title: SEM BAZ2B

description: Library name: SEM_BAZ2B

value: SEM


title: P5_ferret_striatum, scRNAseq

status: Public on Aug 12 2025

type: SRA

city: San Francisco

first: Alex

last: Pollen

state: CA

country: USA

institute: University of California San Francisco

description: Library name: P5_ferret_striatum

library_source: transcriptomic single cell

data_processing:
Genes were quantified using CellRanger v7.0.1, ambient RNA was removed using Cellbender v0.2.1, inhibitory neurons were isolated used conserved markers (DLX1/2/5/6, GAD1/2)
Assembly: GRCr8 (rat), mOrycun1.1 (rabbit), mMonDom1.pri (opossum), SugarGlider_lib1_testN_pseudohap (Sugar glider), ASM1176430v1.1 (ferret), SusScrofa11.1 (pig)
Supplementary files format and content: barcodes.csv contains cell metadata
Supplementary files format and content: genes.csv contains gene metadata
Supplementary files format and content: matrix.mtx contains raw cells by genes CellRanger and Cellbender matrix

molecule: polyA RNA

organism: Mustela putorius furo

source_name: striatum

extract_protocol:
Regions of interest were dissected and tissue was dissociated in papain. Whole cells from pig, ferret, opossum, rat, and rabbit were resuspended in PBS supplemented with 0.04% BSA for Chromium 10X processing, mouse cells were resuspended in PBS supplemented with 0.1% BSA and sorted for Nkx2.1-cre;Ai14 expression using BD FACSAria Fusion for Chromium 10X processing.
Library was constructed according to manufacturer's protocol

tag: tissue

value: striatum

tag: cell line

value: WT, P5

tag: cell type

value: developing brain


title: patterned induced neurons, C1_A4-3, Pan troglodytes, 2N, minusKCl, piN_Rep1 (RNA-seq)

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

description:
Library name: C1_A4-3_minusKCl_1
piN_human-chimp_gene_counts.txt

library_source: transcriptomic

data_processing:
RNA-seq data from the human and chimpanzee diploids, autotetraploids, and allotetraploids was analyzed as previously described (Song et al., 2021). Briefly, sequencing reads were trimmed for adapter sequences and assessed for sequencing quality using trimgalore v0.6.6 with cutadapt v2.5 (Martin, 2011) and fastqc v0.11.5 (Andrews et al., 2010). Reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to a composite human-chimpanzee genome (hg38 and panTro6). The number of uniquely-mapped reads (MAPQ=255) that overlap each gene was counted using featureCounts from the subread v2.0.0 package (Liao et al., 2014).
For CRISPR inhibition experiments, UMIs were extracted using umi_tools v1.1.2 (Smith et al., 2017) and adapter sequences were trimmed using cutadapt v2.5 (Martin, 2011). Sequencing quality was assessed with fastqc v0.11.5 (Andrews et al., 2010). Reads that map to rDNA (https://www.ncbi.nlm.nih.gov/nuccore/U13369.1) were removed, and remaining reads were aligned using STAR v2.7.9a with two-pass mapping (Dobin et al., 2013) to either the hg38 or panTro6 genome, as appropriate. Reads were then de-duplicated based on UMIs using umi_tools, and the number of reads that overlap each gene was counted using featureCounts from the subread v2.0.0 package with default parameters (Liao et al., 2014).
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: gene count files

molecule: total RNA

organism: Pan troglodytes

growth_protocol:
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into neural progenitor cells (NPCs) using the StemDiff SMADi Neural Induction Kit (STEMCELL Technologies, cat #08582) as per the manufacturer’s instructions. On D7, cells were split using Accutase (Millipore, cat #SCR005) and infected with lentivirus (if applicable). Cells were harvested at D14 for sequencing.
Stem cell lines were routinely propagated feeder-free in mTeSR Plus (STEMCELL Technologies, cat #100-0276), and differentiated into patterned induced neurons (piNs) via induction of doxycycline-inducible NGN2 and as described in Nehme et al., 2018. Cells were harvested on D28

extract_protocol:
NPCs at D14 or piNs at D28 were collected in Trizol and RNA was extracted with the Direct-Zol Miniprep Kit (Zymo Research, cat #R2052) or the Direct-Zol Microprep Kit (Zymo Research, cat #R2062). Cells infected with lentivirus were collected by FACS prior to RNA extraction.
RNA sequencing libraries were made with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara Bio) or with the WatchMaker RNA Library Prep Kit with Polaris Depletion (WatchMaker Genomics) and the Twist UMI Adapter System - TruSeq Comp, 96 Samples Plate A (Twist Biosciences, cat #105041).

treatment_protocol: If applicable, cells were infected with lentivirus.

value: patterned induced neurons

value: N

tag: ploidy

tag: kcl treatment

value: minusKCl

tag: batch


title: EHEC Vehicle 1

city: Madison

first: Vanessa

last: Sperandio

state: WI

address: 1550 Linden Dr

department: Medical Microbiology & Immunology

institute: University of Wisconsin - Madison

description: Library name: V1

data_processing:
Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads.
Demultiplexing, quality control, and adapter trimming was performed with bcl- convert (v4.2.4)
Assembly: GCA_000008865.2
Supplementary files format and content: tab-delimited tsv  file includes RPKM values for each Sample

organism: Escherichia coli O157:H7

growth_protocol: WT EHEC was grown in low-glucose DMEM until late log phase with either methanol as vehicle, 10 µM serotonin, 500 µM indole or both of them together.

extract_protocol:
RNA was extracted through TRIzol chloroform extraction method. Extracted RNA was treated with InvitroGen Turbo DNA-free kit and purified by SPRi (RNAClean XP).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: Vehicle, 10 µM serotonin, 500 µM indole or both of them together was added to the growth medium in a filution of 1:1000.

tag: strain

tag: genotype

value: WT

tag: treatment

value: Methanol


title: P5_ferret_cortex, scRNAseq

description: Library name: P5_ferret_cortex

source_name: cortex

value: cortex


title: EHEC Vehicle 2

description: Library name: V2


title: patterned induced neurons, C1_A4-3, Pan troglodytes, 2N, 6hrKCl, piN_Rep1 (RNA-seq)

description:
Library name: C1_A4-3_6hrKCl_1
piN_human-chimp_gene_counts.txt


title: HJ-23-2

city: JiangSu

first: Zhang Meiqi

last: Zhang

address: 59 Cangwu Road, Haizhou District, Lianyungang City

country: China

institute: 江苏海洋大学

data_processing:
Raw data quality assessed with FastQC.
Quality trimming using Trimmomatic.
Alignment with HISAT2.
Redundancy and insertion fragment distribution analysis with RSeQC.Uniformity and genome structure distribution analysis with Qualimap.
Gene coverage and sequencing distribution analysis with BEDTools.
Assembly: HISAT2
Supplementary files format and content: The counts matrices provide gene expression counts across different samples. RSEM quantification files contain estimated expression levels for each gene and transcript. Quality control reports from FastQC are also included to visualize and assess the sequencing data quality.

organism: Homo sapiens

source_name: Colorectal Carcinoma

growth_protocol: After reaching 80% density, HCT116 cells were divided into two groups, with no less than 5×10^6 cells in each group. One group was treated with 30µM HJ-23 drug, and the other group was treated with DMSO as a control. Both groups of cells were incubated at 37°C. One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer. Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

value: Colorectal Carcinoma

value: Colorectal cells

value: HJ-25, 30 μM, 24 hours


title: EHEC Serotonin 3

description: Library name: S3

value: 10 µM serotonin


title: Visium_JKPF2_3

status: Public on Aug 11 2025

city: Tokyo

first: Yu

last: Fujita

address: 3-25-8 Nishishinbashi

country: Japan

institute: The Jikei University School of Medicine

description:
Library name: Visium_JKPF2_3
10x Genomics

data_processing:
(Spatial) Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.       (scRNA-seq) Raw sequencing data were processed using 10x Cell Ranger pipeline (version 6.1.2, 10X Genomics) to generate FASTQ files.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned_fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Library strategy: Spatial Transcriptomics

source_name: IPF lung

extract_protocol:
(Spatial )Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat.     (scRNA-seq) The isolated lung tissue fragments were mechanically minced and dissociated using enzymes, according to the protocol of a lung dissociation kit (130-095-927; Miltenyi Biotec, Bergisch Gladbach, Germany). After dissociation, the viability of single cells was confirmed to be > 90% using trypan blue staining. The cells were then washed using phosphate-buffered saline (PBS) supplemented with 0.1% bovine serum albumin (BSA, Sigma-Aldrich), filtered using 70- and 40-μm filters, centrifuged at 300 × g for 10 min, and resuspended in PBS supplemented with 1% BSA.
(Spatial) Spatial transcriptome sequencing libraries were prepared with 10XGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.    (scRNA-seq) Cells were counted and resuspended in PBS supplemented with 0.1% BSA for the single-cell library construction using a 10X Genomics platform (10X Genomics). The target number of captured cells ranged from 3,000 to 8,000. The samples were tested using a Chromium single-cell 3’ GEM and library & gel bead kit v3.1. Briefly, the cells were loaded into each channel and then partitioned into gel beads in an emulsion in the Chromium Controller, where cell lysis and barcoded RNA RT occurred, followed by amplification, fragmentation, and 5′ adaptor and sample index attachment. Sequencing was performed using a HiSeq X instrument (Illumina, San Diego, CA, USA)

value: IPF lung


title: Visium_JKPF3_2

description:
Library name: Visium_JKPF3_2
10x Genomics


title: OD0.5_ABC141_biorep1

first: Suzana

middle: P

last: Salcedo

state: Wisconsin

address: 2015 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description:
Library name: Expo_ABC141_1
Column name in raw counts file Expo_1.abc141_kh.sorted_SCJSCESTW.unique.bam

data_processing:
Bowtie2 v. 2.5.2 with the parameter -very-sensitive-local (to enable soft-trimming and maximise the hit rate) was used to align sequencing reads with the reference genome. gDNAx package v1.6.0 was used to assess genomic DNA contamination in RNA-seq data and filter out potential DNA reads (Calvo-Serra & Castelo, 2025). FeatureCounts v2.0.6 was used to count the number of uniquely mapped reads. DESeq2 v1.44.0 was used to reveal genes differentially expressed between exponential and stationary phases, (false discovery rate cutoff = 0.05) (Love et al., 2014). Gene Ontology (GO) term overrepresentation analysis was performed by kegga method of the limma v3.60.6 R package (Phipson et al., 2016).
Assembly: PRJNA1255660
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Acinetobacter baumannii

source_name: bacterial cell

growth_protocol: A. baumannii ABC141 was grown overnight in LB at 37°C under shaking, which corresponds to 15 h of growth and an OD600 between 2.2 and 2.5. This culture was diluted in LB to an OD600 of 0.1 before incubation under shaking at 37°C until reaching an OD600 of 0.5.

extract_protocol:
An ice-cold 5% (v/v) phenol, 95% (v/v) ethanol ultra-pure solution was prepared, and 2/5 volume was added to 28 mL of the exponential or 15 ml of the ON cultures and incubated on ice for 1h. Samples were pelleted by centrifugation at 3220 × g at 4°C for 10 min and cell pellets were subsequently dissolved in 1 mL ice cold TRIzol and transferred into a Phase-Lock-Tube (VWR, #2302830). Four hundred μL of chloroform was added and the solution was shaken without vortexing for 10 s followed by 3 min incubation at RT. Tubes were centrifuged at full speed for 15 min before the aqueous phase was transferred to a new 1.5 mL tube. RNA was precipitated by the addition of 450 μL of isopropanol and incubation for 30 min at RT. After 30 min, the RNA was pelleted by centrifugation at full speed in a microcentrifuge, and the pellet was washed with 350 μL of ethanol (75%), incubated for 10 min and centrifuged for 10 min at full speed in a microcentrifuge. The wash step was repeated three times before discarding the remaining supernatant, air-drying the pellet and resuspending the RNA with 25 μL of RNase-free water, followed by a 5 min incubation at 65°C at 900 rpm agitation. The RNA extractions were stored at -80°C before assessing their quality using a 1/10 dilution of the extraction using the 4200 TapeStation (Agilent Technologies).
Total RNA was sent to Core Unit Systems Medicine (SysMed) sequencing facility for RNA-seq (University of Würzburg, Germany), where DNase I digestion and rRNA depletion (RiboCop) was performed. Library for the sequencing was prepared using the NEBNext Multiplex Small RNA Library Prep kit. Sequencing was performed on the Illumina NextSeq-500 Mid Output KT v2.5 (150 cycles).

value: bacterial cell


title: Visium_JKPF3_3

description:
Library name: Visium_JKPF3_3
10x Genomics


title: Visium_JKPF3_1

description:
Library name: Visium_JKPF3_1
10x Genomics


title: Visium_JKPF2_1

description:
Library name: Visium_JKPF2_1
10x Genomics


title: EHEC Serotonin 1

description: Library name: S1


title: SEM BCL6

city: Oxford

first: Alastair

last: Smith

state: England

address: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: SEM_BCL6

library_source: genomic

data_processing:
FASTQ fils were quality checked using FastQC version v0.12.1. Adapter sequences were removed and low quality reads were trimmed using trim_galore version 0.6.10 using the following parameters: --2colour 20. Reads were aligned to the reference genome hg38 using bowtie2 version 2.5.1 with with default parameters. and blacklisted regions (https://github.com/Boyle-Lab/Blacklist) were removed using bedtools. BigWig files were generated using deepTools bamCoverage 3.5.5 with the following parameters: --extendReads -bs 1 --normalizeUsing RPKM  --minMappingQuality 10 --maxFragmentLength 2000 --minFragmentLength 1 --samFlagInclude 3 --samFlagExclude 4. Peak calling was performed using lanceotron v1.2.6 with the following parameters: -c 0.5
Assembly: hg38
Supplementary files format and content: Bigwigs

molecule: genomic DNA

source_name: SEM

extract_protocol:
ChIP-seq
Briefly, 10^7 cells were single-fixed (1% formaldehyde for 10 min) for histone modifications or double-fixed (2 mM disuccinimidyl glutarate for 30 min, then 1% formaldehyde for 30 min) for transcription/chromatin factors, then lysed with 120 µl SDS lysis buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS) and sonicated using a Covaris ME220 (Woburn, MA) to generate 200–300 bp fragments. Insoluble material was pelleted, then the supernatant was diluted 10× and pre-cleared for 30 min at 4 °C with rotation using 5 µl protein A- and G-coupled dynabeads (ThermoFisher Scientific). An input sample was taken, then 2 µg antibody was added to the sample before incubation overnight at 4 °C with rotation. The antibodies used are detailed in Supplementary Table 3. Protein A- and G-coupled dynabeads were used to isolate antibody-chromatin complexes, after which the beads were washed three times with RIPA buffer (50 mM HEPES-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP40 and 0.7% sodium deoxycholate) and once with Tris-EDTA. Samples were eluted with SDS lysis buffer, RNase A- and proteinase K-treated and crosslinks were reversed at 65 °C overnight. DNA was purified by PCR purification column (Qiagen) and analyzed by qPCR, relative to input. PCR primer sequences are given in Supplementary Table 4. For ChIP-seq, libraries were generated using the Ultra II library preparation kit (NEB), then sequenced by paired-end sequencing with a 75-cycle high-output Nextseq 500 kit (Illumina).

tag: disease state

value: acute lymphoblastic leukemia (ALL)


title: Visium_JKPF1_1

description:
Library name: Visium_JKPF1_1
10x Genomics


title: P14_ferret_cortex, scRNAseq

description: Library name: P14_ferret_cortex

value: WT, P14


title: Male CTL_3

city: Jackson

first: Harry

last: Pantazopoulos

state: MS

address: 2500 North State Street

department: Psychiatry and Human Behavior

institute: University of Mississippi Medical Center

description: Library name: 1158_10169_Control

data_processing:
Sequence reads were aligned to MacaM genome with the basespace application RNA-Seq Alignment (Version: 2.0.1 [workflow version 3.19.1.12+master]) that conducted both splice aware genome alignment with STAR alignment (version 2.6.1a) and transcriptome quantification with Salmon (version 0.11.2).
Assembly: MacaM genome with the basespace application RNA-Seq Alignment (Version: 2.0.1 [workflow version 3.19.1.12+master])
Supplementary files format and content: Processed data (raw count matrix) can be found in the CSV file 'Control_vs_Ethanol.genes.counts.csv'

organism: Macaca mulatta

source_name: hippocampus

extract_protocol:
Total RNA was extracted from tissue samples using the Invitrogen PureLink RNA Mini kit with Trizol (Life Technologies; Carlsbad, CA, USA) according to the manufacture’s protocol.
Library preparation employed the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (San Diego, CA, USA), per manufacturer’s protocol using up to 1 ug of RNA per sample

value: hippocampus

tag: Sex

value: male


title: Male CTL_1

description: Library name: 1158_10167_Control


title: Male CTL_5

description: Library name: 1158_10171_Control


title: Male CTL_2

description: Library name: 1158_10168_Control


title: Male ALCOHOL_6

description: Library name: 1158_10066_Ethanol


title: Male ALCOHOL_7

description: Library name: 1158_10067_Ethanol


title: Male ALCOHOL_3

description: Library name: 1158_10062_Ethanol


title: Male CTL_4

description: Library name: 1158_10170_Control


title: Male ALCOHOL_2

description: Library name: 1158_10061_Ethanol


title: Male ALCOHOL_5

description: Library name: 1158_10065_Ethanol


title: SEM AFF1C

description: Library name: SEM_AFF1C

value: SEM


title: Male ALCOHOL_1

description: Library name: 1158_10060_Ethanol


title: Visium_JKPF2_2

description:
Library name: Visium_JKPF2_2
10x Genomics


title: Visium_JKPF1_2

description:
Library name: Visium_JKPF1_2
10x Genomics


title: Visium_JKPF3_5

description:
Library name: Visium_JKPF3_5
10x Genomics


title: Male ALCOHOL_4

description: Library name: 1158_10063_Ethanol


title: U-CLL patient number 52

type: genomic

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

country: Spain

institute: IDIBAPS

hyb_protocol: According to manufacturer instructions

scan_protocol: According to manufacturer instructions

data_processing:
CpGs with a pvalue ≤0.01 in more than 10% of the samples were removed
SNP associated CpGs were removed
Sex associated CpGs were removed
Individual-specific CpGs were removed
The data was normalized using the SWAN algorithm after the filtering steps
Charalampopoulou2025_UCLL_betavalues.csv: comma-separated file containing methylation beta values of each sample. The beta values range from 0 to 1, where 0 represents unmethylated and 1 methylated CpGs.

label: Cy3 and Cy5

source_name: Peripheral Blood

label_protocol: According to manufacturer instructions

extract_protocol: According to manufacturer instructions

value: Peripheral Blood

value: Peripheral Blood Mononuclear Cells

value: chronic lymphocytic leukemia (CLL)


title: U-CLL patient number 49


title: U-CLL patient number 50


title: U-CLL patient number 51


title: U-CLL patient number 48


title: U-CLL patient number 44


title: U-CLL patient number 47


title: U-CLL patient number 43


title: U-CLL patient number 41


title: U-CLL patient number 40


title: U-CLL patient number 37


title: U-CLL patient number 45


title: U-CLL patient number 46


title: U-CLL patient number 42


title: U-CLL patient number 35


title: U-CLL patient number 34


title: U-CLL patient number 39


title: U-CLL patient number 32


title: U-CLL patient number 38


title: U-CLL patient number 31


title: U-CLL patient number 27


title: Liver DNA - 7101

city: Wilrijk

first: Evelien

last: Van Dijck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

hyb_protocol: bisulfite converted DNA was amplified and hybridized to human Infinium MethylationEPIC arrays (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan and standard recommended Illumina scanner setting

data_processing: ChAMP package R version 4.4.1

source_name: MASH F0-Fno MASLD

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted from 22 liver biopsies using the DNeasy Blood & Tissue Kit (Qiagen, Hilden Germany) according to the manufacturer’s protocol

value: liver

tag: age

tag: gender

tag: bmi

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: masld

tag: bpsyst

tag: bpdiast

tag: alcohol

tag: smoke

tag: bdmed


title: U-CLL patient number 25

tag: tissue

tag: cell type

tag: genotype


title: Liver DNA - 7140

source_name: MASL

tag: age

tag: gender

tag: bmi

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: krea

tag: asat


title: U-CLL patient number 36

tag: tissue

tag: cell type

tag: genotype


title: Liver DNA - 6566

tag: age

tag: gender

tag: bmi

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: masld

tag: bpsyst

tag: bpdiast

tag: alcohol

tag: smoke

tag: bdmed


title: Liver DNA - 7703

tag: tissue

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: krea

tag: asat


title: Liver DNA - 6850

source_name: no MASLD

tag: age

tag: gender

tag: bmi

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: masld

tag: bpsyst

tag: bpdiast

tag: alcohol


title: Liver DNA - 7416

source_name: MASH F2-F4

tag: tissue

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: smoke

tag: bdmed


title: Liver DNA - 7417

tag: age

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: masld

tag: bpsyst


title: U-CLL patient number 23

tag: tissue

tag: cell type

tag: genotype


title: Liver DNA - 6999

tag: age

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: bpdiast

tag: alcohol

tag: smoke

tag: bdmed


title: Liver DNA - 6545

tag: tissue

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: masld

tag: bpsyst


title: Liver DNA - 7425

tag: age

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: bpdiast

tag: alcohol


title: U-CLL patient number 24

tag: tissue

tag: cell type

tag: genotype


title: Liver DNA - 7965

tag: age

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: masld

tag: bpsyst

tag: smoke

tag: bdmed


title: Liver DNA - 5892

tag: tissue

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: bpdiast

tag: alcohol


title: Liver DNA - 7322

tag: age

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: masld

tag: bpsyst


title: Liver DNA - 7340

tag: tissue

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: smoke

tag: bdmed


title: Liver DNA - 6811

tag: age

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: bpdiast

tag: alcohol


title: U-CLL patient number 17

tag: tissue

tag: cell type

tag: genotype


title: Liver DNA - 6847

tag: age

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: masld

tag: bpsyst

tag: smoke

tag: bdmed


title: Liver DNA - 6493

tag: tissue

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: bpdiast

tag: alcohol


title: Liver DNA - 7361

tag: age

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: masld

tag: bpsyst


title: U-CLL patient number 16

tag: tissue

tag: cell type

tag: genotype


title: Liver DNA - 8125

tag: age

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: bpdiast

tag: alcohol

tag: smoke

tag: bdmed


title: Liver DNA - 7323

tag: tissue

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: masld

tag: bpsyst


title: U-CLL patient number 14

tag: cell type

tag: genotype


title: U-CLL patient number 15


title: U-CLL patient number 33


title: U-CLL patient number 29


title: U-CLL patient number 30


title: U-CLL patient number 28


title: Liver DNA - 7487

tag: age

tag: gender

tag: bmi

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: ballooning

tag: inflammation

tag: fibrosis

tag: bpdiast

tag: alcohol

tag: smoke

tag: bdmed


title: U-CLL patient number 26

tag: tissue

tag: cell type

tag: genotype


title: U-CLL patient number 6


title: U-CLL patient number 4


title: U-CLL patient number 3


title: U-CLL patient number 2


title: U-CLL patient number 1


title: U-CLL patient number 22


title: U-CLL patient number 20


title: iPSC-derived neural precursor cell, MCT8-deficient, rep 3

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

description:
Library name: Sample 13
S13

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of 1 mismatch in the indexing read.
The FASTQ files were aligned to gencode hg38 transcriptome  with STAR (v.2.7.8a) using the Partek Flow platform.
Aligned reads were quantified to the annotation model (Partek E/M) and normalized to counts per million.
Assembly: Human, hg38
Supplementary files format and content: Partek_hRGCs_MCT8_WT_Gene_counts.txt: Counts table, samples per row, columns by features.

source_name: Monolayer of neural precursor cells

growth_protocol: We followed the protocols of StemCell Technologies for neural induction (SCT 08581)

extract_protocol:
RNA extraction with PureLink Mini Kit from ThermoFischer (12183018A) and DNAse treatment on column (roche, #
Samples of total RNA were sent to the Genomic facility at the University of Chicago for library preparation and sequencing. Libraries were paired-end sequenced with NovaSeq 6000, S4 flow

treatment_protocol: Change media for fresh media supplemented with 1nM T4

value: Monolayer of neural precursor cells

tag: cell line

value: human induced pluripotent stem cells

value: MCT8 deficient

tag: treatment

value: maintenance medium


title: U-CLL patient number 21


title: iPSC-derived neural precursor cell, MCT8-deficient, rep 2

description:
Library name: Sample 12
S12


title: U-CLL patient number 19


title: iPSC-derived neural precursor cell, MCT8-deficient, rep 1

description:
Library name: Sample 11
S11


title: U-CLL patient number 18


title: iPSC-derived neural precursor cell, control, treated with 1nM T4, rep 1

description:
Library name: Sample 6
S6

value: WT

value: maintenance medium + 1nM T4


title: U-CLL patient number 13


title: U-CLL patient number 12


title: iPSC-derived neural precursor cell, control, rep 4

description:
Library name: Sample 4
S4


title: U-CLL patient number 11


title: U-CLL patient number 10


title: U-CLL patient number 9


title: iPSC-derived neural precursor cell, control, rep 2

description:
Library name: Sample 2
S2


title: U-CLL patient number 8


title: U-CLL patient number 7


title: U-CLL patient number 5


title: vec, ATO (1 μg/ml )+DAC (5 μM), 24 h

city: Shanghai

first: Huaxin

address: Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 6

data_processing:
Raw sequence reads were initially processed using fqC (Babraham Institute, Cambridge, UK) for quality control, then adapter sequences and poor-quality reads were removed using Cutadapt. Quality-filtered reads were then mapped to the human genome using the Salmon (version 1.10.0) (Patro et al., 2017) software, and only uniquely mapped reads were kept.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Blood

growth_protocol: THP-1 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 37℃ under 5% CO2.

extract_protocol:
Total RNA was isolated using total RNA Purification Kit (B518651, Sangon Biotech). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 cells were treated with indicated compound for 24 h.

value: Blood

value: Myeloid malignant cell line

value: Empty vector

value: ATO (1 microg/ml )+DAC (5 microM) for 24 h


title: Liver Invariant Natural Killer T cells (iNKT), Diethylnitrosamine (DEN), 38-42 weeks, Hepatocellular carcinoma 2

city: Vari

first: Mihalis

last: Verykokakis

address: Fleming 34

country: Greece

institute: BSRC Alexander Fleming

data_processing:
Base calling was performed using bcl2fastq software.
Fastq files were mapped to mouse genomic build mm10 using a two-step alignment process. In the first round, reads were mapped with hisat2 (Kim et. al)using the default parameters and then, the unmapped reads were mapped with bowtie2 (Ben Langmead & Steven L Salzberg, 2012) using the --local and --very-sensitive parameters.
Assembly: mm10
Supplementary files format and content: RNA-seq analysis was conducted with the Bioconductor package metaseqR2 (https://pubmed.ncbi.nlm.nih.gov/32778872/). Raw reads were estimated through metaseqR2 and were normalized with the DESEQ algorithm. Differential gene expression was conducted with the PANDORA algorithm by combining the algorithms DESeq2, edgeR, limma NBPSeq, and NOISeq analyzed using the DESeq algorithm. Genes exhibiting a meta-p-valueDESeq p-value < 0.05 and a fold change greater than 1.0 or less than −1.0 on the log2 scale (corresponding to a 2-fold change in the natural scale) were considered differentially expressed. The volcano plot was generated using ggplot2. The analyses can be found in scripts metaseqR2.R and volcano.R.

organism: Mus musculus

source_name: Hepatocellular Carcinoma (Liver)

growth_protocol: All mice were maintained at the Biomedical Sciences Research Center (BSRC) Alexander Fleming Animal Facility. Experimental procedures were conducted in accordance with the guidelines established by the Institutional Animal Care and Use Committee of BSRC Alexander Fleming.

extract_protocol:
To isolate hepatic lymphocytes, livers were placed in a 100 μm filter and homogenized with FACS buffer (HBSS, 0.25% BSA, 25 mg/ml DNase I, 0.1% NaN3). Samples were subsequently centrifuged at 1500 rpm for 5 min at 4oC, and pellets were resuspended in 8 ml of Percoll mixture (for 10 ml Percoll mixtures: 0.4 ml 10X PBS, 4 ml Percoll, and 5.6 ml 1X PBS). Samples were centrifuged at 2000 rpm for 20 min at 20oC without braking. Red blood cells were lysed with H2O, and lymphocytes were resuspended in 1 ml FACS Buffer after centrifugation at 1500 rpm for 5 min at 4oC. Lymphocytes were incubated with PBS57-loaded CD1d tetramers  and anti-TCRb for 30 min on ice and in the dark  in the presence of anti-mouse CD16/32 Fc block and propidium iodide. iNKT cells were sorted as CD1dLoaded PBS57 tetramer+TCRb+ cells in a FACSAria III. RNA was extracted using RNAeasy micro kit.
QuantSeq-LEXOGEN (3’ mRNA-seq Library Prep Kit for Ion Torrent)

treatment_protocol: one i.p. injection wth 25 mg/kg Diethylnitrosamine (DEN) in 15-day old male C57BL/6 WT mice. Mice were euthanzed between 38-42 weeks old

value: Hepatocellular Carcinoma (Liver)

value: Invariant Natural Killer T cells (iNKT)

value: Diethylnitrosamine (DEN)


title: Liver Invariant Natural Killer T cells (iNKT), Diethylnitrosamine (DEN), 38-42 weeks, Hepatocellular carcinoma 1


title: Liver Invariant Natural Killer T cells (iNKT), Healthy 2

source_name: Healthy Liver

value: Healthy Liver

value: PBS


title: Liver Invariant Natural Killer T cells (iNKT), Healthy 1


title: Liver Invariant Natural Killer T cells (iNKT), Diethylnitrosamine (DEN), 38-42 weeks, Hepatocellular carcinoma 3


title: iPSC-derived neural precursor cell, MCT8-deficient, rep 5

description:
Library name: Sample 15
S15


title: p53-R282W + IRF7 KD (#2), DMSO, 24 h

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 3

value: TP53-R282W; IRF7 knockdown (clone #2)

value: DMSO for 24 h


title: CHD-040-21

city: Perugia

first: Roberta

last: La Starza

address: Piazzale Menghini 9

department: Department of Medicine and Surgery

country: Italy

institute: University of Perugia

hyb_protocol: DNA was restriction digested, ligated, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing: Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 4.2 (ChAS) software with filters set at 50 Kb for Copy Number Alterations (CNAs) and 10 Mb for copy neutral Loss Of Heterozygosity (cnLOH). Our data refer to NetAffx Build 33.2 (hg19) database

label: Biotin

source_name: Unsorted Peripheral Blood Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow/peripheral blood cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis

tag: subtype

value: immature

tag: stage of disease

value: diagnosis


title: iPSC-derived neural precursor cell, control, treated with 1nM T4, rep 3

description:
Library name: Sample 8
S8

value: Monolayer of neural precursor cells

value: human induced pluripotent stem cells


title: iPSC-derived neural precursor cell, control, treated with 1nM T4, rep 5

description:
Library name: Sample 10
S10

value: WT


title: iPSC-derived neural precursor cell, control, treated with 1nM T4, rep 2

description:
Library name: Sample 7
S7

value: maintenance medium + 1nM T4


title: iPSC-derived neural precursor cell, MCT8-deficient, rep 4

description:
Library name: Sample 14
S14

value: MCT8 deficient

value: maintenance medium


title: iPSC-derived neural precursor cell, control, treated with 1nM T4, rep 4

description:
Library name: Sample 9
S9


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 1 day in suspension, biol rep1

city: Galveston

first: Nehal

last: Dwivedi

state: Texas

address: 301 University Blvd

institute: The University of Texas Medical Branch Galveston

description: Library name: TpmApop_1d_1

data_processing:
Differential expression analysis was performed using Novogene’s Novomagic platform, employing the DESeq2 pipeline with adjusted p-value (padj) < 0.05 and |log₂FoldChange| > 1 as significance thresholds.
Assembly: hg38
Supplementary files format and content: counts, FPKM for each sample

growth_protocol: MDA-EV and MDA-Tpm2.1 cells were maintained in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 1% penicillin–streptomycin, and 2 µg/mL puromycin at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen®, Germantown, MD, USA; Cat. #74104) according to the manufacturer’s protocol
Library construction was done by Novogene Co. Ltd. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: MDA-EV and MDA-Tpm2.1 cells were cultured under attached conditions (tissue culture plates) for 6 hours, and under suspension conditions (ultra-low attachment plates) for 5 hours, 1 day, 2 days, and 4 days. For MDA-Tpm2.1 cells culuted under suspension conditions, the apoptotic and non-apoptotic populations were separated at each time point using the Annexin V MicroBead Kit (Miltenyi Biotec), following the manufacturer’s protocol, which isolates cells based on Annexin V binding.

value: epithelial cell

value: Tpm2.1 overexpression

value: Tpm2.1 overexpression, Apoptosis separation, in suspension

tag: treatment time

value: 1 day


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 2 dasy in suspension, biol rep1

description: Library name: TpmApop_2d_1

value: 2 days


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 1 day in suspension, biol rep2

description: Library name: TpmApop_1d_2


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 5 hours in suspension, biol rep2

description: Library name: TpmApop_5h_2

value: 5 hours


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 4 dasy in suspension, biol rep1

description: Library name: TpmApop_4d_1

value: 4 days


title: iPSC-derived neural precursor cell, control, rep 3

description:
Library name: Sample 3
S3


title: iPSC-derived neural precursor cell, control, rep 5

description:
Library name: Sample 5
S5


title: vec, DMSO, 24 h

description: Library name: Sample 5

value: Blood

value: Myeloid malignant cell line

value: Empty vector


title: CHD-096-21

source_name: Unsorted Bone Marrow Cells

value: immature

value: remission


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 4 dasy in suspension, biol rep2

description: Library name: TpmApop_4d_2


title: iPSC-derived neural precursor cell, control, rep 1

description:
Library name: Sample 1
S1

value: Monolayer of neural precursor cells

value: human induced pluripotent stem cells


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 4 dasy in suspension, biol rep2

description: Library name: Tpm_NoAp_4d_2

value: Tpm2.1 overexpression, Non-apoptosis separation, in suspension


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 4 dasy in suspension, biol rep1

description: Library name: Tpm_NoAp_4d_1


title: p53-R282W + IRF7 KD (#1), DMSO, 24 h

description: Library name: Sample 1

value: TP53-R282W; IRF7 knockdown (clone #1)

value: DMSO for 24 h


title: p53-R282W + IRF7 KD (#1), ATO (1 μg/ml )+DAC (5 μM), 24 h

description: Library name: Sample 2

value: ATO (1 microg/ml )+DAC (5 microM) for 24 h


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 2 dasy in suspension, biol rep2

description: Library name: Tpm_NoAp_2d_2

value: epithelial cell

value: Tpm2.1 overexpression


title: p53-R282W + IRF7 KD (#2), ATO (1 μg/ml )+DAC (5 μM), 24 h

description: Library name: Sample 4

value: TP53-R282W; IRF7 knockdown (clone #2)


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 2 dasy in suspension, biol rep1

description: Library name: Tpm_NoAp_2d_1

value: 2 days


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 2 dasy in suspension, biol rep2

description: Library name: TpmApop_2d_2

value: Tpm2.1 overexpression, Apoptosis separation, in suspension


title: Skin, WT, Non-lesional, NoTx, Sample 9

city: Ann Arbor

first: J. Michelle

last: Kahlenberg

state: MI

address: NCRC 20-1841, 2800 Plymouth Rd

department: Department of Internal Medicine – Division of Rheumatology and Department of Dermatology

institute: University of Michigan

description: Library name: 11595_sample_9

data_processing:
The reads were trimmed using Cutadapt v4.8 (Martin, 2011).
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010).
Fastq Screen v0.15.3 was used to screen for various types of contamination (Wingett and Andrews, 2018).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Multiqc v1.20 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Assembly: mouse reference genome GRCm38
Supplementary files format and content: Tab-delimited text file includes the raw counts for each sample

source_name: Skin

extract_protocol:
Skin samples were isolated from lesional skin in 12-month-old Ifnk TG mice and from non-lesional skin in both Ifnk TG mice and WT mice. For isolation of RNA from skin tissue, frozen samples were crushed with mortar and pestle prior to homogenization using a handhold tissue homogenizer (Grainger). RNA isolation of skin was done using  For lymph node RNA isolation, inguinal skin-draining lymph nodes were put through a 70µm cell strainer. Homogenates were then lysed in RLT lysis buffer and RNA was purified using RNeasy Plus Mini Kit (Qiagen). Total RNA quantity and purity were determined based on A260nm/A280 nm using a BIOTEK EPOCH plate reader.
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.

treatment_protocol: Prior to irradiation, all mice were weighed, shaved on the back, and placed in a restrainer with facial protection. The mice were irradiated with 250 mJ/cm2 UVB three days per week for two weeks using an UV-2 ultraviolet irradiation system (Tyler Research) which uses cascade-phosphor ultraviolet generators that emit 310 nm of UVB radiation. Irradiated skin was outlined with a black sharpie for identification of irradiated areas during the two-week observation period. After this observation period, skin-draining inguinal lymph nodes were harvested and processed as outlined below.

value: Skin

value: WT Non-lesional

value: NoTx

tag: batch


title: Skin, WT, Non-lesional, NoTx, Sample 10

description: Library name: 11595_sample_10


title: Skin, Ifnk TG, Lesional, NoTx, Sample 6

description: Library name: 11595_sample_6

value: Ifnk TG Lesional


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 5 hours in suspension, biol rep1

description: Library name: TpmNoAp_5h_1

value: 5 hours


title: MDA-MB-231 cells with Tpm2.1 overexpression, Apoptosis fraction, 5 hours in suspension, biol rep1

description: Library name: TpmApop_5h_1


title: Skin, Ifnk TG, Non-lesional, NoTx, Sample 3

description: Library name: 11595_sample_3

value: Ifnk TG Non-lesional


title: MDA-MB-231 cells, control, 5 hours in suspension, biol rep2

description: Library name: EV_5h_2

value: Control

value: Empty vector, in suspension


title: Inguinal lymph node, Ifnk TG, UVTx, Sample 10

description: Library name: 11567_sample_10

source_name: Inguinal lymph node

value: Inguinal lymph node

value: Ifnk TG

value: UVTx


title: MDA-MB-231 cells, control, 5 hours in suspension, biol rep1

description: Library name: EV_5h_1


title: MDA-MB-231 cells, control, adherent, biol rep1

description: Library name: MDA_EV_3

value: Empty vector


title: Skin, Ifnk TG, Non-lesional, NoTx, Sample 2

description: Library name: 11595_sample_2


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 1 day in suspension, biol rep2

description: Library name: Tpm_NoAp_1d_2

value: epithelial cell

value: Tpm2.1 overexpression, Non-apoptosis separation, in suspension

value: 1 day


title: Skin, WT, Non-lesional, NoTx, Sample 8

description: Library name: 11595_sample_8


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 5 hours in suspension, biol rep2

description: Library name: TpmNoAp_5h_2

value: Tpm2.1 overexpression


title: MDA-MB-231 cells with Tpm2.1 overexpression, Non-apoptosis fraction, 1 day in suspension, biol rep1

description: Library name: Tpm_NoAp_1d_1


title: HPNE cells, KRAS(Q61L), Biological Rep 3

city: Charleston

first: Guy

middle: Aaron

last: Hobbs

state: SC

address: 86 Johnathan Lucas, HCC 702

institute: Medical University of South Carolina

description:
Library name: Sample 12
Column name in raw_counts.csv: Q61L_3

data_processing:
Paired-end sequencing was performed at the Vanderbilt VANTAGE core laboratory (Vanderbilt University) to a depth of 25 million reads per library using an Illumina NovaSeq 6000 (RRID:SCR_020150). Sequencing data were analyzed using Partek Flow software. Reads were aligned to the human genome assembly hg38 using spliced transcript alignment to a reference (STAR RRID:SCR_004463) and quantified using an annotation model (Partek E/M RRID:SCR_011860) using hg38.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes Trimmed Mean of M component counts for each sample

source_name: Pancreas

growth_protocol: Stable cell lines were maintained in HPNE stable cell lines were maintained in high-glucose DMEM (Corning, #10-013-CV) supplemented with 10% tetracycline negative fetal bovine serum (Gemini, #100-800-500) in a humidified chamber with 5% CO2 at 37°C without antibiotic treatment. HPNE KRAS mutant cells were generated by stably expressing our HYGRO-pCW5.7 constructs encoding EV, KRASWT, KRASG12D/R, or KRASQ61L.

extract_protocol:
RNA was extracted using the NEBNext Poly(A) mRNA Magnetic Isolation Module.1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs #E7760L).

treatment_protocol: Cells were treated with doxycycline for 48 hours before analysis.

value: Pancreas

value: Human Pancreatic Nestin-Expressing

value: pancreatic ductal epithelial cell

value: KRAS Q61L

value: 2.5 µg/mL doxycycline for 48 hours


title: MDA-MB-231 cells, control, 4 days in suspension, biol rep2

description: Library name: EV_4d_2

value: 4 days


title: Skin, Ifnk TG, Lesional, NoTx, Sample 7

description: Library name: 11595_sample_7

value: Skin

value: Ifnk TG Lesional

value: NoTx


title: Skin, Ifnk TG, Lesional, NoTx, Sample 5

description: Library name: 11595_sample_5


title: Skin, Ifnk TG, Lesional, NoTx, Sample 4

description: Library name: 11595_sample_4


title: Inguinal lymph node, WT, NoTx, Sample 3

description: Library name: 11567_sample_3

value: Inguinal lymph node

value: WT


title: MDA-MB-231 cells, control, 2 days in suspension, biol rep1

description: Library name: EV_2d_1

value: Control

value: Empty vector, in suspension

value: 2 days


title: MDA-MB-231 cells, control, 2 days in suspension, biol rep2

description: Library name: EV_2d_2

value: epithelial cell


title: Inguinal lymph node, WT, NoTx, Sample 2

description: Library name: 11567_sample_2


title: MDA-MB-231 cells, control, 1 day in suspension, biol rep2

description: Library name: EV_1d_2

value: 1 day


title: Liver DNA - 7993

value: liver

tag: age

tag: gender

tag: bmi

tag: ffm

tag: fm

tag: fmperc

tag: cttot

tag: ctvisc

tag: ctsubc

tag: chol

tag: hdl

tag: tg

tag: ldl

tag: homa

tag: krea

tag: asat

tag: alat

tag: alkfosf

tag: ggt

tag: steatosis

tag: masld

tag: bpsyst


title: MDA-MB-231 cells, control, 1 day in suspension, biol rep1

description: Library name: EV_1d_1

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: treatment time


title: Inguinal lymph node, WT, UVTx, Sample 9

description: Library name: 11567_sample_9

tag: tissue

value: UVTx

tag: batch


title: HPNE cells, KRAS(G12R), Biological Rep 2

description:
Library name: Sample 8
Column name in raw_counts.csv: G12R_2

value: Pancreas

value: Human Pancreatic Nestin-Expressing

value: KRAS G12R

value: 0.5 µg/mL doxycycline for 48 hours


title: Inguinal lymph node, Ifnk TG, UVTx, Sample 11

description: Library name: 11567_sample_11

value: Ifnk TG


title: MDA-MB-231 cells, control, 4 days in suspension, , biol rep1

description: Library name: EV_4d_1

value: 4 days


title: Inguinal lymph node, Ifnk TG, UVTx, Sample 12

description: Library name: 11567_sample_12


title: MDA-MB-231 cells with Tpm2.1 overexpression, adherent,  biol rep2

description: Library name: MDA_Tpm2_4

value: Tpm2.1 overexpression


title: Inguinal lymph node, WT, NoTx, Sample 1

description: Library name: 11567_sample_1

value: NoTx


title: MDA-MB-231 cells with Tpm2.1 overexpression, adherent,  biol rep1

description: Library name: MDA_Tpm2_3


title: Inguinal lymph node, Ifnk TG, NoTx, Sample 6

description: Library name: 11567_sample_6

value: Inguinal lymph node


title: HPNE cells, KRAS(G12D), Biological Rep 2

description:
Library name: Sample 5
Column name in raw_counts.csv: G12D_2

value: pancreatic ductal epithelial cell

value: KRAS G12D

value: 0.25 µg/mL doxycycline for 48 hours


title: Inguinal lymph node, WT, UVTx, Sample 7

description: Library name: 11567_sample_7

value: WT


title: MDA-MB-231 cells, control, adherent, biol rep2

description: Library name: MDA_EV_4

value: epithelial cell

value: Control

value: Empty vector


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_12

first: Haley

middle: Elizabeth

last: Gause

institute: UCSF

description: Library name: gnoto_CaEfM2

data_processing:
trimming/filtering: fastp (ver: 0.20.1), parameters: "--adapter_sequence='AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' -x"
alignment: star (ver: 2.7.9a), parameters: "--outSAMmultNmax 10,  --alignIntronMax 4000 --alignIntronMin 4"
filter out reads less than 30bp in length:  samtools (ver:1.14), parameters: "view --expr 'length(seq)>30'  -O {outputfolder} -o {outputfilename} {inputfilename}"
extract gene counts: subread (ver: 2.0.1)
Assembly: CGD Candida albicans Assembly 22 (C_albicans_SC5314_version_A22-s07-m01-r105_chromosomes.fasta)
Assembly: Enterococcus_faecalis_og1rf.ASM17257v2.dna.chromosome.Chromosome.fa
Supplementary files format and content: CaSTAR_mRNA_counts_above30bp.txt, , EfSTAR_gene_counts_above30bp.txt: counts matrix with raw counts per gene. Columns are sample names, genes are column names
Supplementary files format and content: *_normcounts.csv: normalized count per gene using DESeq2 count normalization
Supplementary files format and content: *.bam: BAM files of alignment of reads to genome generated by STAR, then filtered to contain only reads that were greater than 30bp in length. These BAM files were used to generate the count files

organism:
Enterococcus faecalis
Candida albicans
Mus musculus

source_name: cecum contents

growth_protocol: gnotobiotic mice were gavaged with 100µL cells in PBS. Cecum was harvested 4 days post-gavage and contents were harvested into RNA-later stabilization solution

extract_protocol:
RNA extracted following the protocol found at: dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1
rRNA depletion using siTOOLS riboPOOL probes: filamentous fungi, pan-bacteria, and Mus musculus (probes used when species is present). Followed manufacturer protocol for one-step depletion followed by NEB Monarch RNA Clean Up 10ug kit (NEB #T2030) per provided protocol. 5 ng of rRNA depleted RNA was used to prepare libraries using CORALL Total RNA-seq kit according to provided protocols.
RNA extracted following the protocol found at: dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1

value: cecum contents

tag: strain 1

tag: strain 2

tag: genotype 1

tag: genotype 2

tag: genotype 3

value: BALB/c

tag: sex 3

value: male


title: HPNE cells, KRAS(G12D), Biological Rep 1

description:
Library name: Sample 4
Column name in raw_counts.csv: G12D_1

value: Pancreas

value: Human Pancreatic Nestin-Expressing


title: Inguinal lymph node, Ifnk TG, NoTx, Sample 5

description: Library name: 11567_sample_5

value: Ifnk TG


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_9

description: Library name: gnoto_CaEfF1

value: female


title: HPNE cells, KRAS(Q61L), Biological Rep 2

description:
Library name: Sample 11
Column name in raw_counts.csv: Q61L_2

value: KRAS Q61L

value: 2.5 µg/mL doxycycline for 48 hours


title: Inguinal lymph node, Ifnk TG, NoTx, Sample 4

description: Library name: 11567_sample_4

value: Inguinal lymph node

value: NoTx


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_6

description: Library name: 23F3_gnoto_Candida-albicans_Enterococcus-faecalis

growth_protocol: gnotobiotic mice were gavaged with 100µL cells in PBS. Cecum was harvested 10 days post-gavage and contents were harvested into RNA-later stabilization solution


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_5

description: Library name: 23F2_gnoto_Candida-albicans_Enterococcus-faecalis


title: HPNE cells, KRAS(G12D), Biological Rep 3

description:
Library name: Sample 6
Column name in raw_counts.csv: G12D_3

value: pancreatic ductal epithelial cell

value: KRAS G12D


title: HPNE cells, EV, Biological Rep 1

description:
Library name: Sample 1
Column name in raw_counts.csv: EV_1

value: KRAS WT


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_3

description: Library name: 23M4_gnoto_Candida-albicans_Enterococcus-faecalis

value: WT


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_10

description: Library name: gnoto_CaEfF3


title: CRLM2_Colon_CD45+

city: Rozzano, Milan

first: Paolo

last: Marzano

address: Via Alessandro Manzoni 56

institute: Humanitas Research Hospital

description:
Library name: CRLM2_Colon_CD45+
10x Genomics

data_processing:
Fastq files were processed with Cellranger v7.1.0 (10X Genomics), using default parameters. The scRNA-seq reads were aligned to the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference. Only mapped reads with valid barcodes and unique molecular identifiers (UMIs) were retained to compute a gene expression matrix containing the number of UMI for every cell and gene.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: Matrix files in h5 format

molecule: cytoplasmic RNA

source_name: Peritumoral Colon

extract_protocol:
The peritumoral colon and liver tissue samples were surgically sampled from tissue-area adjacent to the tumor mass. These were then chopped into small fragments, digested in HBSS+/+ containing 2 mg/ml of Collagenase Type I solution (Gibco), 2% FBS (Sigma Aldrich), 50 µg/ml DNAse I (Sigma Aldrich) and 10mM HEPES (Sigma-Aldrich), and subsequently incubated for 35 min at 37°C in the same solution. The resulting single-cell suspension was filtered through a 100 µm cell strainer and erythrocytes were lysed with BD Lysing Buffer. Cells were pelleted, counted, and frozen according to the slow freezing procedure in standard cryo-vials (1 ml cell suspension in the cryopreservation medium) and stored at -80 until use. Next, the cells were thawed, washed in PBS, stained with Live/dead Aqua Fluorescent Reactive Dye (Thermo Fisher Scientific) and mouse anti-human CD45 antibody 2D1 (BD Biosciences) at 4°C for 20 minutes and sorted by FACS Melody cell sorter (BD Biosciences). Freshly PBMCs were isolated through Lympholyte®-H Cell Separation density gradient solution (Cedarlane Laboratories) according to the manufacturer’s instructions and frozen in Fetal Bovine Serum (FBS, Sigma Aldrich) supplemented with 10% of the cryoprotective dimethyl sulfoxide (DMSO, PanReac AppliChem).
Libraries for scRNA-seq were generated using a microfluidic-based approach on the Chromium Single-Cell Platform using the Chromium Single-Cell 5′ Library and Gel Bead Kit (10X Genomics, 1000006), according to the manufacturer’s instructions. In brief, thawed samples were evaluated for viability prior to scRNA-seq analysis, and all were ≥95% viable. Single cells were individually loaded onto a Chromium single-cell controller (10X Genomics) to generate single-cell gel beads-in-emulsion (GEMs). Captured cells were then lysed and the released RNA was barcoded through reverse transcription in individual GEMs. The concentration of the scRNA-seq libraries was assessed using an Agilent 4200 TapeStation system. The libraries were sequenced using an Illumina Novaseq6000 sequencer with a paired-end 150-bp (PE150) reading strategy (performed by CapitalBio Technology).

value: Peritumoral Colon

value: CD45+ TILs

tag: run

tag: lane

tag: age

tag: Sex

value: Male


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_4

city: San Francisco

description: Library name: 23F1_gnoto_Candida-albicans_Enterococcus-faecalis

value: cecum contents

value: BALB/c


title: CRLM2_Blood

description:
Library name: CRLM2_Blood
10x Genomics

value: Peripheral Blood

value: PBMCs


title: HPNE cells, KRAS(Q61L), Biological Rep 1

description:
Library name: Sample 10
Column name in raw_counts.csv: Q61L_1

value: Pancreas

tag: cell line

value: Human Pancreatic Nestin-Expressing


title: HPNE cells, KRAS(G12R), Biological Rep 3

description:
Library name: Sample 9
Column name in raw_counts.csv: G12R_3

tag: cell type

value: KRAS G12R

value: 0.5 µg/mL doxycycline for 48 hours


title: CRLM1_Blood

description:
Library name: CRLM1_Blood
10x Genomics

value: Female


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_13

description: Library name: gnoto_CaEfM3

value: male


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_14

description: Library name: gnoto_CaEfM6


title: HPNE cells, KRAS(G12R), Biological Rep 1

description:
Library name: Sample 7
Column name in raw_counts.csv: G12R_1

value: pancreatic ductal epithelial cell

tag: genotype


title: Nudt21-Lysm_LPS_3h-4

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

description: Library name: Sample 16

data_processing:
Raw reads were trimed using fastp
Trimed reads were aligned to the reference genome using bowtie2
PCR duplicates were removed using umi tools
Samtools were used to sort, convert and index alignment files
Deeptools were used to generate bigwig files
Assembly: GRCm38
Supplementary files format and content: bigwig files

source_name: Bone marrow

growth_protocol: L-929 conditioned medium (LCM) was used as a source of macrophage colony-stimulating factor (M-CSF). L-929 cells (ATCC no. CCL-1) were cultured in DMEM containing 10% fetal bovine serum (FBS) and 2% Glutamine until confluence. The conditioned medium was harvested, centrifuged to remove cells, and stored at −80°C until use. BMM culture medium consisted of DMEM supplemented with antibiotics, 10% FBS, and 20% L929 conditioned medium.  For BMM isolation, mice were euthanized, and femurs were collected under aseptic conditions in sterile PBS. Bone marrow was flushed from the femurs using Dulbecco’s phosphate-buffered saline (PBS) without calcium and magnesium and passed through a 70-µm cell strainer to obtain a single-cell suspension. The cells were centrifuged at 1,200 rpm for 5 minutes at room temperature, and the pellet was resuspended in BMM culture medium. Cells were plated in non–tissue culture-treated Petri dishes and incubated at 37°C with 5% CO₂ for 7 days to allow differentiation into macrophages. After differentiation, BMMs were detached by gentle scraping, centrifuged, and resuspended in DMEM. Macrophages were either used immediately for analysis or replated for further experimental treatments.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 17 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina). PAC-seq as described in Routh et al, 2017.

treatment_protocol: 1 ug/ml LPS for 3 hrs.

value: Bone marrow

value: Bone marrow drived macrophage

tag: treatment

value: 1 ug/ml LPS for 3 hrs.


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_7

description: Library name: 23F4_gnoto_Candida-albicans_Enterococcus-faecalis

value: WT

value: female


title: Inguinal lymph node, WT, UVTx, Sample 8

description: Library name: 11567_sample_8

value: Inguinal lymph node

value: UVTx


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_2

description: Library name: 23M3_gnoto_Candida-albicans_Enterococcus-faecalis

value: cecum contents

value: BALB/c


title: Nudt21-Lysm_LPS_3h-2

description: Library name: Sample 14


title: Nudt21-Lysm_Con-4

description: Library name: Sample 12


title: 451LuR 36 h PUFA/Fe3+ 3

city: Leuven

first: Sahar

last: Motamedi

address: Herestraat 49, Nieuwstraat

department: Oncology

institute: KU Leuven

description: Library name: Sample48

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads by CASAVA base recognition (Base Calling).
QC control: error rate (Phred score), GC content distribution, removing reads with adaptor contamination and with MAPQ<10  and with >5nt/100nt mismatches
Assembly: Assembly: mm10 using HISAT2
Supplementary files format and content: The files consists of the FPKM reads for all analyzed genes.

source_name: Melanoma

extract_protocol:
RNA was isolated using the PureLink™ RNA Mini Kit (12183018A, Invitrogen).
standard library, poly-A enrichment

value: Melanoma

value: 451Lu R


title: gnotobiotic_Enterococcus-faecalis_5

description: Library name: 21F2_gnoto_Enterococcus_faecalis

organism:
Enterococcus faecalis
Mus musculus


title: HPNE cells, EV, Biological Rep 3

description:
Library name: Sample 3
Column name in raw_counts.csv: EV_3

value: Pancreas

value: Human Pancreatic Nestin-Expressing

value: KRAS WT

value: 2.5 µg/mL doxycycline for 48 hours


title: Nudt21-Lysm_Con-3

description: Library name: Sample 11


title: HPNE cells, EV, Biological Rep 2

description:
Library name: Sample 2
Column name in raw_counts.csv: EV_2


title: CRLM2_Liver_CD45+

description:
Library name: CRLM2_Liver_CD45+
10x Genomics

source_name: Peritumoral Liver

value: Peritumoral Liver

value: CD45+ TILs

value: Male


title: CRLM3_Colon_CD45+

description:
Library name: CRLM3_Colon_CD45+
10x Genomics

value: Peritumoral Colon

value: Female


title: CRLM1_Liver_CD45+

description:
Library name: CRLM1_Liver_CD45+
10x Genomics


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_8

description: Library name: gnoto_CaEfM5

value: WT

value: male


title: CRLM3_Liver_CD45+

description:
Library name: CRLM3_Liver_CD45+
10x Genomics


title: gnotobiotic_Enterococcus-faecalis_7

description: Library name: 21F4_gnoto_Enterococcus_faecalis

value: female


title: Nudt21-Lysm_LPS_3h-1

description: Library name: Sample 13

value: Bone marrow

value: Bone marrow drived macrophage

value: 1 ug/ml LPS for 3 hrs.


title: 451LuR 36 hCTRL3

description: Library name: Sample45

value: Melanoma


title: gnotobiotic_Enterococcus-faecalis_6

description: Library name: 21F3_gnoto_Enterococcus_faecalis

value: cecum contents

value: BALB/c


title: Nudt21-Lysm_Con-2

description: Library name: Sample 10


title: CRLM1_Colon_CD45+

description:
Library name: CRLM1_Colon_CD45+
10x Genomics


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_11

description: Library name: gnoto_CaEfM1


title: gnotobiotic_Candida-albicans_Enterococcus-faecalis_1

description: Library name: 23M2_gnoto_Candida-albicans_Enterococcus-faecalis


title: Nudt21-Lysm_Con-1

description: Library name: Sample 9


title: gnotobiotic_Enterococcus-faecalis_4

description: Library name: 21M4_gnoto_Enterococcus_faecalis


title: 451LuR 36 h PUFA/Fe3+ 1

description: Library name: Sample46

value: 451Lu R


title: Lysm_LPS_3h-3

description: Library name: Sample 7

value: Lysm-Cre


title: Lysm_Con-1

description: Library name: Sample 1


title: Lysm_LPS_3h-4

description: Library name: Sample 8


title: 451LuR 36 h CTRL2

description: Library name: Sample44


title: Lysm_LPS_3h-2

description: Library name: Sample 6


title: Replica Set S2, Library 2

description:
Library name: Sub2_B
CS01_T4_D50_40

data_processing:
The produced fastq files were analyzed with the Parse Bioscience pipeline suite 1.0.4. The suite performed reads demultiplexing and aligned the reads against a STAR-produced index reference from the Ensembl human whole genome reference GRCh38, as provided by Parse (hg38_v1.0.3), followed by the calculation of read counts per feature per cell.
The spipe pipeline version V1.0.3 from ParseBiosciences was used to process fastq files, ran in mode all per library, and combined using as input the output per library.
Assembly: hg38
Supplementary files format and content: parse_pipeline_samples.xlsx: Excel with 6 sheets, Parse pipeline notes, samples with full metadata and samples table per sequencing library used to recapitulate the analysis.
Supplementary files format and content: cell_metadata.csv: CSV file with metadata per cell.
Supplementary files format and content: all_genes.csv: CSV file with gene list, feature table with ID, name and genome.
Supplementary files format and content: DGE.mtx: Mtx sparse matrix format for raw counts of genes per cell.
Supplementary files format and content: anndata.h5ad: h5ad file, HDF5 format with AnnData object that includes counts, cell metadata and features information

source_name: cerebral organoid

growth_protocol: Cerebral organoids were generated and growth till day 20 following the StemCell echnologies kit (SCT 08570). From that point on, organoids were culture in BrainPhys and the supplements SM1, N2A, NEAA (Gibco), Glutamax (Gibco), insulin (MilliporeSigma), BME (MilliporeSigma), and 2 ng/mL brain-derived neurotrophic growth factor (Tocris). Every 3 days, half of the medium was replaced with a fresh one)

extract_protocol:
Organoids were recollected in a 15 mL polypropylene (Falcon) tube to wash with PBS 3 times. As a dissociation reagent, 1 mL of trypsin 0.5% — EDTA (10×) with 50 μM Y-27632, 40 U/μL RNase inhibitor, and 1 U DNase I was added to the organoids and kept on 37°C in a Vari-Mix Platform Rocker at 30 rpm for 15 minutes. Every 5 minutes, we mechanically disrupted the organoids until it was homogenized into single cells. Afterward, we proceeded to the inactivation of trypsin with 1 mL Advanced DMEM/F12 mix containing Bovine Albumin Fraction V (7.5% solution) 50 μM Y-27632, 40 U/μL RNase inhibitor, and 1U DNase I. We collected and filtered the cells trhough a cell strainer. We then add another 1 mL Advanced DMEM/F12 mix to recover any left cells from the strainer. We took 10 μL of single-cell medium mixed with 10 μL Trypan Blue (0.4%) to count the number of single cells to proceed with their fixation. We carried out the fixation of at least 1 × 105 required single cells, following the protocol described in the Evercode fixation kit (Parse Bioscience).
The preparation for the cell barcoding and the posterior library for sequencing was performed with Evercode WT Mini, Chemistry v2 (Parse Bioscience). The Genomics Core facility of the University of Chicago performed the sequencing using a HiSeq Illumina platform, paired end.

treatment_protocol: From day 7 to day 50, the culture medium was supplemented with 1nM T4

value: cerebral organoid

value: CS03ictr and CS58iMCT8

value: iPSC-derived cerebral organoid

value: Wildtype and MCT8-deficient

value: Replica S2, Library 2


title: Replica Set S1, Library 2

description:
Library name: Sub2_A
CS01_T4_D50_37

value: Replica S1, Library 2


title: gnotobiotic_Enterococcus-faecalis_2

description: Library name: 21M2_gnoto_Enterococcus_faecalis

value: WT


title: Lysm_LPS_3h-1

description: Library name: Sample 5


title: Replica set S1, Library 1

description:
Library name: Sub1_A
CS01_D50_22

value: Replica S1, Library 1


title: Lysm_Con-4

description: Library name: Sample 4


title: Nudt21-Lysm_LPS_3h-3

description: Library name: Sample 15


title: Lysm_Con-3

description: Library name: Sample 3


title: Lysm_Con-2

description: Library name: Sample 2


title: 451LuR 36 h CTRL1

description: Library name: Sample43


title: gnotobiotic_Enterococcus-faecalis_3

description: Library name: 21M3_gnoto_Enterococcus_faecalis

value: male


title: 451Lu 36 h PUFA/Fe3+ 3

description: Library name: Sample42


title: BMDM treated with thrombin-activated platelets 3

city: Würzburg

first: Clement

last: Cochain

address: Josef Schneider Str.2 Haus D16

country: Germany

institute: University Hospital Würzburg

data_processing:
Demultiplexed FASTQ files were generated with bcl-convert v.4.0.3 (Illumina).
To assure high sequence quality, Illumina reads were quality- and adapter-trimmed via Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
Processed reads were subsequently mapped to the mouse genome (GCF_000001635.27/GRCm39) using STAR v2.7.2b with default parameters but including transcript annotations from RefSeq annotation version 109 for GRCm39.
This annotation was also used to generate read counts on exon level summarized for each gene via featureCounts v1.6.4 from the Subread package
Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (parameters: -s 2 -t exon -M -O --fraction).
Assembly: mm10
Supplementary files format and content: csv;raw read counts

source_name: bone marrow derived macrophage

growth_protocol: To obtain bone marrow derived macrophages, total bone marrow cells were obtained from the tibia and femur of C57BL6/J mice and cultured for 7 days (10ml at 2 million cells/ml in 10cm cell culture dishes) in RPMI containing 100 U/ml penicillin and streptomycin, 50µM of β-Mercaptoethanol, 10% fetal calf serum and 15% L929-cell conditioned medium as a source of M-CSF. Medium was refreshed on day 3 and 6 of the culture, and macrophages were detached with Accutase and harvested on Day 7. 400,000 macrophages were plated in wells of a 12-well plate and left to attach overnight in complete medium. Macrophages were then incubated in starvation medium (RPMI supplemented with 0.5%FCS) for 4 hours before initating treatment.

extract_protocol:
RNA extraction was performed with the Nucleo Spin RNA extraction kit (Macherey-Nagel, 740955.50) following the manufacturer’s instructions.
Libraries were prepared using TruSeq Stranded mRNA library prep kits (Illumina) according to the manufacturer's instructions

treatment_protocol: Macrophages were treated for 4 hours with vehicle (PBS), thrombin alone (0.01 U/mL), resting platelets, or thrombin-activated platelets (0.01 U/mL thrombin). Platelets had previously been purified from the blood of C57BL6/J mice.

value: bone marrow derived macrophage

value: Thrombin-activated platelets


title: Col-0-H2O_RNAseq_rep3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file includes normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C for 12 d.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Single-end sequencing libraries were built for RNA-seq (DNBSEQ platform, 50bp), paired-end sequencing libraries were built for RNA-seq (Illumina Novaseq 6000 platform, 150bp).

treatment_protocol: 12d Col-0 seedlings from MS media were transferred to H2O (Col-H2O), liquid MS (Col-MS), or liquid MS with AZD8055 (Col-AZD) for 4d; 12d drmy1 and gtb123 from MS media were transferred to liquid MS (drmy1-MS and gtb123-MS) for 4d.

value: seedlings

value: wild type

value: 12 days


title: cell line MCF7-wt

type: RNA

city: Kyiv

first: Serhii

last: Kropyvko

address: 150, Zabolotnogo str.

department: Department of Functional Genomics

country: Ukraine

institute: Institute of Molecular Biology and Genetics NAS of Ukraine

description: total RNA from cell line MCF7-wt

data_processing: The qPCR was performed with CFX96 (BioRad). Normalization was performed with CFX manager software (BioRad) via deltaCq against control gene amplification signal.

label: FAM, ROX, HEX

source_name: cell line MCF7-wt

label_protocol: 2μg of total RNA was pre-treated with DNase I (Thermo Fisher Scientific, USA), according to the manufacturer's recommendations, to remove residues of genomic DNA. After that, cDNA synthesis was performed in 20μl according to the manufacturer's recommendations using RevertAid H Minus reverse transcriptase (Thermo Fisher Scientific, USA).

growth_protocol: cells were cultivated in DMEM with 10% FBS with antibiotics streptomycin and penicilin at 37C in 5% CO2

extract_protocol: Total RNA was isolated from 5x10^6 cells via guanidinium isothiocyanate method using innuSOLV reagent (Analityk Jena) or RNA Go (BioLabTech) in accordance with the manufacturer's recommendations


title: gnotobiotic_Enterococcus-faecalis_1

description: Library name: 21M1_gnoto_Enterococcus_faecalis

value: cecum contents

value: BALB/c


title: 451LuR 36 h PUFA/Fe3+ 2

description: Library name: Sample47

value: Melanoma

value: 451Lu R


title: 451Lu 36 h PUFA/Fe3+ 2

description: Library name: Sample41


title: 451Lu 36 h CTRL1

description: Library name: Sample37


title: Col-0-H2O_RNAseq_rep2


title: cell line MCF7+TKS4L

description: total RNA from cell line MCF7+TKS4L

source_name: cell line MCF7+TKS4L


title: cell line MCF7+TKS4b

description: total RNA from cell line MCF7+TKS4b

source_name: cell line MCF7+TKS4b


title: S.pombe cells, Rapalink-1 treated (100nM) - duplicate 2

city: London

first: Charalampos

last: Rallis

address: Mile End Road

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

description:
R2
gene_fkpm.xls
RvsM_deg_all

data_processing:
Raw data (raw reads) in fastq formats was processed using in-house perl scripts (Novogene, Cambridge) to obtain clean data by removing reads containing adapter, ploy-N and low quality reads from raw data.
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.
Mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FKPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential gene expression analysis of two conditions/groups (two biological replicates per condition) was performed using DESeq2R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expressiondatausing a model based on the negative binomial distribution. The resultingP-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05found by DESeq2 were assigned as differentially expressed.
Assembly: Index of the reference genome was built using Hisat2 v2.0.5
Supplementary files format and content: FKPM counts for genes under untreated and treated conditions (for Rapamycin and Rapalink-1)
Supplementary files format and content: differentially expressed gene lists for untreated, Rapamycin and Rapalink-1 treated samples in three combinations (untreated vs Rapamycin, untreated vs Rapalink-1, Rapamycin vs Rapalink-1)

organism: Schizosaccharomyces pombe

source_name: yeast/fungi

growth_protocol: Fission yeast wildtype (972-) cells were grown in complete YES medium supplemented with 3% glucose. Cultures were incubated at 32°C at 132 RPM for the duration of the experiment.

extract_protocol:
Yeast cells were harvested after 5 hours treatment with Rapamycin/Rapalink-1 (and untreated control), washed with DEPC water and pelleted. 750uL of TES and subsequently acidic phenol-chloroform was added, mixed and incubated at 65°C for 1 hour with repeated vortexing every 10 minutes for 10 seconds each. Samples were placed on ice for 1 minute, vortexed for 20 seconds and then centrifuged for 15 minutes at 4°C and 20,000 rcf. To pre-spun yellow phase-lock tubes, 700uL of acidic phenol-chloroform and 700uL of the water phase from samples were added and the tube was inverted multiple times to mix together, after which the tubes were centrifuged for 5 minutes at 4°C as previously described. To pre-spun phase-lock tubes, 700uL of chloroform:isoamyl alcohol (24:1) and 700uL of water phase from samples from yellow phase-lock tubes were mixed together and centrifuged at 4°C as before. To precipitate RNA, 500uL of water phase from the previous step were added to 2ml eppendorf tubes containing 1.5ml of 100% EtOH (cold) and 50uL of 3M NaAc pH 5.2, vortexed for 10 seconds and then incubated at -70°C for 30 minutes. The samples were then centrifuged again for 10 minutes at 20,000 rcf and 4°C. The supernatant was discarded and 500uL of 70% EtOH (in DEPC water at 4°C) was added and the tube was inverted to mix the sample. Majority of the supernatant was aspirated and the samples were spun down again briefly (5 seconds). The remaining superntant was removed and the pellet was allowed to air dry for 5 minutes at room temperature. Lastly, the pellet was resuspended in 100uL of DEPC water and incubated for 1 minute at 65°C. The pellet was then pipetted until dissolved and then gently vortexed for 10 seconds. RNA concentrations were measured using Qubit as per manufacturers' instructions. The samples were further processed by RNAeasy (Qiagen) cleanup with on column DNase treatments before double elution.
RNA library formed by polyA capture and Illumina 150bp paired-end sequencing (Novogene, Cambridge)

treatment_protocol: 2x 50ml mother cultures of fission yeast wildtype were grown to OD 0.2 and subsequently divided into three flasks of 20ml final culture each.Two cultures were untreated, two treated with 100nM of Rapamycin and two with 100nM of Rapalink-1. After 5 hours, cells were spun down, pelleted and stored at -80°C for RNA extraction.

value: yeast/fungi

value: Rapalink-1 (100nM) 5 hours


title: BMDM treated with thrombin-activated platelets 4


title: 451Lu 36 hCTRL3

description: Library name: Sample39


title: cell line MCF7-deltaTKS4

description: total RNA from cell line MCF7-deltaTKS4

source_name: cell line MCF7-deltaTKS4


title: M238 36 h PUFA/Fe3+ 2

description: Library name: Sample35


title: Replica Set S2, Library 1

description:
Library name: Sub1_B
CS01_D50_24

value: cerebral organoid

value: CS03ictr and CS58iMCT8

value: iPSC-derived cerebral organoid

value: Wildtype and MCT8-deficient

value: Replica S2, Library 1


title: 451Lu 36 h CTRL2

description: Library name: Sample38


title: 451Lu 36 h PUFA/Fe3+ 1

description: Library name: Sample40


title: BMDM treated with Thrombin 3

value: Thrombin 0.1U/ml


title: BMDM treated with thrombin-activated platelets 2

value: bone marrow derived macrophage


title: S. pombe cells, Rapamycin treated (100nM) - duplicate 1

description:
M1
gene_fkpm.xls
MvsC_deg_all

value: WT

value: Rapamycin (100nM) 5 hours


title: 443_NeGFP_HuCh

city: Edinburgh

first: Hannah

last: Long

address: Crewe Rd South

department: MRC Human Genetics Unit

institute: University of Edinburgh

description:
Library name: 2_443
10x Genomics

data_processing:
Cell Ranger (10x Genomics, v7.1.0) was used to create FASTQ files and perform alignment, filtering, barcode and UMI counting. A custom reference genome was created from GRCz11 using the Lawson Lab transcriptome annotation (downloaded from https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/, (Lawson et al. 2020)) and manually annotated eGFP and mCherry sequences.
Assembly: A custom reference genome was created from GRCz11 using the Lawson Lab transcriptome annotation (downloaded from https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/, (Lawson et al. 2020)) and manually annotated eGFP and mCherry sequences.
Supplementary files format and content: 444_NeCh_HuGFP_Seurat

organism: Danio rerio

source_name: dissected heads

extract_protocol:
Embryos were dechorionated and placed into 0.5x Danieau’s solution with tricaine (MS-222) anaesthetic. Embryo cranial regions were dissected using a scalpel blade and collected into 0.5x Danieau’s solution on ice. The samples were washed twice using 0.5x Danieau’s solution and once with FACSmax (Amsbio) after centrifugation at 300 x g for 1 min at 4°C. Finally, samples were resuspended in 500 μL FACSmax and passed through a 35-μm cell strainer to obtain single-cells. Cells were sorted based on fluorescence using the CytoFLEX SRT (Beckman Coulter).
Up to 40,000 sorted cells per sample were processed for scRNA-seq and Illumina library preparation using the 10x Genomics Chromium single-cell 3′ gene expression technology (v3.1) by the IGC FACS facility. Sequencing of the resulting libraries was carried out on the NextSeq 2000 platform (Illumina Inc.) using the NextSeq 1000/2000 P3 Reagents (100 cycles) v3 Kit, aiming for ∼50,000 reads per cell.

value: dissected heads

tag: Stage


title: BMDM treated with Thrombin 2


title: S0005 Single cell RNAseq on HBEC and OS-17 cocultured

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description: Library name: S0005

data_processing:
Raw data and initial processing was performed using Cell Ranger (10X Genomics) with reads mapped to the mm10 version of the mouse genome (mouse tumor samples), the hg38 version of the human genome (human patient samples), or a mixed genome containing both (xenograft samples).
Assembly: mm10/hg38/mm10 and hg38
Supplementary files format and content: Compressed tar file containing output from cellranger count including: barcodes.tsv.gz, filtered_feature_bc_matrix.h5, metrics_summary.csv, web_summary.html, features.tsv.gz, matrix.mtx.gz, raw_feature_bc_matrix.h5

source_name: Mixture of HBEC and OS-17

growth_protocol: All cell lines utilized herein were routinely authenticated with STR and mycoplasma testing through Laboratory Corporation of America. Cells utilized for experiments were within 20 passage doublings after reviving from liquid nitrogen storage. OS-17 cells, a human osteosarcoma cell line, were derived from an early passage of the OS-17 patient-derived xenograft, grown from a primary femur biopsy at St. Jude’s Children’s Research Hospital in Memphis and was a gift from Dr. Peter Houghton. Cells were maintained in RPMI (Corning, 10-040-CV) with 10% fetal bovine serum (FBS) (Atlanta Biologicals, S11150H). HBEC3-KT cells were obtained from American Type Culture Collection (ATCC, CRL-4051) and maintained in Airway Epithelial Cell Basal Medium (ATCC, PCS-300-030) with the Bronchial Epithelial Cell Growth Kit (ATCC, PCS-300-040). HBEC:OS-17 organotypic co-culture were established as follows: HBEC were grown to confluence on 0.4µm inserts (Corning, 353090) with HBEC media in upper and lower chambers. OS-17 cells (50,000), were plated into top chamber in DMEM/F12 (Corning, 10-090-CV) + 1% FBS with HBEC media in lower chamber. Cultures were maintained until 72 hours prior to processing for single-cell RNA-sequencing. All animal experiments were carried out in accordance with the Institutional Animal Care and Use Committee (IACUC, protocols AR15-00022 and AR14-00045) of the Research Institute at Nationwide Children’s Hospital (Columbus, OH) guidelines. The approved protocols aimed to minimize the number of mice used and to minimize any pain or distress. All manipulations occurred under sterile conditions in a laminar flow hood. Staff performed all surgical procedures under general anesthesia and aseptic conditions. Mice used were 6-8 weeks-old CB17SC scid-/- (RRID: IMSR_TAC:cb17sc) female mice for the OS-17 models. Mice were maintained under barrier conditions.

extract_protocol:
Lungs harvested from mice were processed using the human tumor dissociation kit (Miltenyi Biotec, 130-095-929) with a GentleMacs Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427). HBEC mono-cultures, OS-17 monocultures, or HBEC:OS-17 co-cultures (72 hours) were gently trypsinized and dissociated into single cell suspensions.
Following dissociation into single cell suspension, single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3′RNA-sequencing system (10X Genomics) with the Reagent Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer’s instructions. cDNA library quality and quantity were determined using an Agilent 2100 bioanalyzer using the High Sensitivity DNA Reagents kit (Agilent, 5607-4626) and then sequenced.

value: Mixture of HBEC and OS-17


title: Col-0-AZD_RNAseq_rep1

tag: tissue

value: seedlings

value: wild type

value: 12 days


title: BMDM treated with thrombin-activated platelets 1

value: Thrombin-activated platelets


title: M238 36 h PUFA/Fe3+ 3

description: Library name: Sample36

value: Melanoma


title: Col-0-H2O_RNAseq_rep1


title: M238 36 hCTRL3

description: Library name: Sample33


title: Col-0-AZD_RNAseq_rep3


title: 444_NeCh_HuGFP

description:
Library name: 5_444
10x Genomics


title: BMDM treated with resting platelets 4

value: Resting platelets


title: drmy1-MS_RNAseq_rep2


title: S.pombe cells, wildtype, untreated - duplicate 1

description:
C1
gene_fkpm.xls
MvsC_deg_all

value: yeast/fungi

value: Untreated


title: Col-0-AZD_RNAseq_rep2


title: M238 36 h PUFA/Fe3+ 1

description: Library name: Sample34


title: S0001 Single cell RNAseq on HBEC and OS-17 cells mixed during processing

description: Library name: S0001


title: S. pombe cells, Rapamycin treated (100nM) - duplicate 2

description:
M2
gene_fkpm.xls
RvsM_deg_all


title: HPCs, HG+PRDM16 lenti-virus, 24 h, rep3

city: Wuhan

first: Ben

last: Tang

address: JieFang Avenue

department: Department of Nephrology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website  directly.
The number of perfect clean tags for each gene was calculated and then normalized in fragments per kilo bases per million mapped Reads (FPKM) using the described method.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HPC

growth_protocol: HPCs were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen)
The mRNA purified by Oligo(dT)-attached magnetic beads was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis and purified using AMPure XP Beads. The cDNA library was constructed through repair, PCR amplification, and purification. Qubit 2.0 and Agilent 2100 bioanalyzer were used for quantification.

treatment_protocol: HPCs were treated with high glucose and transfected with NC or PRDM16 overexprssing lenti-virus for 24 h.

value: HPC

value: Human Podocyte

value: High glucose+PRDM16 lenti-virus transfection


title: BMDM treated with Thrombin 4

value: Thrombin 0.1U/ml


title: HPCs, HG+PRDM16 lenti-virus, 24 h, rep2


title: S.pombe cells, wildtype, untreated - duplicate 2

description:
C2
gene_fkpm.xls
RvsC_deg_all


title: BMDM treated with Thrombin 1

value: bone marrow derived macrophage


title: gtb123-MS_RNAseq_rep3


title: M238 36 h CTRL1

description: Library name: Sample31


title: S.pombe cells, Rapalink-1 treated (100nM) - duplicate 1

description:
R1
gene_fkpm.xls
RvsC_deg_all

value: WT

value: Rapalink-1 (100nM) 5 hours


title: drmy1-MS_RNAseq_rep3


title: M257 36 h PUFA/Fe3+ 2

description: Library name: Sample29


title: BMDM treated with resting platelets 3


title: M257 36 h PUFA/Fe3+ 3

description: Library name: Sample30


title: BMDM treated with resting platelets 2


title: M238 36 h CTRL2

description: Library name: Sample32


title: M257 36 h PUFA/Fe3+ 1

description: Library name: Sample28


title: HPCs, HG+PRDM16 lenti-virus, 24 h, rep1


title: BMDM treated with resting platelets 1


title: gtb123-MS_RNAseq_rep2


title: HPCs, HG+NC lenti-virus, 24 h, rep3

value: High glucose+NC lenti-virus transfection


title: BMDM treated with vehicle 4

value: Vehicle (PBS)


title: HPCs, HG+NC lenti-virus, 24 h, rep2


title: gtb123-MS_RNAseq_rep1

value: seedlings


title: Col-0-MS_RNAseq_rep3

value: wild type


title: M257 36 hCTRL3

description: Library name: Sample27


title: BMDM treated with vehicle 3


title: HPCs, HG+NC lenti-virus, 24 h, rep1


title: Col-0-MS_RNAseq_rep2

value: 12 days


title: drmy1-MS_RNAseq_rep1


title: M257 36 h CTRL1

description: Library name: Sample25


title: BMDM treated with vehicle 1


title: M257 36 h CTRL2

description: Library name: Sample26


title: IP_1967_FLAG_rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

extract_protocol:
Arabidopsis seedlings were cross-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

tag: chip antibody

value: SIGMA, F1804


title: Normal dermal cells, with AA, rep 4

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

description:
Library name: NDF_AA_4
column name in raw_FPKM_TPM_readcounts_allsamples.xlsx, GeneMappingSummary.xls, GenomeMappingSummary.xls : NDF_AA_4

data_processing:
The SOAPnuke software was used to filter out low-quality reads, with remaining clean reads aligned to the reference human genome (Homo Sapiens GRCh37) and using HISAT2 and Bowtie2 software. Transcripts per million (TPM) values were used for all analyses. The R script used to generate the figures in this manuscript is available as a Supplementary File provided with the original publication.
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: Excel file provides Raw FPKM, TPM and Read counts for all samples as separate tabs
Supplementary files format and content: Excel file provides genome mapping statistics for all samples
Supplementary files format and content: Excel file provides gene mapping statistics for all samples

source_name: Normal skin

extract_protocol:
Normal and keloid dermal fibroblasts (P8-9) were thawed and seeded in triplicate at a density of 26,300 cells/cm² (near confluency), and left overnight to adhere and spread. Cells were cultured in complete medium (high-glucose Dulbecco's Modified Eagle Medium (DMEM) with GlutaMAX and pyruvate (Gibco, #31966021) + 10% FBS and 1% penicillin/streptomycin (Sigma-Aldrich, #P0781)) with or without supplementation with 50μg/mL ascorbic acid for 5 days, with media changes every other day. After 5 days, triplicate wells were combined into 350μL RLT buffer (Qiagen, #74104), supplemented with 1% beta-mercaptoethanol (PanReac AppliChem, #A1108.0100) before being frozen at -80°C until downstream analysis. This experiment was repeated on serial passages, P8 & P9, which were used as technical replicates (N=4).   RNA was purified using the RNeasy Mini kit (Qiagen, #74104) following manufacturer’s instructions, and quantified using a Qubit high sensitivity RNA assay (Invitrogen, #Q32852). RNA quality was ascertained by Bioanalyzer 2100 (Agilent). RNA Integrity Number (RIN) values above 9 were used.
RNA from P8-9 normal and keloid fibroblasts cultured with and without ascorbic acid were shipped to BGI Genomics Co. Ltd., Hong Kong for library preparation and sequencing using the BGISEQ platform.

treatment_protocol: Experiment was conducted in 4 technical batches (rep 1-4). We processed all samples in the same library preparation and sequencing run.

value: Normal skin

tag: passage

value: Passage 9

value: With AA


title: Col-0-MS_RNAseq_rep1


title: IP_1967_FLAG_rep1