234


title: Preterm infant blood miRNA - C08 (BPD)


title: MNT-214

description: Library name: MNT-214


title: CRC372ORG

description:
Library name: CRC372ORG
Column name in raw_counts_pdtos.txt: CRC372ORG


title: Preterm infant blood miRNA - C07 (Control)

value: Control


title: MNT-197

description: Library name: MNT-197


title: PNC022_B1

tag: age at biopsy

tag: histology cathegory

value: ACR


title: MX_234

description: Library name: MX_234


title: MT_309

description: Library name: MT_309


title: CRC390ORG

description:
Library name: CRC390ORG
Column name in raw_counts_pdtos.txt: CRC390ORG

tag: passage

tag: sequencing batch


title: MNT-192

description: Library name: MNT-192


title: MNT-179

description: Library name: MNT-179


title: MNT-173

description: Library name: MNT-173


title: CRC262ORG

description:
Library name: CRC262ORG
Column name in raw_counts_pdtos.txt: CRC262ORG


title: Preterm infant blood miRNA - C06 (Control)

tag: disease status

tag: gestational age (weeks)

value: grade 1


title: Preterm infant blood miRNA - C05 (Control)

tag: birth weight (g)

tag: age at sampling (days of life)

value: yes


title: MNT-158

description: Library name: MNT-158


title: MNT-130

description: Library name: MNT-130


title: Preterm infant blood miRNA - C04 (Control)

tag: rds

tag: surfactant administration


title: CRC946ORG

description:
Library name: CRC946ORG
Column name in raw_counts_pdtos.txt: CRC946ORG

value: rectum


title: CRC504ORG

description:
Library name: CRC504ORG
Column name in raw_counts_pdtos.txt: CRC504ORG


title: MNT_434

description: Library name: MNT_434


title: Preterm infant blood miRNA - C03 (Control)

tag: mechanical ventilation from birth

tag: ivh


title: MNT_359

description: Library name: MNT_359

tag: tissue


title: Preterm infant blood miRNA - C02 (Control)

value: no

value: grade 2


title: MNT_347

description: Library name: MNT_347


title: CRC516ORG

description:
Library name: CRC516ORG
Column name in raw_counts_pdtos.txt: CRC516ORG

tag: cell line

tag: cell type


title: MNT_327

description: Library name: MNT_327


title: MNT_317

description: Library name: MNT_317


title: Preterm infant blood miRNA - B12 (Control)


title: CRC197ORG

description:
Library name: CRC197ORG
Column name in raw_counts_pdtos.txt: CRC197ORG


title: MNT_309

description: Library name: MNT_309


title: Preterm infant blood miRNA - B11 (Control)


title: CRC994ORG

description:
Library name: CRC994ORG
Column name in raw_counts_pdtos.txt: CRC994ORG


title: MNT_217

description: Library name: MNT_217


title: MLN_359

description: Library name: MLN_359


title: CRISPRi lncRNA screen ML-2 replicate 2 Population Doubling 18

city: Frankfurt

first: Robert

last: Winkler

state: Hesse

address: Theodor-Stern-Kai 7

department: Department of Pediatrics

institute: Goethe University Frankfurt

description:
Library name: ML-2.R2.T2
Column name in counttable_screen_filtered.txt: ML-2.R2.T2

data_processing:
50 bp single-end reads were quantified using MAGeCK count 0.5.9.5 with the CRISPRi lncRNA library reference.
Screen hits were identified using the MAGeCK MLE algorithm 0.5.9.5 with copy number variation correction (--cnv-norm) and --norm-method none (counts were pre-normalized by total read count).
Assembly: GRCh38
Supplementary files format and content: counttable_screen_filtered.txt: Tab-delimited text file containing library-size normalized sgRNA counts. Columns: sgRNA (sgRNA identifier), Gene (target gene name), and one column per sample with normalized count values.
Library strategy: CRISPR Screen

growth_protocol: Human myeloid leukemia cell lines K562, THP-1, ML-2, M-07e, SKNO-1 and NOMO-1 were procured from DSMZ (Braunschweig, Germany). All cell lines were maintained as per the supplier's recommendations and were subjected to routine testing for Mycoplasma contamination.

extract_protocol:
Genomic DNA was extracted from samples at the beginning and end of the screen using the JetFlex Genomic DNA Purification Kit (Thermo Fisher Scientific).
The integrated sgRNA cassettes were amplified by PCR (NEBNext High-Fidelity 2x PCR Master Mix, New England Biolabs), gel-purified (GeneJET Gel Extraction Kit, Thermo Fisher Scientific), and sequenced on an Illumina HiSeq 2000 instrument (50 bp single-end).

treatment_protocol: Stable cell lines expressing the CRISPRi effector were generated with pLKO5d.SFFV.dCas9-KRAB.MeCP2.P2A.BSD. A custom CRISPRi library targeting a comprehensive list of lncRNAs assembled from GENCODE v25, LNCipedia 4.0 and NONCODE v4 was cloned into the SGL40C.EFS.dTomato vector (Addgene #89395) via BsmBI restriction sites. The library comprises three to nine sgRNAs per target, tiling the 250 bp window immediately downstream of the annotated transcription start site, and incorporates non-targeting controls against luciferase and positive depletion controls targeting essential genes such as MYC, MYB, and RPL9. Cells were transduced with the lentiviral library at 30% efficacy and then cultured for 18 population doublings, ensuring a library representation of at least 1000-fold was maintained throughout.

value: acute myeloid leukemia

tag: replicate

tag: timepoint

value: Population Doubling 18


title: CRISPRi lncRNA screen ML-2 replicate 2 Day 0

description:
Library name: ML-2.R2.T0
Column name in counttable_screen_filtered.txt: ML-2.R2.T0

value: Day 0


title: Preterm infant blood miRNA - B09 (Control)


title: CRC648ORG

description:
Library name: CRC648ORG
Column name in raw_counts_pdtos.txt: CRC648ORG


title: CRISPRi lncRNA screen ML-2 replicate 1 Population Doubling 18

description:
Library name: ML-2.R1.T2
Column name in counttable_screen_filtered.txt: ML-2.R1.T2


title: CRC967ORG

description:
Library name: CRC967ORG
Column name in raw_counts_pdtos.txt: CRC967ORG


title: CRISPRi lncRNA screen K562 replicate 2 Population Doubling 18

description:
Library name: K562.R2.T2
Column name in counttable_screen_filtered.txt: K562.R2.T2

value: chronic myelogenous leukemia


title: Preterm infant blood miRNA - B07 (Control)


title: CRC911ORG

description:
Library name: CRC911ORG
Column name in raw_counts_pdtos.txt: CRC911ORG


title: CRISPRi lncRNA screen K562 replicate 1 Population Doubling 18

description:
Library name: K562.R1.T2
Column name in counttable_screen_filtered.txt: K562.R1.T2


title: MT_217

description: Library name: MT_217


title: Preterm infant blood miRNA - B06 (Control)


title: CRISPRi lncRNA screen K562 replicate 1 Day 0

description:
Library name: K562.R1.T0
Column name in counttable_screen_filtered.txt: K562.R1.T0


title: CRC299ORG

description:
Library name: CRC299ORG
Column name in raw_counts_pdtos.txt: CRC299ORG


title: CRISPRi lncRNA screen K562 replicate 2 Day 0

description:
Library name: K562.R2.T0
Column name in counttable_screen_filtered.txt: K562.R2.T0


title: CRISPRi lncRNA screen M07e replicate 2 Population Doubling 18

description:
Library name: M07e.R2.T2
Column name in counttable_screen_filtered.txt: M07e.R2.T2


title: Preterm infant blood miRNA - B05 (Control)


title: CRISPRi lncRNA screen M07e replicate 2 Day 0

description:
Library name: M07e.R2.T0
Column name in counttable_screen_filtered.txt: M07e.R2.T0


title: CRC158ORG

description:
Library name: CRC158ORG
Column name in raw_counts_pdtos.txt: CRC158ORG


title: CRISPRi lncRNA screen M07e replicate 1 Population Doubling 18

description:
Library name: M07e.R1.T2
Column name in counttable_screen_filtered.txt: M07e.R1.T2


title: CRISPRi lncRNA screen M07e replicate 1 Day 0

description:
Library name: M07e.R1.T0
Column name in counttable_screen_filtered.txt: M07e.R1.T0


title: Preterm infant blood miRNA - B04 (BPD)

value: BPD


title: CRC989ORG

description:
Library name: CRC989ORG
Column name in raw_counts_pdtos.txt: CRC989ORG


title: CRISPRi lncRNA screen THP-1 replicate 2 Population Doubling 18

description:
Library name: THP-1.R2.T2
Column name in counttable_screen_filtered.txt: THP-1.R2.T2


title: CRISPRi lncRNA screen THP-1 replicate 2 Day 0

description:
Library name: THP-1.R2.T0
Column name in counttable_screen_filtered.txt: THP-1.R2.T0


title: MNT_404

description: Library name: MNT_404


title: Preterm infant blood miRNA - B03 (BPD)


title: MNT_381

description: Library name: MNT_381


title: MNT_370

description: Library name: MNT_370


title: CRC298ORG

description:
Library name: CRC298ORG
Column name in raw_counts_pdtos.txt: CRC298ORG


title: CRC226ORG

description:
Library name: CRC226ORG
Column name in raw_counts_pdtos.txt: CRC226ORG


title: Preterm infant blood miRNA - C01 (BPD)


title: CRISPRi lncRNA screen THP-1 replicate 1 Population Doubling 18

description:
Library name: THP-1.R1.T2
Column name in counttable_screen_filtered.txt: THP-1.R1.T2


title: CRISPRi lncRNA screen THP-1 replicate 1 Day 0

description:
Library name: THP-1.R1.T0
Column name in counttable_screen_filtered.txt: THP-1.R1.T0


title: CRC481ORG

description:
Library name: CRC481ORG
Column name in raw_counts_pdtos.txt: CRC481ORG


title: Preterm infant blood miRNA - B02 (BPD)


title: CRISPRi lncRNA screen NOMO-1 replicate 2 Population Doubling 18

description:
Library name: NOMO-1.R2.T2
Column name in counttable_screen_filtered.txt: NOMO-1.R2.T2


title: CRISPRi lncRNA screen NOMO-1 replicate 2 Day 0

description:
Library name: NOMO-1.R2.T0
Column name in counttable_screen_filtered.txt: NOMO-1.R2.T0


title: Preterm infant blood miRNA - B01 (BPD)


title: CRC314ORG

description:
Library name: CRC314ORG
Column name in raw_counts_pdtos.txt: CRC314ORG


title: CRISPRi lncRNA screen NOMO-1 replicate 1 Population Doubling 18

description:
Library name: NOMO-1.R1.T2
Column name in counttable_screen_filtered.txt: NOMO-1.R1.T2


title: MNT_261

description: Library name: MNT_261


title: CRISPRi lncRNA screen NOMO-1 replicate 1 Day 0

description:
Library name: NOMO-1.R1.T0
Column name in counttable_screen_filtered.txt: NOMO-1.R1.T0


title: CRC259ORG

description:
Library name: CRC259ORG
Column name in raw_counts_pdtos.txt: CRC259ORG


title: CRISPRi lncRNA screen SKNO-1 replicate 2 Population Doubling 18

description:
Library name: SKNO-1.R2.T2
Column name in counttable_screen_filtered.txt: SKNO-1.R2.T2


title: Preterm infant blood miRNA - B10 (Control)


title: CRC836ORG

description:
Library name: CRC836ORG
Column name in raw_counts_pdtos.txt: CRC836ORG


title: Preterm infant blood miRNA - A12 (BPD)


title: CRISPRi lncRNA screen SKNO-1 replicate 2 Day 0

description:
Library name: SKNO-1.R2.T0
Column name in counttable_screen_filtered.txt: SKNO-1.R2.T0


title: Preterm infant blood miRNA - A11 (BPD)


title: CRISPRi lncRNA screen SKNO-1 replicate 1 Population Doubling 18

description:
Library name: SKNO-1.R1.T2
Column name in counttable_screen_filtered.txt: SKNO-1.R1.T2


title: CRC860ORG

description:
Library name: CRC860ORG
Column name in raw_counts_pdtos.txt: CRC860ORG


title: CRISPRi lncRNA screen SKNO-1 replicate 1 Day 0

description:
Library name: SKNO-1.R1.T0
Column name in counttable_screen_filtered.txt: SKNO-1.R1.T0


title: CRC930ORG_2

description:
Library name: CRC930ORG_2
Column name in raw_counts_pdtos.txt: CRC930ORG_2


title: Preterm infant blood miRNA - A10 (BPD)


title: H1993 cells, PHA665752 resistance

city: Goyang-si

first: Yu-Ra

last: Choi

address: 323, Ilsan-ro, Ilsandong-gu

institute: national cancer center

description:
Library name: HPR_S2
HPR_S2

data_processing:
FastQC tool was employed to assess the quality of the raw reads
the STAR 2 pass tool was utilized to align the RNA sequencing data to the GRCh38
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each samples
Supplementary files format and content: csv file includes FPKM values for each samples

growth_protocol: The cell was maintained in RPMI-1640, a medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using TRIzol (#15596026; Ambion, Austin, TX, USA) and a chloroform protocol.
RNA libraries for RNA-seq were prepared using Truseq library prep kit following manufacturer's protocols

treatment_protocol: The MET-TKI-acquired resistant cell line was established by continuously treating the parental H1993 cell line with increasing concentrations of PHA665752, starting from 1nM to 1uM. The resistant cell line was maintained with 1uM PHA665752 and was cultured in a drug-free medium for 1 week before performing all experiments.

value: Lung cancer

tag: treatment


title: H1993 cells

description:
Library name: H1993
H1993

value: DMSO


title: HMLE, V5-TWIST1, ChIP, doxy

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
ChIP‐seq NGS reads were aligned to the human reference genome hg19 through the BWA aligner using default settings.
Peaks were called using the MACS2 software (v2.0.10) with the option “– mfold=7,30 ‐p 0.00001”, thus outputting only enriched regions withP‐value<10−5.
Assembly: hg19
Supplementary files format and content: excel file containing all the MACS2 peaks (p<0.00001)
Supplementary files format and content: bigWig

source_name: breast

extract_protocol:
The preparation and processing of ChIP‐seq samples were performed as previously described (Sabò et al, 2014; PMID:25043028).
The ChIP protocol  was performed as previously described (Sabò et al, 2014; PMID:25043028), with an anti V5 antibody (Abcam, ab9116 ChIP grade, 10ug). DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013 PMID:23429716) and sequenced on an Illumina HiSeq 2000.

value: breast

value: HMLE

value: female

tag: chip antibody

value: V5 (Abcam, ab9116)

value: doxycycline 1 ug/mL

tag: genotype


title: CRC212ORG

description:
Library name: CRC212ORG
Column name in raw_counts_pdtos.txt: CRC212ORG

value: Patient-derived tumor organoids

tag: passage

tag: sequencing batch


title: HMLE, TWIST1-V5, ChIP, doxy


title: CRC621ORG

description:
Library name: CRC621ORG
Column name in raw_counts_pdtos.txt: CRC621ORG


title: MX_197

description: Library name: MX_197

value: xenograft tumor


title: Preterm infant blood miRNA - A09 (BPD)

tag: disease status

tag: gestational age (weeks)

value: grade 1

value: yes


title: HMLE, V5-TWIST1, ChIP, no doxy

value: untreated