title: DMA-tumor

description: Gene expression data from urinary bladder tumors of DMA-treated male rats

source_name: urinary bladder, DMA-induced tumors


title: Sample: 7 [Control]

status: Public on Aug 09 2023

type: genomic

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

hyb_protocol: Converted DNA (500 ng ) was hybridized to an Infinium HumanMethylation450 BeadChip (Illumina Inc.) and scanned using HiScanSQ (Illumina Inc.).

scan_protocol: HiScanSQ (Illumina Inc.)

data_processing: Data preprocessing and methylation-level extraction were performed using GenomeStudio Software (Illumina Inc.).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: liver

label_protocol: Bisulfite conversion of genomic DNA was performed using EZ DNA Methylation-Gold Kit (Zymo Research, Irving, CA).

extract_protocol: DNA was extracted from frozen tissue samples with DNA NucleoSpin® Tissue (Macherey-Nagel, Düren, Germany), according to the manufacturer’s instructions.

tag: tissue

value: liver

tag: condition

value: Control


title: Control

type: RNA

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Rat array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: urinary bladder, control male rats

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: TRIzol® Reagent was performed according to the manufacturer's instructions.

treatment_protocol: Male 6-week-old F344 rats were treated with 0 (Control) or 200 ppm dimethylarsinic acid (DMA) in drinking water for 4 weeks.

value: urinary bladder

tag: strain

value: F344 rats

tag: age

value: 10 weeks

tag: gender

value: male

tag: treatment


title: D1.5_1_XAV

type: SRA

city: Stanford

first: Sivakamasundari

last: Vijayakumar

state: CA

address: 265 Campus Drive, Lokey Stem Cell Building, Rm G3105

department: Institute for Stem Cell Biology and Regenerative Medicine

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
skewer (v0.2.2)  was used to trim adaptor sequences - skewer x -AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG; skewer y- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTANNNNNNNNGATCTCGGTGGTCGCCGTATCATT
using Salmon (v1.7.0) trimmed reads were mapped to GRCh38 reference cDNA and ncRNA sequences from ensemble (release 95) (http://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/)
read counts were quantifed using Salmon (v1.7.0)
counts were normalized using DESeq2 R package
Assembly: GRCh38
Supplementary files format and content: mapped raw counts text file for all samples ("All_samples_rawcounts.csv")

source_name: hPSC

growth_protocol: hPGCLC differentiation protocol

extract_protocol:
Cells were dissociated with acutase and washed twice in wash buffer (0.04% Bovine Serum Albumin in Ca2+/Mg2+-free PBS), filtered using 40um strainer and counted on the Countess II automated cell counter (Thermo Fisher).
Library construction by Truseq; 8bp dual indices
RNA seq libraries were prepared by Truseq and seqeunced on HiSeq4000, 2x150bp, paired-end

treatment_protocol: untreated or XAV939 or CHIR99021 or Base media

tag: time point

tag: cell line

value: hPSC

tag: cell type

value: differentiated hPSC

tag: replicate

value: XAV


title: DMA

source_name: urinary bladder, DMA-treated male rats

value: DMA-treated


title: Sample: 6 [Control]


title: D1.5_3_Base_Media


title: Two-Donor-SSNseq-CAR-T-ex-vivo-5P, SSN-derived cDNA

city: Houston

first: Pawel

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description:
10x Genomics
Sample 6-2
Exp6_barcodes.tsv.gz
Exp6_features.tsv.gz
Exp6_matrix.mtx.gz

data_processing:
Gene expressing reads were aligned to the GRCh38 genome (human) using the 10x Genomics Cell Ranger, with the pipeline cellranger count or multi. Small RNA counts were retrieved through cellranger count using the pattern containing group barcodes and sequences derived from constant regions of corresponding small RNAs.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Human CAR T cells

extract_protocol:
Lentiviral barcoded human primary CAR T cells were pooled and loaded into a Chromium Controller (10x Genomics).
10x Chromium Next GEM Single Cell 3' Reagent Kits v3.1 or 5' Reagent Kits V2 (with Feature Barcoding technology for CRISPR Screening) was used to construct the mRNA, small RNA and/or TCR libraries, according to the manufacturer’s protocol (CG000316_RevD or CG000510 Rev B).

value: Human CAR T cells

tag: fraction

value: small RNA


title: D1.5_3_CHIR

value: CHIR


title: BMDM WT, LPS 60 min sample 27

city: Madrid

first: Ana

last: Cuenda

state: Madrid

address: C. Darwin, 3

department: DEPARTMENT OF IMMUNOLOGY AND ONCOLOGY

country: Spain

institute: National Biotechnology Centre (CNB-CSIC)

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_27_SAM

data_processing:
The RSEM package (version 1.2.31) in conjunction with the STAR alignment algorithm (version 2.5.2a) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser 15 on February 19, 2016. Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3). Genes with a false discover rate <0.05 were judged to be differentially expressed.
Supplementary files format and content: tab-delimited text includes raw counts for each Sample
Supplementary files format and content: tab-delimited text includes edger analysis for paired Samples

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Bone marrow derived macrophages were

extract_protocol:
RNA was isolated from 1 x 10xe6 BMDM from WT or p38γ/δKIKO male mice using the RNeasy kit (QIAGEN).
Biological replicate libraries were prepared using the TruSeq RNA library prep kit (Illumina)

treatment_protocol: Lipopolysacharide 100 ng/ml

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophages

tag: genotype

value: WT

value: Lipopolysacharide 100 ng/ml

tag: time

value: 60 minutes


title: Two-Donor-SSNseq-CAR-T-ex-vivo-5P, mRNA-derived cDNA

description:
10x Genomics
Sample 6-1
Exp6_barcodes.tsv.gz
Exp6_features.tsv.gz
Exp6_matrix.mtx.gz

value: mRNA


title: BMDM WT, LPS 60 min sample 26

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_26_SAM


title: D1.5_2_Base_Media


title: Sample: 4 [Control]

value: liver

value: Control


title: D1.5_1_Base_Media


title: 3plex-SSNseq-CAR-T-in-vivo-3P, SSN-derived cDNA

description:
10x Genomics
Sample 5b-2
Exp5b_barcodes.tsv.gz
Exp5b_features.tsv.gz
Exp5b_matrix.mtx.gz


title: BMDM WT, LPS 60 min sample 25

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_25_SAM


title: Sample: 5 [Control]


title: BMDM KIKO, LPS 30 min sample 24

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_24_SAM

value: p38g knock in/p38d knock out

value: 30 minutes


title: 3plex-SSNseq-CAR-T-in-vivo-3P, mRNA-derived cDNA

description:
10x Genomics
Sample 5b-1
Exp5b_barcodes.tsv.gz
Exp5b_features.tsv.gz
Exp5b_matrix.mtx.gz


title: D1_3_CHIR

value: hPSC

value: differentiated hPSC


title: Sample: 3 [Control]


title: D1_2_CHIR


title: BMDM KIKO, LPS 30 min sample 23

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_23_SAM


title: Two-Donor-SSNseq-CAR-T-ex-vivo-3P, SSN-derived cDNA

description:
10x Genomics
Sample 5a-2
Exp5a_barcodes.tsv.gz
Exp5a_features.tsv.gz
Exp5a_matrix.mtx.gz


title: BMDM KIKO, LPS 30 min sample 22

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_22_SAM


title: Two-Donor-SSNseq-CAR-T-ex-vivo-3P, mRNA-derived cDNA

description:
10x Genomics
Sample 5a-1
Exp5a_barcodes.tsv.gz
Exp5a_features.tsv.gz
Exp5a_matrix.mtx.gz


title: Sample: 1 [Control]

description: Control


title: D1_1_CHIR


title: D1_3_XAV

value: XAV


title: BMDM KIKO, LPS 30 min sample 21

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_21_SAM


title: KO_H3K27ac.r2

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

library_source: genomic

data_processing:
The reads were aligned to the mouse genome (mm9 ) and Drosophila genome (dm6) using the Bowtie2 alignment package (Langmead & Salzberg.  Nat Methods 9, 357-359, 2012). Aligned reads were sorted and indexed using Samtools (v1.11)93. Sambamba (v0.8.0) was used to filter out unmapped, multi-mapped and duplicate reads( Li, H. et al. Bioinformatics 25, 2078-2079, 2009). bamCoverage from deepTools (v3.3.2) was used with spike-in (Drosophila) reads as a normalization factor to extract bigwig files for visualization of the data (Ramirez et al. Nucleic Acids Res 42, 2014).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files

source_name: T cells

extract_protocol:
ChIPseq was done essentially as previously described (Cernilogar et al. Nucleic Acids Res, 2019  PMID 31350899)  but with the inclusion of a spike-in strategy to allow for relative quantification of the detected ChIP signal in control versus experiment (Egan et al. PloS One, 2012 PMID 27875550). Briefly, 300 thousand FACS-sorted cross-linked cells (1% formaldehyde, 10min RT) were lysed in 100 ul Buffer-B-0.3 (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0,3%SDS, 1x protease inhibitors -Roche) and sonicated in a microtube (Diagenode; C300010011) using a Bioruptor Pico device until most of the DNA fragments were 200-500 base pairs long (settings: temperature 4°C, 20 cycles with 30 seconds On/30 seconds Off). After shearing, lysates were centrifuged 10min, 4°C, 12000g and supernatant diluted with 1 volume of Dilution Buffer (1mM EGTA 300 mM NaCl, 2% Triton x-100, 0.2% sodium deoxycholate, 1x protease inhibitors-Roche). Sonicated chromatin, supplemented with 50ng of Drosophila spike-in chromatin (Active Motif 53083),  was then incubated 4h at 4°C on a rotating wheel with 2 ug of H3K27ac (Diagenode C15410174) and 1ug H2Av (Active Motif 61686) antibodies conjugated to 15 µl of Protein-G Dynabeads (Thermofisher). Beads were washed five times with Buffer-A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors) and once with Buffer-C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (20mg/ml) for 1 hour at 55°C and 8 hours at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 hour at 55°C. Finally, DNA was purified with SPRI AMPure XP beads (Beckman Coulter) (sample-to-beads ratio 1:2). Purified DNA was used as input for library preparation with MicroPlex Library Preparation Kit v2 (Diagenode, cat. C05010012) and processed according to the manufacturer´s instruction. Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.
MicroPlex Library Preparation Kit v2 (Diagenode, cat. C05010012)

value: T cells

value: Tamoxifen

tag: antibody

value: anti-H3K27ac (Diagenode; Pab-174-050)


title: WT_H3K27ac.r2


title: D1_2_XAV


title: Exp12.2_ND4_CCI_P110_s2

city: Medford

first: David

last: Kaplan

state: MA

address: 4 Colby street

department: Biomedical Engineering

institute: Tufts University

data_processing:
Raw sequencing reads (.fastq files) were uploaded to the Tufts University Galaxy Server (52) for analysis, first utilizing FastQC (https://www.bioinformatics.babraham.ac.uk/) for quality control before reading alignment with RNA STAR (53) (reference genome GRCh38.p13, https://www.ncbi.nlm.nih.gov/) and quantification using featureCounts (54).
Differentially expressed gene lists were created using the DESeq2 R package (55) by comparing injury and Sham conditions, with or without P110 treatment. Gene set enrichment analyses (GSEA) were performed using the desktop software (https://www.gsea-msigdb.org/gsea/index.jsp) (56, 57) using MitoCarta3.0 (58) and custom curated mitochondrial pathway (59) databases. Heatmaps were generated using the pheatmap R package.
Gene module co-expression analyses were performed with the CEMiTool R package (60, 61), GSEA using the Reactome pathway database (https://reactome.org/), and signed interaction network analysis utilizing high confidence STRING protein-protein interactions (STRING score > 700).
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: ND41866*C/iNSC/pr. Astrocytes

growth_protocol:
The hiNSC cell line was previously generated from dermis-derived human fibroblasts, isolated from human neonatal foreskin fibroblasts through direct reprogramming (45). hiNSCs were handled following a previously established protocol (3). The cells were maintained in media composed of KnockOut DMEM (Invitrogen) supplemented with 1% GlutaMax (Invitrogen); 20% KnockOut Serum Replacement (Invitrogen); 1% Anti- Anti (Invitrogen); 0.2% β-mercaptoethanol (Invitrogen); 800 mL of 10 µg/mL basic fibroblast growth factor (Invitrogen) added proportionally to aliquots of media upon use. Media was changed daily. In brief, hiNSCs were expanded and subcultured on top of inactivated mouse embryonic fibroblasts. When cells reached 70-80% confluency, they were lifted from the plates via incubation with TrypLE solution for 1 min at 37°C, followed by quenching with 6mL of hiNSCs expansion media. Cells were then collected and pelleted by centrifugation at 3,000 rpm for 2 minutes. For further expansion, pellets were gently disrupted with a 10 ml pipette, and the colony suspension was transferred to an inactivated MEFs layer; for 3D seeding, the pellet was rigorously pipetted to obtain single-cell suspensions. For expansion, hiNSCs colonies were seeded from 1 dish into 20 (15cm2).
Human primary astrocytes (Sciencell research laboratories, cat. no. 1800) were expanded on 20 µg/mL poly-L-lysine (Sigma, P4832) coated surfaces up to passage 5 following established protocols from the manufacturer. Astrocytes were maintained in astrocyte media supplemented with astrocyte growth factors (1%), Fetal Bovine Serum (2%), and Anti-Anti (1%) from Sciencell research laboratories (cat.no. 1801); media was changed every 3 days. In brief, when astrocytes were 70-80% confluent, they were lifted from the plate via incubation in 0.25% Trypsin/EDTA for 3 minutes at 37°C, followed by quenching with complete astrocyte media. Next, the cell suspension was collected from the plates and pelleted by centrifugation at 1,000 rpm for 5 minutes. Cells were re-seeded at 350,000 cells/cm2.
Two iPSC lines from healthy donors (YZ1 and ND418664) were differentiated into microglia following a previously established protocol (26, 27). iPSCs were expanded in colonies on a Matrigel layer in mTeSR1 Embryonic stem cell media (StemCell Technologies, cat.no. 85850) as directed by batch instructions from the manufacturer. Each differentiation round required one vial of frozen iPSCs. The iPSCs were thawed and incubated in mTeSR1 media supplemented with 0.5 µM Rock Inhibitors (StemCell Technologies, cat.no. 72304) for 24h at 37°C, with daily media changes until iPSC colonies were near each another. To lift the colonies, 2 mL of ReLeSR (StemCell Technologies, cat.no. 05872) solution was applied for 30 seconds at room temperature, followed by 3 minutes of incubation at 37°C after the ReLeSR was aspirated. Media was added to the plates and the side of the plates was gently tapped to detach the cells. After collecting and centrifuging the cells at 300xg for 5 minutes, the cells were split into a 1:6 ratio and re-plated in mTeSR1 media. The following day, the mTeSR1 media was replaced with E8 media (StemCell Technologies, cat.no. 05990), preferable for microglia differentiation. A second splitting followed the same passaging protocol summarized above, following the addition of the E8 media at least once before differentiation.
To initiate iPSC differentiation to hematopoietic stem cells, the iPSCs were seeded in 6-well plates coated in phenol-red free Matrigel with hematopoietic differentiation media (StemCell Technologies, cat.no. 05310). The media was changed following the manufacturer’s protocol. After 11 days, early progenitors of hematopoietic cells were collected and counted and then seeded in 6-well plates coated with phenol-red free Matrigel (~400,000 cells/well); 2 mL of microglia differentiation media composed of DMEM-F12 phenol red-free media supplemented with 2% B-27 and 0.5% N2 supplements, 1% Glutamax, 5 µg/mL Insulin, 2% Insulin-Transferin-Selenite, 1% Non-essential amino acids, and 400µM monothioglycerol was added to each well with freshly infused 100 ng/mL interleukin- 34 (IL-34), 25 ng/mL macrophage colony-stimulating factor (MCSF), and 50 ng/mL transforming growth factor beta (TGFβ) growth factors. Then 1 ml of fresh media was supplemented with IL-34 (R&D systems, cat. No. 5265-IL-010), MCSF (Invitrogen, cat.no. PHC9501), and TGFβ (Fisher, cat.no. 5018578) growth factors every other day. On days 12 and 24 of growth, 5 mL of the 6 mL of media in each well was removed and centrifuged to remove the media with accumulated waste. The cells were resuspended in 1 mL of media and replated into the respective well. On day 25 of growth, the media was supplemented with 100 ng/mL fractalkine (Invitrogen, cat.no. 10636H08H50) and 100 ng/mL OX-2 membrane glycoprotein (CD200) (R&D systems, cat.no. 27712CD050) growth factors in addition to the previously described growth factors.
Hematopoietic stem cells and iPSC-derived microglia were characterized for cell-specific marker expression after each round of differentiation. Live cells were stained with a panel of markers: clusters of differentiation 43, 34, 235, 41, 45, 117 (CD43, CD34, CD235, CD41, CD45, c-kit), triggering receptor expressed on myeloid cells 2 (TREM2), transmembrane protein 119 (TMEM119), and C-X3-C motif chemokine receptor 1 (CX3CR1) and imaged with a Leica SP8 Confocal microscope (Leica Microsystems).
The system for generating 3D human tricultures was modified from our earlier published protocols of 3D rat, mouse, and human neuronal monocultures (17, 47, 48). When hiNSCs, primary astrocytes, and HMC3s reached nearly 100% confluency, they were collected and pelleted as described in the individual culture methods and then combined to achieve the following ratio: 2:0.5:0.1 million neurons, astrocytes, and microglia, respectively. The same ratio was used for cocultures for the respective cell types. Immediately before seeding the triculture cell solution, previously prepared PLO- and laminin-coated silk scaffolds were placed in 96-well plates, and a vacuum manifold was used to remove excess liquid. Calculations were performed so that each 40mL of cell suspension contained 2:0.5:0.1 million neurons, astrocytes, and microglia. Then 40mL of the cell suspension was pipetted onto the semi-dried scaffolds and incubated for 30 minutes at 37°C to allow the cells to attach. After this, 150mL of Neuronal media was added to each well. Neuronal media was composed of NeuroBasal medium supplemented with 2% B-27, 1% Anti-Anti, 1% Glutamax, and 1% astrocytes growth factors. The scaffolds were placed in a tissue culture incubator (37°C, 5% CO2 in a humidified atmosphere). The following day, the cell-seeded scaffolds were transferred to new 96-well plates. To each scaffold, 100mL of collagen type I solution (Corning or R&D systems, 3 mg/mL with a pH adjusted to 7.0-7.2 with NaOH) was added and then incubated for 30 minutes at 37°C to allow the collagen gel to crosslink. Next, 150mL of neural media was added to all scaffolds and incubated for 24h at 37°C. The following day, the brain-like tissues were moved into 48-well plates with 1 ml of Neuronal media in each well. Media was changed every fourth day until the tissues were used for injury studies, as controls, or for analysis 6 weeks after seeding.

extract_protocol:
Scaffolds were collected and stored at -80˚C. Upon isolation, samples were thawed on ice and incubated with 600µL of Lysis Buffer from RNeasy Kit (Qiagen, Catalog No. 74106). During incubation, samples were cut up using small scissors and continued to sit in a lysis buffer for approximately 20 minutes. The lysed samples were placed onto QIAshredder Mini Spin (Qiagen) columns and spun at 10,000 rpm for 2 minutes. An equal amount of 70% ethanol was added to the supernatant and mixed thoroughly. The ethanol-containing mixture was spun in two rounds through the RNeasy Mini Spin column (Qiagen) at 10,000rpm for 1 minute each; the flow through was discarded. In a new collection tube, 400µL of RNA wash from SurePrep RNA/DNA/Protein Purification Kit (Fisher Scientific, Catalog No. BP2802-50) was added to the RNeasy column and spun at the same setting for 1 minute; the flow through was discarded. After the first RNA Wash, 30µL of DNase and RDD buffer (1:7 ratio) containing solution from the RNase-Free DNase Set (Qiagen, Catalog No. 79254) was incubated on the columns at room temperature for 15 minutes before a second and third round of RNA was performed as well as a final spin to ensure the column was dry. The column was placed into a 1.5mL microcentrifuge tube, and 22uL of RNA Elution Solution (Fisher Scientific) was added to the center of the column and spun at 12,000rpm for 1 minute. Samples were then read on the NanoDrop 2000 spectrophotometer and stored at -80˚C before sequencing.
Approximately 1μg of total RNA for each sample underwent RNA quality control analyses before library preparation and bulk mRNA sequencing, as previously described (50, 51). RNA integrity numbers (RIN) were determined with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), which indicated minimal RNA degradation. Illumina Novaseq sequencers generated paired-end reads (150bp) at a read depth of 20 million reads (50).
RNA libraries for RNA-seq were prepared by Novogene

treatment_protocol:
At six weeks, the 3D brain-like tissues were placed on a flat weigh boat and subjected to contusion injury using a pneumatic cylinder with a 5 mm flat tip impactor at a velocity of 6m/s, penetration depth 0.6mm, and a dwell time duration of 200 ms (17). Sham tissues were handled similarly to the injured tissues but without receiving the contusion injury. Following injury or sham protocol, the tissues were incubated at 37°C in 5% CO2 in a humidified atmosphere until the indicated time marks for analysis of lactate dehydrogenase (LDH) and glutamate release in the medium, cell death, neural network stricture, western blot, and mitochondria health.
Dynamin-related protein 1 (Drp1) – mitochondria fission 1 protein (Fis1) peptide inhibitor P110 was purchased from Tocris Bioscience (cat. No.68971) (16). For each independent experiment, a new vial of P110 was freshly reconstituted in deionized water at 1 mg/mL.  Immediately following injury or sham treatment, tissues were treated with either 2.4mL of a) P110 (reconstituted) to achieve 1 µM concentration or b) control treatment (deionized water). Tissues were then incubated at 37°C in 5% CO2 and a humidified atmosphere until the indicated time marks for analysis of LDH and glutamate release in the medium, cell death, neural network structure, protein expression, and mitochondrial health.

value: ND41866*C/iNSC/pr. Astrocytes

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes

tag: p110 treatment

value: P110 treatment

tag: cci treatment

value: 6 weeks in culture, 24 hours after controlled cortical impact injury


title: BMDM KIKO, LPS 30 min sample 19

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_19_SAM

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophages

value: Lipopolysacharide 100 ng/ml


title: D1_1_XAV


title: Exp12.2_ND4_CCI_P110_s1

value: WT


title: BMDM WT, LPS 30 min sample 18

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_18_SAM


title: Exp12.2_ND4_Sham_P110_s2

value: 6 weeks in culture, 24 hours after sham treatment


title: D1_3_Base_Media


title: KO_H3K27ac.r1


title: Exp12.2_ND4_CCI_CTRL_s2

value: no treatment


title: WT_H3K27ac.r1


title: BMDM WT, LPS 30 min sample 17

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_17_SAM

value: 30 minutes


title: BMDM WT, LPS 30 min sample 16

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_16_SAM


title: D1_2_Base_Media

value: hPSC

value: differentiated hPSC


title: Sample: 2 [Control]

value: liver

value: Control


title: KO_1415 plus Arg

city: Shanghai

first: Shuangquan

last: Yan

address: 800 Dongchuan RD. Minhang District

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were filtered by seqtk to obtain clean reads for data analysis.
Bowtie2 (version: 2-2.0.5)was applied to Genome mapping with local alignment after pretreatment.
htseq is used to count the fragments of each gene after tophat comparison, and then TMM (trimmed mean of m values) method is used to normalize. Finally, the FPKM value of each gene is calculated by perl script.
Genome_build: Mycobacterium_smegmatis_MC2_155_uid57701
Supplementary_files_format_and_content: xls files include FPKM values for each Sample
Supplementary_files_format_and_content: xls files include raw gene counts for every gene and every sample

organism: Mycolicibacterium smegmatis

source_name: whole cells

growth_protocol: M.smegmatis were growth in the 7H9 liqid medium (OD600=0.8).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat# 74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
According to the standard Illumina protocols(rRNA removal, fragmentation, first strand cDNA  and second strand synthesis, terminal repair, 3 'end plus A ligation, enrichment).

treatment_protocol: The cells were centrifuged and washed twice with 1 * PBS, and then resuspended and cultured in the M9 medium for 6 hours (Arg and NH4Cl as the sole nitrogen source, separately).

value: treat with 5mM L-Arginine for 6 hours

value: MSMEG_1415 knockout


title: KO_1415

value: NO


title: Exp12.2_ND4_CCI_CTRL_s1

value: ND41866*C/iNSC/pr. Astrocytes

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes


title: D1_1_Base_Media


title: BMDM WT, LPS 30 min sample 13

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_13_SAM

value: Bone marrow


title: WT plus Arg

value: Wild type


title: Exp12.2_ND4_Sham_CTRL_s2


title: BMDM KIKO, LPS 30 min sample 20

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_20_SAM

value: BMDM

value: Bone marrow derived macrophages

value: p38g knock in/p38d knock out


title: D0.5_3_Base_Media


title: BMDM KIKO, 0 min sample 12

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_12_SAM

value: Lipopolysacharide 100 ng/ml

value: 0 minutes


title: D0.5_2_Base_Media


title: WT


title: Exp12.2_ND4_Sham_CTRL_s1

value: WT

value: no treatment

value: 6 weeks in culture, 24 hours after sham treatment


title: D0.5_1_Base_Media

value: hPSC

value: differentiated hPSC


title: Exp12.2_YZ1_CCI_P110_s2

source_name: YZ1/iNSC/pr. Astrocytes

value: YZ1/iNSC/pr. Astrocytes

value: P110 treatment

value: 6 weeks in culture, 24 hours after controlled cortical impact injury


title: BMDM KIKO, 0 min sample 11

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_11_SAM


title: BMDM KIKO, 0 min sample 9

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_9_SAM


title: Exp12.2_YZ1_Sham_P110_s2


title: Exp12.2_YZ1_CCI_P110_s1


title: D0_1_Untreated

value: Untreated


title: D0_3_Untreated


title: △fnr, vehicle, stationary, rep 2

city: San Francisco

first: Peter

middle: J

last: Turnbaugh

address: 513 Parnassus Ave, HSW 1501

institute: University of California, San Francisco

library_source: other

data_processing:
Samples were dual-end sequenced (2 x 75 bp) using the NextSeq Mid Output platform
Reads were mapped to the E. coli K12 BW25113 genome sequence (NCBI Reference Sequence: GCA_000750555.1) using Bowtie2
and HTSeq  was used to count the number of reads to E. coli genes.
Differential gene expression was analyzed using limma
Assembly: Reads were mapped to the E. coli K12 BW25113 genome sequence (NCBI Reference Sequence: GCA_000750555.1) using Bowtie2
Supplementary files format and content: comma seperated file containing raw counts for each sample

molecule: other

organism: Escherichia coli

growth_protocol: 100 ml of overnight cultures of both wt and Δfnr E. coli were grown in LB supplemented with 0.05% L-Cysteine under anaerobic conditions. Overnight culture OD600 nm was measured for both cultures and normalized to a starting OD600 nm of 0.05 in 100ml of LB with 0.05% L-Cysteine in 12 replicates for each strain. OD600 nm was monitored until mid-exponential phase for each strain (previously determined).

extract_protocol:
1 μl of TRI Reagent (Sigma Aldrich catalog number T9424) was added to bacterial pellets and incubated for 10 mins, samples were then transferred to 2 ml Lysing Matrix E tubes (MP Biomecials, catalog number 116914050). Cells were lysed for 5 mins in the bead beater at room temperature. 200 μl of chloroform was added. Samples were vortexed for 15 sec and incubated at room temperature for 10 mins. Samples were then centrifuged at 16,000 x g for 15 mins at 4°C. 500 μl of the upper aqueous phase was transferred to a new tube, 500 μl of 100% ethanol added, and vortexed to mix. Mixture was transferred to a spin column (PureLink RNA Mini Kit; Life Technologies; catalog number 12183025) and centrifuged at ≥12,000 x g for 30 sec, discarding flow-through, until all of the material had been added to the column. To the spin column, 350 µl Wash Buffer I (PureLink RNA Mini Kit; Life Technologies; catalog number 12183025) was added, then the column was centrifuged at ≥12,000 x g for 30 sec, discarding flow-through. 80 μl of PureLink DNase mix was added to the column and incubated at room temperature for 15 mins. 350 μl of Wash Buffer I (Purelink RNA mini kit) was added and the column spun at >12000 x g for 30 sec. The column was transferred to a new collection tube, and 500 µl Wash Buffer II was added, followed by centrifugation at ≥12,000 x g for 30 sec, discarding flow-through. The column was centrifuged at ≥12,000 x g for 60 sec and dried, then moved to a collection tube. 50 µl RNase-free water was added, and the column was incubated at room temperature for 1 min. Finally, the column was centrifuged for 1 min at ≥12,000 x g, retaining the flow-through, which contained total RNA.
Samples were DNase treated again using TURBO-DNase (Ambion; ThermoFisher catalog number AM2238) and incubated at 37°C for 30 mins. RNA Ampure XP Beads were used to clean up the reactions. 1.8 volumes of the RNA Ampure XP beads were added to 1 volume of RNA sample and allowed to sit for 5 mins at room temperature. Tubes were placed on a magnetic stand until the liquid cleared. Then liquid was removed and beads washed with 200 μl of 100% Ethanol. Samples were incubated for 30 sec, then removed. This was repeated twice more. Samples were allowed to dry for 5 mins, removed from the magnetic stand, and 30 μl of RNase-free water was added. This was incubated for 2 min at room temperature then placed back on the magnetic rack where liquid was collected after turning clear.

treatment_protocol: At mid-exponential 3 replicates for each strain were treated with a final concentration of 250 μM FD&C Red No. 40 in DMSO, or 1% DMSO. After 45 mins of exposure, 15 ml of the sample was removed for RNA extraction, while the remaining volume was used for proteomics. Both volumes samples were spun down to pellet cells, supernatant removed, and cell pellets were flash frozen in liquid nitrogen then stored at -80°C. The remaining samples were allowed to reach stationary phase, then they were treated with a final concentration of 250 μM FD&C Red No. 40 in DMSO, or 1% DMSO. Samples were processed the same way as for mid-exponential.

value: delta-fnr

value: DMSO

tag: growth phase

value: stationary


title: Exp12.2_YZ1_Sham_P110_s1

tag: tissue

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes


title: BMDM KIKO, 0 min sample 7

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_7_SAM

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophages


title: △fnr, vehicle, stationary, rep 3


title: BMDM WT, 0 min sample 6

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_6_SAM

value: Lipopolysacharide 100 ng/ml

value: 0 minutes


title: Exp12.2_ND4_Sham_P110_s1

value: ND41866*C/iNSC/pr. Astrocytes

value: WT


title: Exp12.2_YZ1_CCI_CTRL_s2

value: no treatment


title: △fnr, Red 40, stationary, rep 3

value: FD&C Red No. 40


title: △fnr, vehicle, stationary, rep 1


title: D0_2_Untreated

value: hPSC

value: differentiated hPSC


title: Exp12.2_YZ1_CCI_CTRL_s1

value: YZ1/iNSC/pr. Astrocytes

value: 6 weeks in culture, 24 hours after controlled cortical impact injury


title: BMDM WT, 0 min sample 5

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_5_SAM


title: △fnr, Red 40, stationary, rep 2

value: delta-fnr


title: BMDM WT, 0 min sample 4

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_4_SAM


title: △fnr, Red 40, stationary, rep 1


title: Exp12.2_YZ1_Sham_CTRL_s2

value: 6 weeks in culture, 24 hours after sham treatment


title: D35S_A7 scRNA-seq

description: sc-RNA-seq

data_processing:
Basecalling was performed using Illumina Casava software
Samples were demultiplexed using Illumina bcl2fasq software
Sequenced reads were processed, aligned and counts summarised using Cellranger 2.2.0 pipeline
mapped data was further analyzed using Seurat V2 R package
Monocle V2 R package was used for trajectory inference
Genome_build: hg19
Supplementary_files_format_and_content: Matrix.mtx is matrix a file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: barcodes. tsv files with cell barcodes for every cell in the sample
Supplementary_files_format_and_content: genes. tsv files of gene identifier for every gene
Supplementary_files_format_and_content: csv files with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: csv files with raw gene counts for all 5000 randomly down sampled cells

source_name: Day 3.5 differentiated PGCLCs, sorted for CXCR4+PDGFRA-GARP- .

extract_protocol:
Cells were dissociated with acutase and washed twice in wash buffer (0.04% Bovine Serum Albumin in Ca2+/Mg2+-free PBS), filtered using 40um strainer and counted on the Countess II automated cell counter (Thermo Fisher). For each cell population, 10,400 cells were loaded per lane on the 10x Genomics Chromium chip, with the goal of capturing 6,000 cells.
Library construction by 3’ prime V2 chemistry Chromium single cell gene expression kit.

value: differentiated, PGCLC protocol

tag: sorting

value: sorted


title: BMDM WT, 0 min sample 3

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_3_SAM

value: Bone marrow


title: D35U_A6 scRNA-seq

description: sc-RNA-seq

source_name: Day 3.5 differentiated PGCLCs, unsorted

value: unsorted


title: BMDM KIKO, 0 min sample 10

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_10_SAM

value: BMDM

value: Bone marrow derived macrophages

value: p38g knock in/p38d knock out


title: wt, vehicle, stationary, rep 3

tag: strain

value: wt

value: DMSO

value: stationary


title: wt, vehicle, stationary, rep 2


title: D05_A3 scRNA-seq

description: sc-RNA-seq

source_name: Day 0.5 differentiated


title: Exp12.2_YZ1_Sham_CTRL_s1

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes

value: WT

value: no treatment


title: wt, vehicle, stationary, rep 1


title: BMDM WT, 0 min sample 1

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_1_SAM

value: Lipopolysacharide 100 ng/ml

value: 0 minutes


title: BMDM WT, 0 min sample 2

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_2_SAM


title: Exp9.2_ND4_CCI_P110_s2

value: ND41866*C/iNSC/pr. Astrocytes

value: P110 treatment

value: 6 weeks in culture, 24 hours after controlled cortical impact injury


title: Exp9.2_ND4_CCI_P110_s1


title: Exp9.2_ND4_Sham_P110_s2

value: 6 weeks in culture, 24 hours after sham treatment


title: wt, Red 40, stationary, rep 2

value: FD&C Red No. 40


title: H9_A2 scRNA-seq

description: sc-RNA-seq

source_name: hPSC, H9

value: hPSC

value: undifferentiated

value: unsorted


title: B16F10-dCas9 cells, sgMc1r, aMSH+IFNg-2

city: Beijing

first: Yazhong

last: Cui

address: 7 Science Park Road ZGC Life Science Park, Beijing

institute: National institute of biological sciences, Beijing

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: Excel files include RPKM values for each Sample.

growth_protocol: B16F10 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using TRIZON reagent.
RNA libraries for RNA-seq were prepared by Berry Genomics (Beijing, China).

value: mouse melanoma

value: Mc1r knockdown

value: aMSH+IFNg

value: 12 hours


title: DE_A5 scRNA-seq

description: sc-RNA-seq

source_name: Day2 differentiated Definitive endoderm

value: Definitive endoderm

value: differentiated, DE protocol


title: wt, Red 40, stationary, rep 1

value: wt

value: stationary


title: Exp9.2_ND4_Sham_P110_s1

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes

value: WT


title: △fnr, vehicle, midexponential, rep 3

value: delta-fnr

value: DMSO

value: midexponential


title: B16F10-dCas9 cells, sgMc1r, aMSH-2

value: aMSH


title: B16F10-dCas9 cells, sgMc1r, aMSH+IFNg-1


title: △fnr, vehicle, midexponential, rep 2


title: Female PXR-KO EtOH-fed 4

city: Seattle

first: Julia

middle: Yue

state: WA

address: 4225 Roosevelt Way NE Suite #100

department: Occupational and Health Sciences

institute: University of Washington

hyb_protocol: standard Affymetrix protocols

scan_protocol: GeneChip Scanner 3000 7G Pluse with autoloader

data_processing: R using oligo package. Probes IDs annotated using the clariomsmousehttranscriptcluster.db package. The mean probe intensities higher than log2(100) in at least one group were selected for further analysis. Differential analysis between control and EtOH-exposed groups of the same genotype and sex was determined using the Linear Models for Micoarray Data (limma) package.

label_protocol: Sense-strand cDNA

extract_protocol: Affymetrix GeneChip array was used after the total RNA extraction from liver tissues.

value: female

tag: diet

value: EtOH

value: PXR-KO

value: Liver


title: Exp9.2_ND4_CCI_CTRL_s2

value: ND41866*C/iNSC/pr. Astrocytes

value: no treatment

value: 6 weeks in culture, 24 hours after controlled cortical impact injury


title: △fnr, vehicle, midexponential, rep 1


title: Exp9.2_ND4_CCI_CTRL_s1


title: B16F10-dCas9 cells, sgMc1r, untreat-2

value: mouse melanoma

value: Mc1r knockdown

value: untreated

value: 12 hours


title: Exp9.2_ND4_Sham_CTRL_s2

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes

value: 6 weeks in culture, 24 hours after sham treatment


title: △fnr, Red 40, midexponential, rep 3

value: delta-fnr

value: FD&C Red No. 40


title: B16F10-dCas9 cells, sgMc1r, untreat-1


title: Female PXR-KO control-fed 4

tag: gender

value: control


title: Female PXR-KO EtOH-fed 1


title: Female PXR-KO EtOH-fed 3


title: Female PXR-KO EtOH-fed 2


title: Female PXR-KO control-fed 3


title: △fnr, Red 40, midexponential, rep 2

tag: treatment

value: midexponential


title: B16F10-dCas9 cells, sgControl, aMSH+IFNg-2

value: WT

value: aMSH+IFNg


title: B16F10-dCas9 cells, sgControl, aMSH+IFNg-1


title: B16F10-dCas9 cells, sgMc1r, aMSH-1

value: aMSH


title: Exp9.2_YZ1_CCI_P110_s2

value: YZ1/iNSC/pr. Astrocytes

value: P110 treatment


title: B16F10-dCas9 cells, sgControl, aMSH-1


title: B16F10-dCas9 cells, sgControl, aMSH-2


title: Exp9.2_YZ1_CCI_P110_s1


title: Female PXR-KO control-fed 2

value: female

value: PXR-KO

value: Liver


title: Exp9.2_YZ1_Sham_P110_s2


title: Female PXR-KO control-fed 1


title: wt, vehicle, midexponential, rep 2

value: wt

value: DMSO


title: wt, vehicle, midexponential, rep 1


title: B16F10-dCas9 cells, sgControl, untreat-2

value: mouse melanoma

value: untreated

value: 12 hours


title: Exp9.2_YZ1_Sham_P110_s1

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes

value: 6 weeks in culture, 24 hours after sham treatment


title: Exp9.2_YZ1_CCI_CTRL_s2

value: no treatment

value: 6 weeks in culture, 24 hours after controlled cortical impact injury


title: Male PXR-KO EtOH-fed 4

value: male

value: EtOH


title: B16F10-dCas9 cells, sgControl, untreat-1

value: WT


title: Male PXR-KO EtOH-fed 3


title: wt, Red 40, midexponential, rep 3

value: FD&C Red No. 40

value: midexponential


title: wt, Red 40, midexponential, rep 2


title: Male PXR-KO EtOH-fed 2


title: Exp9.2_ND4_Sham_CTRL_s1

value: ND41866*C/iNSC/pr. Astrocytes


title: △fnr, Red 40, midexponential, rep 1

value: delta-fnr


title: Tumoral samples, 496; treatment: control

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

data_processing:
RNA-seq processing:
Read adapters and polyA tails were removed with bbduk.sh, following the Lexogen recommendations. Processed reads were analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19 (--library-type fr-secondstrand in TopHat), allowing two mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM20.GRCm38.Ensembl95). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm38
Supplementary files format and content: Normalized counts obtained with DESeq2

source_name: BC tumors from the miR-203 KI-PyMT mice

growth_protocol: Tg (MMTV-PyMT); miR-203 (KI/KI) and Tg (MMTV-PyMT); miR-203 (+/+) mice were euthanized and tumors were extracted. Two random pieces were snap frozen and stored at −80°C, two random pieces were fixed in formalin for histopathological analysis and immunohistochemistry, and the remainder was processed for the isolation of viable cells. The remaining tissue was minced, washed with 10 mL AdDF+++ (Advanced DMEM/F12 containing 1x Glutamax, 10 mM HEPES, and antibiotics) and digested in 10 mL BC organoid expansion medium (10% homemade R-Spondin 1 conditioned medium; 5 nM Neuregulin 1-Peprotech 100-03; 5 ng/ml FGF7, Peprotech 100-19; 20 ng/ml FGF10, Peprotech 100-26; 5 ng/ml EGF, Peprotech AF-100-15; 100 ng/ml Noggin, Peprotech 120-10C; 500nM A83-01, Tocris 2939; 5 microM Y-27632, Abmole; 500 nM SB202190, Sigma S7067; 1X B27 supplement, Gibco 17504-44; 1,25 mM N-Acetylcysteine, Sigma A9165; 5mM Nicotinamide, Sigma N0636; 1X Glutamax, Invitrogen 12634-034; 10mM Hepes, Invitrogen 15630-056; 100U/ml  Penicillin/Streptomycin, Invitrogen 15140-122; Primocin, Invitrogen Ant-pm-1 and Advanced DMEM/F12, Invitrogen 12634-034) containing 1-2 mg·ml-1collagenase (Sigma, C9407) on an orbital shaker at 37°C for 1-2 h. The digested tissue suspension was sequentially sheared using 10 mL and 5 mL plastic and flamed glass Pasteur pipettes. After every shearing step the suspension was strained over a 100 μm filter with retained tissue pieces entering a subsequent shearing step with ∼10ml AdDF+++. 2% FCS were added to the strained suspension before centrifugation at 400 rcf. The pellet was resuspended in 10ml AdDF+++ and centrifuged again at 400 rcf. In case of a visible red pellet, erythrocytes were lysed in 2 mL red blood cell lysis buffer (Roche, 11814389001) for 5 min at room temperature before the addition of 10ml AdDF+++ and centrifugation at 400 rcf. The pellet was resuspended in 10 mg·ml-1 cold Cultrex growth factor reduced BME type 2 (Trevigen, 3533-010-02) and 40 μL drops of BME-cell suspension were allowed to solidify on pre-warmed 24-well suspension culture plates (Greiner, M9312) at 37°C for 20 min. Upon completed gelation, 400 μL of BC organoid expansion medium was added to each well and plates transferred to humidified 37°C / 5% CO2 incubators. Medium was changed every 4 days and organoids were passaged every week: organoids were resuspended in 2 mL cold AdDF+++ and mechanically sheared through flamed glass Pasteur pipettes. When necessary, very dense organoids were dissociated by resuspension in 2 mL TrypLE Express (Invitrogen, 12605036), incubation for 1-5 min at room temperature, and mechanical shearing through flamed glass Pasteur pipettes. Following the addition of 10 mL AdDF+++ and centrifugation at 300 rcf. or 400 rcf. respectively, organoid fragments were resuspended in cold BME and reseeded as above at ratios (1:1 to 1:6) allowing the formation of new organoids. Single cell suspensions were initially seeded at high density and reseeded at a lower density after ∼1 week. In order to prevent misidentification and/or cross-contamination of BC organoids, we cultured every line physically separate, implemented the use of a laboratory management system. All organoid lines were frequently tested and resulted in all cases negative in the MycoAlert mycoplasma detection kit (Lonza, LT07-318).

extract_protocol:
For RNAseq, total RNA was extracted using the miRVana miRNA isolation kit (ThermoFisher), following the manufacturer´s recommendations. Between 0.8 and 1 µg of total RNA was extracted from organoids after dissociating the Matrigel/BME form the cultures (as indicated above). RIN (RNA integrity number) numbers were always in the range of 9 to 10 (Agilent 2100 Bioanalyzer).
250ng of total RNA samples were used. Average sample RNA Integrity Number was 9.1 (range 8.2-9.8) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. [This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation]. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq 2500 with v4 Chemistry by following manufacturer's protocols.
QuantSeq 3‘ mRNA-Seq

treatment_protocol: For epithelial differentiation, we used the media defined by Lonza (MEGM Mammary Epithelial Cell Growth Medium and Bullekit). Basically, this media has been optimized for the growth of mammary epithelial cells in a serum-free environment and includes BPE, hEGF, Insulin, Hydrocortisone and GA-1000 (Lonza CC-3150). FGF2 treatment (2 nM; Sigma) induces mammary branching as published before [33]. For inducing transient miR-203 over-expression, ColA1(miR-203/miR-203); Rosa26(rtTA/rtTA) organoid cultures were treated with Dox (1 ug/ml; Invitrogen) during 5 days. After that, Dox withdrawal was standardized for the cultures during following several passages (usually 2 weeks) unless other time points are indicated in the text. In this inducible system, we always test that insert expression is uniquely dependent on Dox, and becomes absolutely undetectable after Dox withdrawal. As a control of the treatment itself, Dox was also added and tested in wild-type organoids.

tag: clone

value: mouse mammary gland tumor-derived organoids

value: control

tag: sample type

value: tumoral


title: wt, vehicle, midexponential, rep 3

value: wt

value: DMSO


title: Male PXR-KO EtOH-fed 1

value: PXR-KO

value: Liver


title: Male PXR-KO control-fed 4


title: wt, Red 40, midexponential, rep 1


title: Exp9.2_YZ1_Sham_CTRL_s2

value: YZ1/iNSC/pr. Astrocytes

tag: cell line

value: iPSC-derived microglia/iNSC-derived neurons/primary astrocytes

value: 6 weeks in culture, 24 hours after sham treatment


title: Exp9.2_YZ1_Sham_CTRL_s1

value: no treatment


title: cortex, MAP2K, experiment

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNA-Seq: High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
RNA-Seq: Gene expression levels were reported as fragments per kilobase of exon per million fragments mapped (FPKM).
RNA-Seq: Genes with a p value <0.05 were considered would be called as differentially expressed.
Assembly: mm10

source_name: cortex

extract_protocol:
scRNA-Seq: Briefly, mouse embryos were dissected out and immediately submerged in fresh ice-cold Hanks balanced salt solution (Gibco 12175-095). The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit (Miltenyi Biotec, catalog no. 130-092-628) according to the manufacturer’s instructions.
scRNA-Seq: The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000 or Illumina Hiseq4000.
RNA-Seq: The E14.5 cortex tissues from Rosa-fgf8/Rosa-mek1dd mice and littermate controls were dissected.
RNA-Seq: Total RNA was isolated using an RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. RNA-seq libraries were prepared according to the Illumina HiSeq 4000 protocol. The gene expression level was reported with fragments per kilobase of exon model per million mapped reads (FPKM)

value: cortex


title: cortex, MAP2K, control

description: 10x Genomics

value: WT


title: Tumoral samples; 476; treatment: MEGM

value: MEGM media


title: FEOS-3

city: ChangSha

first: dingyu

last: Wu

address: 87 Xiangya Road

institute: Xiangya Hospital

data_processing:
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model. Differential expression was assessed by DEseq/DESeq2/edgeR/DEGseq using read counts as input.
The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05. All the differentially expressed genes were used for heat map analysis and KEGG ontology enrichment analyses. For KEGG enrichment analysis, a P-value < 0.05 was used as the threshold to determine significant enrichment of the gene sets.
Pre-processing of sequencing reads / Quality Control.
1) Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: :TRAILING:20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
2) Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Quantification of gene expression level.
Paired-end reads were aligned to the mouse reference genome mm10/hg19/rn6 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
Differential expression analysis.
The statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(foldchange)| > 1 using theDEseq/DESeq2/edgeR/DEGseq software. Finally, a hierarchical clustering analysis was performed using the R language package gplots according to the RPKM values of differential genes in different groups. And colors represent different clustering information, such as the similar expression pattern in the same group, including similar functions or participating in the same biological process.
GO terms and KEGG pathway enrichment analysis.
In order to identify the Gene Ontology (GO) annotations and pathways in which differentially expressed genes were enriched, GO term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the ?clusterProfiler?package in RBioconductor /KOBAS3.0 software.
In the present study, the clusterProfiler package in R Bioconductor/ KOBAS3.0 was used to identify and visualize the GO terms and KEGG pathways enriched by all differentially expressed genes.
Co-expression network of differentially expressed lncRNAs/mRNAs.
To investigate the potential functions of differentially expressed lncRNAs and the interactions between mRNAsand lncRNAs, we constructed alncRNA/mRNA transcripts co-expression network. The co-expression networkwas constructed by calculating the Pearson correlation coefficient and P value between multiple genes.
In our study, the transcripts were filtered using a COR of >0.85 and a P-value of <0.05. Then we chose XXXXX DEmRNA transcripts that were enriched in reproduction-related pathways and all DE lncRNAs to construct a
coexpressionnetwork, theco-expression network was illustrated using Cytoscape software.
Analysis of the protein-protein interaction (PPI) network of DEGs.
In order to explore the correlation between these DEGs, the interaction network of protein-protein internet (PPI) was constructed using the STRING database and visualized in Cytoscape software.

source_name: Adipose

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA).
The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: Adipose

tag: cell type

value: Adipose-derived mesenchymal stem cells

value: CEFFE+osteogenic induction


title: Male PXR-KO control-fed 2

source_name: liver

value: male


title: Tumoral samples, 476; treatment:DOX

value: mouse mammary gland tumor-derived organoids

value: DOX


title: FEOS-2


title: Male PXR-KO control-fed 1

value: control


title: Exp9.2_YZ1_CCI_CTRL_s1

value: 6 weeks in culture, 24 hours after controlled cortical impact injury


title: FEOS-1


title: Tumoral samples; 476; treatment: control

value: tumoral


title: NCOS-3

value: osteogenic induction


title: HFD3-Epi

city: Jinan

first: Xiujing

last: Feng

state: China

address: School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China

institute: Shandong First Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Epididymal fat

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Epididymal fat

value: HFD

value: untreatment


title: HFD2-Epi


title: HFD1-Epi


title: Female WT EtOH-fed 3

value: female

value: EtOH

value: Liver


title: Non-tumoral samples, 474; treatment:control

value: non-tumoral


title: NCOS-2

value: Adipose


title: ND3-Epi

value: ND


title: Tumoral samples; 476; treatment: MEGM+DOX

value: MEGM media + DOX


title: Female WT EtOH-fed 4

value: WT


title: Female WT EtOH-fed 2


title: Tumoral samples, 496; treatment: MEGM media

value: mouse mammary gland tumor-derived organoids

value: MEGM media


title: NCOS-1

value: Adipose-derived mesenchymal stem cells


title: Male PXR-KO control-fed 3

value: male

value: control

value: PXR-KO


title: ND2-Epi

value: Epididymal fat


title: Female WT EtOH-fed 1


title: ND1-Epi


title: AML24

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

description: 10X Genomics

data_processing:
Sequencing reads were demultiplexed and aligned to GRCh38 reference using the CellRanger pipeline (mkfastq and count, 10x GENOMICS, v3.1.0).
Assembly: GRCh38
Supplementary files format and content: Tab separated values files
Supplementary files format and content: matrix files

source_name: Peripheral blood

extract_protocol:
The cells were encapsulated into single droplets using Chromium Controller (10x GENOMICS) according to the manufacturer's protocol.
Libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 or v3 (10x GENOMICS) according to the manufacturer's protocol.

treatment_protocol: Human AML patient cells were thawed from cryopreservation and sorted on 7AAD- to eliminate dead cells. AML1 was also sorted on CD45+CD33+ cells to remove non-myeloid cells. Xenografted cells were sorted on human CD45+CD33+ to purify human leukemic cells.

value: Peripheral blood

value: Primary patient cells

value: AML patient leukemic cells


title: Tumoral samples, 366; treatment: DOX

value: DOX

value: tumoral


title: Tumoral samples, 366; treatment: control


title: Non-tumoral samples, 474; treatment: MEGM

value: non-tumoral


title: Female WT control-fed 3

value: female

value: Liver


title: AML8_xeno

description: 10X Genomics

source_name: Xenograft bone marrow

value: Xenograft bone marrow

value: Xenografted patient cells

value: AML leukemic cells sort purified from xenograft


title: E13.5 Female Section9.5

city: Guangzhou

first: Guangdun

last: Peng

state: Guang dong

address: Building 3, KaiYuan Road, Huangpu District

department: Center for Cell Lineage and Atlas

institute: Bioland Laboratory

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Quality control and adapter trimming on Raw reads were implemented with fastp-0.21.0
Clean reads were mapped to mouse reference genome and gene annotations (mm10-3.0.0) using the Space Ranger
Count matrix were extracted by loading the output directory of Space Ranger into Seurat
Spots were filtered with cut-offs at a minimum of 1,000 detected genes and a maximum of 10% mitochondrial counts, except for section 6.5 (S6.5) of the female mouse, a minimum of 500 detected genes and a maximum of 10% mitochondrial counts were applied for S6.5.
Assembly: mm10-3.0.0
Supplementary files format and content: count_mtx.tsv.gz: expression matrix
Supplementary files format and content: meta.csv.gz: spot annotation metadata
Supplementary files format and content: coordinates_merge.csv.gz: merged barcodes and coordinates for spots
Supplementary files format and content: scalefactors_json: scalefactors in json format
Supplementary files format and content: png file: Image of tissue
Library strategy: Spatial Transcriptomics

source_name: embryo

extract_protocol:
Collected embryos were embedded in Tissue freezing medium and stored at -80°C until sectioning. The whole embryo tissue was serially cryo-sectioned along craniocaudal axis at 10μm, and about 1000 sections were harvested. Considering the morphology and uniform sampling, 10 sections from a male embryo and 4 sections from a female embryo were selected for spatial transcriptomic analysis by 10x Genomics Visium platform.
These sections were then used for spatial transcriptomic analysis by 10x GenomicsVisium platform according to manufacturer’s construction.

value: embryo

tag: developmental stage

value: embryonic day 13.5

tag: Sex


title: AML20

description: 10X Genomics


title: Non-Tumoral samples, 474; treatment: DOX

value: mouse mammary gland tumor-derived organoids


title: Non-Tumoral samples, 474; treatment: control

value: control


title: blood, donor 22-0010

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

institute: UHN

description:
barcodes.tsv.gz
matrix.mtx.gz
Metadata.txt
features.tsv.gz

data_processing:
Seq-Well3 libraries were pre-processed using the DropSeq pipeline with the tools v.2.3.0. Pooled libraries were demultiplexed using bcl2fastq v.2.20.0.422. Read alignment was done using STAR 2. Sequencing data were aligned to GRCh38 (hg38) reference genome.
CellRanger-processed filtered feature matrices were analyzed using Seurat version 3.1.5.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-separated metadata information

source_name: blood

extract_protocol:
After taking samples from the patients, samples were maintained on ice and immediately processed. After quality control steps, red blood cells were depleted (StemCell Technolopgies Inc.). Cells were washed, counted, and subjected to scRNAseq.
Samples were prepared as outlined by the Seq-Well S3 Reagent Kit user guide.
Cells were diluted to 75,000 cells/mL. A suspension of 200 µL was then loaded onto Seq-Well S3 arrays pre-loaded with mRNA capture beads. Fresh samples were directly processed on site whereas frozen samples were placed horizontally in 50 mL conical tubes and stored at -80 °C. Once ready, samples proceeded with hybridization, bead isolation, and reverse transcription. Samples underwent Illumina Nextera XT Library preparation. Sequencing was performed on either a NextSeq 500/550 instrument with a High Output Flowcell and a 75-cycle kit (PE 20/50) or a NovaSeq 6000 instrument with a S4S4 Flowcell and a 100-cycle kit. Samples were demultiplexed and sequenced to an average depth of 1M reads per Seq-Well array.

value: blood

tag: individual

value: No Treatment

tag: disease state

value: Healthy


title: liver, donor 22-0010

value: liver


title: E13.5 Female Section8.5


title: liver, donor 22-0004


title: E13.5 Ref Section9

value: male


title: Female WT control-fed 2

tag: genotype

value: WT


title: E13.5 Female Section7.5


title: SuSa 72hr post release, scRNA-seq

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

description: 10x Genomics 3' v3.1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: SuSa

extract_protocol:
Cryobanked cells were thawed, washed with cold media +10%FBS, then cold PBS with 1% BSA. Cells were then filtered through a 35uM filter and resuspended to 1,000cells/ul and kept on ice until processed.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: SuSa

value: testicular germ cell tumor

tag: timepoint

value: 72hr post release


title: Female WT control-fed 4

value: female

value: Liver


title: E13.5 Female Section6.5


title: AML8

description: 10X Genomics

value: Peripheral blood

value: Primary patient cells

value: AML patient leukemic cells


title: SuSa 24hr post release, scRNA-seq

description: 10x Genomics 3' v3.1

value: 24hr post release


title: Female WT control-fed 1


title: blood, donor 22-0002


title: E13.5 Ref  Section8

value: embryo

value: embryonic day 13.5


title: Male WT EtOH-fed 3

value: EtOH


title: SuSa log phase, scRNA-seq

description: 10x Genomics 3' v3.1

value: at log phase


title: Male WT EtOH-fed 4


title: KLE 72hr post release, scRNA-seq

description: 10x Genomics 3' v3.1

source_name: KLE

value: KLE

value: Endometrial adenocarcinoma


title: Male WT EtOH-fed 2

value: male


title: Male WT control-fed 4

value: control

value: WT


title: E13.5 Ref  Section7


title: liver, donor 22-0002

value: liver

value: No Treatment

value: Healthy


title: Male WT control-fed 3

value: Liver


title: blood, donor 22-0004

value: blood


title: E13.5 Ref Section10


title: KLE 48hr post release, scRNA-seq

description: 10x Genomics 3' v3.1

value: 48hr post release


title: SuSa 48hr post release, scRNA-seq

description: 10x Genomics 3' v3.1

value: SuSa

value: testicular germ cell tumor


title: blood, donor 30-1025

value: CHB


title: E13.5 Ref  Section6

value: embryo

value: embryonic day 13.5


title: Male WT EtOH-fed 1

value: EtOH


title: liver, donor 30-1025


title: blood, donor 30-1024


title: liver, donor 30-1024


title: E13.5 Ref  Section4


title: E13.5 Ref  Section5


title: AML2_xeno

description: 10X Genomics

value: Xenograft bone marrow

value: Xenografted patient cells

value: AML leukemic cells sort purified from xenograft


title: E13.5 Ref  Section3

value: male


title: KLE log phase, scRNA-seq

description: 10x Genomics 3' v3.1

value: KLE

value: Endometrial adenocarcinoma

value: at log phase


title: YIP2_S6_L002_R1_001

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l lncRNA_CRISPRi_sgRNA_library --control-sgrna lncRNA_CRISPRi_sgRNA_CTRL --norm-method control -n sgrna.count --sample-label D0,D21 --fastq files.fq”. MAGeCK test module was then applied with parameters “mageck test -k sgrna.count -c D0 -t D21 --norm-method control --keep-tmp -n D21_D0 --control-sgrna lncRNA_CRISPRi_sgRNA_CTRL”, to identify the lncRNAs that showed a  significant differential selection (|log2(fold-change)| ≥ 1 and p < 0.05) between the D0 and D21 groups. Based on a custom second-best script, the gene-level results were summarized for the lncRNAs accroding to the library map.
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V25 transcriptome with tophat (v2.1.1). The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2 (1.22.2).
For the eCLIP data: YeoLab's eCLIP (v0.7.1) was used to call the significant peaks (p < 0.05 & FC > 1.2)

growth_protocol: The U87 and U251 cells were cultured in the Dulbecco’s modified Eagle’s medium (DMEM, Hyclone #SH30022.01) supplemented with 10% Fetal Bovine Serum (FBS, Gibco#10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI).

extract_protocol:
The genome DNA was extracted by using QIAamp DNA Mini Kit (QIAGEN) for each replicate. Total RNA was isolated from U251 cells using RNeasy Mini Kit (QIAGEN #74104) and was treated with DNase I (QIAGEN #79254).
Two rounds of PCR were employed to prepare the next-generation-sequencing (NGS)-ready sgRNA libraries with the KAPA HiFi HotStart ReadyMix (Roche # KK2602). The RNA-seq library were constructed with TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594).The eCLIP libraries were generated from U251 cells in biological duplicates with the kit (Eclipse Bioinnovations Inc, #ECEK-0001) according to the standard single-end eCLIP protocol.

treatment_protocol: For eCLIP-seq experiments, U251 cells stably expressing FLAG-tagged YBX1 were crosslinked by 254-nm UV light (400 mJ/cm2) .

value: glioblastoma

value: tumor


title: AML1

description: 10X Genomics

value: Peripheral blood

value: Primary patient cells

value: AML patient leukemic cells (sort purified)


title: Tumor margin, rep3

city: Wuhan

first: Yan

last: Wei

address: Bayi road 229

institute: wuhan university

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: tumor

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: orthotopic injection 2 × 105 MDA-MB-231 cells into the fourth pair of mammary fat pad

value: epithelial cell

value: WT

value: orthotopic injection


title: blood, donor 30-1023

value: blood

value: No Treatment

value: CHB


title: Tumor margin, rep2


title: Tumor margin, rep1


title: Male WT control-fed 2

value: control

value: Liver


title: Male WT control-fed 1

value: male


title: E13.5 Ref  Section2

value: embryo

value: embryonic day 13.5


title: YIP1_S5_L002_R1_001


title: liver, donor 30-1023

value: liver


title: E13.5 Ref Section1


title: blood, donor 30-1022


title: YINPUT2_S8_L002_R1_001

value: glioblastoma


title: Embroid body, TCM media, day 8, rep3 [Day8-EXP3_L002]

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

institute: University of Calgary

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 in two lanes to obtain ~33M reads per sample.
Library quality was assessed with FASTQC
Reads were then aligned with STAR using the GrCM38/mm10 build.
Count tables were assembled with htseq-count using the reverse strand and intersection-nonempty settings
Assembly: mm10
Supplementary files format and content: Tab delimited raw counts are provided for all samples per lane

growth_protocol: R1 mESCs (Nagy et al. 1993) with GFP stably expressed from the Myh6 promoter were grown in Dulbecco’s modified Eagle’s medium (DMEM, 15% FBS, 1mM sodium pyruvate, 1x antimycotic/antibiotic and LIF). EB were generated by growing mESCs for 48 h in 400um Aggrewell™(Stem Cell Technologies) with 600 cells per well. Aggregates grown in suspension in a petri dish on a rotary orbital shaker for until day 4. On day 4 EBs were plated on 0.2% gelatin-coated plates with 15 EBs/well. Day 0-8 were in base or TCM differenitation media.

extract_protocol:
Total RNA was isolated from Ebs at day 4 or 8 of differentiation with the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol.
Libraries were constructed with the Ultra II Directional RNA Library Prep, using poly-A capture for mRNA enrichment.

treatment_protocol: Differentiation media wa either base medium (10% FBS, 1mM sodium pyruvate, 1x antmyoctiv/antibiotic and 50uM BMEin DMEM) or TCM (50% base medium, 50% base conditioned by mTSCs for 3 days)

tag: state

value: Embryoid bodies

value: mECS

value: Myh6-GFP+, WT

value: TCM


title: Tumor core, rep2

tag: tissue

value: tumor

value: epithelial cell


title: YINPUT1_S7_L002_R1_001


title: Embroid body, TCM media, day 8, rep3 [Day8-EXP3_L001]


title: KLE 24hr post release, scRNA-seq

description: 10x Genomics 3' v3.1

value: KLE

value: Endometrial adenocarcinoma

value: 24hr post release


title: liver, donor 30-1022

value: No Treatment

value: CHB


title: Tumor core, rep1

value: WT

value: orthotopic injection


title: blood, donor 30-1021

value: blood


title: liver, donor 30-1021


title: Embroid body, TCM media, day 8, rep2 [Day8-EXP2_L002]


title: Human skin, cutaneous squamous cell carcinoma, cSCC5

city: Heidelberg

first: Manuel

last: Rodríguez-Paredes

address: Im Neuenheimer Feld 280

institute: German Cancer Center (DKFZ)

data_processing:
Alignment of the raw fastq-data with CellRanger v4.0.0 to reference genome.
Quality control, data filtering and sample combination with CellRanger v4.0.0.
Assembly: hg19
Supplementary files format and content: Seurat object after QC with CellRanger containing count matrix.

source_name: skin

extract_protocol:
Fresh human skin tissue was kept in MACS Tissue Storage Solution (Miltenyi Biotec, cat. no. 130-100-008) at most overnight. It was then enzymatically and mechanically dissociated using the Whole Skin Dissociation kit for human material (Miltenyi Biotec, cat. no. 130-101-540) and the Gentle MACS Dissociator device (Miltenyi Biotec), following the manufacturer's instructions. The resulting cell suspensions were filtered through 70µm cell strainers (Falcon, cat. no. 10788201) and the Dead Cell Removal Kit (Miltenyi Biotec, cat. no. 130-090-101) was then used to remove apoptotic and dead cells.
About 20,000 single cells per sample were used to prepare sequencing libraries with the Chromium Single Cell Reagent kit (v3.1 chemistry) from 10X Genomics (cat. no. 1000128), following the manufacturer's instructions. Library quality was checked with the Qubit dsDNA HS Assay kit (Life Technologies, cat. no. Q32851), and cDNA integrity was assessed with D1000 ScreenTapes (Agilent Technologies, cat. no. 5067-5582). Finally, pairwise sequencing (26 + 96bp) was performed with a NovaSeq 6000 device (Illumina).

value: skin

value: male

tag: age

tag: diagnosis

value: cutaneous squamous cell carcinoma

tag: grading


title: Human skin, cutaneous squamous cell carcinoma, cSCC4


title: Embroid body, TCM media, day 8, rep2 [Day8-EXP2_L001]

value: Embryoid bodies


title: liver, donor 20-3002

value: liver

value: NUC treatment


title: O3-TX-ATAC-seq_2

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq and HiC-seq reads  were aligned to the hg19 or mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Assembly: mm9, hg19
Supplementary files format and content: tab-delimited text files include count values for RNA-seq, and peaks for ATAC-seq, and interaction contact file for HIC-seq samples.

source_name: OCI-AML3 leukemia cells

growth_protocol: Total bone marrow LK cells were isolate from WT and NPM1C+ KI mice, and were sorted with Lin- and Kit+ markers.  Human OCI-AML3 leukemia cells were culture with alpha-MEM supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ATAC-seq samples derived according to Nextera Tn5 Transposase kits. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.  HiC-seq libraries were prepared according to KAPA HyperPrep Kits (KK8500).

treatment_protocol: Immediately extract total RNA from OCI-AML3 AML cells with and without Selinexor (KPT-330, XPO1 inhibitor) treatment.

tag: cell types

value: Human-derived acute myeloid leukemia

value: peripheral blood

tag: disease

value: acute myeloid leukemia


title: O3-TX-ATAC-seq_1


title: Embroid body, TCM media, day 8, rep1 [Day8-EXP1_L002]

value: mECS

value: Myh6-GFP+, WT

tag: treatment

value: TCM


title: Human skin, cutaneous squamous cell carcinoma, cSCC3


title: Tumor core, rep3

value: tumor

value: epithelial cell


title: Embroid body, base media, day 8, rep3 [Day8-CON3_L002]

value: base


title: O3-WT-ATAC-seq_2


title: blood, donor 20-3001

value: CHB


title: Human skin, cutaneous squamous cell carcinoma, cSCC1


title: Embroid body, base media, day 8, rep3 [Day8-CON3_L001]


title: liver, donor 20-3001


title: Human skin, Bowen's disease, BD3

description: same donor as BD2 but from different body part

value: Bowen's disease

value: early invasive


title: O3-WT-ATAC-seq_1


title: blood, donor 20-1003

value: blood

value: No Treatment


title: O3-NW-RNA-seq_2


title: Embroid body, base media, day 8, rep2 [Day8-CON2_L002]

value: Embryoid bodies


title: Human skin, Bowen's disease, BD2

description: same donor as BD3 but from different body part

value: skin

value: male


title: O3-NW-ATAC-seq_2

value: Human-derived acute myeloid leukemia


title: O3-NW-RNA-seq_1

value: peripheral blood


title: blood, donor 20-3002

value: NUC treatment


title: O3-NW-ATAC-seq_1

value: acute myeloid leukemia


title: Embroid body, base media, day 8, rep2 [Day8-CON2_L001]

value: mECS

value: Myh6-GFP+, WT


title: liver, donor 20-1003

value: liver


title: Embroid body, TCM media, day 8, rep1 [Day8-EXP1_L001]

value: TCM


title: Human skin, Bowen's disease, BD1


title: blood, donor 20-1002


title: O3-TX-RNA-seq_2


title: Human skin, cutaneous squamous cell carcinoma, cSCC2

value: cutaneous squamous cell carcinoma


title: Embroid body, base media, day 8, rep1 [Day8-CON1_L002]

value: base


title: Embroid body, base media, day 8, rep1 [Day8-CON1_L001]


title: O3-TX-RNA-seq_1


title: Embroid body, TCM media, day 4, rep3 [Day4-EXP3_L002]


title: O3-WT-RNA-seq_2


title: blood, donor 10-1007

value: CHB


title: Human skin, healthy UVR-exposed, EH1

value: healthy


title: O3-WT-RNA-seq_1


title: liver, donor 10-1007


title: Embroid body, TCM media, day 4, rep3 [Day4-EXP3_L001]


title: Dropseq-T2D4

city: Cleveland

first: Shanshan

last: Zhang

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

data_processing:
The sequenced Drop-Seq libraries yield 50-base paired-end reads (PE50). The first 20bp of read 1 are cellular and molecular barcodes (base 1-12 cell barcode, base 13-20 UMI). We trimmed base 21-50 of read 1 before further analysis. We first remove all data with the quality score of read 1 (base 1-20) lower than 10. Read 2 was trimmed at 3’ end to remove ployA tails of at least 6 bases and trimmed at 5’ if template switching oligo (TSO) adapter sequence appears. Clean reads were then aligned to hg19  using STAR with default settings. We only keep uniquely mapped reads on gene exons. We next filtered out PCR duplicates with the same coordinates, cell barcode, and UMI. We then grouped the reads by cell barcode and generated the digital UMI-count matrix after counting transcripts for every gene with every cell barcode.
Supplementary_files_format_and_content: cell~gene matrix from each donor

source_name: human islet T2D4

growth_protocol: To dissociate islets into single cells, cells were washed once in HBSS (Sigma-aldrich, #6648) and incubated in Accutase (Innovative Cell Technologies, #AT104) at 37°C for 20-25 min. The islets were broken up gently with a 5 ml pipette every 5 min. When >95% of the islets were digested into single cells, PIM(S) medium were added to neutralize the Accutase. Single cells were washed again with HBSS and resuspended in HBSS at the concentration of 2 x 105/mL for Drop-Seq analysis.

extract_protocol:
We performed Drop-Seq following the protocol as previously described (Macosko et al., 2015). Briefly, three pump-controlled syringes with cell suspension (200,000 cells/mL), barcoded beads in lysis buffer (120,000 beads/mL), and droplet generation oil were connected to a microfluidic device under microscope supervision. During droplets generation, we set the cell and bead flow speed at 4,000uL/hr, and the oil speed at 15,000uL/hr. The droplets are collected into 50mL falcon tubes (usually less than 5mL). Under this setting, most droplets have at most one beads or one cell.
Following droplet breakage,we performed 1st strand cDNA synthesis on beads followed by SMART-PCR (Macosko et al., 2015). Finally, the resulting full-length cDNA library are prepared for sequencing exactly following the published Drop-Seq protocol (Macosko et al., 2015).

tag: tag

value: no treat

value: drop-seq

value: no


title: blood, donor 10-1006

value: blood


title: Embroid body, TCM media, day 4, rep2 [Day4-EXP2_L002]

value: Embryoid bodies

tag: cell line


title: O3-TX-HIC-seq

value: Human-derived acute myeloid leukemia


title: Dropseq-T2D3

source_name: human islet T2D3


title: liver, donor 10-1006


title: Embroid body, TCM media, day 4, rep2 [Day4-EXP2_L001]

tag: cell type


title: blood, donor 10-1005

value: No Treatment


title: Dropseq-T2D2

source_name: human islet T2D2


title: O3-WT-HIC-seq

value: peripheral blood


title: Human skin, healthy UVR-exposed, EH3

value: skin

value: male


title: Embroid body, TCM media, day 4, rep1 [Day4-EXP1_L002]

value: mECS

value: Myh6-GFP+, WT


title: Cebpa_activated_OCIAML3_2

value: acute myeloid leukemia


title: Embroid body, TCM media, day 4, rep1 [Day4-EXP1_L001]

value: TCM


title: liver, donor 10-1005

value: liver


title: Cebpa_activated_OCIAML3_1


title: Human skin, healthy UVR-exposed, EH2


title: blood, donor 10-1003

value: NUC treatment

value: CHB


title: Pu1_activated_OCIAML3_3


title: Embroid body, base media, day 4, rep3 [Day4-CON3_L001]

value: base


title: Dropseq-HT6

source_name: human islet HT6

value: no treat

value: drop-seq


title: Dropseq-T2D1

source_name: human islet T2D1

value: no


title: Pu1_activated_OCIAML3_2


title: O3-NW-HIC-seq


title: Embroid body, base media, day 4, rep2 [Day4-CON2_L002]

value: Embryoid bodies


title: liver, donor 10-1003


title: Pu1_activated_OCIAML3_1

value: Human-derived acute myeloid leukemia


title: Dropseq-HT5

source_name: human islet HT5


title: Embroid body, base media, day 4, rep2 [Day4-CON2_L001]


title: Microcapsule_EB, scRNA-seq

city: Nijmegen

first: Rebecca

middle: Regina

last: Snabel

state: Gelderland

address: Geert Grooteplein 26-28

department: Molecular Developmental Biology

country: Netherlands

institute: RIMLS

description:
3A1_DRRAGN_StemCellsCavitation_d6_Z04_S8
Microcapsule_EB_d6

data_processing:
Trimming and mapping of reads was performed with seq2science v0.6.0 (available in Zenodo, https://doi.org/10.5281/zenodo.4451349).
kb-python (v0.26.4) was used for pseudoalignment against the GRCh38 genome, to quantify UMI counts per cell.
Scater (v1.20.1) was used to preprocess and perform quality control, Seurat (v4.0.4) was used for SCTransform HVG-selection, normalization and further downstream analysis.
Assembly: GRCh38
Supplementary files format and content: seurat_metadata.csv: Metadata with an entry for each single cell.
Supplementary files format and content: seurat_sf_genes.tsv: Gene names, row names for the count matrix.
Supplementary files format and content: seurat_sf_barcodes.tsv: Cell barcodes, column names for the count matrix.
Supplementary files format and content: seurat_sf_counts.mtx: Raw gene count sparse matrix, with cells in columns and genes in rows.
Supplementary files format and content: seurat_SCT_scaled_counts.csv: Scaled counts matrix, as used for dimensionality reductions (PCA and UMAP).
Supplementary files format and content: seurat_umap_embedding.csv: UMAP embedding coordinates used for visualizing the cells in 2D.

source_name: hPSC reporter lines MESP1(mCherry/NKX2-5(eGFP), ACTN2(mRubyII)/NKX2-5(eGFP)

extract_protocol:
TrypLE (Gibco) dissociation of cells before sorting into 384-well plates.
CEL-Seq2 protocol in 384-well plates, with ERCC spike-ins.
Libraries were multiplexed and sequenced on NextSeq500 Illumina.

value: hPSCs


title: Dropseq-HT4

source_name: human islet HT4


title: Dropseq-HT3

source_name: human islet HT3


title: hPSCs, scRNA-seq

description:
3A1_DRRAGN_StemCell_d1_Z02_S10
hPSCs_d1

value: hPSC reporter lines MESP1(mCherry/NKX2-5(eGFP), ACTN2(mRubyII)/NKX2-5(eGFP)


title: Ctrl_OCIAML3_2

value: peripheral blood


title: Embroid body, base media, day 4, rep1 [Day4-CON1_L002]


title: Cardiac_microcapsule, scRNA-seq

description:
3A1_DRRAGN_CardiacSpheroid_d21_Z01_S1
Cardiac_microcapsule_d21

value: hPSC-derived CM


title: Dropseq-HT7

source_name: human islet HT7


title: Control_cardiac, scRNA-seq

description:
3A1_DRRAGN_CardiacEB_d21_Z03_S1
Control_cardiac_d21


title: Dropseq-HT2

source_name: human islet HT2


title: U251YBX1SI3_S6

city: Houston

value: glioblastoma

value: tumor


title: ATII cells, siRNA LKB1, rep3

city: Southampton

first: Yihua

last: Wang

address: University Road

country: United Kingdom

institute: University of Southampton

data_processing:
Quality control of RNA-seq raw paired data was performed using FastQC  and MultiQC.
Trim Galore was used to trim adapters, reads with low quality (<30) and short length (<50 bp).
RNA-seq reads were mapped to Homo_sapiens.GRCh38.100 using Hisat2 with default codes.
Sam files were transformed into bam files using samtools.
The read counts of each genes were summarized using featureCounts.
Assembly: Homo_sapiens.GRCh38.100
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

source_name: ATII

growth_protocol: ATII cells (kindly provided by Prof Julian Downward) were cultured in DCCM-1 (Biological Industries Ltd.) supplemented with 10% NBCS (Life Technologies), 1% penicillin, 1% streptomycin and 1% L-glutamine (from Sigma Aldrich) and were kept at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop Spectophotometer 2000c (Thermo Fisher Scientific). A total amount of 3 μg RNA per sample was used as input material for library construction.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, Massachusetts, USA) following manufacturer’s instruction. Libraries were pooled in equimolar and sequenced using the paired-end strategy (2 × 150) on the Illumina NovaSeq 6000 platform following the standard protocols (Novogene, UK).

treatment_protocol: ATII cells were transfected with STK11 or control siRNA oligos at a final concentration of 35 nM using DharmaFECT 2 reagent (Dharmacon).

value: ATII

value: alveolar epithelial type II (ATII) cells

value: WT

value: 35uM siRNA against LKB1 (STK11), 72hours


title: Ctrl_OCIAML3_1

value: acute myeloid leukemia


title: Embroid body, base media, day 4, rep3 [Day4-CON3_L002]

value: mECS

value: Myh6-GFP+, WT

value: base


title: Dropseq-HT1

source_name: human islet HT1

value: no treat

value: drop-seq

value: no


title: Embroid body, base media, day 4, rep1 [Day4-CON1_L001]

value: Embryoid bodies


title: Hi-C.beta6

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only first 36 bases were used for mapping. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed. For every loop anchor, we first count Hi-C reads from the anchor to every fragment within 2Mb range and then map the contact fragments to ~5kb anchor resolution. We used HiCorr to correct bias in raw contacts between every two anchors, and apply DeepLoop on the bias-corrected contact ratio from HiCorr. The file column names are "anchor_loc1", "anchor_loc2", "raw_reads","HiCorr_bias_corrected.ratio","DeepLoop_enhanced"
Genome_build: hg19
Supplementary_files_format_and_content: The file column names are "anchor_loc1", "anchor_loc2", "raw_reads","HiCorr_bias_corrected.ratio","DeepLoop_enhanced"

source_name: human islet sorted beta cells

extract_protocol:
Human islets were purchased from Prodo Labs (Cat# HIR-001). After receiving, the islets were well dispersed and washed with complete PIM(S) media (Prodo Labs, Cat# PIM-S001GMP) by centrifuging at 180g for 2 minutes.  The supernatant was removed with about 2-3ml of media left. The islet pellets were then gently resuspended in complete PIM(S) media, and transferred to a 6-well non-tissue culture treated plate. After recovering in a cell incubator for overnight, the islets were digested to single cells. Briefly, the islets were pelleted and washed with HBSS without Ca++/Mg++ (Sigma, Cat# H6648-1L), and then digested with Accutase (Life Technologies, Cat# A1110501) in a 6-well non-treated plate at 37ºC for about 5 minutes. The digested cells were filtered through a 40?m cell strainer to obtain single cells, and the cell number and viability were observed after washing twice with HBSS. To prepare for low input Hi-C, the single cells were firstly fixed with BD cytofix/ cytoperm buffer (BD, Cat# 51-2090KZ) for 20 minutes and washed with BD perm/ Wash buffer before stained with desired antibodies for alpha cells (BD Biosciences, BV421 mouse anti-glucagon, Cat# 565891) and beta cells (BD Biosciences, Alexa Flour 647 Mouse Anti-Insulin, Cat# 565689). The cells were sorted out using BD FACS ARIA II.
We followed our previous easy Hi-C protocol to generate the eHi-C libraries. In order to make it compatible to low input sorted cells, we made a few changes. Briefly, about 20-30k sorted alpha or beta cells were applied for each library. Nuclei were extracted and digested with HindIII before proximity ligation. The chromatin ligates were then digested DpnII before constructing self-circles. The circuited DNAs were then linearized with a second digestion of HindIII. All the recovered DNAs were used to generate libraries. We followed the standard protocol to generate the libraries with modified Truseq adapters containing a regular sample index (i7) and a random fragment index (i5: NNNNNN).

value: Hi-C


title: Hi-C.beta5


title: ATII cells, siRNA LKB1, rep1


title: ATII cells, siRNA LKB1, rep2


title: U251YBX1SI2_S5


title: Mutant Animal 1, Airway cells, scRNAseq

city: St Louis

first: Amjad

last: Horani

address: 660S Euclid Ave

institute: Washington University

description:
10x Genomics
mALI_counts.txt.gz
mALI_meta.txt

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: trachea

growth_protocol: Cells were differentiated and maintained at ALI conditions

extract_protocol:
Airway cells were isolated after incubation in trypsin for 5 minutes and mechanical dissociation. The isolated cells were resuspended in tryspin for  and incubated at 37 °C for 5 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (PBS+0.04% BSA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains a primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up, amplified, and the apropiated sized fragments were selected for subsequent library construction.

value: Primary airway cells

value: trachea

tag: strain

value: DNAAF5 Mutant

value: 12 weeks old


title: Mutant Animal 3, Airway cells, scRNAseq


title: U251YBX1SI1_S4

value: glioblastoma

value: tumor


title: WT Animal 3, Airway cells, scRNAseq

value: WT


title: liver, donor 20-1002

source_name: liver

value: liver

value: No Treatment

value: CHB


title: ATII cells, siRNA Control, rep2

value: ATII

value: alveolar epithelial type II (ATII) cells

value: 35uM control siRNA, 72hours


title: U251YBX1NC3_S3


title: WT Animal 2, Airway cells, scRNAseq


title: ATII cells, siRNA Control, rep1


title: Hi-C.beta3

value: no treat


title: Hi-C.beta4


title: Hi-C.beta2


title: WT Animal 1, Airway cells, scRNAseq


title: 3D co-cultured LKB1-depleted ATII + MRC5, rep3

source_name: ATII + MRC5

growth_protocol: ATII cells (kindly provided by Prof Julian Downward) were cultured in DCCM-1 (Biological Industries Ltd.) supplemented with 10% NBCS (Life Technologies), 1% penicillin, 1% streptomycin and 1% L-glutamine (from Sigma Aldrich). MRC5 cells were obtained from the European Collection of Authenticated Cell Cultures (ECACC) and were cultured in DMEM (Thermo Fisher Scientific). Both cell culture media were supplemented with 10% FBS (Thermo Fisher Scientific), 1% penicillin/streptomycin and glutamine (Thermo Fisher Scientific). All cells were kept at 37 °C and 5% CO2.

treatment_protocol: Aggregation of 3D cultures was achieved using Nanoshuttle-PL (Greiner Bio-One). Briefly, MRC5 fibroblasts at 80% confluence were treated with Nanoshuttle-PL for 24 h, before trypsinisation as normal. Cells are then pipetted onto cell repellant 96-well plates sat on a magnetic drive and left to incubate at 37 °C and 5% CO2 for a minimum of 3 h on the magnetic drive to enable the spheroid to form. The process was then repeated for control or LKB1-depleted ATII cells so they could then grow around the existing fibroblast spheroid. LKB1-depleted ATII cells were generated by transfection with LKB1 (STK11) siRNA oligos at a final concentration of 35 nM using DharmaFECT 2 reagent (Dharmacon).

value: ATII + MRC5

value: alveolar epithelial type II (ATII) cells + human lung fibroblast

value: LKB1-depleted ATII cells co-cultured with MRC5 in 3D for 5 days


title: Hi-C.beta1

value: Hi-C


title: Mutant Animal 2, Airway cells, scRNAseq

value: Primary airway cells

value: trachea


title: 3D co-cultured LKB1-depleted ATII + MRC5, rep2


title: ATII cells, siRNA Control, rep3


title: 3D co-cultured LKB1-depleted ATII + MRC5, rep1


title: Hi-C.alpha7

source_name: human islet sorted alpha cells


title: Hi-C.alpha6


title: U251DARS-AS1SI3_S6


title: U251DARS-AS1SI2_S5


title: U251YBX1NC2_S2