title: KD_3

city: Shanghai

first: Zouyu

address: 1508 Longhang Road

institute: Jinshan Hospital of Fudan University

description:
Library name: sample6
FPKM.KD_3

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

source_name: HeLa

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: HeLa

value: cervical cancer cells

value: STEAP3 koncodown


title: sAAb_6310 [6310_2_Ivan_Gerling]

status: Public on Dec 31 2024

type: RNA

city: Gainesville

first: Alexandra

middle: E.

last: Cuaycal

state: FL

address: 1275 Center Drive

department: Infectious Diseases and Immunology/Biomedical Engineering

country: USA

institute: University of Florida

hyb_protocol: Amplified RNA samples were hybridized according to Nugen protocols on the Affymetrix Fluidics Station 450.

scan_protocol: Samples were scanned on a GCS3000 7G (Affymetrix).

data_processing: Raw signal intensity values from all arrays were Robust Multichip Average (RMA)  background corrected, quantile normalized, median polish summarized, and log2transformed. Processing was carried out using Partek Genomics Suite, version 6.5.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Laser capture-microdissected islet from nPOD donor 6310

label_protocol: The RNA was amplified using Nugen Pico WTA amplification kit, fragmented and labeled using the Nugen Encore Biotin Module according to Nugen protocols.

extract_protocol: Total islet RNA was extracted using the PicoPure RNA kit (ThermoFisher). DNAse treatment was performed using recombinant DNase I (RNase-free DNAse kit, Worthington Biochemical Corporation).

treatment_protocol: 10 um thick OCT pancreas sections were used to laser-microdissect single islets from dehydrated slides with a Leica 7000 LMD microscope.

tag: tissue

value: Fresh frozen pancreas section


title: sAAb_6310 [6310_3_Ivan_Gerling]


title: Col-0 wild type, control condition, biological replicate #2

type: SRA

city: Chuncheon

first: Dong-Hoon

last: Jeong

state: Gangwon-do

address: Room #8306, Department of Life Science, 1 Hallymdaehak-gil

department: Dept. of Life Science

country: South Korea

institute: Hallym University

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v20.0.4
Assembly: TAIR10
Supplementary files format and content: Exel file including TPM values for each Sample

organism: Arabidopsis thaliana

source_name: Seven-day-old seedlings

growth_protocol: Arabidopsis thaliana ecotype Columbia (Col-0) was used in this study. Arabidopsis Plants were grown under long-day conditions (16h light/8h dark) at 22°C on 1/2 MS medium with 1% sucrose and 0.6% plant agar, adjusted to pH 5.7. The T-DNA insertion lines including prp43a-1(SALKseq_42682), prp43bs-1(WiscDsLox508D09) were obtained from Arabidopsis Biological Resource Center (ABRC).

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings using Quick-RNA Plant Miniprep Kit (Zymo Research).
RNA-seq libraries were constructed using TruSeq Stranded mRNA library preparation kit (Illumina) and paired-end sequencing was performed to produce 2 X 75-bp reads using the Illumina Miseq platform.

treatment_protocol: Seedlings were gown on ½ MS medium. 7 days after germination (DAG) seedlings were treated with 38°C for 16 hours.

value: Seven-day-old seedlings

tag: genotype

value: Col-0 wild type

tag: treatment

value: No treatment


title: F_Cyp2bnull 4

city: Clemson

first: Jazmine

last: Eccles

state: SC

address: 132 Long Hall

institute: Clemson University

data_processing:
PE150 strategy by Novogene. HISAT2 was used to map clean reads.
Assembly: GRCm39
Supplementary files format and content: Excel file containing raw counts performed by Novogene named "gene_count.xls"

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA extractions were performed on 20 mg of liver tissue previously stored at -80C. RNA was extracted with TRIzol (Life Technology, Carlsbad, CA USA) and chloroform. Quality was checked via Nanodrop (Thermo Fisher Scientific, Walkham, MA USA) to ensure both A260/280 and A260/230 values were about 2.0.
Library construction was performed by Novogene (Sacramento, CA USA) using messenger RNA purified from total RNA. Quality was checked with Qubit (Thermo Fisher Scientific, Walkham, MA USA).

value: Liver

tag: Sex

value: F

value: 20-hour fast


title: KD_2

last: Zhao

country: China

description:
Library name: sample5
FPKM.KD_2

tag: cell line

tag: cell type


title: Col-0 wild type, control condition, biological replicate #1


title: sAAb_6310 [6310_6_Ivan_Gerling]


title: sAAb_6310 [6310_12_Ivan_Gerling]


title: F_Cyp2bnull 3


title: F_Cyp2bnull 2


title: KD_1

description:
Library name: sample4
FPKM.KD_1


title: sAAb_6310 [6310_10_Ivan_Gerling]


title: NC_3

description:
Library name: sample3
FPKM.NC_3

value: WT


title: F_Cyp2bnull 1


title: NC_2

description:
Library name: sample2
FPKM.NC_2


title: M_Cypb2null 4

value: M


title: NC_1

description:
Library name: sample1
FPKM.NC_1


title: Experimental ECs, Smu1 RNAi, rep2

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description: Library name: Smu1_iRNA_Exp_b

data_processing:
Raw reads were mapped with vast-tools align v2.5.1 for dm6 (VASTDB library: vastdb.dme.23.06.20.tar.gz)
Assembly: dm6
Supplementary files format and content: cRPKM and raw gene counts from vast-tools align

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were grown at 18°C, 25°C or 29°C on standard medium

extract_protocol:
RNA from the different biological replicas was isolated using RNeasy Mini kit (QIAGEN). cDNA synthesis, library preparation and amplification (Pico Profiling) followed González-Roca et al. 2010 (PLoS ONE).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: Escort cells from experimental ovaries carrying a Smu1 RNAi construct


title: Control ECs, Smu1 RNAi, rep2

description: Library name: Smu1_iRNA_Ctrl_b

value: Escort cells from control ovaries


title: Experimental ECs, Smu1 RNAi, rep1

description: Library name: Smu1_iRNA_Exp_a


title: TFCs+CpCs, 4w-old, rep2

description: Library name: Niches_4w_b

value: Terminal filament cells + cup cells from 4w-old ovaries


title: M_Cypb2null 3


title: M_Cypb2null 2


title: Hep.G2.MeOH.conc8.rep3

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: hepg.meoh.0.08.H12
cell lysate
hepg.meoh.0.08.H12

library_source: other

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using DESeq2 and Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

source_name: liver

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to extract of interest 24 hours after seeding at 35,000 cells per well

value: liver

value: Hep G2

value: hepatocyte


title: sAAb_6310 [6310_1_Ivan_Gerling]


title: TFCs+CpCs, 4w-old, rep1

description: Library name: Niches_4w_a


title: Hep.G2.MeOH.conc8.rep2

description:
Library name: hepg.meoh.0.08.H08
cell lysate
hepg.meoh.0.08.H08


title: M_Cypb2null 1


title: Hep.G2.MeOH.conc8.rep1

description:
Library name: hepg.meoh.0.08.H04
cell lysate
hepg.meoh.0.08.H04


title: TFCs+CpCs, 1w-old, rep2

description: Library name: Niches_1w_b

value: Terminal filament cells + cup cells from 1w-old ovaries


title: sAAb_6181 [6181_7_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6181

value: Fresh frozen pancreas section


title: sAAb_6310 [6310_11_Ivan_Gerling]


title: sAAb_6181 [6181_8_Ivan_Gerling]


title: ND_6232 [6232-1_9_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6232


title: ND_6232 [6232-1_8_Ivan_Gerling]


title: Hep.G2.MeOH.conc7.rep3

description:
Library name: hepg.meoh.0.15.G12
cell lysate
hepg.meoh.0.15.G12


title: TFCs+CpCs, 1w-old, rep1

description: Library name: Niches_1w_a


title: Control ECs, Smu1 RNAi, rep1

description: Library name: Smu1_iRNA_Ctrl_a


title: E12.5 Wnt9b Knockout out mouse 2 mesonephros

city: Madison

first: Fei

state: WI

address: 2015 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

data_processing:
R studio platform was used for data analysis. Raw data was uploaded to R to be analyzed.  All data analysis followed default normalization.
The library package was loaded into R and the coded functions were input prior to data upload.  The raw counts were loaded in to R.
The samples were defined and groups were factored in for sorting and grouping of the samples for comparison
Finally to get DEG, we filtered our gene counts, performed DESeq2 statistical analysis and compared Wnt9b+/+ and Wnt9b-/- male mesonephros.
The DEGs were then filterd based on TPM  to create the data table.
Assembly: GRCm39.110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: E12.5 Male Mesonephros

extract_protocol:
RNA was harvested using PicoPure RNA Isolation Kit from Applied Biosystems cat# 12204001
Upond recieval of samples, a quality check is performed to check for RNA amount and purity. Then the library is contruction using polyA enrichment to capture Poly(A) and remove rRNA. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Upon fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.  Once cDNA synthesis is finished, 250-300bp insert cDNA library was prepared. The library was ready once overhangs were converted to ends, purified and libraries were assesed for quality and 150bp paired-end reads were generated.

value: E12.5 Male Mesonephros

value: Knockout


title: E12.5 Wnt9b Knockout out mouse 3 mesonephros


title: ECs, 4w-old, rep2

description: Library name: ECs_4w_b

value: Escort cells from 4w-old ovaries


title: Hep.G2.MeOH.conc7.rep2

description:
Library name: hepg.meoh.0.15.G08
cell lysate
hepg.meoh.0.15.G08


title: E12.5 Wnt9b Knockout out mouse 1 mesonephros


title: ND_6131 [IG97_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6131


title: ECs, 4w-old, rep1

description: Library name: ECs_4w_a


title: E12.5 Wnt9b control mouse 3 mesonephros

value: Heterozygous


title: sAAb_6147 [6147_1_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6147


title: ECs, 1w-old, rep2

description: Library name: ECs_1w_b

value: Escort cells from 1w-old ovaries


title: Hep.G2.MeOH.conc7.rep1

description:
Library name: hepg.meoh.0.15.G04
cell lysate
hepg.meoh.0.15.G04


title: Hep.G2.MeOH.conc6.rep3

description:
Library name: hepg.meoh.0.3.F12
cell lysate
hepg.meoh.0.3.F12


title: E12.5 Wnt9b control mouse 2 mesonephros


title: ND_6073 [IG96_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6073


title: Hep.G2.MeOH.conc6.rep2

description:
Library name: hepg.meoh.0.3.F08
cell lysate
hepg.meoh.0.3.F08


title: ECs, 1w-old, rep1

description: Library name: ECs_1w_a


title: ND_6099 [IG95_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6099


title: E12.5 Wnt9b control mouse 1 mesonephros


title: Hep.G2.MeOH.conc6.rep1

description:
Library name: hepg.meoh.0.3.F04
cell lysate
hepg.meoh.0.3.F04


title: mock-infected pMG_2

city: Seoul

first: Soo-Jin

last: Oh

address: Guro-go

institute: Korea University

description: (Duplicate) mock-infected primary microglia followed by vehicle treatment

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 or GRCh38 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39, GRCh38
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Brain

growth_protocol: primary microglia were cultured in DMEM/F12(Ham's)-supplemetned with FBS, P/S, grwoth factors, etc.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: HSV1 were inoculated into cells @ MOI 10 and/or 30 μM ALT001 were treated in SF DMEM

value: Brain

value: Primary cell

value: microglia


title: Hep.G2.MeOH.conc5.rep3

description:
Library name: hepg.meoh.0.6.E12
cell lysate
hepg.meoh.0.6.E12


title: ND_6232 [6232-1_6_Ivan_Gerling]


title: mock-infected pMG_1

description: mock-infected primary microglia followed by vehicle treatment


title: MGH-U3-KO-Erdafitinib-1

city: wuhan

first: 砚超

last: 余

state: 湖北

address: xinhua street

institute: huazhong university of science and technology

data_processing:
Download the reference genome and gene model annotation file directly from the genome website. Use HISAT2 (v2.2.1) to build an index of the reference genome, and use HISAT2 (v2.2.1) to align paired-end clean reads with the reference genome, with parameters “–phred33 --no-mixed --no-discordant”.
Assembly: mm10
Supplementary files format and content: processed data.txt

source_name: bladder

extract_protocol:
Agarose gel electrophoresis: analyze sample RNA integrity and whether there is DNA contamination; NanoPhotometer spectrophotometer: detect RNA purity (OD260/280 and OD260/230 ratio); Agilent 2100 bioanalyzer: accurately detect RNA integrity.
The starting RNA for library construction is total RNA, with a total amount >=800ng. The library construction kit used in library construction is BGI’s NEBNext® UltraTM RNA Library Prep Kit. mRNA with polyA tail is enriched by Oligo(dT) magnetic beads, and then the obtained mRNA is randomly broken in NEB Fragmentation Buffer with divalent cations. Using the fragmented mRNA as a template, random oligonucleotides as primers, cDNA first strand is synthesized in M-MuLV reverse transcriptase system, then RNA strand is degraded by RNaseH and cDNA second strand is synthesized in DNA polymerase I system with dNTPs as raw materials. The purified double-stranded cDNA is end-repaired, A-tailed and ligated with sequencing adapters, and AMPure XP beads are used to select cDNA of about 200bp, PCR amplification and AMPure XP beads purification of PCR products are performed to obtain the library. After the library construction is completed, Qubit2.0 Fluorometer is used for preliminary quantification, dilute the library to 1.5ng/ul, then use Agilent 2100 bioanalyzer to detect the insert size of the library, after the insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (library effective concentration higher than 2nM), to ensure the library quality.

value: bladder

value: MGH -U3

value: KO

value: Erdafitinib


title: Hep.G2.MeOH.conc5.rep2

description:
Library name: hepg.meoh.0.6.E08
cell lysate
hepg.meoh.0.6.E08

value: liver


title: ND_6232 [IG93_Ivan_Gerling]


title: MGH-U3-WT-Erdafitinib-3

value: WT


title: HSV1-infected w/ ALT pMG_2

description: (Duplicate) HSV1-infected primary microglia followed by ALT001 treatment


title: ND_6131 [IG92_Ivan_Gerling]


title: Hep.G2.MeOH.conc5.rep1

description:
Library name: hepg.meoh.0.6.E04
cell lysate
hepg.meoh.0.6.E04

value: Hep G2

value: hepatocyte


title: ND_6316 [IG98_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6316

value: Fresh frozen pancreas section


title: Hep.G2.MeOH.conc4.rep3

description:
Library name: hepg.meoh.1.2.D12
cell lysate
hepg.meoh.1.2.D12


title: HSV1-infected w/ ALT pMG_1

description: HSV1-infected primary microglia followed by ALT001 treatment


title: MGH-U3-WT-Erdafitinib-2


title: MGH-U3-KO-Erdafitinib-2


title: HSV1-infected pMG_2

description: (Duplicate) HSV1-infected primary microglia followed by vehicle treatment


title: ND_6230 [IG90_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6230


title: Hep.G2.MeOH.conc4.rep2

description:
Library name: hepg.meoh.1.2.D08
cell lysate
hepg.meoh.1.2.D08


title: MGH-U3-WT-Erdafitinib-1


title: MGH-U3-KO-Erdafitinib-3


title: HSV1-infected pMG_1

description: HSV1-infected primary microglia followed by vehicle treatment


title: Hep.G2.MeOH.conc4.rep1

description:
Library name: hepg.meoh.1.2.D04
cell lysate
hepg.meoh.1.2.D04


title: ND_6234 [IG91_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6234


title: ND_6279 [IG84_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6279


title: ALT-treated pMG_1

description: mock-infected primary microglia followed by ALT001 treatment


title: SW780-DMSO

data_processing:
Download the reference genome and gene model annotation file directly from the genome website. Use HISAT2 (v2.2.1) to build an index of the reference genome, and use HISAT2 (v2.2.1) to align paired-end clean reads with the reference genome, with parameters “–phred33 --no-mixed --no-discordant”.
Supplementary files format and content: processed data.xls

value: DMSO


title: ALT-treated pMG_2

description: (Duplicate) mock-infected primary microglia followed by ALT001 treatment


title: Hep.G2.MeOH.conc3.rep2

description:
Library name: hepg.meoh.2.5.C08
cell lysate
hepg.meoh.2.5.C08


title: Hep.G2.MeOH.conc3.rep3

description:
Library name: hepg.meoh.2.5.C12
cell lysate
hepg.meoh.2.5.C12


title: Hep.G2.MeOH.conc2.rep3

description:
Library name: hepg.meoh.5.B12
cell lysate
hepg.meoh.5.B12


title: Hep.G2.MeOH.conc3.rep1

description:
Library name: hepg.meoh.2.5.C04
cell lysate
hepg.meoh.2.5.C04


title: Hep.G2.MeOH.conc2.rep2

description:
Library name: hepg.meoh.5.B08
cell lysate
hepg.meoh.5.B08


title: ND_6234 [IG82_Ivan_Gerling]


title: HD2_co-culture_NPC_3(IsoHD2_Org_IsoHD2_iMac)

first: Wei Jie

last: Wong

address: Chong Qing Nan Road 280

institute: shanghai jiaotong univeristy

data_processing:
The clean paired-ends reads were aligned to the GRCh38.96 human genome reference using kallisto (version 0.46.1) with parameters "–bootstrap-samples=100". The transcript-level estimated counts belonging to the same gene were then aggregated into the matrix of gene-level counts (TPM) implemented in the R package tximport (version 1.14.2).
Assembly: GRCh38.96 human genome
Supplementary files format and content: TPMs

source_name: fibroblasts

extract_protocol:
RNA was harvested using Trizol according to the manufacturer’s instructions. 5 uL of total RNA was used for the construction of the sequencing libraries.
RNA samples were first converted to complementary DNA (cDNA) using the Takara HT kit according to the manufacturer’s instruction

value: fibroblasts

value: donor-derived

value: iPSC

tag: group

value: Isogenic control

value: Forebrain + iMac co-culture


title: HD2_co-culture_NPC_2(IsoHD2_Org_IsoHD2_iMac)


title: MGH-U3-DMSO


title: GpBL4w3

city: New Haven

first: Jain

state: CONNECTICUT

address: 1 Gilbert St, TAC BUILDING, S220

institute: YALE UNIVERSITY

description: BDL 4weeks-3

data_processing:
Reads were trimmed using Trim Galore (v0.5.0) and mapped to the mouse reference genome (mm10) using HISAT2 (v2.1.0).  Gene expression levels were quantified using StringTie (v1.3.3b) with gene models (v27) from the GENCODE project.Differentially expressed genes (DEGs) were identified using DESeq2 (v1.22.1)
Assembly: mm10
Supplementary files format and content: xls file of normalized count

source_name: Liver

extract_protocol:
For RNA-seq analysis, 2 to 5×104 LyECs were sorted directly into 500 µl of TRIzol reagent and total RNA was extracted.
rRNA depletion library

value: Liver

value: Lymphatic endothelial cell

value: Bile duct ligation


title: GpBL2w3

description: BDL 2weeks-3


title: HD2_co-culture_NPC_1(IsoHD2_Org_IsoHD2_iMac)


title: SW780-Erdafitinib

value: bladder


title: ND_6293 [IG81_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6293


title: GpBL4w1

description: BDL 4weeks-1


title: GpBL4w2

description: BDL 4weeks-2


title: Hep.G2.MeOH.conc2.rep1

description:
Library name: hepg.meoh.5.B04
cell lysate
hepg.meoh.5.B04

source_name: liver


title: GpBL2w2

description: BDL 2weeks-2


title: MGH-U3-Erdafitinib

value: MGH -U3


title: HD2_co-culture_neurons_3(IsoHD2_Org_IsoHD2_iMac)


title: ND_6099 [IG72_Ivan_Gerling]


title: Hep.G2.MeOH.conc1.rep3

description:
Library name: hepg.meoh.10.A12
cell lysate
hepg.meoh.10.A12


title: ND_6099 [IG8_Ivan_Gerling]


title: ND_6232 [6232-1_10_Ivan_Gerling]


title: GpBL2w1

description: BDL 2weeks-1


title: ND_6336 [IG71_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6336


title: ND_6131 [IG73_Ivan_Gerling]


title: HD2_co-culture_neurons_2(IsoHD2_Org_IsoHD2_iMac)


title: ND_6293 [IG74_Ivan_Gerling]


title: ND_6098 [IG83_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6098


title: Hep.G2.MeOH.conc1.rep2

description:
Library name: hepg.meoh.10.A08
cell lysate
hepg.meoh.10.A08


title: GpShm3

value: Sham surgery


title: Hep.G2.MeOH.conc1.rep1

description:
Library name: hepg.meoh.10.A04
cell lysate
hepg.meoh.10.A04

value: liver


title: ND_6232 [IG7_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6232


title: ND_6232 [IG62_Ivan_Gerling]


title: GpShm2


title: Hep.G2.H2O2.conc8.rep3

description:
Library name: hepg.h2o2.0.025.H10
cell lysate
hepg.h2o2.0.025.H10


title: GpShm1


title: HD2_co-culture_NPC_2(IsoHD2_Org_Mut_HD2_iMac)

value: WT (Mut)


title: HD2_co-culture_NPC_3(IsoHD2_Org_Mut_HD2_iMac)


title: Hep.G2.H2O2.conc8.rep2

description:
Library name: hepg.h2o2.0.025.H06
cell lysate
hepg.h2o2.0.025.H06

value: Hep G2


title: Old, male, biological replicate 5, technical replicate 1, ST-RNAseq

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: 10x Genomics Visium

data_processing:
Demultiplexed, aligned, extracted barcodes, counted unique molecular identifiers (UMIs), and compiled a feature-barcode matrix for each sample  were made using the Space Ranger software (v2.0.1) (https://www.10xgenomics.com/support/software/space-ranger/latest).
The feature-barcode matrix from Space Ranger was imported into PartekFlow Genomic Analysis Software (Partek Inc.) for further quality assessments.The barcoded spots were filtered by counts at low.cutoff=1 and high.cutoff=38,855, detected genes at  low.cutoff=1 and high.cutoff=8012, % mitochondrial counts at low.cutoff=0, high.cutoff=35%, % ribosomal counts at low.cutoff=0, high.cutoff=14%. Filtered genes with value ≤ 1.0 in at least 99 % of the cells were excluded.
The data were normalized and scaled to counts per million (CPM, add:1.0, log:2.0). PCA was performed, and the top 100 principal components (PCs) were stored by PartekFlow Genomic Analysis Software (Partek Inc.)
The data were then clustered using graph-based cluster analysis with a clustering resolution set to 0.5. Spots on visium image were classified based on histology and Uniform Manifold Approximation and Projection (UMAP) and annotated to the graph-based clusters by PartekFlow Genomic Analysis Software (Partek Inc.)
ANOVA statistics was applied to each age group comparison for differential analysis with sex as a covariate by PartekFlow Genomic Analysis Software (Partek Inc.)
Assembly: mm10
Supplementary files format and content: H5 File
Library strategy: Spatial transcriptomics

source_name: coronal sections of mouse brain

extract_protocol:
Tissue sections were first stained with Hematoxylin-Eosin (H&E), followed by cDNA synthesis, amplification, barcoding, and library construction (see Methods). Following this demonstrated protocol, we obtained high-quality spatially resolved RNA-seq data from these 36 samples and sequenced them on the NovaSeq™ 6000 platform achieving an average coverage of 171 million(round 1) and 101 million(round 2)read pairs per sample.
10 µl (25%) of the total amplified cDNA was used as input to perform enzymatic fragmentation, end repair and A-tailing (10X Genomics, PN1000196). A double-sided size selection was then performed with SPRIselect (Beckman, Coulter B23318). TruSeq read2 primer was added via adaptor ligation (10X Genomics, PN1000196). P5, P7, i7, and i5 sample indices were added via index PCR with the individual dual index TT set A (10X Genomics, 3000431). The cycle number for index PCR was calculated based on the yield of the 25% carry forward cDNA material and 15 cycles were used. A double-sided size selection of the post-index PCR sample was performed with SPRIselect (Beckman, Coulter B23318).

value: coronal sections of mouse brain

tag: strain

tag: age

value: 125 weeks


title: Hep.G2.H2O2.conc8.rep1

description:
Library name: hepg.h2o2.0.025.H02
cell lysate
hepg.h2o2.0.025.H02

value: hepatocyte


title: ND_6316 [IG61_Ivan_Gerling]

value: Fresh frozen pancreas section


title: Old, male, biological replicate 4, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: HD2_co-culture_NPC_1(IsoHD2_Org_Mut_HD2_iMac)

value: fibroblasts

value: donor-derived


title: ND_6098 [IG60_Ivan_Gerling]


title: HD2_co-culture_neurons_3(IsoHD2_Org_Mut_HD2_iMac)

value: iPSC


title: ND_6316 [IG6_Ivan_Gerling]


title: Hep.G2.H2O2.conc7.rep3

description:
Library name: hepg.h2o2.0.05.G10
cell lysate
hepg.h2o2.0.05.G10


title: ND_6234 [IG59_Ivan_Gerling]


title: HD2_co-culture_neurons_2(IsoHD2_Org_Mut_HD2_iMac)

value: Forebrain + iMac co-culture


title: HD2_co-culture_neurons_1(IsoHD2_Org_IsoHD2_iMac)

value: Isogenic control


title: Hep.G2.H2O2.conc7.rep2

description:
Library name: hepg.h2o2.0.05.G06
cell lysate
hepg.h2o2.0.05.G06


title: Old, male, biological replicate 2, technical replicate 2, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440159


title: Hep.G2.H2O2.conc7.rep1

description:
Library name: hepg.h2o2.0.05.G02
cell lysate
hepg.h2o2.0.05.G02


title: HD2_iMicroglia_3

value: iMicroglia differentiation


title: Old, male, biological replicate 1, technical replicate 2, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440155


title: Hep.G2.H2O2.conc6.rep3

description:
Library name: hepg.h2o2.0.1.F10
cell lysate
hepg.h2o2.0.1.F10


title: HD2_iMicroglia_2


title: Old, female, biological replicate 5, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: ND_6234 [IG50_Ivan_Gerling]


title: Old, female, biological replicate 4, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: Hep.G2.H2O2.conc6.rep2

description:
Library name: hepg.h2o2.0.1.F06
cell lysate
hepg.h2o2.0.1.F06


title: HD2_iMicroglia_1


title: Hep.G2.H2O2.conc6.rep1

description:
Library name: hepg.h2o2.0.1.F02
cell lysate
hepg.h2o2.0.1.F02


title: Old, male, biological replicate 3, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: ND_6271 [IG5_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6271


title: Hep.G2.H2O2.conc5.rep3

description:
Library name: hepg.h2o2.0.21.E10
cell lysate
hepg.h2o2.0.21.E10


title: Old, female, biological replicate 3, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: IsoHD2_iMac_3

value: iMac differentiation


title: HD2_co-culture_neurons_1(IsoHD2_Org_Mut_HD2_iMac)


title: Old, female, biological replicate 2, technical replicate 2, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440157


title: Hep.G2.H2O2.conc5.rep2

description:
Library name: hepg.h2o2.0.21.E06
cell lysate
hepg.h2o2.0.21.E06


title: ND_6232 [6232-1_1_Ivan_Gerling]


title: IsoHD2_iMac_2


title: ND_6293 [IG49_Ivan_Gerling]


title: Old, female, biological replicate 1, technical replicate 1, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440152


title: ND_6073 [IG51_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6073


title: Hep.G2.H2O2.conc5.rep1

description:
Library name: hepg.h2o2.0.21.E02
cell lysate
hepg.h2o2.0.21.E02


title: ND_6230 [IG40_Ivan_Gerling]


title: IsoHD2_iMac_1


title: Young, male, biological replicate 5, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium

value: 11 weeks


title: Hep.G2.H2O2.conc4.rep3

description:
Library name: hepg.h2o2.0.42.D10
cell lysate
hepg.h2o2.0.42.D10


title: Young, male, biological replicate 4, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: ND_6271 [IG38_Ivan_Gerling]


title: IsoHD2_iMac_4


title: Mut_HD2_iMac_3


title: Young, male, biological replicate 3, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: Hep.G2.H2O2.conc4.rep1

description:
Library name: hepg.h2o2.0.42.D02
cell lysate
hepg.h2o2.0.42.D02


title: Mut_HD2_iMac_2


title: Hep.G2.H2O2.conc3.rep2

description:
Library name: hepg.h2o2.0.83.C06
cell lysate
hepg.h2o2.0.83.C06


title: Young, male, biological replicate 1, technical replicate 2, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440163


title: ND_6073 [IG48_Ivan_Gerling]


title: Mut_HD2_iMac_1


title: HD1_iMicroglia_3


title: Young, female, biological replicate 5, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: ND_6230 [IG29_Ivan_Gerling]


title: ND_6131 [IG30_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6131


title: ND_6336 [IG28_Ivan_Gerling]


title: ND_6232 [6232_8_Ivan_Gerling]


title: Hep.G2.H2O2.conc3.rep1

description:
Library name: hepg.h2o2.0.83.C02
cell lysate
hepg.h2o2.0.83.C02


title: Hep.G2.H2O2.conc3.rep3

description:
Library name: hepg.h2o2.0.83.C10
cell lysate
hepg.h2o2.0.83.C10


title: HD1_iMicroglia_2


title: Young, female, biological replicate 3, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: Hep.G2.H2O2.conc4.rep2

description:
Library name: hepg.h2o2.0.42.D06
cell lysate
hepg.h2o2.0.42.D06


title: ND_6098 [IG39_Ivan_Gerling]


title: Mut_HD2_iMac_4


title: HD1_iMicroglia_1


title: Hep.G2.H2O2.conc2.rep2

description:
Library name: hepg.h2o2.1.67.B06
cell lysate
hepg.h2o2.1.67.B06


title: Young, male, biological replicate 2, technical replicate 2, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440167


title: Young, female, biological replicate 2, technical replicate 2, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440165


title: ND_6098 [IG19_Ivan_Gerling]


title: IsoHD1_iMac_3


title: Hep.G2.H2O2.conc2.rep1

description:
Library name: hepg.h2o2.1.67.B02
cell lysate
hepg.h2o2.1.67.B02


title: ND_6271 [IG27_Ivan_Gerling]


title: IsoHD1_iMac_2


title: Young, female, biological replicate 1, technical replicate 1, ST-RNAseq_resequencing

description:
10x Genomics Visium
Re-sequenced sample, image file same as GSM7440160


title: Young, female, biological replicate 4, technical replicate 1, ST-RNAseq

description: 10x Genomics Visium


title: Hep.G2.H2O2.conc2.rep3

description:
Library name: hepg.h2o2.1.67.B10
cell lysate
hepg.h2o2.1.67.B10


title: ND_6316 [IG18_Ivan_Gerling]


title: IsoHD1_iMac_1


title: Hep.G2.H2O2.conc1.rep2

description:
Library name: hepg.h2o2.3.33.A06
cell lysate
hepg.h2o2.3.33.A06


title: Mut_HD1_iMac_3


title: Hep.G2.H2O2.conc1.rep1

description:
Library name: hepg.h2o2.3.33.A02
cell lysate
hepg.h2o2.3.33.A02


title: Mut_HD1_iMac_2


title: Hep.G2.DMSO.conc8.rep3

description:
Library name: hepg.dmso.0.08.H11
cell lysate
hepg.dmso.0.08.H11


title: Mut_HD1_iMac_1


title: Hep.G2.DMSO.conc8.rep2

description:
Library name: hepg.dmso.0.08.H07
cell lysate
hepg.dmso.0.08.H07


title: ND_6336 [IG16_Ivan_Gerling]


title: lung epithelial AT2 cell, naïve, CC2

city: St Louis

first: Steven

last: Van Dyken

state: MO

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: lung

growth_protocol: cells were not cultured prior to sequencing

extract_protocol:
RNA wwas harvested using Rneasay mini plus kit (Qiagen).
Takara Clontech SMARTer

treatment_protocol: mice were anesthesized prior to intranasal challenge with 50 microliters of chitin particles or PBS

value: lung

value: epithelial cell

value: AMCase Knockout

value: naïve


title: lung epithelial AT2 cell, naïve, CC1


title: lung epithelial AEP cell, naïve, CC2


title: Hep.G2.DMSO.conc8.rep1

description:
Library name: hepg.dmso.0.08.H03
cell lysate
hepg.dmso.0.08.H03

value: liver

value: Hep G2


title: shRNA_CCDC12_3

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Read counts for each gene were carried out using HT-Seq using the hg38 refSeq refFlat GTF file.
Genes with adjusted P-value < 0.05 and |foldChange| > 2 were defined as differentially expressed genes (DEGs).
Assembly: hg38

extract_protocol:
The total RNA of cells in each group was isolated using RNAiso Plus (TakaRa, 9108) and stored at -80℃. The concentration and purity of RNA were determined using a NanoPhotometer (ThermoFisher Scientific Intertek, Cat. 3100668).
RNA purification, cDNA synthesis and RNA-Seq of each group (n = 3) were performed by Oebiotech company (Shanghai, China). RNA integrity was analyzed through the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). The RNA integrity number ≥ 7 was subjected to the following analysis. The cDNA libraries were constructed through TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA).Shanghai

value: breast cancer

value: WT

value: CCDC12 knock-dwon


title: ND_6232 [IG120_Ivan_Gerling]

value: Fresh frozen pancreas section


title: lung epithelial AT2 cell, naïve, CC3


title: Hep.G2.H2O2.conc1.rep3

description:
Library name: hepg.h2o2.3.33.A10
cell lysate
hepg.h2o2.3.33.A10

value: hepatocyte


title: ND_6279 [IG17_Ivan_Gerling]


title: ND_6232 [IG112_Ivan_Gerling]


title: Hep.G2.DMSO.conc7.rep3

description:
Library name: hepg.dmso.0.15.G11
cell lysate
hepg.dmso.0.15.G11


title: lung epithelial AT2 cell, naïve, WT3


title: lung epithelial AEP cell, naïve, CC1


title: lung epithelial AEP cell, naïve, CC3


title: ND_6279 [IG108_Ivan_Gerling]


title: shRNA_CCDC12_1


title: ND_6232 [6232_7_Ivan_Gerling]


title: ND_6271 [IG107_Ivan_Gerling]


title: ND_6232 [IG109_Ivan_Gerling]


title: Hep.G2.DMSO.conc7.rep2

description:
Library name: hepg.dmso.0.15.G07
cell lysate
hepg.dmso.0.15.G07


title: ND_6073 [IG106_Ivan_Gerling]


title: lung epithelial AEP cell, naïve, WT3


title: ND_6230 [IG102_Ivan_Gerling]


title: NC3

value: control


title: Hep.G2.DMSO.conc7.rep1

description:
Library name: hepg.dmso.0.15.G03
cell lysate
hepg.dmso.0.15.G03


title: NC2


title: lung epithelial AT2 cell, naïve, WT2


title: shRNA_CCDC12_2


title: Hep.G2.DMSO.conc6.rep2

description:
Library name: hepg.dmso.0.3.F07
cell lysate
hepg.dmso.0.3.F07


title: ND_6279 [IG101_Ivan_Gerling]


title: lung epithelial AEP cell, naïve, WT2


title: Hep.G2.DMSO.conc6.rep3

description:
Library name: hepg.dmso.0.3.F11
cell lysate
hepg.dmso.0.3.F11


title: NB4_overexpression_HA-PML/RARα-ΔIDR_replication2

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
The salmon program was used for quantification of transcript expression.
The reference transcriptome was built with the Ensembl gene annotation file and the hg38 genome (GRCh38.98).
|log2(fold change)| >=0.585 and the FDR < 0.01 were used for determining differentially expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing the reads count values

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA). Ribosomal RNAs were depleted according to the manufacturer's protocol (Vazyme, China, N406-01).
RNA-seq libraries were preapared withthe NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, E7530S) according to the manufacturer’s instructions.

treatment_protocol: NB4 cells were infected with lentivirus to knock-down engogenous PML/RARα and replace with empty vector or full-length PML/RARα or phase separation-imcompetent mutants (F158E or ΔIDR) for 72 hours.

value: Acute promyelocytic leukemia cells

value: overexpression HA-tagged ΔIDR mutant PML/RARα with endogenous PML/RARα knock-down


title: Hep.G2.DMSO.conc5.rep3

description:
Library name: hepg.dmso.0.6.E11
cell lysate
hepg.dmso.0.6.E11


title: NB4_overexpression_HA-PML/RARα-ΔIDR_replication1


title: ND_6232 [IG100_Ivan_Gerling]


title: lung epithelial AEP cell, naïve, WT1


title: Hep.G2.DMSO.conc6.rep1

description:
Library name: hepg.dmso.0.3.F03
cell lysate
hepg.dmso.0.3.F03


title: lung epithelial AT2 cell, chitin, CC2

value: chitin


title: NB4_overexpression_HA-PML/RARα-F158E_replication2

value: overexpression HA-tagged F158E mutant PML/RARα with endogenous PML/RARα knock-down


title: lung epithelial AEP cell, chitin, CC2


title: NC1


title: Hep.G2.DMSO.conc5.rep2

description:
Library name: hepg.dmso.0.6.E07
cell lysate
hepg.dmso.0.6.E07


title: NB4_overexpression_HA-PML/RARα-F158E_replication1


title: lung epithelial AT2 cell, chitin, CC1


title: Hep.G2.DMSO.conc5.rep1

description:
Library name: hepg.dmso.0.6.E03
cell lysate
hepg.dmso.0.6.E03


title: lung epithelial AEP cell, chitin, CC1


title: NB4_overexpression_HA-PML/RARα_replication2

value: overexpression HA-tagged full-length PML/RARα with endogenous PML/RARα knock-down


title: NB4_overexpression_HA-PML/RARα_replication1


title: lung epithelial AT2 cell, chitin, WT3

value: lung


title: Hep.G2.DMSO.conc4.rep2

description:
Library name: hepg.dmso.1.2.D07
cell lysate
hepg.dmso.1.2.D07


title: Hep.G2.DMSO.conc4.rep3

description:
Library name: hepg.dmso.1.2.D11
cell lysate
hepg.dmso.1.2.D11


title: ND_6401 [6401_8_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6401


title: NB4_overexpression_empty vector_replication2

value: overexpression empty vector with endogenous PML/RARα knock-down


title: Hep.G2.DMSO.conc4.rep1

description:
Library name: hepg.dmso.1.2.D03
cell lysate
hepg.dmso.1.2.D03


title: Hep.G2.DMSO.conc3.rep3

description:
Library name: hepg.dmso.2.5.C11
cell lysate
hepg.dmso.2.5.C11


title: NB4_overexpression_empty vector_replication1


title: lung epithelial AT2 cell, chitin, WT2

value: epithelial cell


title: lung epithelial AEP cell, chitin, WT2


title: NB4_overexpression_HA-PML/RARα-ΔIDR_IP_BRD4

library_source: genomic

data_processing:
Sequencing reads were aligned to hg38 by Bowtie2 (version 2.2.9). The uniquely mapped and non-redundant reads were left to conduct peak calling.
ChIP-seq peak regions were called using MACS (version 1.4.2) at a p-value cut off of 10e-10 or 10e-5.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. Peaks.xls files were generated using MACS v1.4.2.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the pellets were then re-suspended in ChIP buffer (Active motif) containing 1 mM PMSF and proteinase inhibitor cocktail (Sigma). Chromatin shearing was performed using a Biorupter Pico ultrasonicator device (Diagenode) with 30s ON then 30s OFF for 30 cycles. Solubilized chromatin was used for immunoprecipitation by incubating overnight at 4 °C with chip antibodies. The immunoprecipitation reaction was transferred to the Protein G agarose Column (53039, Active Motif) and incubated for 2 hours at 4 °C, then each column was washed 4 times with 900 μL Wash Buffer AM1 (Active motif). The ChIPed sample was eluted using 100 μL 37 °C Elution Buffer AM4 (Active Motif). Cross-linking was reversed by adding 5 μL Proteinase K and the sample was incubated overnight at 65 °C. Input and ChIPed DNA were purified using a DNA purification column (Active Motif).
DNA libraries were prepared with the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer’s instructions. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: NB4 cells were were infected with lentivirus to knock-down engogenous PML/RARα and replace with empty vector or full-length PML/RARα or phase separation-imcompetent mutants (F158E or ΔIDR) for 72 hours.

value: Acute promyelocytic leukemia (APL) patient-derived cell line

tag: chip antibody

value: BRD4 (Bethyl laboratory, #A301-985)


title: NB4_overexpression_HA-PML/RARα-F158E_IP_BRD4


title: lung epithelial AEP cell, chitin, WT1


title: lung epithelial AEP cell, chitin, WT3


title: NB4_overexpression_HA-PML/RARα_IP_BRD4


title: Hep.G2.DMSO.conc2.rep3

description:
Library name: hepg.dmso.5.B11
cell lysate
hepg.dmso.5.B11

value: liver

value: Hep G2


title: NB4_overexpression_empty vector_IP_BRD4


title: lung epithelial AT2 cell, chitin, CC3

value: AMCase Knockout


title: Hep.G2.DMSO.conc2.rep2

description:
Library name: hepg.dmso.5.B07
cell lysate
hepg.dmso.5.B07


title: ND_6401 [6401_7_Ivan_Gerling]


title: Hep.G2.DMSO.conc3.rep2

description:
Library name: hepg.dmso.2.5.C07
cell lysate
hepg.dmso.2.5.C07


title: lung epithelial AEP cell, chitin, CC3


title: lung epithelial AT2 cell, naïve, WT1

value: WT

value: naïve


title: Hep.G2.DMSO.conc2.rep1

description:
Library name: hepg.dmso.5.B03
cell lysate
hepg.dmso.5.B03

value: hepatocyte


title: lung epithelial AT2 cell, chitin, WT1


title: NB4_overexpression_HA-PML/RARα-ΔIDR_IP_HA

value: HA-Tag Rabbit antibody (Cell Signaling Technology, #3724)


title: Hep.G2.DMSO.conc3.rep1

description:
Library name: hepg.dmso.2.5.C03
cell lysate
hepg.dmso.2.5.C03


title: NB4_overexpression_HA-PML/RARα-F158E_IP_HA


title: NB4_overexpression_HA-PML/RARα_IP_HA


title: Hep.G2.DMSO.conc1.rep3

description:
Library name: hepg.dmso.10.A11
cell lysate
hepg.dmso.10.A11


title: ND_6368 [6368_5_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6368

value: Fresh frozen pancreas section


title: lung epithelial AEP cell, naïve, WT3

data_processing:
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

growth_protocol: isolated cells were immediately processed for sequencing

value: PBS


title: ND_6401 [6401_6_Ivan_Gerling]

data_processing: Raw signal intensity values from all arrays were Robust Multichip Average (RMA)  background corrected, quantile normalized, median polish summarized, and log2transformed. Processing was carried out using Partek Genomics Suite, version 6.5.


title: ND_6368 [6368_1_Ivan_Gerling]


title: Hep.G2.DMSO.conc1.rep2

description:
Library name: hepg.dmso.10.A07
cell lysate
hepg.dmso.10.A07


title: ND_6339 [6339_5_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6339


title: ND_6368 [6368_2_Ivan_Gerling]


title: ND_6401 [6401_5_Ivan_Gerling]


title: ND_6235 [6235_7_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6235


title: Hep.G2.DMSO.conc1.rep1

description:
Library name: hepg.dmso.10.A03
cell lysate
hepg.dmso.10.A03


title: ND_6232 [6232_5_Ivan_Gerling]


title: ND_6339 [6339_3_Ivan_Gerling]


title: Hep.G2.control.rep18

description:
Library name: hepg.ctrl.H09
cell lysate
hepg.ctrl.H09


title: lung epithelial AEP cell, naïve, WT2


title: UMUC3 PDX,GANAB-KD,14days, 4

city: Guangzhou

first: Yuqing

last: Li

address: North campus of Sun Yat-sen University, No.74 of Zhongshan 2nd road, Yuexiu Distinct, Guangzhou, Guangdong

institute: Sun Yat-sen University

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantifed using Space Ranger's default settings
Assembly: mm10
Library strategy: Spatial Transcriptomics

source_name: bladder cancer PDX

extract_protocol:
Samples were fixed with formalin and embedded with paraffin
Spatial transcriptome sequencing librares were prepared with 10xGenomics Visium Spatial Gene Expression Sides & Reagent kit according to manufacturer's construction

value: bladder cancer PDX

value: bladder cancer cell

value: GANAB-KD


title: ND_6339 [6339_7_Ivan_Gerling]


title: lung epithelial AEP cell, naïve, WT1

value: lung


title: UMUC3 PDX,GANAB-KD,14days, 3


title: ND_6368 [6368_3_Ivan_Gerling]


title: NB4_overexpression_empty vector_IP_HA


title: ND_6235 [6235_5_Ivan_Gerling]


title: ND_6235 [6235_2_Ivan_Gerling]


title: ND_6235 [6235_1_Ivan_Gerling]


title: lung epithelial AEP cell, Day 14, WT3

value: Influenza H1N1/PR8 (250 PFU)


title: Hep.G2.control.rep17

description:
Library name: hepg.ctrl.H05
cell lysate
hepg.ctrl.H05


title: UMUC3 PDX,GANAB-KD,14days, 2


title: Hep.G2.control.rep16

description:
Library name: hepg.ctrl.H01
cell lysate
hepg.ctrl.H01


title: lung epithelial AEP cell, Day 14, WT1

value: epithelial cell


title: ND_6339 [6339_1_Ivan_Gerling]


title: Hep.G2.control.rep15

description:
Library name: hepg.ctrl.G09
cell lysate
hepg.ctrl.G09


title: lung epithelial AEP cell, naïve, CC4


title: UMUC3 PDX,GANAB-KD,14days, 1


title: Hep.G2.control.rep14

description:
Library name: hepg.ctrl.G05
cell lysate
hepg.ctrl.G05


title: UMUC3 PDX,WT,14days, 3


title: lung epithelial AEP cell, naïve, CC3


title: ND_6232 [6232_3_Ivan_Gerling]


title: Hep.G2.control.rep13

description:
Library name: hepg.ctrl.G01
cell lysate
hepg.ctrl.G01


title: UMUC3 PDX,WT,14days, 2


title: lung epithelial AEP cell, Day 14, WT2


title: Hep.G2.control.rep12

description:
Library name: hepg.ctrl.F09
cell lysate
hepg.ctrl.F09


title: UMUC3 PDX,WT,14days, 1


title: UMUC3 PDX,WT,7days, 4


title: lung epithelial AEP cell, naïve, CC1


title: lung epithelial AEP cell, naïve, CC2


title: Hep.G2.control.rep11

description:
Library name: hepg.ctrl.F05
cell lysate
hepg.ctrl.F05


title: lung epithelial AEP cell, Day 14, CC3


title: UMUC3 PDX,WT,7days, 3


title: mAAb_6080 [6080_8_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6080


title: mAAb_6158 [6158_2_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6158


title: Hep.G2.control.rep10

description:
Library name: hepg.ctrl.F01
cell lysate
hepg.ctrl.F01


title: lung epithelial AEP cell, Day 14, CC2


title: mAAb_6080 [6080_6_Ivan_Gerling]


title: UMUC3 PDX,WT,7days, 2


title: mAAb_6158 [6158_1_Ivan_Gerling]


title: Hep.G2.control.rep9

description:
Library name: hepg.ctrl.E09
cell lysate
hepg.ctrl.E09


title: mAAb_6080 [6080_7_Ivan_Gerling]


title: UMUC3 PDX,WT,7days, 1


title: lung epithelial AEP cell, Day 14, CC1


title: Hep.G2.control.rep7

description:
Library name: hepg.ctrl.E01
cell lysate
hepg.ctrl.E01


title: D62_sg2.2_noDIFF_noRAPA_3

city: Frankfurt am Main

first: Afsheen

last: Kumar

address: Theodor-Stern-Kai 7

country: Germany

institute: University Hospital Frankfurt am Main

data_processing:
edgeR package in R was used for RNA-seq data analysis
sequence reads were trimmed for removing adapters, leading and trailing low quality or N bases (below quality 3)
scanned the read with a 4-base wide sliding window, a cut was made if the average quality per base drops below 15 (sliding window 4:15)
dropped the read if its below a specified length (36)
trimmed sequences were mapped to human genome build “hg38” using “getInBuiltAnnotation” function in R (Rsubread package)
Read count and normalization were performed using R functions “featureCounts” (Rsubread) and “cpm” (edgeR) respectively
Assembly: hg38
Supplementary files format and content: tab separated file includes normalized counts for each sample

extract_protocol:
RNA was harvested using Nucleospin RNA – 740955.50 .14 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated with Quantseq 3‟-mRNA Library Prep (Lexogen) and sequenced on a HiSeq 2500 V4 (High Output Mode) with a coverage of 10M Raw Reads per sample and a standard read length of 1x50bp (NGS Core Facility Bonn)

value: hNPCs

value: KO


title: mAAb_6267 [6267_8_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6267

extract_protocol: Total islet RNA was extracted using the PicoPure RNA kit (ThermoFisher). DNAse treatment was performed using recombinant DNase I (RNase-free DNAse kit, Worthington Biochemical Corporation).


title: mAAb_6080 [6080_5_Ivan_Gerling]


title: UUO CH6824025 No.23

city: Totsuka-ku, Yokohama

first: Yukari

last: Yasui

state: kanagawa

address: Totsuka-cho 216

department: Research Div.

country: Japan

institute: Chugai Pharmaceutical Co., Ltd.

description: FFPE Spatial Transcriptomics

data_processing:
Raw sequencing data were processed using 10xGenomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to geneexpression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
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 spots
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
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the cordinates specifyng spots
Library strategy: Spatial transcriptomics

source_name: Kidney

extract_protocol:
Prepared FFPE (formalin-fixed, paraffin-embedded) and sectioned at 5 μm thickness.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial for FFPE Gene Expression kit according to the manufacturer's instructions.

treatment_protocol: CH6824025 was orally once daily administered for 8 days.

value: Kidney

tag: model

value: UUO


title: mAAb_6267 [6267_7_Ivan_Gerling]

first: Alexandra

address: 1275 Center Drive

institute: University of Florida


title: D62_sg2.2_noDIFF_noRAPA_2


title: UUO CH6824025 No.21

description: FFPE Spatial Transcriptomics


title: D62_sg2.2_noDIFF_noRAPA_1


title: UUO Vehicle No.19

description: FFPE Spatial Transcriptomics

value: Vehicle


title: Hep.G2.control.rep5

description:
Library name: hepg.ctrl.B05
cell lysate
hepg.ctrl.B05

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using DESeq2 and Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

source_name: liver

value: liver

value: Hep G2


title: mAAb_6267 [6267_6_Ivan_Gerling]


title: Hep.G2.control.rep4

description:
Library name: hepg.ctrl.B01
cell lysate
hepg.ctrl.B01

value: hepatocyte


title: D62_sg2.2_noDIFF_RAPA_3


title: UUO Vehicle No.16

description: FFPE Spatial Transcriptomics


title: mAAb_6267 [6267_5_Ivan_Gerling]


title: Hep.G2.control.rep8

description:
Library name: hepg.ctrl.E05
cell lysate
hepg.ctrl.E05


title: D62_sg2.2_noDIFF_RAPA_2


title: UUO CH6824025 No.24

description: FFPE Spatial Transcriptomics


title: Hep.G2.control.rep3

description:
Library name: hepg.ctrl.A09
cell lysate
hepg.ctrl.A09


title: Hep.G2.control.rep2

description:
Library name: hepg.ctrl.A05
cell lysate
hepg.ctrl.A05


title: D62_sg2.2_noDIFF_RAPA_1


title: UUO CH6824025 No.22

description: FFPE Spatial Transcriptomics


title: Hep.G2.control.rep6

description:
Library name: hepg.ctrl.B09
cell lysate
hepg.ctrl.B09


title: D62_sg2.1_noDIFF_noRAPA_3


title: UUO Vehicle No.18

description: FFPE Spatial Transcriptomics


title: Sham No.13

description: FFPE Spatial Transcriptomics

value: Sham


title: D62_sg2.1_noDIFF_noRAPA_2


title: Hep.G2.control.rep1.

description:
Library name: hepg.ctrl.A01
cell lysate
hepg.ctrl.A01


title: Caco-2.MeOH.conc8.rep3

description:
Library name: caco.meoh.0.08.H12
cell lysate
caco.meoh.0.08.H12

source_name: colon

value: colon

value: epithelial


title: D62_sg2.1_noDIFF_noRAPA_1


title: NC, bio rep 3

city: Minato-ku

first: Wenyu

last: ZHANG

state: Tokyo

address: 4-6-1 Shirokanedai

department: Computational Biology and Medical Sciences

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to the mouse reference genome (mm10) using Rsubread (v2.4.3). Raw counts were obtained from read alignments using refGene for gene counts or RepeatMasker annotation for transposable elements, and then further transferred to CPM using edgeR (v3.32.1). After filtering out low-expression genes with CPM < 1, all CPM values were performed with log2 transformed for further analysis.
Assembly: mm10
Supplementary files format and content: xlsm files include CPM values for each Sample

source_name: mouse bone marrow cells transformed by SETBP1 and ASXL1 mutations

extract_protocol:
Normal murine bone marrow erythroid precursor cell or AEL murine bone marrow leukemic cells in each sample was sorted 10 x10^6 cells and extracted by RNeasy Mini Kit (QIAGEN).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Primary cells

value: WT


title: NC, bio rep 2

value: mouse bone marrow cells transformed by SETBP1 and ASXL1 mutations


title: mAAb_6267 [6267_3_Ivan_Gerling]

last: Cuaycal

value: Fresh frozen pancreas section


title: mAAb_6267 [6267_4_Ivan_Gerling]


title: Caco-2.MeOH.conc8.rep2

description:
Library name: caco.meoh.0.08.H08
cell lysate
caco.meoh.0.08.H08


title: D62_sg2.1_noDIFF_RAPA_3


title: mAAb_6080 [6080_3_Ivan_Gerling]


title: mAAb_6267 [6267_2_Ivan_Gerling]


title: Caco-2.MeOH.conc8.rep1

description:
Library name: caco.meoh.0.08.H04
cell lysate
caco.meoh.0.08.H04


title: mAAb_6197 [6197-01_9_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6197


title: mAAb_6267 [6267_10_Ivan_Gerling]


title: mAAb_6197 [6197-01_3_Ivan_Gerling]


title: mAAb_6267 [6267_13_Ivan_Gerling]


title: mAAb_6197 [6197-01_2_Ivan_Gerling]


title: NC, bio rep 1


title: AEL, bio rep 3


title: D62_sg2.1_noDIFF_RAPA_2


title: Caco-2.MeOH.conc7.rep2

description:
Library name: caco.meoh.0.15.G08
cell lysate
caco.meoh.0.15.G08


title: D62_sg2.1_noDIFF_RAPA_1


title: Caco-2.MeOH.conc7.rep3

description:
Library name: caco.meoh.0.15.G12
cell lysate
caco.meoh.0.15.G12


title: D62_sgNTC_noDIFF_noRAPA_3


title: mAAb_6197 [6197-01_12_Ivan_Gerling]


title: Caco-2.MeOH.conc7.rep1

description:
Library name: caco.meoh.0.15.G04
cell lysate
caco.meoh.0.15.G04


title: D62_sgNTC_noDIFF_noRAPA_2


title: AEL, bio rep 1


title: Caco-2.MeOH.conc6.rep3

description:
Library name: caco.meoh.0.3.F12
cell lysate
caco.meoh.0.3.F12


title: skin tissues-osi-3

city: hangzhou

first: Congying

address: Yuhangtang

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: tab-delimited text files include FPKM calues for each sample

source_name: skin

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: skin

value: osimertinib


title: Caco-2.MeOH.conc6.rep2

description:
Library name: caco.meoh.0.3.F08
cell lysate
caco.meoh.0.3.F08

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol


title: D62_sgNTC_noDIFF_noRAPA_1

value: hNPCs


title: Caco-2.MeOH.conc6.rep1

description:
Library name: caco.meoh.0.3.F04
cell lysate
caco.meoh.0.3.F04


title: skin tissues-osi-2


title: mAAb_6197 [6197-01_11_Ivan_Gerling]


title: mAAb_6197 [6197-01_1_Ivan_Gerling]


title: skin tissues-osi-1


title: AEL, bio rep 2


title: D62_sgNTC_noDIFF_RAPA_2


title: mAAb_6167 [6167-01_8_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6167


title: mAAb_6167 [6167-01_7_Ivan_Gerling]


title: skin tissues-untreat-3

value: control


title: Caco-2.MeOH.conc5.rep3

description:
Library name: caco.meoh.0.6.E12
cell lysate
caco.meoh.0.6.E12


title: Caco-2.MeOH.conc5.rep2

description:
Library name: caco.meoh.0.6.E08
cell lysate
caco.meoh.0.6.E08


title: D62_sgNTC_noDIFF_RAPA_1


title: skin tissues-untreat-2


title: D62_sg2.2_DIFF_noRAPA_3

value: KO


title: Caco-2.MeOH.conc5.rep1

description:
Library name: caco.meoh.0.6.E04
cell lysate
caco.meoh.0.6.E04


title: mAAb_6197 [6197_5_Ivan_Gerling]


title: skin tissues-untreat-1


title: D62_sgNTC_noDIFF_RAPA_3


title: Caco-2.MeOH.conc4.rep3

description:
Library name: caco.meoh.1.2.D12
cell lysate
caco.meoh.1.2.D12


title: Caco-2.MeOH.conc4.rep2

description:
Library name: caco.meoh.1.2.D08
cell lysate
caco.meoh.1.2.D08


title: Caco-2.MeOH.conc4.rep1

description:
Library name: caco.meoh.1.2.D04
cell lysate
caco.meoh.1.2.D04


title: D62_sg2.2_DIFF_noRAPA_2


title: mAAb_6080 [6080_2_Ivan_Gerling]


title: D62_sg2.2_DIFF_RAPA_3


title: MS21026-adipose-44% fat + fiber-pooled-snATAC-seq-rep1

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were conducted using the Cell Ranger ATAC v2.0.0 for snATAC-Seq
For quality control and filtering purposes, snATAC-Seq data, nuclei having a TSS enrichment <4, or <4,000 were removed.
Assembly: GRCm38
Supplementary files format and content: adipose_snATAC.h5ad

source_name: gonadal fat pad

extract_protocol:
Tissue (~100 ug tissue) was homogenized in a pre-warmed lysis buffer in Polytron/dounce. Leave on ice for 5 mins.The homogenate was filtered through 40um filter.The filtrate was placed in centrifuge bottles or tubes and under-layered with 0.25 volumes of sucrose solution (750ul). Nuclei were centrifuged in a pre-chilled swinging bucket rotor (4°C) through the sucrose cushion at 3,000xg for 20 min. The fat layer was removed using fisher plastic pasteur pipette. The supernatant was removed gently by pouring it out.The nuclear pellet under the fat floatation pellet was gently and quickly re-suspended in with 100 ul lysis buffer and transfer to new 1.5 ml Eppendorf tube. Nuclei were centrifuged in a pre-chilled rotor (4°C) at 3000 x g for 5mins. Nuclei were re-suspended in 100ul DPBSB (1% BSA in DPBS). Filter Nuclei sample with a 40-μm pore size filter.
version 1 10x ATAC-seq chemistry

treatment_protocol: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected at sixteen weeks of age.

value: gonadal fat pad

tag: diet

value: 44% fat + fiber

tag: container id

tag: sequencing id


title: MS21024-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: MS21022-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: D62_sg2.2_DIFF_noRAPA_1


title: mAAb_6167 [6167-01_1_Ivan_Gerling]

city: Gainesville


title: D62_sg2.2_DIFF_RAPA_2


title: mAAb_6167 [6167-01_3_Ivan_Gerling]


title: mAAb_6167 [6167-01_4_Ivan_Gerling]


title: Caco-2.MeOH.conc3.rep3

first: Niladri

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

description:
Library name: caco.meoh.2.5.C12
cell lysate
caco.meoh.2.5.C12


title: mAAb_6167 [6167_4_Ivan_Gerling]


title: mAAb_6167 [6167_6_Ivan_Gerling]


title: MS20103-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: MS20101-adipose-10% fat + fiber-pooled-snATAC-seq-rep1

value: 10% fat + fiber


title: D62_sg2.1_DIFF_noRAPA_3


title: Caco-2.MeOH.conc3.rep1

description:
Library name: caco.meoh.2.5.C04
cell lysate
caco.meoh.2.5.C04


title: mAAb_6167 [6167_3_Ivan_Gerling]


title: MS20099-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: D62_sg2.2_DIFF_RAPA_1


title: mAAb_6167 [6167_2_Ivan_Gerling]


title: Caco-2.MeOH.conc2.rep3

description:
Library name: caco.meoh.5.B12
cell lysate
caco.meoh.5.B12


title: MS20097-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: D62_sg2.1_DIFF_noRAPA_1


title: D62_sg2.1_DIFF_RAPA_3


title: Caco-2.MeOH.conc2.rep2

description:
Library name: caco.meoh.5.B08
cell lysate
caco.meoh.5.B08


title: D62_sg2.1_DIFF_noRAPA_2


title: MS20095-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: D62_sg2.1_DIFF_RAPA_2


title: MS20093-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: mAAb_6158 [6158_8_Ivan_Gerling]


title: Caco-2.MeOH.conc3.rep2

description:
Library name: caco.meoh.2.5.C08
cell lysate
caco.meoh.2.5.C08


title: Caco-2.MeOH.conc1.rep3

description:
Library name: caco.meoh.10.A12
cell lysate
caco.meoh.10.A12


title: mAAb_6158 [6158_5_Ivan_Gerling]


title: Caco-2.MeOH.conc2.rep1

description:
Library name: caco.meoh.5.B04
cell lysate
caco.meoh.5.B04


title: MS20091-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: Caco-2.MeOH.conc1.rep2

description:
Library name: caco.meoh.10.A08
cell lysate
caco.meoh.10.A08


title: D62_sg2.1_DIFF_RAPA_1


title: MS20076-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: mAAb_6080 [6080_1_Ivan_Gerling]


title: D62_sgNTC_DIFF_noRAPA_2


title: mAAb_6158 [6158_4_Ivan_Gerling]


title: Caco-2.H2O2.conc8.rep3

description:
Library name: caco.h2o2.0.025.H10
cell lysate
caco.h2o2.0.025.H10


title: hbmsc-0.5kpa-7 days- rep2

city: Chengdu

first: Yu

last: Shen

address: NO.2025 Chengluo Avenue

institute: Chengdu University

description: Passage 3-4 hbmsc were used in this experiment.

hyb_protocol: 12.5 ug of fragmented and labeled cRNA were added and hybridized for 16 hr at 45C on Affymetrix GeneChip Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression Console Software and Affymetrix® Transcriptome Analysis Console (TAC) Softwareis used to analysis the raw data.

label: biotin

source_name: Human bone marrow mesenchymal stem cells,  0.5kpa substrates, 7 days.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: Human bone marrow mesenchymal stem cells P2 were obtained by purchase (HUXMA-01001, Cyagen technology, China), and the cell surface markers and differentiation ability have been verified. Cells were inoculated at 37°C in a 5% CO2 humidified incubator and complete growth  medium (HUXMA-90011, Cyagen technology, China) was used. When the cells are approximately 80 to 90% confluence, they were dissociated with Trypsin-EDTA and passaged.  P3-4 hbmsc were used for follow-up tests.

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

treatment_protocol: The cells were separately seeded on the extracellular subtrates with the rigidity of 32kpa and 0.5kpa. The cells were inoculated at 37°C in a 5% CO2 humidified incubator and the complete medium was replaced every 2 days. The cells were collected for test after 3 days and 7 days after incubation.

tag: time

value: 7 days


title: MS20070-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: MS20064-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: D62_sgNTC_DIFF_RAPA_3


title: hbmsc-0.5kpa-7 days- rep3

value: Human bone marrow mesenchymal stem cells


title: hbmsc-32kpa-7 days- rep3

source_name: Human bone marrow mesenchymal stem cells,  32kpa substrates, 7 days.


title: D62_sgNTC_DIFF_RAPA_2


title: Caco-2.H2O2.conc7.rep3

description:
Library name: caco.h2o2.0.05.G10
cell lysate
caco.h2o2.0.05.G10


title: MS20038-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: hbmsc-32kpa-7 days- rep2


title: MS20062-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: Caco-2.H2O2.conc8.rep1

description:
Library name: caco.h2o2.0.025.H02
cell lysate
caco.h2o2.0.025.H02


title: D62_sgNTC_DIFF_noRAPA_3


title: Caco-2.H2O2.conc7.rep2

description:
Library name: caco.h2o2.0.05.G06
cell lysate
caco.h2o2.0.05.G06


title: MS20072-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: BRD3-KD-plus-LPS-3

city: Changsha

first: Nian

state: Hunan

address: No.110 Xiangya Road

institute: Central south university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts data for each Sample

growth_protocol: THP1 monocytes were maintained in RPMI 1640  supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using E.Z.N.A.® total RNA kit. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library prep kit, and the library quantity was determined using the Picogreen method.

treatment_protocol: lipopolysaccharide (100ng/ml) for 3h

value: Human monocytes

value: BRD3 knockdown

value: lipopolysaccharide


title: hbmsc-0.5kpa-7 days- rep1


title: D62_sgNTC_DIFF_noRAPA_1


title: Caco-2.H2O2.conc7.rep1

description:
Library name: caco.h2o2.0.05.G02
cell lysate
caco.h2o2.0.05.G02

value: colon

value: epithelial


title: Caco-2.MeOH.conc1.rep1

description:
Library name: caco.meoh.10.A04
cell lysate
caco.meoh.10.A04


title: hbmsc-32kpa-7 days- rep1


title: Caco-2.H2O2.conc8.rep2

description:
Library name: caco.h2o2.0.025.H06
cell lysate
caco.h2o2.0.025.H06


title: hbmsc-0.5kpa-3 days- rep3

source_name: Human bone marrow mesenchymal stem cells,  0.5kpa substrates, 3 days.

value: 3 days


title: hbmsc-0.5kpa-3 days- rep2


title: D62_sgNTC_DIFF_RAPA_1

value: WT


title: BRD3-KD-plus-LPS-2


title: MS20032-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: MS20036-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: MS20027-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: non-Alzheimer's Disease_Biological replicate 10

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

description: Transcriptome expression profiling of postmortem human hippocampus non-AD brain

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Human Transcriptome Array (HTA) 2.0. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into the Transcriptome Analysis Console (TAC) Software 4.0 and CHP files were generated.

source_name: Postmortem human hippocampus brain

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Postmortem human hippocampus were cut out from each brain and preserved at −80 °C until RNA preparation. Written informed consent for all subjects was obtained from their families. Neuropathologic changes were examined as described previously (PMID: 20739649).

extract_protocol: Total RNA was isolated using a combination of Isogen and the RNeasy Mini Kit, according to the manufacturers’ instructions.

tag: gender

value: Male


title: BRD3-KD-3

value: PBS


title: Caco-2.H2O2.conc6.rep1

city: Sainte-Anne-de-Bellevue

description:
Library name: caco.h2o2.0.1.F02
cell lysate
caco.h2o2.0.1.F02


title: MS20020-adipose-10% fat + fiber-pooled-snATAC-seq-rep1


title: BRD3-KD-plus-LPS-1


title: BRD3-KD-2


title: hbmsc-32kpa-3 days- rep3

source_name: Human bone marrow mesenchymal stem cells,  32kpa substrates, 3 days.


title: non-Alzheimer's Disease_Biological replicate 9


title: hbmsc-32kpa-3 days- rep2


title: non-Alzheimer's Disease_Biological replicate 8


title: Caco-2.H2O2.conc5.rep3

description:
Library name: caco.h2o2.0.21.E10
cell lysate
caco.h2o2.0.21.E10


title: hbmsc-0.5kpa-3 days- rep1


title: Caco-2.H2O2.conc5.rep2

description:
Library name: caco.h2o2.0.21.E06
cell lysate
caco.h2o2.0.21.E06


title: BRD3-KD-1


title: Caco-2.H2O2.conc6.rep3

description:
Library name: caco.h2o2.0.1.F10
cell lysate
caco.h2o2.0.1.F10


title: non-Alzheimer's Disease_Biological replicate 7

value: Female


title: LPS-3h-3


title: Caco-2.H2O2.conc5.rep1

description:
Library name: caco.h2o2.0.21.E02
cell lysate
caco.h2o2.0.21.E02


title: MS20015_Pool-7-islets-10% fat + fiber-pooled-rep1

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were conducted using the Cell Ranger software v6.1.1 for scRNA-Seq
Demuxlet software was used to separate cells originating from different strain genetic backgrounds in the pooled samples.
For quality control and filtering purposes, in scRNA-Seq data low-quality single cells having <500 islet expressed genes; >20% islet mitochondrial transcripts; or >50% ribosomal transcripts were filtered out. In addition, genes mapping to less than three single cells per sequenced library were also removed.
Assembly: GRCm38
Supplementary files format and content: islet_scRNA.h5ad

source_name: islets of Langerhans

growth_protocol: Isolated Islets are centrifuged at 180 rcf x 3 minutes, supernatant removed, then transferred to 24 well non-tissue culture treated plate after adding one mL complete RPMI. Islets are then placed in a 37 incubator overnight. Next day, islets are transferred to a 15ml conical tube, centrifuged at 180 rcf x 3 minutes, supernatant removed. Islets are resuspended in 1-2 ml Accutase, pipetted up and down every 30 seconds while watching islet “clumps” dissociate into single cell suspension. 2-3 ml RPMI is added to complete medium to stop dissociation and pipetted gently to mix. Dissociated cells are pipetted through 20 um strainer into fresh 15ml conical tube. Centrifuge again at 230 rcf x 3 minutes, supernatant removed. Cell pellet is resuspended in 2-3 ml RPMI complete medium and mixed by pipetting again. Lastly, cell pellet is resuspended in volume of medium or buffer required for standard single cell capture. Countess used for cell count and viability estimates.

extract_protocol:
Dissociation protocol for islets; after overnight incubation, cells were dissociated prior to loading on the 10X Chromium
version 3 10x Genomics RNA-seq chemistry

value: islets of Langerhans


title: MS20045_STC6197-islets-44% fat + fiber-pooled-rep1


title: hbmsc-32kpa-3 days- rep1


title: Caco-2.H2O2.conc6.rep2

description:
Library name: caco.h2o2.0.1.F06
cell lysate
caco.h2o2.0.1.F06


title: MS20022-adipose-44% fat + fiber-pooled-snATAC-seq-rep1


title: Caco-2.H2O2.conc4.rep3

description:
Library name: caco.h2o2.0.42.D10
cell lysate
caco.h2o2.0.42.D10


title: LPS-3h-2


title: non-Alzheimer's Disease_Biological replicate 5


title: MS20046_STC6198-islets-44% fat + fiber-pooled-rep1


title: LPS-3h-1


title: MS20065_STC6326-islets-44% fat + fiber-pooled-rep1


title: non-Alzheimer's Disease_Biological replicate 4


title: Caco-2.H2O2.conc4.rep2

description:
Library name: caco.h2o2.0.42.D06
cell lysate
caco.h2o2.0.42.D06


title: Control-3


title: Caco-2.H2O2.conc4.rep1

description:
Library name: caco.h2o2.0.42.D02
cell lysate
caco.h2o2.0.42.D02


title: MS20007_Pool-1-islets-10% fat + fiber-pooled-rep1


title: MS20066_STC6327-islets-44% fat + fiber-pooled-rep1


title: non-Alzheimer's Disease_Biological replicate 6


title: non-Alzheimer's Disease_Biological replicate 2


title: Caco-2.H2O2.conc3.rep3

description:
Library name: caco.h2o2.0.83.C10
cell lysate
caco.h2o2.0.83.C10


title: non-Alzheimer's Disease_Biological replicate 3


title: Control-2


title: non-Alzheimer's Disease_Biological replicate 1


title: 71_D7

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7

data_processing:
Human: Raw sequencing reads in the fastq files were mapped with STAR version 2.7.1a to the Gencode release 36 based on the GRCh38.p12 reference human genome with the corresponding GTF files.
Table counts was obtained with FeatureCounts function in the package subread, version 1.6.4
Assembly: GRCh38.p12
Supplementary files format and content: txt file containing the table counts obtained with FeatureCounts

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7

extract_protocol:
Quick-RNA microprep
NGS libraries with Globin/Ribosome depletion were prepared according to the manual Protocol for use with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) (New England Biolabs) (versión 1.0, 7/20) and Protocol for use with FFPE RNA, NEBNext rRNA Depletion for Illumina® (NEB #E6310) (New England Biolabs) (Version 3.1, 5/20)  Library Prep Kit for Illumina® (New England Biolabs) (Version 1.0, 4/17)

value: peripheral blood

tag: disease state

tag: batch


title: Control-1

tag: genotype


title: Caco-2.H2O2.conc3.rep2

last: Basu

description:
Library name: caco.h2o2.0.83.C06
cell lysate
caco.h2o2.0.83.C06

tag: tissue

tag: treatment


title: MS20077_STC6682-islets-44% fat + fiber-pooled-rep1


title: MS20078_STC6912-islets-10% fat + fiber-pooled-rep1


title: Caco-2.H2O2.conc3.rep1

description:
Library name: caco.h2o2.0.83.C02
cell lysate
caco.h2o2.0.83.C02

tag: cell line


title: Alzheimer's Disease_Biological replicate 8

description: Transcriptome expression profiling of postmortem human hippocampus AD brain


title: Alzheimer's Disease_Biological replicate 6


title: Caco-2.H2O2.conc2.rep2

description:
Library name: caco.h2o2.1.67.B06
cell lysate
caco.h2o2.1.67.B06

tag: cell type


title: Caco-2.H2O2.conc2.rep3

description:
Library name: caco.h2o2.1.67.B10
cell lysate
caco.h2o2.1.67.B10


title: MS20079_STC6913-islets-44% fat + fiber-pooled-rep1


title: Alzheimer's Disease_Biological replicate 7


title: 70_D7


title: MS20082_STC6916-islets-10% fat + fiber-pooled-rep1


title: Caco-2.H2O2.conc2.rep1

description:
Library name: caco.h2o2.1.67.B02
cell lysate
caco.h2o2.1.67.B02


title: 70_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0


title: 71_D0


title: Alzheimer's Disease_Biological replicate 5


title: MS20083_STC6917-islets-44% fat + fiber-pooled-rep1


title: 69_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7


title: Alzheimer's Disease_Biological replicate 4


title: MS20073_STC6680-islets-44% fat + fiber-pooled-rep1


title: Caco-2.H2O2.conc1.rep3

description:
Library name: caco.h2o2.3.33.A10
cell lysate
caco.h2o2.3.33.A10


title: 69_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0


title: MS21007_STC11425-islets-10% fat + fiber-pooled-rep1


title: Caco-2.H2O2.conc1.rep2

description:
Library name: caco.h2o2.3.33.A06
cell lysate
caco.h2o2.3.33.A06


title: Alzheimer's Disease_Biological replicate 3


title: 68_D7


title: Alzheimer's Disease_Biological replicate 2


title: Caco-2.H2O2.conc1.rep1

description:
Library name: caco.h2o2.3.33.A02
cell lysate
caco.h2o2.3.33.A02


title: MS21011_STC11426-islets-10% fat + fiber-pooled-rep1


title: Caco-2.DMSO.conc8.rep3

description:
Library name: caco.dmso.0.08.H11
cell lysate
caco.dmso.0.08.H11


title: Alzheimer's Disease_Biological replicate 1


title: 68_D0


title: 67_D0


title: MS21015_STC11428-islets-10% fat + fiber-pooled-rep1


title: Colon of mice gavaged by Bacteroides thetaiotaomicron biol rep6

city: Shanghai

first: Shuo

last: Xu

address: Zhizaoju Road

institute: Shanghai ninth people's hospital

description: Library name: CS7

data_processing:
RNA-seq
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: RNA-seq
Supplementary files format and content: TPL2021071189.tar.gz

source_name: Colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Colon

value: primary

value: tissue

value: wt

value: Drug stimulation


title: MS21017_STC11429-islets-44% fat + fiber-pooled-rep1

value: 44% fat + fiber


title: Caco-2.DMSO.conc8.rep1

description:
Library name: caco.dmso.0.08.H03
cell lysate
caco.dmso.0.08.H03

source_name: colon


title: 66_D0


title: Colon of mice gavaged by Bacteroides thetaiotaomicron biol rep4

description: Library name: CS5


title: MS21019_STC11430-islets-10% fat + fiber-pooled-rep1

value: 10% fat + fiber


title: Caco-2.DMSO.conc7.rep3

description:
Library name: caco.dmso.0.15.G11
cell lysate
caco.dmso.0.15.G11


title: 65_D0


title: Colon of mice gavaged by Bacteroides thetaiotaomicron biol rep3

description: Library name: CS4


title: MS21025-adipose-44% fat + fiber-pooled-RNA-seq rep1

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were conducted using the Cell Ranger software v6.1.1 for scRNA-Seq
Demuxlet software was used to separate cells originating from different strain genetic backgrounds in the pooled samples.
For quality control and filtering purposes, in scRNA-Seq data low-quality single cells having <400 (adipose) expressed genes; >10% (adipose) mitochondrial transcripts; or >50% ribosomal transcripts were filtered out. In addition, genes mapping to less than three single cells per sequenced library were also removed.
Assembly: GRCm38
Supplementary files format and content: adipose_snRNA.h5ad

extract_protocol:
Tissue (~100 ug tissue) was homogenized in a pre-warmed lysis buffer in Polytron/dounce. Leave on ice for 5 mins.The homogenate was filtered through 40um filter.The filtrate was placed in centrifuge bottles or tubes and under-layered with 0.25 volumes of sucrose solution (750ul). Nuclei were centrifuged in a pre-chilled swinging bucket rotor (4°C) through the sucrose cushion at 3,000xg for 20 min. The fat layer was removed using fisher plastic pasteur pipette. The supernatant was removed gently by pouring it out.The nuclear pellet under the fat floatation pellet was gently and quickly re-suspended in with 100 ul lysis buffer and transfer to new 1.5 ml Eppendorf tube. Nuclei were centrifuged in a pre-chilled rotor (4°C) at 3000 x g for 5mins. Nuclei were re-suspended in 100ul DPBSB (1% BSA in DPBS). Filter Nuclei sample with a 40-μm pore size filter.
Version 3, 10x Genomics RNA-seq chemistry

treatment_protocol: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected after at sixteen weeks of age.

value: gonadal fat pad


title: MS21005_STC11424-islets-44% fat + fiber-pooled-rep1


title: 63_D7


title: Caco-2.DMSO.conc7.rep1

description:
Library name: caco.dmso.0.15.G03
cell lysate
caco.dmso.0.15.G03

value: colon


title: Caco-2.DMSO.conc6.rep3

description:
Library name: caco.dmso.0.3.F11
cell lysate
caco.dmso.0.3.F11

value: epithelial


title: MS21023-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: 63_D0


title: Colon of mice gavaged by Bacteroides thetaiotaomicron biol rep2

description: Library name: CS3


title: MS21013_STC11427-islets-10% fat + fiber-pooled-rep1


title: Caco-2.DMSO.conc8.rep2

description:
Library name: caco.dmso.0.08.H07
cell lysate
caco.dmso.0.08.H07


title: Colon of mice gavaged by Bacteroides thetaiotaomicron biol rep1

description: Library name: CS2


title: MS21021-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: Caco-2.DMSO.conc6.rep2

description:
Library name: caco.dmso.0.3.F07
cell lysate
caco.dmso.0.3.F07


title: MS20102-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: Colon of mice gavaged by Bacteroides thetaiotaomicron

description: Library name: CS1


title: 61_DO


title: 62_D0


title: Colon of mice gavaged by Bacteroides thetaiotaomicron biol rep5

description: Library name: CS6


title: Caco-2.DMSO.conc6.rep1

description:
Library name: caco.dmso.0.3.F03
cell lysate
caco.dmso.0.3.F03


title: MS20100-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: Colon of mice gavaged by PBS biol rep6

description: Library name: CH7


title: Caco-2.DMSO.conc5.rep3

description:
Library name: caco.dmso.0.6.E11
cell lysate
caco.dmso.0.6.E11


title: Caco-2.DMSO.conc7.rep2

description:
Library name: caco.dmso.0.15.G07
cell lysate
caco.dmso.0.15.G07


title: MS20098-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: 61_D7


title: Colon of mice gavaged by PBS biol rep5

description: Library name: CH6


title: 65_D7


title: Caco-2.DMSO.conc5.rep2

description:
Library name: caco.dmso.0.6.E07
cell lysate
caco.dmso.0.6.E07


title: 59_D7


title: Caco-2.DMSO.conc5.rep1

description:
Library name: caco.dmso.0.6.E03
cell lysate
caco.dmso.0.6.E03


title: Colon of mice gavaged by PBS biol rep4

description: Library name: CH5


title: Colon of mice gavaged by PBS biol rep3

description: Library name: CH4


title: 58_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7


title: MS20096-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: Colon of mice gavaged by PBS biol rep2

description: Library name: CH3


title: MS20092-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: 59_D0


title: 58_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0


title: Caco-2.DMSO.conc4.rep3

description:
Library name: caco.dmso.1.2.D11
cell lysate
caco.dmso.1.2.D11


title: Colon of mice gavaged by PBS

description: Library name: CH1


title: MS20090-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: Caco-2.DMSO.conc4.rep1

description:
Library name: caco.dmso.1.2.D03
cell lysate
caco.dmso.1.2.D03


title: MS20075-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: Caco-2.DMSO.conc4.rep2

description:
Library name: caco.dmso.1.2.D07
cell lysate
caco.dmso.1.2.D07


title: 57_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0


title: 57_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19


title: Colon of mice gavaged by PBS biol rep1

description: Library name: CH2


title: Caco-2.DMSO.conc3.rep3

description:
Library name: caco.dmso.2.5.C11
cell lysate
caco.dmso.2.5.C11


title: MS20071-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: BL/6 LSK with ILC2sn from ILC2s with IL-33 3

city: Bern

first: Pascal

last: Naef

address: Murtenstrasse 35

country: Switzerland

institute: University of Bern

data_processing:
fastp was used to process the raw reads (removing reads containing adapter and poly-N sequences and low-quality reads) (at Novogene)
Clean reads were mapped using the Spliced Transcripts Alignment to a Reference (STAR) software (at Novogene)
Quantification (read counts) was done using FeatureCounts
Assembly: mm10
Supplementary files format and content: Csv file contains the raw reads for each sample (per row)

source_name: Lin-sca1+cKit+ (LSK)

growth_protocol: BL/6 mice were sacrificed and the long bones, hips, and spines were harvested, crushed, and AcK lysed. The single cells were purified for lin- cells (CD3-CD19-Gr1-Ter119-) by magnetic cell separation (MACS), and stained for the purification of ILC2s (lin-cKit-sca1+CD25+CD127+) LSKs (lin-cKit+sca1+). The ILC2s and LSKs were sorted using an ARIA III from BD.

extract_protocol:
LSKs were suspended in RLT lysis buffer (Quiagen) and sent to Novogene Europe on dry ice for RNA isolation.
RNA libraries for RNA-seq were prepared using NEBNext Ultra TM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Sorted ILC2s were cultured in IMDM 10% (5'000 cells per 100ul), supplemented with rmIL-2 (50U/ml) and rmIL-7 (50ng/ml), +/- rmIL-33. After 24h, the ILC2 conditioned supernatant (ILC2sn) was harvested from the wells and frozen at -80°
Sorted LSKs were cultred in IMDM 10% (25000 cells per 100ul), either with or without IL-33, or in ILC2sn (originating from ILC2s treated with or without rmIL-33)

value: Lin-sca1+cKit+ (LSK)

value: BL/6 WT

value: 24h culture +SCF +Flt3L + ILC2sn (+ IL-33)


title: Caco-2.DMSO.conc3.rep2

description:
Library name: caco.dmso.2.5.C07
cell lysate
caco.dmso.2.5.C07


title: 56_D7


title: BL/6 LSK with ILC2sn from ILC2s with IL-33 2


title: MS20069-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: 56_D0


title: Caco-2.DMSO.conc3.rep1

description:
Library name: caco.dmso.2.5.C03
cell lysate
caco.dmso.2.5.C03


title: MS20094-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: BL/6 LSK with ILC2sn from ILC2s with IL-33 1


title: 55_D0


title: BL/6 LSK with ILC2sn from ILC2s w/o IL-33 4

value: 24h culture +SCF +Flt3L + ILC2sn (no IL-33)


title: Caco-2.DMSO.conc2.rep2

description:
Library name: caco.dmso.5.B07
cell lysate
caco.dmso.5.B07


title: 53_D0


title: MS20061-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: BL/6 LSK with ILC2sn from ILC2s w/o IL-33 3


title: MS20037-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: 52_D7


title: Caco-2.DMSO.conc2.rep1

description:
Library name: caco.dmso.5.B03
cell lysate
caco.dmso.5.B03


title: MS20035-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: BL/6 LSK with ILC2sn from ILC2s w/o IL-33 2


title: Caco-2.DMSO.conc2.rep3

description:
Library name: caco.dmso.5.B11
cell lysate
caco.dmso.5.B11


title: BL/6 LSK with ILC2sn from ILC2s w/o IL-33 1


title: 52_D0


title: Caco-2.DMSO.conc1.rep3

description:
Library name: caco.dmso.10.A11
cell lysate
caco.dmso.10.A11


title: MS20028-adipose-44% fat + fiber-pooled-RNA-seq rep1


title: BL/6 LSK with IL-33 2

value: 24h culture +SCF +Flt3L + IL-33


title: Caco-2.DMSO.conc1.rep2

description:
Library name: caco.dmso.10.A07
cell lysate
caco.dmso.10.A07


title: MS20063-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: MS20023-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: Caco-2.DMSO.conc1.rep1

description:
Library name: caco.dmso.10.A03
cell lysate
caco.dmso.10.A03


title: Caco-2.control.rep18

description:
Library name: caco.ctrl.H09
cell lysate
caco.ctrl.H09


title: 51_D0


title: BL/6 LSK with IL-33 3


title: MS20021-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: BL/6 LSK with IL-33 1


title: 49_D0


title: Caco-2.control.rep17

description:
Library name: caco.ctrl.H05
cell lysate
caco.ctrl.H05


title: 50_D0


title: 48_D0


title: MS20019-adipose-10% fat + fiber-pooled-RNA-seq rep1


title: BL/6 LSKs w/o IL-33 4

value: 24h culture +SCF +Flt3L


title: BL/6 LSKs w/o IL-33 3


title: MS21020-Islets-10% fat + fiber-pooled-rep1

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were conducted using the Cell Ranger ATAC v2.0.0 for snATAC-Seq
Demuxlet software was used to separate cells originating from different strain genetic backgrounds in the pooled samples.
For quality control and filtering purposes, snATAC-Seq data, nuclei having a TSS enrichment <4, or <4,000 were removed.
Assembly: GRCm38
Supplementary files format and content: islet_snATAC.h5ad

extract_protocol:
Dissociation protocol for islets; after overnight incubation, cells were dissociated prior to loading on the 10X Chromium
version 1 10x ATAC-seq chemistry

value: islets of Langerhans


title: Caco-2.control.rep16

description:
Library name: caco.ctrl.H01
cell lysate
caco.ctrl.H01


title: 47_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7

value: peripheral blood


title: BL/6 LSKs w/o IL-33 2