title: 12367726_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 16

value: Grade III


title: 12600485_surgery (BC360 9.15.2023)

status: Public on Apr 22 2026

type: RNA

city: Oklahoma City

first: Suresh

last: Niture

state: OK

address: 800 NE 10th St, Department Of Radiation Oncology

country: USA

institute: Department of Radiation Oncology, Stephenson Cancer Center, Oklahoma Unive

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 18

hyb_protocol: Panel standard is a DNA oligo blend containing all BC360 and IO 360 probe target sequences, that is run on each cartridge within the experiment for normalization of non-PAM50 genes; while reference sample is an RNA oligo blend containing PAM50 probe target sequences for PAM50 genes.

scan_protocol: nCounter technology provides a robust method for multiplexing up to 800 gene expression targets using direct detection technology. The simple, efficient workflow requires just 15 minutes hands-on time for most panels using an automated benchtop processing system and produces highly reproducible data, requiring no amplification or technical replicates in less than 24 hours. This workflow rapidly accelerates biomarker validation and biomarker development, providing gene expression data you can count on.

data_processing:
nCounter Analysis System and nSolver Analysis Software
Housekeeper Normalization for non-TIS and non-PAM50 Genes
Genes are normalized using a ratio of the expression value to the geometric mean of all housekeeping genes on the panel.
Housekeeper Normalization for TIS Genes
Genes in the TIS signature are normalized using a ratio of the expression value to the geometric mean of the housekeeper genes used only for the TIS signature.
Housekeeper Normalization for PAM50 Genes
Genes in the PAM50 signature are normalized using a ratio of the expression value to the geometric mean of the housekeeper genes used only for the PAM50 signature.
Panel Standard Normalization for non-PAM50 Genes
Genes not in the PAM50 signature are additionally normalized using a ratio of the housekeeper-normalized data and a panel standard run on the same cartridge as the observed data. In the absence of a panel standard column, values from panel standard run on the same codeset lot as the observed data may be substituted. If a cartridge is missing a panel standard run, the average of all panel standards present is substituted for that cartridge.
Reference Sample Normalization for PAM50 genes
Genes in the PAM50 signature are additionally normalized using a ratio of the housekeeper-normalized data and a reference sample run on the same codeset lot from a NanoString archive is used.
Final Adjustments
The housekeeper-normalized and panel standard-normalized data is Log(2) transformed. A constant of 8 is added to TIS so that it is on the same scale as investigational use only (IUO) TIS, making scores comparable across research use only (RUO) and IUO assays. Other non-TIS signatures are also adjusted with constants to express values in a similar range.
Differential Expression Analysis
Grouping Variable
Differential expression is fit on a per gene or per signature basis using a linear model for analyses without a blocking factor. The statistical model uses the expression value or signature score as the dependent variable and fits a grouping variable as a fixed effect to test for differences in the levels of that grouping variable.
Expression(gene or signature)= μ+Group+ε
P-values are adjusted within each analysis, gene or signature, and on the grouping variable level difference t-test using the Benjamini and Yekutieli False Discovery Rate (FDR) adjustment to account for correlations amongst the tests. All models are fit using the limma package in R.

label: Photocleavable oligonucleotide

molecule: total RNA

organism: Homo sapiens

source_name: primary breast cancer

label_protocol: The nanoString (nCounter Run) technology was used, and two approaches were applied for tumor analysis: 1) The nCounter® Breast Cancer 360™ panel and 2) PanCancer IO 360 panel.  Breast Cancer 360™ data analysis report provides a unique 360° view of gene expression for the breast tumor microenvironment and immune response, and PanCancer IO 360 panel provides a unique 360 ° view of gene expression for the tumor, microenvironment, and immune response. 19 BC samples passed all QCs, which include 5 Pre-RT (biopsy), and 14 post-RT (surgery). Three samples failed housekeeping geomean QC and were excluded from the analysis. Two-panel standards were used for normalization.  In IO 360 panel, 20 samples passed all QCs. 2 samples failed housekeeping geomean QC and were excluded from the analysis. One panel standard was used for normalization.

growth_protocol: Breast Cancer Patients were recruited at Myco College of Medicine, Jacksonville, FL. The study was conducted through a protocol approved by the Myco College of Medicine Institutional Review Board (IRB)

extract_protocol: Paraffin-embedded tissue biopsy samples from 20 BC patients (5 biopsy and  15 post RT surgical) were used to extract total RNA. We used whole sections of biopsy and surgical tissue for RNA extraction. RNA samples were isolated using the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The quality and concentration of RNA were estimated using the NanoDrop ND-1000 spectrophotometer. Further analysis of RNA integrity was performed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer.

treatment_protocol: n this cohort study, we isolated 20 tumor tissues from 20 breast cancer patients, of which 5 tumors were collected during diagnosis and biopsy.  These patients were treated with standard radiation therapy (RT), and treatment included a total of 30 Gy radiation in three weeks.

tag: tissues

value: primary breast cancer

tag: race

value: Not Hispanic or Latino

tag: histology

value: Grade II

tag: Sex

value: Female

tag: Stage

tag: age


title: CTi003-A_d0_fresh_Rep2

type: SRA

city: Hannover

first: Maximilian

last: Schinke

address: Nikolai-Fuchs-Str. 1

country: Germany

institute: Fraunhofer ITEM

description: Library name: Sample 4

library_source: transcriptomic

data_processing:
Sequencing, QC and mapping and counting was performed by Novogene Co., Ltd.
Sequence reads were trimmed for adapters. Reads containing N >10% and low quality reads with Qscore of over 50% bases of the read <=5 were removed.
Clean reads were mapped to reference genome using HISAT2. Mapped regions were classified as exon, intron, or intergenic region
Assembly: Homo_sapiens_Ensemble_94_gene (Novogene Co., Ltd.)
Supplementary files format and content: csv file includes raw count values for each sample
Supplementary files format and content: csv file FPKM  values for each sample

source_name: blood

growth_protocol: iPSC-Mac were harvested weekly from adherent differentiation in X-VIVO™ 15 medium + 2 U/mL penicillin-streptomycin, 2mM L-glutamine, 50 µM β-mercaptoethanol (all from Gibco) supplemented with 25 ng/mL hIL-3 and 50 ng/mL human macrophage colony stimulating factor (hM-CSF, Peprotech)).

extract_protocol:
On day 3, the cells were washed with PBS and resuspended in RNA lysis buffer. RNA isolation was performed with the Direct-zol RNA Microprep Kit (Zymo Research) according to manufacturer’s instructions.
Library construction was performed at Novogene Co., Ltd.

treatment_protocol: Freshly harvested cells were terminally differentiated for three days in either X-VIVO medium supplemented with 50ngmL hM-CSF or RPMI1640 medium (incl. L-glutamine, Gibco) + 10% heat-inactivated FBS (FBS superior), 2 U/mL penicillin-streptomycin supplemented with 50ngmL hM-CSF

tag: tissue

value: blood

tag: cell type

value: iPSC-derived macrophage

tag: genotype

value: WT

tag: treatment

value: no treatment


title: CTi003-A_d3_RPMI+FCS_Rep2

description: Library name: Sample 6

value: RPMI differentiation


title: 1-spr-expnx-OPNn

city: Madrid

first: Leonardo

middle: Daniel

last: Garma

state: Madrid

address: Melchor Fernández Almagro 3

country: Spain

institute: Spanish National Cancer Research Center

description: Library name: 1-spr-expnx-OPNn

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 (Illumina).
Assembly: hg38
Supplementary files format and content: Tab-separated values of raw counts for each sample

organism: Mus musculus

source_name: Splenocyte-derived cell cultures

extract_protocol:
After 48h in co-culture, 1x Brefeldin A (BioLegend, #420601) was added. Splenocytes were collected for FACS analysis and RNAseq analysis. RNA was extracted using RNAeasy Mini Plus Kit (Qiagen, #74134) and quantified in LabChip GX Touch Nucleic Acid Analyzer (PerkinElmer). RNA quality was determined by Agilent's 2100 Bioanalyzer Lab-Chip technology. Only samples with RNA Integrity Number (RIN)>7 was used for sequencing.
Total RNA samples (300ng; with average RIN/RQS 7.5, range 2.5-9.5) were converted into sequencing libraries using the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used, in which random primers featuring a 6 nt long Unique Molecular Identifier tag are used {to be addressed for bias correction at data analysis}. Directional cDNA libraries, stranded in the sense orientation {--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq, --rna-strandness F in HISAT}, were completed by PCR and sequenced in a single read format on an NovaSeq X Illumina instrument.

value: Splenocyte-derived cell cultures

value: Splenocyte

value: Exposed to RAW cells cultured under normoxia without SPP1


title: CTi003-A_d3_XVIVO_Rep2

description: Library name: Sample 5

value: X-VIVO differentiation


title: GM05386_noTGFb_rep1

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Département de microbiologie et infectiologie

country: Canada

institute: Université de Sherbrooke

description: Library name: 48h_rep1

data_processing:
Sequence reads were trimmed using Trimmomatic (V0.39) and the following parameters: ILLUMINACLIP:adapters.fa:2:30:10, LEADING:20, TRAILING:20, and MINLEN:45. The quality of the reads was assessed using FastQC (V0.11.9).
The transcriptome of the human genome GRCh38 was created using gffread (cufflinks V2.2.1) with the Ensembl annotation and genome files (V109).
Kallisto (V0.48.0) was used to align the reads to the transcriptome and to quantify the transcripts. The transcript abundance was combined to obtain the gene level quantification.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes TPM vlues for each sample

source_name: fibroblasts

growth_protocol: GM 05386 primary skin fibroblasts (Coriell Institute for Medical Research) were maintained in Alpha Modification of Eagle’s medium (AMEM) supplemented with 20 mL of 10% heat activated FBS (VWR, CA76327-086), 5 mL of 5% L-glutamine (Wisent, 609-065-EL), 5 mL of 5% penicillin-streptomycin (VWR, CA45000-652), 800 uL of amphotericin B (Wisent, 450-105-QL), 5 mL of 5% sodium pyruvate (Wisent, 600-110-EL), 25 uL of 40ug/mL of fibroblast growth factor β (FGFβ) (Wisent, 511-126-QU), and 125 uL of 0.2% heparin (Sigma, H3393-50KU). The cells were passage twice a week with a seeding cell volume of 1 X 106 cells. Prior to cell seeding, the T-75 flasks used for its passages are always coated with 5 mL of 1ug/mL fibronectin (Sigma-Aldrich, F1141) diluted in PBS (with Ca & Mg) (Corning #21-030-CV) overnight at 4°C or 4 hours in 37oC incubator to aid adhesion and proliferation of the cells, followed by aspiration and washing of the flask with 5 mL of PBS w/o Ca & Mg.

extract_protocol:
RNA extraction was performed using a hybrid trizol-column protocol. Briefly, the upper aqueous phase after chloroform phase separation was then transferred and diluted with an equal volume of 70% ethanol, followed by transfer to a RNeasy mini spin column (Qiagen, 74104) as the manufacturer`s recommendation. RNA extracts were DNAse treated using the RNAse free DNAse set (Qiagen, 79254), and their quality checked by Agilent Bioanalyzer for the RNA integrity (RIN value). Library preparation and sequencing was performed by Genome Québec
Libraries were generated from 20 ng of total RNA as following: mRNA enrichment and cDNA synthesis was achieved with theNEBNext Single Cell Low Input RNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the KAPA Library Quantification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Primary skin fibroblast (GM05386) cells of 5 to 10 passage numbers were used for this experiment. The cells were seeded in 6-well per 1 mL of complete media (for RNA-Seq analysis) and 96-well per 200 uL of complete media (for qRT-PCR analysis) plates and kept for 3 days until it reaches 70 to 80% confluency. Afterwards, the supernatant was aspirated and fresh media without FBS was added followed by the addition of a 1 ug/mL TGF-β (Abeomics, 32-1763-10) stock to reach a final concentration of 10 ng/mL. Cells were kept in an incubator and harvested after 2 days.

value: fibroblasts

tag: cell line

value: fibroblast

value: normal

value: untreated

tag: batch


title: 1-spr-exphx-OPNp

description: Library name: 1-spr-exphx-OPNp

value: Exposed to RAW cells cultured under hypoxia with SPP1


title: GM05386_noTGFb_rep2

description: Library name: 48h_rep2


title: CTi003-A_d3_XVIVO_Rep1

description: Library name: Sample 2


title: 1-spr-lavnx-OPNn

description: Library name: 1-spr-lavnx-OPNn

value: Exposed to RAW cells cultured under normoxia without SPP1, after media wash


title: CTi003-A_d3_RPMI+FCS_Rep1

description: Library name: Sample 3


title: GM05386_TGFb_rep1

description: Library name: 48h_TGFb_rep1

value: TGFβ


title: 12627839_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 14

value: primary breast cancer

value: Not Hispanic or Latino

value: Grade I

value: Female


title: 1-spr-exphx-OPNn

description: Library name: 1-spr-exphx-OPNn

value: WT

value: Exposed to RAW cells cultured under hypoxia without SPP1


title: TM039_KAN57

city: Göttingen

first: Lena-Christin

last: Conradi

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

institute: University Medical Center Göttingen

description: Library name: PDO8_KAN57

data_processing:
The raw reads were quality controlled using fastqc (RRID: SCR_014583) and checked for both microbial and mouse contamination using Kraken (RRID: SCR_005484) and fastq screen (RRID: SCR_000141), respectively. Next, the sequence reads were trimmed using trimmomatic (RRID: SCR_011848), mapped to the reference genome (Ensembl, genome assembly GRCh38.p13) using star (RRID: SCR_004463), and finally the features were quantified using htseq‐count (RRID: SCR_011867).
Assembly: genome assembly GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: PDOs from primary PDAC tissue

extract_protocol:
RNA was isolated with Quick-RNA miniprep (Zymo Research, #R1055), according to the manufacturer's instructions.
Library preparation for RNA-Seq was performed on the STAR Hamilton NGS automation platform using the Illumina Stranded mRNA Prep Kit (Cat. No. 20040534) together with the Illumina RNA UD Indexes Set A, Ligation with 96 Indexes (Cat. No. 20091646), starting from 50 ng of total RNA.

treatment_protocol: PDOs untreated or treated with 40 µM PFKFB3-inhibitor KAN0438757 for 24 h

value: PDOs from primary PDAC tissue


title: CTi003-A_d0_fresh_Rep1

description: Library name: Sample 1

value: blood

value: iPSC-derived macrophage

value: no treatment


title: 12295292_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 13

value: Grade II


title: TM039_ctrl

description: Library name: PDO8_ctrl

value: control


title: 7680218_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 11

value: Hispanic or Latino


title: 12703144_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 10


title: TM056_KAN57

description: Library name: PDO7_KAN57


title: 1-spm-expnx-OPNp

description: Library name: 1-spm-expnx-OPNp

value: Splenocyte-derived cell cultures

value: Splenocyte

value: Exposed to cell culture media of RAW cells cultured under normoxia with SPP1


title: 7779018_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 12


title: TM056_ctrl

description: Library name: PDO7_ctrl


title: High dose of D-glucose-2,RNA

city: Jinan

first: Xiaochen

last: Tian

address: Beiyuan Street,

country: China

institute: The Second Hospital of Shandong University

description: Library name: Sample 8

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean  reads were separately aligned to reference genome with orientation mode using HISAT2 software.
Assembly: GRCh38 reference genome
Supplementary files format and content: csv files include TPM values for each Sample

molecule: polyA RNA

source_name: kidney

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at ShenZhen BGl Genomics Co., Ltd. (ShenZhen, China) according to the manufacturer’s instructions. The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

value: kidney

value: podocyte cells

value: Epithelial Cell


title: High dose of D-glucose-1,RNA

description: Library name: Sample 7


title: In_vivo_GF, sub4, DNA, Rep3

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description:
Library name: sample24
Column name in GF_Sub4_Counts: GIS590

library_source: genomic

data_processing:
Sequencing reads were aligned to the oligonucleotide library using BWA (PMID: 20080505). After alignment, any oligonucleotides with fewer than 10 reads in either the DNA or RNA samples were excluded from downstream analysis.
To assess oligonucleotide activity and identify robust functional Cis-Regulatory Elements (fCREs), three statistical tools were employed within the R programming environment (version 4.3.3): DESeq2 (version 1.42.1), EdgeR (version 4.0.16), MPRAnalyzer (version 1.20.0).
Assembly: hg38
Supplementary files format and content: processed files include counts >10 for each tested elements for each replicate
Supplementary files format and content: annotation of column names in counts file to associate column names with replicate number and condition

molecule: genomic DNA

source_name: Liver

growth_protocol: Human liver cancer cell line HepG2 was cultured in DMEM-high glucose (Thermo Fisher) with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) from HepG2 or Rneasy midi kit (Qiagen) from mouse liver. DNA was extracted using mini-prep kit (Qiagen)
Plasmid DNA library preparation: we used 200 ng DNA as a template and each library was assigned unique i5 and i7 primers to aid in demultiplexing post-sequencing. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) with the following program (98°C for 3min; 98°C for 15s, 65°C for 30s, 7°2C for 45s and repeat for 17 cycles); 72°C for 2min). PCR reactions from each sample were combined and purified using 0.8X KAPA HyperPure Beads (Roche). RNA library preparation: we first isolated mRNA from 40 ug of total RNA from each sample using Dynabead Oligo-dT25 beads (Invitrogen) for HepG2 samples. We used 600 ug of total RNA to isolate mRNA for mouse liver samples. RNA was treated with Turbo DNase (Thermo Fisher Scientific) to remove contaminating DNA, and reverse-transcribed with SuperScript III (Thermo Fisher Scientific) using gene-specific RT primers. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) and 10 uM P7_UMI_Primer with the following program (98°C for 60s; 65°C for 30s; 72°C for 45s). Samples were purified using 1.4X KAPA HyperPure Beads (Roche) and eluted with 20uL water at 37°C for 3 min at 300 rpm on the thermomixer. Purified samples from the earlier step were used as a template per PCR reaction. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche), 10 uM junction_fwd primer, and 10 uM P7_junction_rev primer with the following program (98°C for 90s; 98°C for 15s, 65°C for 30s, 72°C for 40s and repeat for 22 cycles; 72°C for 2min). Samples were purified using 0.8X KAPA HyperPure Beads (Roche) and eluted with 20uL water at 37°C for 3 min at 300 rpm on the thermomixer. Lastly, each library was assigned a unique i5 primer to aid in demultiplexing post-sequencing The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) and 10uM P7_seqready rev primers with the following program (98°C for 90s; 98°C for 15s, 65°C for 30s, 72°C for 40s and repeat for 8 cycles; 72°C for 2min). PCR reactions from each sample were combined and purified using 0.8X KAPA HyperPure Beads (Roche). Samples were eluted with an appropriate amount of water at 37°C for 3 min at 300 rpm on the thermomixer. Sample concentration post-purification was measured using Qubit™ dsDNA Quantification Assay Kits (Invitrogen).

value: Liver

value: Germ-free


title: 1-spm-exphx-OPNp

description: Library name: 1-spm-exphx-OPNp

value: WT

value: Exposed to cell culture media of RAW cells cultured under hypoxia with SPP1


title: TM016_KAN57

description: Library name: PDO6_KAN57

value: PDOs from primary PDAC tissue


title: Medium dose of D-glucose-3,RNA

description: Library name: Sample 6


title: 12589546_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 9

value: primary breast cancer

value: Not Hispanic or Latino

value: Female


title: TM037_KAN57

description: Library name: PDO5_KAN57


title: Medium dose of D-glucose-2,RNA

description: Library name: Sample 5


title: High dose of D-glucose-3,RNA

description: Library name: Sample 9


title: TM016_ctrl

description: Library name: PDO6_ctrl


title: In_vivo_GF, sub4, DNA, Rep2

description:
Library name: sample23
Column name in GF_Sub4_Counts: GIS588


title: In_vivo_GF, sub4, DNA, Rep1

description:
Library name: sample22
Column name in GF_Sub4_Counts: GIS587


title: 7951254_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 8

value: Grade II


title: 1-spm-exphx-OPNn

description: Library name: 1-spm-exphx-OPNn

value: Exposed to cell culture media of RAW cells cultured under hypoxia without SPP1


title: 12357728_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 7

value: Grade I


title: In_vivo_GF, sub4, RNA, Rep3

description:
Library name: sample21
Column name in GF_Sub4_Counts: GIS569


title: 12627839_biopsy (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 5


title: 6589688_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 6


title: TM037_ctrl

description: Library name: PDO5_ctrl

value: control


title: TM078_KAN57

description: Library name: PDO4_KAN57


title: In_vivo_GF, sub4, RNA, Rep2

description:
Library name: sample20
Column name in GF_Sub4_Counts: GIS567


title: 12589546_biopsy (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 4


title: 7814749_biopsy (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 3


title: In_vivo_GF, sub4, RNA, Rep1

description:
Library name: sample19
Column name in GF_Sub4_Counts: GIS566


title: Normal dose of D-glucose-2,RNA

description: Library name: Sample 2


title: Medium dose of D-glucose-1,RNA

description: Library name: Sample 4


title: Normal dose of D-glucose-3,RNA

description: Library name: Sample 3


title: Normal dose of D-glucose-1,RNA

description: Library name: Sample 1


title: TM078_ctrl

description: Library name: PDO4_ctrl


title: 4569357_biopsy (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 2


title: TM061_KAN57

description: Library name: PDO3_KAN57


title: In_vivo_GF, sub3, DNA, Rep3

description:
Library name: sample18
Column name in GF_Sub3_Counts: GIS586


title: HEK-293, pH 6.6, DMSO, repeat 3

city: Moscow

first: Anastasia

middle: Nikolaevna

last: Kazakova

address: Malaya Pirogovskaya

country: Russia

institute: Lopukhin Federal research and clinical center of physical-chemical medicine of Federal medical biological agency

description:
Library name: ph6-rep3
Column name in salmon_tximport_counts.txt: ph6_rep3

data_processing:
Unprocessed RNA-Seq reads were trimmed using Trimmomatic (v. 0.39) and Trimgalore (v. 0.6.6), wherein adapter/index sequences were trimmed, and reads shorter than 35 nucleotides were filtered.
Transcript-level abundances were quantified using the quasi-mapping approach with Salmon (v. 1.5.1) on the hg38 Gencode reference transcriptome with default parameters.
Transcript-level abundances were then aggregated to gene-level abundances using the tximport R/Bioconductor package. Differential gene expression analysis was carried out with the DESeq2 R/Bioconductor package using the Wald test, applying an FDR cutoff of 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt files include counts for genes for each sample

growth_protocol: HEK-293 cells were were cultured in a humidified 5% CO2 incubator at 37 ◦C, tested for mycoplasma contamination, and grown in 6-well plates in in Dulbecco's Modified Eagle Medium (DMEM) (Paneco, Russia) supplemented with a 1% penicillin/streptomycin mixture (Paneco, Russia), 2 mM glutamine (Paneco, Russia), and 10% fetal bovine serum (Capricorn Scientific, USA) to a confluency of approximately 60-70%.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen, USA) and treated with RQ1 Rnase-Free DNAse I (Promega, USA) to remove residual gDNA.
Libraries were prepared using KAPA mRNA Capture Kit (Roche, Switzerland) and KAPA RNA HyperPrep Kit (Roche, Switzerland). Libraries were purified using KAPA HyperPure Beads (Roche, Switzerland), and size distribution and quality were assessed using a High Sensitivity DNA chip (Agilent Technologies, USA). Libraries were quantified using the Quant-iT DNA Assay Kit, High Sensitivity (Thermo Fisher Scientific, USA). Sequencing was performed on the NextSeq 1000 (Illumina, USA) using the NextSeq 1000/2000 P2 Reagents (200 Cycles), with 2% PhiX (Illumina) added as an internal control.

treatment_protocol: HEK-293 cells that were treated with SRPIN 350 (10 μM) in DMEM (pH 7.4), for 48 hours; or with an equal volume of DMSO in DMEM (pH 7.4) for 48 hours; or with an equal volume of DMSO in acidified DMEM (pH 6.6) for 48 hours

value: pH 6.6, DMSO


title: In_vivo_GF, sub3, DNA, Rep2

description:
Library name: sample17
Column name in GF_Sub3_Counts: GIS585


title: TM061_ctrl

description: Library name: PDO3_ctrl


title: LN_3

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: Library name: LN_3

data_processing:
Sequenced libraries were processed with deepTools(Ramírez et al. 2016) v_2.0, using STAR(Kaminow et al. 2021)v_2.7.10, for trimming and mapping, and feature Counts(Liao et al. 2014) v_2.0.3 to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies)(R Core Team 2013) with DESeq2(Love et al. 2014) v_1.36 to generate normalized read counts
Assembly: mm10
Supplementary files format and content: matrix of raw gene counts per sample

source_name: Spleen and Lymph node

extract_protocol:
RNA extraction, library preparation using SMART-Seq® v4, and Illumina sequencing were performed at Admera Health.
RNA extraction, library preparation using SMART-Seq® v4, and Illumina sequencing were performed at Admera Health.

value: T cells

tag: media

value: Th2 polarizing conditions

value: Spleen and Lymph node


title: HEK-293, pH 6.6, DMSO, repeat 1

description:
Library name: ph6-rep1
Column name in salmon_tximport_counts.txt: ph6_rep1


title: LN_1

description: Library name: LN_1


title: TM027_KAN57

description: Library name: PDO2_KAN57


title: LN_2

description: Library name: LN_2


title: In_vivo_GF, sub3, DNA, Rep1

description:
Library name: sample16
Column name in GF_Sub3_Counts: GIS582


title: TM027_ctrl

description: Library name: PDO2_ctrl


title: HEK-293, pH 6.6, DMSO, repeat 2

description:
Library name: ph6-rep2
Column name in salmon_tximport_counts.txt: ph6_rep2


title: In_vivo_GF, sub3, RNA, Rep3

description:
Library name: sample15
Column name in GF_Sub3_Counts: GIS565


title: 6589688_biopsy (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 1


title: TM065_KAN57

description: Library name: PDO1_KAN57


title: IL33_2

description: Library name: IL33_2


title: HEK-293, pH 7.4, SRPIN340, repeat 1

description:
Library name: SRPIN340-rep1
Column name in salmon_tximport_counts.txt: SRPIN340_rep1

value: pH 7.4, SRPIN340


title: IL33_3

description: Library name: IL33_3


title: In_vivo_GF, sub3, RNA, Rep1

description:
Library name: sample13
Column name in GF_Sub3_Counts: GIS561

value: Liver


title: HEK-293, pH 7.4, DMSO, repeat 1

description:
Library name: control-rep1
Column name in salmon_tximport_counts.txt: DMSO_rep1

value: pH 7.4, DMSO


title: IL33_1

description: Library name: IL33_1


title: TM068

description: Library name: PDO10


title: IL2_3

description: Library name: IL2_3


title: HEK-293, pH 7.4, SRPIN340, repeat 2

description:
Library name: SRPIN340-rep2
Column name in salmon_tximport_counts.txt: SRPIN340_rep2


title: In_vivo_GF, sub3, RNA, Rep2

description:
Library name: sample14
Column name in GF_Sub3_Counts: GIS564

value: Germ-free


title: HEK-293, pH 7.4, DMSO, repeat 2

description:
Library name: control-rep2
Column name in salmon_tximport_counts.txt: DMSO_rep2


title: In_vivo_GF, sub2, DNA, Rep2

description:
Library name: sample11
Column name in GF_Sub2_Counts: GIS580


title: IL2_2

description: Library name: IL2_2


title: TM065_ctrl

description: Library name: PDO1_ctrl


title: In_vivo_GF, sub2, DNA, Rep3

description:
Library name: sample12
Column name in GF_Sub2_Counts: GIS581


title: Spleen-IL27_2

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

institute: Shanghai Children's Medical Center

description: Library name: Sample 20

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCm39 or GRCh38 whole genome using STAR 2.7.11a  with parameters  --runMode alignReads --runThreadN 5  --genomeLoad NoSharedMemory  --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
The gene expression level (TPM) was calculated according to the Sequencing depth and gene length, and the DEG matrix was analyzed with the R package DESeq2.
Assembly: Mus_musculus.GRCm39 and Homo_sapiens.GRCh38
Supplementary files format and content: txt files includes raw counts for every sample

source_name: Spleen

extract_protocol:
Bone marrow cells and splenic cells were prepared using standard procedures. Specific cellular subsets were isolated by fluorescence-activated cell sorting (FACS) where indicated. Sorted cell populations were lysed directly in TRIzol reagent (Invitrogen) for RNA extraction. Total bone marrow cells and cultured human mesenchymal stromal cells (hMSCs) were directly lysed in TRIzol without prior sorting. Lysates were stored at −80 °C prior to RNA isolation according to the manufacturer’s instructions.
Total RNA extracted using TRIzol reagent was subjected to quality control prior to library preparation. RNA sequencing libraries were constructed using standard RNA-seq library preparation protocols by commercial service providers (BGI Genomics and OE Biotech). Libraries were prepared following manufacturer-recommended procedures and sequenced on Illumina sequencing platforms to generate paired-end reads.

value: Spleen

value: B cells


title: TM063

description: Library name: PDO9

value: PDOs from primary PDAC tissue


title: TM056

description: Library name: PDO7


title: IL2_1

description: Library name: IL2_1


title: In_vivo_GF, sub2, RNA, Rep3

description:
Library name: sample9
Column name in GF_Sub2_Counts: GIS559


title: In_vivo_GF, sub2, DNA, Rep1

description:
Library name: sample10
Column name in GF_Sub2_Counts: GIS578


title: Spleen-IL27_1

description: Library name: Sample 19


title: TM078

description: Library name: PDO4


title: In_vivo_GF, sub2, RNA, Rep2

description:
Library name: sample8
Column name in GF_Sub2_Counts: GIS557


title: Spleen-Ctrl_2

description: Library name: Sample 18

value: AAV-Ctrl


title: CD3_2

description: Library name: CD3_2


title: Spleen-Ctrl_1

description: Library name: Sample 17


title: TM061

description: Library name: PDO3


title: RNA-Seq of mus musculus:E12.5 ZIKV placenta CSA-3

city: 厦门市

first: CHEN

last: JIAHAO

state: 陈嘉濠

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

institute: 厦门大学

description: Library name: CSA-3

data_processing:
Gene expression levels are quantified with featureCounts. Differential gene expression analysis was performed using DESeq2 (v1.32.0), with a significance threshold set at p-value < 0.05 and fold change > 1.5.
Assembly: mm39
Supplementary files format and content: excel flies include FPKM values for each Sample

source_name: placenta

extract_protocol:
Total RNA from placental tissue was extracted using TRIzol reagent(Invitrogen, 15596018)
High-depth transcriptomic sequencing was conducted on the BGISEQ-500 platform (China, BGI). The obtained raw sequencing reads are aligned to the mouse reference genome (GRCm39) using HISAT2 alignment tools.

value: placenta

value: wt

value: CSA


title: TM027

description: Library name: PDO2


title: CD3_1

description: Library name: CD3_1


title: In_vivo_GF, sub2, RNA, Rep1

description:
Library name: sample7
Column name in GF_Sub2_Counts: GIS560


title: BAT, KO-3

city: San Antonio

first: Xiaoli

last: Sun

state: TX

address: 7703 Floyd Curl Dr

department: Pharmacology

description: Library name: BAT_KO-3

data_processing:
All data were aligned to the mm10 assembly of the mouse genome, and all subsequent data analysis was performed using HOMER, and detailed instructions for analysis can be found at http://homer.salk.edu/homer/ . Mapped data were analyzed with HOMER's "analyzeRepeats.pl" function with options -raw -condenseGenes and -count exons. Differential expression was performed using Homer's getDiffExpression.pl function, which uses DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Raw counts for each sample.

source_name: Brown adipose tissue

extract_protocol:
Tissues were homogenized in TRIzol reagent and total RNA was isolated using PureLink RNA Mini Kit following manufacturer’s instructions (Life Technologies).
RNA quality was assessed by Agilent 4200 TapeStation System. Sequencing libraries were prepared in biological replicates from polyA enriched mRNA. RNA-seq libraries were prepared from poly(A)-enriched mRNA as previously described (PMID:31761566). Libraries were then size selected by beads selection, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and sequenced on a Nextseq 2000 system at the Genome Sequencing Facility of the University of Texas Health Science Center at San Antonio.

value: Brown adipose tissue

tag: tissue type

value: BAT

value: KO

value: HFD


title: RNA-Seq of mus musculus:E12.5 ZIKV placenta CSA-2

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: CSA-2


title: In_vivo_GF, sub1, DNA, Rep2

description:
Library name: sample5
Column name in GF_Sub1_Counts: GIS574


title: TM037

description: Library name: PDO5


title: TM065

description: Library name: PDO1


title: RNA-Seq of mus musculus:E12.5 ZIKV placenta CSA-1

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: CSA-1


title: BAT, KO-1

institute: University of Texas Health Science Center at San Antonio

description: Library name: BAT_KO-1


title: CD3_3

description: Library name: CD3_3

value: T cells

value: Th2 polarizing conditions


title: In_vivo_GF, sub1, DNA, Rep1

description:
Library name: sample4
Column name in GF_Sub1_Counts: GIS573


title: BAT, KO-2

description: Library name: BAT_KO-2


title: In_vivo_GF, sub1, DNA, Rep3

description:
Library name: sample6
Column name in GF_Sub1_Counts: GIS575


title: In_vivo_GF, sub1, RNA, Rep3

description:
Library name: sample3
Column name in GF_Sub1_Counts: GIS553


title: RNA-Seq of mus musculus:E12.5 WT placenta CTRL-3

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: CTRL-3

value: zikv


title: SW480 cells, pCMV6-HKDC1_2

city: Taipei City

first: KuoHsing Chen

address: No.57, Ln. 155, Sec. 3, Keelung Rd.

country: Taiwan

institute: National Taiwan University Cancer Center

description: Library name: SH1

data_processing:
Trimmed sequence reads were mapped to GRCh38.98 using HISAT2(v2.1.0)
The read count matrix was normalized across all samples using the TMM method and converted into transcripts per million (TPMs) for further analysis. Pre-ranked gene-set enrichment analysis (GSEA) was performed using the function implemented by the R package clusterProfiler on the gene sets from MSigDB (v7.4). The genes were ranked based on the score of sign(log2FC) *–log10(p-value), where log2FC and p-value were obtained by performing differential expression analysis using the R package limma procedure.
Assembly: GRCh38.98
Supplementary files format and content: counts2_all samples.csv

growth_protocol: Cells were maintained in RPMI-1640 containing 10% fetal bovine serum, 2 mmol/L L-glutamine (Life Technologies, Carlsbad, CA, USA), PSA (10,000 units/ml penicillin, 10 mg/ml mg/mL streptomycin, and 25μg/ml amphotericin B; Biological Industries, Kibbutz Beit Haemek, Israel). The cells were cultured at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted using Tri Reagent (Ambion, Austin, TX, USA), and the RNA concentration and quality were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Total RNA with A260/A280 = 1.8-2.0 and RNA integrity number >8.0, were used for further experiments.
Total RNA (1–2 μg) was purified using poly-T oligo–attached magnetic beads to isolate mRNA. The purified mRNA was fragmented into small pieces using divalent cations at elevated temperature. First-strand cDNA was synthesized using reverse transcriptase and random primers, followed by second-strand cDNA synthesis with DNA polymerase I and RNaseH. The resulting cDNA fragments underwent end repair, addition of a single adenine (“A”) base at the 3′ ends, and ligation of sequencing adapters. Finally, the adapter-ligated products were purified and enriched by PCR to generate the sequencing-ready cDNA library.

treatment_protocol: pCMV6-HKDC1 (RC221178) and pCMV6-Entry vectors were purchased from OriGene Technologies (Rockville, MD, USA). Transfection was performed in Opti-MEM™(Gibco) using a mix containing Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) and 10 μg plasmid, for 24 h at 37 °C and 5% CO2. The Transfection was stopped after 24 h by replacing the medium containing the plasmid with standard medium in which the cells were routinely cultured. Transfection was validated by HKDC-1 expression in protein lysates.

value: colon cancer


title: SW480 cells, pCMV6-HKDC1_3

description: Library name: SH2


title: BAT, WT-3

description: Library name: BAT_WT-3

value: Wildtype


title: BAT, WT-2

description: Library name: BAT_WT-2


title: SW480 cells, pCMV6-HKDC1_1

description: Library name: SH


title: RNA-Seq of mus musculus:E12.5 WT placenta CTRL-2

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: CTRL-2


title: BAT, WT-1

description: Library name: BAT_WT-1


title: In_vivo_GF, sub1, RNA, Rep1

description:
Library name: sample1
Column name in GF_Sub1_Counts: GIS554

value: Liver

value: Germ-free


title: RNA-Seq of mus musculus:E12.5 WT placenta CTRL-1

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: CTRL-1


title: SW480 cells, pCMV6-Entry_3

description: Library name: SE2


title: eWAT, KO-3

description: Library name: eWAT_KO-3

source_name: White adipose tissue

value: White adipose tissue

value: eWAT


title: DMSO_1%_6h_+ MTB_(MOI10)_6h_3

city: Zürich

first: Johannes

last: Nemeth

address: Rämistrasse 100

department: Department of Infectious Diseases and Hospital Epidemiology

country: Switzerland

institute: University Hospital Zurich

description: Library name: DMSO_6h_INF_6h_3

data_processing:
Sequencing and cluster generation was performed on the NovaSeqX using paired-end 2×150 bp reads following standard protocols. Raw reads were cleaned with fastp (v0.20.0) by removing adapters and poly-x sequences (>9 nt).
Assembly: Pseudo-alignment to the mouse genome (GRCm39) and gene quantification (GENCODE v31) were done with Kallisto (v0.46.1).
Supplementary files format and content: Further analysis in R (v4.4.0) included DEG detection using DESeq2 (v1.45.0) with glm (p ≤ 0.05, log₂FC ≥ 0.5), heatmap generation via ComplexHeatmap (v2.21.0), and PCA using Stats (v4.4.0). GSEA was performed with fgsea (v1.31.0) using the Mouse Hallmark Gene set (mouse_H_v5p2, MSigDB), considering pathways with adjusted p < 0.05, ranked by NES. Enriched pathway visualization was based on averaged log₂FC values using org.Mm.eg.db (v3.8.2)36 with pathview (v1.45.0)37, graphite (v1.51.0)38,39, and png (v0.1-8)40. Transcription factor enrichment was performed using the ulm approach in decoupleR (v2.12.0) on t-values (-log10(pvalue)*(log2 ratio)) from DEG referencing CollecTRI database downloaded from https://saezlab.github.io/decoupleR/reference/get_collectri.html. Unless stated otherwise, plots were generated with ggplot2 (v3.5.1) and shiny (v1.9.1).

source_name: macrophage

growth_protocol: BMDMs were differentiated in R10+ 50 ng/ml mCSF for six days, detached with ice-cold PBS + 2 mM EDTA, and reseeded at 1×10⁶ cells/well in 6-well plates with 2 mL R10  and left to reattach over night.

extract_protocol:
RNA isolation was performed using the Qiagen RNeasy Mini Kit with β-mercaptoethanol (10 µL/mL RLT buffer) and QiaShredder homogenization.
RNA quality was assessed via Fragment Analyzer; only samples with 260/280 ratios of 1.8–2.1 and 28S/18S ratios of 1.5–2 were used. mRNA libraries were prepared using the Illumina® Stranded mRNA Prep Ligation Kit, with poly-A enrichment, reverse-transcription, fragmentation, end-repairing and adenylated before ligation of an anchor. Fragments with anchors at both ends were enriched by PCR with UDI indexing. Library quality and concentration were validated via Fragment Analyzer, yielding ~260 bp smears. Libraries were normalised to 10 nM in 10 mM Tris-Cl (pH 8.5) with 0.1% Tween 20.

treatment_protocol: After 24 h adhesion, uninfected samples were treated with 1% DMSO or 1 µg/mL CFZ for six h at 37°C, 5% CO₂, 90% humidity. Infected samples received the same treatment, followed by warm PBS washes and infection with MTB at MOI 10 for six hours. All samples were washed before RNA isolation.

value: macrophage


title: RNA-Seq of mus musculus:E12.5 WT placenta C3

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: C3

value: placenta


title: SW480 cells, pCMV6-Entry_2

description: Library name: SE1


title: RNA-Seq of mus musculus:E12.5 WT placenta C2

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: C2

value: wt


title: SW480 cells, pCMV6-Entry_1

description: Library name: SE


title: In_vivo_GF, sub1, RNA, Rep2

description:
Library name: sample2
Column name in GF_Sub1_Counts: GIS552


title: RNA-Seq of mus musculus:E12.5 WT placenta C1

address: 福建省福州市闽侯县南通镇苏坂村苏坂东路38号

description: Library name: C1


title: COLO320DM cells, pCMV6-HKDC1_3

description: Library name: CH2


title: DMSO_1%_6h_+ MTB_(MOI10)_6h_2

description: Library name: DMSO_6h_INF_6h_2


title: eWAT, KO-2

description: Library name: eWAT_KO-2


title: eWAT, WT-3

description: Library name: eWAT_WT-3


title: DMSO_1%_6h_3

description: Library name: DMSO_6h_3


title: COLO320DM cells, pCMV6-HKDC1_1

description: Library name: CH


title: eWAT, WT-2

description: Library name: eWAT_WT-2


title: DMSO_1%_6h_+ MTB_(MOI10)_6h_1

description: Library name: DMSO_6h_INF_6h_1


title: Liver AAV-hDC-SIGN-HFHC-3

city: Nantong

first: Chunhua

last: Wan

state: Jiangsu

address: No. 9 Seruan Road

institute: Nantong University

description: fpkm_D3, read_count_D3

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6).
HISAT2 (v2.1.0) was applied to align the clean reads to the reference genome
Bowtie2(v2.3.4.3) was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GRCm38
Supplementary files format and content: FPKM and raw counts values for each Sample

growth_protocol: We studied C57BL/6 mice on a HFHC NASH diet or a control diet for 16 Weeks.

extract_protocol:
Liver tissue was homogenized using TRIzol, followed by total RNA extraction using chloroform and isopropanol.
Subsequently, RNA libraries were prepared by the BGI China facility.

treatment_protocol: We injected mice with AAV9-CD68-EGFP or AAV9-CD68-hDC-SIGN in the tail vein after 8-week-feeding.

tag: strain

value: Male

tag: time


title: Liver AAV-hDC-SIGN-HFHC-4

description: fpkm_D4, read_count_D4


title: COLO320DM cells, pCMV6-Entry_3

description: Library name: CE2


title: DMSO_1%_6h_1

description: Library name: DMSO_6h_1


title: eWAT, WT-1

description: Library name: eWAT_WT-1


title: CFZ 1ug_ml_6h_+ MTB_(MOI10)_6h_3

description: Library name: CLO_1ug_ml_6h_INF_6h_3


title: eWAT, KO-1

description: Library name: eWAT_KO-1


title: Liver AAV-hDC-SIGN-HFHC-1

description: fpkm_D1, read_count_D1


title: COLO320DM cells, pCMV6-HKDC1_2

description: Library name: CH1


title: Liver AAV-hDC-SIGN-HFHC-2

description: fpkm_D2, read_count_D2


title: COLO320DM cells, pCMV6-Entry_1

description: Library name: CE


title: COLO320DM cells, pCMV6-Entry_2

description: Library name: CE1


title: iWAT, KO-3

description: Library name: WiAT_KO-3

value: iWAT


title: DMSO_1%_6h_2

description: Library name: DMSO_6h_2


title: iWAT, KO-2

description: Library name: WiAT_KO-2


title: CFZ 1ug_ml_6h_+ MTB_(MOI10)_6h_1

description: Library name: CLO_1ug_ml_6h_INF_6h_1


title: CFZ 1ug_ml_6h_+ MTB_(MOI10)_6h_2

description: Library name: CLO_1ug_ml_6h_INF_6h_2


title: CT30_Human TS cell, EVT differentition D6, scRNA-Seq, replicate 1

city: Kansas City

first: Michael

last: Soares

state: KS

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

description: Library name: CT30_D6_1

library_source: transcriptomic single cell

data_processing:
Sequencing data was demultiplexed and converted to FASTQ files using the Cell Ranger pipeline (v. 7.0.1). Reads were aligned to the reference human genome GRCh38, and count tables were generated. Filtered counts were converted using Seurat (v 5.2.0). The resulting Seurat objects were merged, and low-quality cells were filtered out (gene detected >100 and <15% mitochondrial DNA). Additionally, the R package doubletfinder was used to mark doublet cells, which were not found in the preparations
Counts from filtered cells were normalized, scaled, and integrated using the Seurat 2000 variable features “vst” method. The dimensionality of the data was reduced using principal component analysis using Seurat’s “RunPCA” with 20 principal components. Cells were clustered using Seurat’s nearest neighbor clustering and the Louvain algorithm. The clusters were visualized using Uniform Manifold Approximation and Projection (UMAP). Various resolutions were determined using the clustree R package. The final resolution parameter was 0.22.
Assembly: GRCh38.p13
Supplementary files format and content: The Excel file contains separate sheets for each cluster, with rows corresponding to genes and columns reporting logFC and p-values

source_name: human trophoblast stem cells- CT30 (Okae et.al)

growth_protocol: Human Triophoblast Stem cells  were grown and differentiated in the dish for 8 days into extravillous trophoblast cells media

extract_protocol:
TS cells were collected in the stem state (D0) and at days 3, 6, and 8 (D3, D6, D8) of EVT cell differentiation. At the time of harvest, cells were incubated with TrypLE (12604039, Gibco) for 15 min at 37°C. Detached cells were then neutralized with 0.3% BSA in PBS, centrifuged for 3 min at 500 × g, and resuspended in 0.3% BSA in PBS. Cells were washed three times with 0.1% BSA in PBS. Cells were counted, and viability was assessed prior to submission for library preparation.
The 10X Genomics Single Cell 3’ Expression v3.1 library preparation was performed using the 10X Genomics Chromium X. The second strand cDNA amplification was performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The QC and quantification of the cDNA was determined using the Agilent TapeStation 4200 HS D5000 ScreenTape assay (5067-5592, Agilent). Validation of the single cell library was conducted using the Agilent TapeStation 4200 D1000 ScreenTape assay. Single cell library quantification was completed using a Roche LightCycle 96 using FastStart Essential Green Master (06402712001, Roche) and KAPA Library Quantification DNA Standards (KK4903, Illumina). Library concentrations were adjusted to 2 nM and pooled. The library pool was diluted for final on-board clustering concentration of 130 pM on a NovaSeq 6000. The sequencing was performed using a NovaSeq 6000 100 cycle Reagent Kit v1.5 (20028401, Illumina) and NovaSeq X Plus 100 cycle Reagent Kit (20104703, Illumina) with an asymmetrical sequencing profile (read 1 - 28 cycles: i7 index read - 10 cycles: i5 index read - 10 cycles: read 2-90 cycles).

value: extravillous trophoblast

value: WT

value: EVT differentiation

value: day 6


title: iWAT, KO-1

description: Library name: WiAT_KO-1

value: KO

value: HFD


title: CFZ 1ug_ml_6h_3

description: Library name: CLO_1ug_ml_6h_3


title: Liver AAV-CON-HFHC-1

description: fpkm_C1, read_count_C1


title: Liver AAV-hDC-SIGN-NCD-3

description: fpkm_B4, read_count_B4


title: CT29_Human TS cell, EVT differentition D6, scRNA-Seq, replicate 1

description: Library name: CT29_D6_1

source_name: human trophoblast stem cells- CT29 (Okae et.al)


title: iWAT, WT-3

description: Library name: iWAT_WT-3


title: CFZ 1ug_ml_6h_2

description: Library name: CLO_1ug_ml_6h_2


title: Liver AAV-CON-HFHC-2

description: fpkm_C2, read_count_C2


title: Human TS cell, EVT differentition D8, scRNA-Seq, replicate 2

description: Library name: CT27_D8_2

source_name: human trophoblast stem cells- CT27 (Okae et.al)

value: day 8


title: Liver AAV-CON-HFHC-3

description: fpkm_C3, read_count_C3


title: CT27_Human TS cell, EVT differentition D6, scRNA-Seq, replicate 1

description: Library name: CT27_D6_3

value: human trophoblast stem cells- CT27 (Okae et.al)


title: Liver AAV-hDC-SIGN-NCD-1

description: fpkm_B1, read_count_B1

value: Liver


title: iWAT, WT-1

description: Library name: iWAT_WT-1

value: Wildtype


title: CFZ 1ug_ml_6h_1

description: Library name: CLO_1ug_ml_6h_1


title: iWAT, WT-2

description: Library name: iWAT_WT-2

value: White adipose tissue


title: Liver AAV-hDC-SIGN-NCD-2

description: fpkm_B2, read_count_B2


title: Liver AAV-CON-NCD-3

description: fpkm_A4, read_count_A4


title: Human TS cell, EVT differentition D8, scRNA-Seq, replicate 1

description: Library name: CT27_D8_1


title: In_vivo_GF, sub5, RNA, Rep3

description:
Library name: GIS429
Column name in GF_Sub5_Counts: GIS429

value: Germ-free


title: 24h, 3 mice pooled, scRNAseq GEX

city: Munich

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

institute: LMU Hospital

description: 10x Genomics

data_processing:
The demultiplexing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: brain

extract_protocol:
Mice were perfused with ice-cold saline and brains were gently removed. The hemispheres were split, the white matter and meninges were removed with forceps. The tissue was dissociated using the papain dissociation system (#LK003150, Worthington Biochemical Corporation) according to the manufacturer’s protocol and an incubation time of 15min. The cell suspension was cleared from dead cells and cell debris using the dead cell removing kit (#130-090-101, Miltenyi). Propidium iodide negative live single cells were flow cytometrically sorted using a BD Fusion cell sorter into RPMI medium containing 5% fetal bovine serum. The cell suspension was centrifuged and washed with PBS containing 0.04% bovine serum albumin (BSA). The cells were resuspended in PBS containing 0.04% BSA for a concentration of 1,200cells/µl, counted and loaded into the Chromium Next GEM Chip G (PN-1000127, 10x Genomics) for a target recovery of 10,000 cells according to the 10x Genomics Next GEM Single Cell 3‘ v3.1 (Dual Index) kit protocol (Step 1, CG000315, Rev E) for GEM preparation (PN-1000296, 10x Genomics) and run in a 10x Genomics Chromium Controller. After GEM preparation, the protocol of the kit was followed for post GEM-RT Cleanup & cDNA amplification (Step 2) and 3‘gene expression library construction (Step 3). Single-cell libraries were sequenced using an Illumina HiSeq 1500 sequencer with a sequencing depth of >20,000 reads per cell.
Libraries were performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: TIA was performed using a modification of the intraluminal filament technique as previously described1, animals were anesthetized (isoflurane in 30%O2/70%N2O) and received an incision between ear and eye to expose the temporal skull. A laser Doppler probe was placed over the skull above the middle cerebral artery (MCA) territory. Animals were then placed in a supine position. After a midline neck incision, the common carotid artery and left external carotid artery were isolated and ligated, a 2mm silicon-coated filament (Doccol, #602112PK5Re) was inserted into the internal carotid artery, through the external carotid artery, until the occlusion of the MCA, checked by a corresponding laser Doppler flow reduction. After 5minutes (TIA), 15minutes or 30minutes of MCA occlusion (MCAo), the filament was removed. For the survival period, animals were kept in their homecage with facilitated access to water and food. Exclusion criteria: Mice without a reduction in blood flow to <20% of the baseline, controlled by a laser Doppler flow, were excluded from the analysis.

value: brain

value: 24h post stroke


title: Human TS cell, EVT differentition D6, scRNA-Seq, replicate 2

description: Library name: CT27_D6_2


title: Liver AAV-CON-NCD-2

description: fpkm_A2, read_count_A2


title: In_vivo_GF, sub5, RNA, Rep1

description:
Library name: GIS430
Column name in GF_Sub5_Counts: GIS430


title: In_vivo_GF, sub5, RNA, Rep2

description:
Library name: GIS427
Column name in GF_Sub5_Counts: GIS427


title: Liver AAV-CON-NCD-1

description: fpkm_A1, read_count_A1


title: naive, 3 mice pooled, scRNAseq GEX

description: 10x Genomics

value: naive


title: Human TS cell, EVT differentition D6, scRNA-Seq, replicate 1

description: Library name: CT27_D6_1


title: In_vivo, sub5, RNA, Rep1

description:
Library name: AML271
Column name in Liver_Sub5_Counts: AML271


title: control_DT40 rep2

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: Library name: 188368

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.4
bowtie2 mapping against hg19 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with HOMER for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command

organism: Gallus gallus

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan)

extract_protocol:
Cells were cross-linked in falcon tube. The DNA was fragmented, biotynilated at both ends, and ligated at newly blunted ends together. Biotinylated DNA was captured and prepared for paired-end Illumina sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.

value: avian leukosis virus (ALV) induced bursal lymphoma cell line


title: hMSC-IL27-1

description: Library name: Sample 15

source_name: hMSC

value: hMSC


title: hMSC-IL27-2

description: Library name: Sample 16


title: In_vivo, sub5, RNA, Rep3

description:
Library name: AML268
Column name in Liver_Sub5_Counts: AML268


title: In_vivo, sub4, RNA, Rep1

description:
Library name: AML266
Column name in Liver_Sub4_Counts: AML266


title: Human TS cell, EVT differentition D3,scRNA-Seq, replicate 2

description: Library name: CT27_D3_2

value: extravillous trophoblast

value: day 3


title: hMSC-Ctrl-2

description: Library name: Sample 14

value: Ctrl


title: Human TS cell, EVT differentition D3,scRNA-Seq, replicate 1

description: Library name: CT27_D3_1

value: WT

value: EVT differentiation


title: WAPL-_AID_+_aux_DT40 rep1

description: Library name: 179961


title: In_vivo, sub5, RNA, Rep2

description:
Library name: AML269
Column name in Liver_Sub5_Counts: AML269


title: CCNB1: Human TS cells (CT27), CCNB1 shRNA  treated, replicate 3

description: Library name: CCNB1_KD3

data_processing:
Raw data obtained from the sequencing facility was converted to fastq format using bcl2fastq (v2.20.0.422) and data quality was inspected using FastQC (v0.11.9)
Reads from fastq files were mapped to the rat reference genome (Rnor_5.0.7) using CLC Bio Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark)
The raw count files were imported into R (v4.2.2) and analyzed to obtain differentially expressed genes by using DESeq2 (v1.38.3)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample (each column represent the condition and each row represents the gene)

growth_protocol: Human Triophoblast Stem cells  were grown and differentiated in the dish for 8 days into EVT cells

extract_protocol:
Total RNA was isolated using the Trizol reagent according to the manufacturer’s instructions (Thermo-Fisher)
Extracted RNA was used as template for cDNA isolation with the High Capacity cDNA Reverse Transcription kit (Applied Biosystems). cDNA libraries were prepared and sequenced using a NovaSeq 6000 by the KUMC Genomics Core

treatment_protocol: Human Triophoblast Stem cells  were treated with control shRNA,  CEBPB, ADAMTS20 or CCNB1 shRNA before differentiation into EVT cells.

value: CCNB1 shRNA

value: Day 8


title: In_vivo, sub4, RNA, Rep2

description:
Library name: AML265
Column name in Liver_Sub4_Counts: AML265


title: Human TS cell, stem state,scRNA-Seq, replicate 1

description: Library name: CT27_D0_1

value: human trophoblast stem cells- CT27 (Okae et.al)

value: day 0


title: WAPL-_AID_+_aux_DT40 rep2

description: Library name: 188371


title: 3d, 3 mice pooled, scRNAseq GEX

description: 10x Genomics

value: 3d post stroke


title: control3

city: Changsha

first: Kun

last: Liu

state: Hunan

address: 36 Lushan Road

institute: Hunan Normal University

description: Library name: sample3

data_processing:
We utilized the “read10X” function within the Seurat V5 R package to import the single-cell expression matrix file. Subsequently, the “CreateSeuratObject” function was employed to convert the single-cell transcriptome data into a Seurat object for further analysis and visualization. Cells were filtered out if the gene count was below 200 or above 8000, as well as if the mitochondrial and ribosome gene expression exceeded 5%. This stringent filtering strategy ensured that only high-quality cells were retained for subsequent analysis. To integrate datasets, we used the “Find Integration Anchors” function with the parameter “dims = 1:20”. To eliminate batch effects across different samples, the Harmony R package was applied. Clusters within the dataset were identified using the “Find Clusters” function with a resolution 0.6.
Assembly: hg18
Supplementary files format and content: matrix files

source_name: femoral head

extract_protocol:
Following surgery, the discarded samples were promptly collected, carefully packaged in sterile bags, and placed in an ice box to maintain optimal conditions. The samples were then rapidly transported to the laboratory for further processing. All procedures adhered to strict ethical guidelines to ensure the protection of participant privacy.  After obtaining the femoral head samples, the tissue was processed into bone fragments. These fragments were then digested using a digestion solution. Following the removal of red blood cells and dead cells, CD45-ALPL+ osteoblasts were enriched using magnetic bead sorting.
Single-cell transcriptome sequencing was performed using the 10x Genomics platform (Chromium™ Controller, USA). Library construction was carried out according to the guidelines outlined in the Single Cell 3' Library & Gel Bead Kit V3 manual provided by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v3-chemistry).

value: femoral head

value: bone tissue cells

value: osteoblast and other cell type


title: In_vivo, sub4, RNA, Rep3

description:
Library name: AML263
Column name in Liver_Sub4_Counts: AML263

value: Liver


title: control2

description: Library name: sample2


title: In_vivo, sub4, RNA, Rep4

description:
Library name: AML262
Column name in Liver_Sub4_Counts: AML262


title: hMSC-Ctrl-1

description: Library name: Sample 13


title: PDS5-B-_-PDS5-A-_AID_+_aux_DT40 rep4

description: Library name: HG23YBGXM_1


title: control_DT40 rep1

description: Library name: 179958


title: control1

description: Library name: sample1


title: Human TS cell, stem state,scRNA-Seq, replicate 2

description: Library name: CT27_D0_2


title: CCNB1: Human TS cells (CT27), CCNB1 shRNA  treated, replicate 1

description: Library name: CCNB1_KD1


title: CCNB1: Human TS cells (CT27), CCNB1 shRNA  treated, replicate 2

description: Library name: CCNB1_KD2


title: In_vivo, sub3, RNA, Rep1

description:
Library name: AML261
Column name in Liver_Sub3_Counts: AML261


title: CCNB1: Human TS cells (CT27), control shRNA  treated, replicate 3

description: Library name: CCNB1_CTR_3

value: Control shRNA


title: PDS5-B-_-PDS5-A-_AID_+_aux_DT40 rep2

description: Library name: 215252_S2

value: avian leukosis virus (ALV) induced bursal lymphoma cell line


title: Stag2KO_5PhIAA_rep3

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

description: Library name: Sample 13

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same bait and prey coordinates and the same bait-prey junction sequence.
Assembly: mm9

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl pro-B lines were maintained in RPIM1640 medium supplemented with 10% FBS, 50 uM 2-Mercaptoethanol, 100 U/ml Penicillin-Streptomycin and 2 mM L-Glutamine.

extract_protocol:
DNA was lysed overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
Genomic DNA was extracted from G1 arrested cells. 2 to 4 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98o 2min, 1cycle; 95o 30sec, 58o 30sec, 72o 90sec, 80 cycles; 72o 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25o 1 hour, 22 o 3 hours, 16 o overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 15 cycles; 72o 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 12 cycles; 72o 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to illumina sequencing platforms with paired-end 300 bp or 150 bp sequencing.

treatment_protocol: RAG complementation and 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest.

value: v-Abl transformed pro-B cell line

value: Stag2-/-, Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days


title: CCNB1: Human TS cells (CT27), control shRNA  treated, replicate 2

description: Library name: CCNB1_CTR_2

value: extravillous trophoblast


title: Stag2KO_5PhIAA_rep2

description: Library name: Sample 12


title: PDS5-B-_-PDS5-A-_AID_+_aux_DT40 rep3

description: Library name: 215253


title: ESCO1-_-ESCO2-_AID_WAPL-_AID_+_aux_DT40 rep2

description: Library name: 188370


title: PDS5-B-_-PDS5-A-_AID_+_aux_DT40 rep1

description: Library name: 215252_S1


title: In_vivo, sub2, RNA, Rep2

description:
Library name: AML229
Column name in Liver_sub2_Counts: AML229


title: CCNB1: Human TS cells (CT27), control shRNA  treated, replicate 1

description: Library name: CCNB1_CTR_1


title: ESCO1-_-ESCO2-_AID_WAPL-_AID_+_aux_DT40 rep1

description: Library name: 179960


title: In_vivo, sub2, RNA, Rep1

description:
Library name: AML227
Column name in Liver_sub2_Counts: AML227


title: ADAMTS20: Human TS cells (CT27), ADAMTS20 shRNA  treated, replicate 3

description: Library name: ADAMTS20_KD_3

value: ADAMTS20 shRNA


title: Stag2KO_5PhIAA_rep1

description: Library name: Sample 11


title: In_vivo, sub1, RNA, Rep1

description:
Library name: AML256
Column name in Liver_Sub1_Counts: AML256


title: ESCO1-_-ESCO2-_AID_+_aux_DT40 rep2

description: Library name: 188369


title: In_vivo, sub3, RNA, Rep2

description:
Library name: AML260
Column name in Liver_Sub3_Counts: AML260


title: Esco1_Stag2KO_5PhIAA_rep2

description: Library name: Sample 49

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same bait and prey coordinates and the same bait-prey junction sequence.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

extract_protocol:
DNA was lysed overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
Genomic DNA was extracted from G1 arrested cells. 2 to 4 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98o 2min, 1cycle; 95o 30sec, 58o 30sec, 72o 90sec, 80 cycles; 72o 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25o 1 hour, 22 o 3 hours, 16 o overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 15 cycles; 72o 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 12 cycles; 72o 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to Mi-Seq machine (Illumina) with paired-end 300 bp sequencing.

treatment_protocol: RAG complementation and 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest. For induction of dCas9-blockade, 2 ug/ml doxycycline was added 4 hours prior to G1 arrest.

value: Esco1-AID2, Stag2-/-, Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days.


title: ESCO1-_-ESCO2-_AID_+_aux_DT40 rep1

description: Library name: 179959


title: In_vivo, sub1, RNA, Rep2

description:
Library name: AML255
Column name in Liver_Sub1_Counts: AML255


title: ADAMTS20: Human TS cells (CT27), ADAMTS20 shRNA  treated, replicate 1

description: Library name: ADAMTS20_KD_1

value: Day 8


title: Esco1_Stag2KO_5PhIAA_rep3

description: Library name: Sample 50


title: ADAMTS20: Human TS cells (CT27), control shRNA  treated, replicate 3

description: Library name: ADAMTS20_CTR_3

value: human trophoblast stem cells- CT27 (Okae et.al)


title: Esco1_Stag2KO_5PhIAA_rep1

description: Library name: Sample 48


title: Esco1_5PhIAA_rep3

description: Library name: Sample 44

value: Esco1-AID2, Emu-Bcl2+, RAG1(D708A)


title: In_vivo, sub1, RNA, Rep3

description:
Library name: AML254
Column name in Liver_Sub1_Counts: AML254


title: In_vivo, sub1, RNA, Rep4

description:
Library name: AML253
Column name in Liver_Sub1_Counts: AML253


title: Femur_3-Phlebotomy

city: Bethesda

first: Eva

last: Mezey

state: MD

address: 30 Convent Dr.

department: NIDCR

institute: NIH

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.7.3a in single-pass mode. With the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --alignSJoverhangMin 3 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: Custom mm10/GRCm38.vM23 + ERCCs + standard transgenes
Supplementary files format and content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: Femur bone

extract_protocol:
Osteocytes enriched bone fractions were isolated from frontal, parietal and femur and processed into total RNA.
Sequencing libraries were prepared by the Illumina Nextera XT method following manufacturer’s recommendations (Illumina, San Diego, CA). The multiplexed libraries were sequenced in a HiSeq1500 instrument in 126bp paired end mode.

value: Femur bone

tag: mouse strain

value: 12 weeks

value: WT

value: Phlebotomy


title: Femur_2-Phlebotomy


title: ADAMTS20: Human TS cells (CT27), ADAMTS20 shRNA  treated, replicate 2

description: Library name: ADAMTS20_KD_2


title: ADAMTS20: Human TS cells (CT27), control shRNA  treated, replicate 2

description: Library name: ADAMTS20_CTR_2


title: Femur_1-Phlebotomy


title: s60KL3

city: Fukuoka

first: Takanori

last: Shinjo

state: fukuoka

address: Maidashi 3-1-1

department: Section of Periodontology

country: Japan

institute: Kyushu University

description: Library name: Sample 36

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Epididymal adipose tissue

extract_protocol:
The total RNA was isolated from eWAT using TRIzol Reagent (nitrogen) and purified using PureLink Mini Prep kit (Thermo Scientific) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

value: Epididymal adipose tissue

value: 60%HFD feeding for 10 weeks, experimental peridontitis for 2weeks


title: ADAMTS20: Human TS cells (CT27), control shRNA  treated, replicate 1

description: Library name: ADAMTS20_CTR_1

value: Control shRNA


title: Femur_2-Control

value: Control


title: Esco1_5PhIAA_rep1

description: Library name: Sample 42

value: v-Abl transformed pro-B cell line


title: s60KL1

description: Library name: Sample 34


title: Femur_3-Control


title: CEBPB: Human TS cells (CT27), CEBPB shRNA  treated, replicate 3

description: Library name: CEBPB_KD_3

value: CEBPB shRNA


title: CEBPB: Human TS cells (CT27), CEBPB shRNA  treated, replicate 1

description: Library name: CEBPB_KD_1

value: extravillous trophoblast


title: s60K3

description: Library name: Sample 33

value: 60%HFD feeding for 10 weeks


title: Femur_1-Control


title: Degron_Ctr_rep1

description: Library name: Sample 39

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: CEBPB: Human TS cells (CT27), control shRNA  treated, replicate 3

description: Library name: CEBPB_ CTR_3


title: PBS_CD8_Rep3

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description: Library name: PR3CD8

data_processing:
Read quality was checked with FastQC
Raw reads were trimmed with TrimGalore, using the -rrbs flag
Trimmed reads were aligned to the mouse reference genome from Ensembl GRCm38 with Bismark using default parameters
CpG level methylation information was obtained with bismark methylation extractor
Assembly: GRCm38
Supplementary files format and content: bismark coverage files containing CpG level methylated and unmethylated counts

extract_protocol:
Splenocytes were stained with antibodies against CD4 and CD8 and sorted using BD Symphony S6. Sorted CD4+ and CD8+ T cells were collected into flow buffer for further downstream epigenetic analysis. DNA isolation was performed on sorted T cells using Puregene Cell kit (Qiagen) according to manufacturer’s guidelines. Zymo Clean and Concentrator Kit was used to clean up the collected DNA. DNA concentration was measured using Qubit Fluorometer 1X high sensitivity assay, and the DNA quality was measured using Nanodrop.
100ng DNA was used per sample. A 2 hour digestion using Mspl restriction enzyme (new England biolabs) was perfomed to enrich for CpG dense regions. Library preparation was performed using NEBNext Ultra II Modules (New England Biolabs) using methylated adaptors. Ampure XP magnetic beads (Beckman Coulter) were used to obtain an average size of approximately 200bp from the DNA fragments. Next, we used the EZ DNA Methylation-Gold Kit (Zymo Research) to perform bisulphite conversion. PCR amplification of DNA was performed using Q5U polymerase and NEBNext Multiplex Oligos for Illumina (New England Biolabs). After quantifying the libraries using Qubit fluorometer, they were normalized and sequenced at the OHSU MPSSR sequencing core.

treatment_protocol: Mice were treated with Aza  (1 mg/kg) or PBS, given IP, for three weeks, with 5 day dosing and a 2 day break

value: Spleen

value: T-Cells

value: FTL-ITD+/- TET2-/-

value: PBS

value: M


title: s60KL2

description: Library name: Sample 35


title: Wapl-AID2_Stag2KO_5PhIAA_rep3

description: Library name: Sample 38

value: Wapl-AID2, Stag2-/-, Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days.


title: PBS_CD8_Rep2

description: Library name: PR2CD8


title: Esco1_5PhIAA_rep2

description: Library name: Sample 43

value: Esco1-AID2, Emu-Bcl2+, RAG1(D708A)


title: CEBPB: Human TS cells (CT27), CEBPB shRNA  treated, replicate 2

description: Library name: CEBPB_KD_2

value: human trophoblast stem cells- CT27 (Okae et.al)

value: Day 8


title: Degron_Ctr_rep3

description: Library name: Sample 41


title: s60K1

description: Library name: Sample 31

value: Epididymal adipose tissue


title: Degron_Ctr_rep2

description: Library name: Sample 40


title: CEBPB: Human TS cells (CT27), control shRNA  treated, replicate 2

description: Library name: CEBPB_ CTR_2

value: Control shRNA


title: s60K2

description: Library name: Sample 32


title: Human TS cell, EVT differentition D8, replicate 3

description: Library name: CT27_D8_3

value: WT

value: EVT differentiation

value: day 8


title: Wapl-AID2_Stag2KO_5PhIAA_rep2

description: Library name: Sample 37

value: v-Abl transformed pro-B cell line


title: s60WL1

description: Library name: Sample 28

value: 60%HFD feeding for 10 weeks, experimental peridontitis for 2weeks


title: Wapl-AID2_Stag1KO_5PhIAA_rep2

description: Library name: Sample 34

value: Wapl-AID2, Stag1-/-, Emu-Bcl2+, RAG1(D708A)


title: s60WL3

description: Library name: Sample 30


title: Wapl-AID2_Stag2KO_5PhIAA_rep1

description: Library name: Sample 36


title: Wapl-AID2_Stag1KO_5PhIAA_rep3

description: Library name: Sample 35


title: Human TS cell, EVT differentition D8, replicate 2

description: Library name: CT27_D8_2

value: extravillous trophoblast


title: PBS_CD4_Rep2

description: Library name: PR2CD4_CC

value: Spleen

value: T-Cells

value: FTL-ITD+/- TET2-/-


title: s60W3

description: Library name: Sample 27

value: 60%HFD feeding for 10 weeks


title: s60WL2

description: Library name: Sample 29


title: Human TS cell, EVT differentition D8, replicate 1

description: Library name: CT27_D8_1


title: CEBPB: Human TS cells (CT27), control shRNA  treated, replicate 1

description: Library name: CEBPB_ CTR_1


title: s60W1

description: Library name: Sample 25


title: Aza_CD8_Rep3

description: Library name: A3_CD8

value: Azacitidine

value: M


title: Human TS cell, EVT differentition D6, replicate 1

description: Library name: CT27_D6_1

value: human trophoblast stem cells- CT27 (Okae et.al)

value: day 6


title: Wapl-AID2_CTCF-Nm_5PhIAA_rep2

description: Library name: Sample 31

value: Wapl-AID2, CTCF(Y226A/F228A), Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days.


title: PBS_CD4_Rep3

description: Library name: PR3CD4_CC

value: PBS


title: s60W2

description: Library name: Sample 26

value: Epididymal adipose tissue

value: WT


title: Wapl-AID2_Stag1KO_5PhIAA_rep1

description: Library name: Sample 33

value: v-Abl transformed pro-B cell line


title: Human TS cell, EVT differentition D6, replicate 3

description: Library name: CT27_D6_3

value: EVT differentiation


title: s40KL2

description: Library name: Sample 23

value: 40%HFD feeding for 10 weeks, experimental peridontitis for 2weeks


title: s40KL3

description: Library name: Sample 24


title: Human TS cell, EVT differentition D6, replicate 2

description: Library name: CT27_D6_2

value: extravillous trophoblast


title: Aza_CD8_Rep2

description: Library name: A2_CD8_CC

value: Spleen

value: F


title: Wapl-AID2_CTCF-Nm_5PhIAA_rep1

description: Library name: Sample 30


title: Wapl-AID2_CTCF-Nm_5PhIAA_rep3

description: Library name: Sample 32


title: Aza_CD4_Rep2

description: Library name: A2_CD4_CC

value: T-Cells

value: FTL-ITD+/- TET2-/-


title: Aza_CD8_Rep1

description: Library name: A1_CD8_CC

value: Azacitidine


title: PBS_CD4_Rep1

description: Library name: PR1CD4

value: M


title: Aza_CD4_Rep3

description: Library name: A3_CD4_CC


title: Aza_CD4_Rep1

description: Library name: A1_CD4_CC


title: Human TS cell, EVT differentition D3 ,replicate 3

description: Library name: CT27_D3_3

value: human trophoblast stem cells- CT27 (Okae et.al)

value: day 3


title: Human TS cell, EVT differentition D3 ,replicate 1

description: Library name: CT27_D3_1


title: s40K3

description: Library name: Sample 21

value: 40%HFD feeding for 10 weeks


title: Wapl-AID2_CTCF-Nm_untreated_rep1

description: Library name: Sample 28

value: Wapl-AID2, CTCF(Y226A/F228A), Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: s40KL1

description: Library name: Sample 22

value: Epididymal adipose tissue


title: TT-seq in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 3

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: CHD4cd_ADNPwt_TTseq_fusion_r3

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 and repeat sensitive settings according to Teissandier et al (Mobile DNA, 2019) (--outFilterType BySJout --outFilterMultimapNmax 100000  --outFilterMismatchNmax 3 --winAnchorMultimapNmax 20000 --alignMatesGapMax 350 --seedSearchStartLmax 30 alignTranscriptsPerReadNmax 30000  --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300  --seedNoneLociPerWindow 1000--outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax --limitBAMsortRAM 10000000000).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by using samtools and bedtools to calculate per base coverage, then counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
For RNA-seq, RNA was collected using RNAeasy miniprep kit (Qiagen) according to manufacturer's instructions. For TT-seq, RNA was isolated using Trizol according to manufacturer's instructions.
Libraries were prepared using TruSeq Ilumina total RNA-seq

tag: genetic background

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)


title: Human TS cell, stem state,replicate 3

description: Library name: CT27_D0_3

value: WT

value: EVT differentiation

value: day 0


title: Human TS cell, EVT differentition D3 ,replicate 2

description: Library name: CT27_D3_2

value: extravillous trophoblast


title: Wapl-AID2_5PhIAA_rep3

description: Library name: Sample 27

value: v-Abl transformed pro-B cell line

value: Wapl-AID2, Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days.


title: Wapl-AID2_5PhIAA_rep2

description: Library name: Sample 26


title: s40K2

description: Library name: Sample 20


title: Wapl-AID2_5PhIAA_rep1

description: Library name: Sample 25


title: s40WL3

description: Library name: Sample 18

value: 40%HFD feeding for 10 weeks, experimental peridontitis for 2weeks


title: Human TS cell, stem state,replicate 2

description: Library name: CT27_D0_2


title: Wapl-AID2_CTCF-Nm_untreated_rep2

description: Library name: Sample 29


title: TT-seq in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 2

description: Library name: CHD4cd_ADNPwt_TTseq_fusion_r2


title: TT-seq in CHD4cd (catalytic dead)-ADNPwt fusion mESC, replicate 1

description: Library name: CHD4cd_ADNPwt_TTseq_fusion_r1


title: Human TS cell, stem state,replicate 1

description: Library name: CT27_D0_1


title: Wapl-AID2_untreated_rep3

description: Library name: Sample 24


title: TT-seq in CHD4wt-ADNPwt fusion mESC, replicate 2

description: Library name: CHD4wt_ADNPwt_TTseq_fusion_r2


title: DMSO_Input

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

description: Library name: DMSO Input

data_processing:
The cleaned FASTQs were aligned using Bowtie2 (2.4.4) to the human reference genome GRCh38.
The duplicated reads were removed using picard (2.26.2) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
ChIP-seq peaks for BN1 were identified using MACS2 (version 2.2.7.1) by pooling HA-tagged bams and input bams.
Peaks were annotated by HOMER (4.11).
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak, merged narrowPeak (except for input samples)

source_name: Blood cell

extract_protocol:
FACS-sorted BN1 K562 cells were processed by HA ChIP
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: Blood cell

value: Leukemia cells

value: GFP+


title: Wapl-AID2_untreated_rep1

description: Library name: Sample 22


title: Wapl-AID2_untreated_rep2

description: Library name: Sample 23


title: s40WL1

description: Library name: Sample 16


title: Dox_Input

description: Library name: Dox Input


title: TT-seq in CHD4wt-ADNPwt fusion mESC, replicate 1

description: Library name: CHD4wt_ADNPwt_TTseq_fusion_r1


title: s40W3

description: Library name: Sample 15

value: 40%HFD feeding for 10 weeks


title: PBS_CD8_Rep1

description: Library name: PR1CD8

value: Spleen

value: T-Cells

value: FTL-ITD+/- TET2-/-

value: PBS

value: M


title: Stag2KO_CTCF-Nm_rep2

description: Library name: Sample 20

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: s40WL2

description: Library name: Sample 17

value: Epididymal adipose tissue

value: WT


title: LJP-treated I/R mouse brain, replicate 3

city: zhanjiang

first: tangming

last: guan

address: No. 57, South Renmin Avenue, Xiashan District

institute: Affiliated Hospital of Guangdong Medical University

description:
Library name: F3
Ischemic hemisphere from I/R + LJP mouse, replicate 3

data_processing:
Paired-end 150 bp sequencing was performed on an Illumina platform at Ribobio.
Raw reads were filtered to remove adapters and low-quality reads. Clean reads were aligned to the mouse reference genome.
Gene expression levels were quantified using featureCounts.
Differentially expressed genes (DEGs) were identified using DESeq2 with the thresholds:
Assembly: Mus musculus GRCm39 (mm10)
Supplementary files format and content: The processed data file (gene_count_matrix.txt) contains raw read counts for all genes across 12 samples.

source_name: Brain

growth_protocol: Mice were housed under standard conditions with a 12-hour light/dark cycle, constant temperature (22±1℃), and ad libitum access to food and water.

extract_protocol:
Total RNA was isolated from ischemic hemispheres using Magzol Reagent (Magen) following the manufacturer’s instructions. RNA quantity and quality were assessed using K5500 spectrophotometer (Kaiao) and Agilent 2200 TapeStation.
Poly(A)+ mRNA was enriched using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), fragmented to ~200 bp, and processed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina. Libraries were validated using Agilent 2200 TapeStation and Qubit (Thermo Fisher).

treatment_protocol: Cerebral ischemia-reperfusion injury was induced by transient middle cerebral artery occlusion (tMCAO). Mice in the LJP group were treated with Laminaria japonica polysaccharide (LJP); vehicle group received saline; sham group underwent sham surgery.

value: Brain

value: I/R + LJP


title: Stag2KO_CTCF-Nm_rep1

description: Library name: Sample 19

value: v-Abl transformed pro-B cell line


title: BN1_1

description: Library name: BN1 HA_ChIP_1

value: GFP+ BRD9-NUTM1


title: Stag2KO_CTCF-Nm_rep3

description: Library name: Sample 21


title: BN1_2

description: Library name: BN1 HA_ChIP_2


title: LJP-treated I/R mouse brain, replicate 4

description:
Library name: F4
Ischemic hemisphere from I/R + LJP mouse, replicate 4


title: TT-seq in CHD4wt-ADNPwt fusion mESC, replicate 3

description: Library name: CHD4wt_ADNPwt_TTseq_fusion_r3

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)


title: Stag2KO_rep6

description: Library name: Sample 18

value: Stag2-/-, Emu-Bcl2+, RAG1(D708A)


title: s40W2

description: Library name: Sample 14


title: LJP-treated I/R mouse brain, replicate 1

description:
Library name: F1
Ischemic hemisphere from I/R + LJP mouse, replicate 1


title: LJP-treated I/R mouse brain, replicate 2

description:
Library name: F2
Ischemic hemisphere from I/R + LJP mouse, replicate 2


title: BxPC-3_NC-1_2

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA28800

data_processing:
Sequencing was performed on the NovaSeq 6000 platform in 101-base single-end mode.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver.2.3.5.1 and SAMtools ver.1.2.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: pancreas

extract_protocol:
Total RNA was extracted from cells using the QIAGEN RNeasy Micro Kit.
The cDNA libraries were constructed according to the manufacturer's instructions using TruSeq stranded mRNA kit (Illumina, San Diego, CA).

value: pancreas

value: negative control treatment


title: BxPC-3_miR-4711-5p_2

description: Library name: GA28802

value: miRNA treatment


title: NKL2

description: Library name: Sample 11

value: ND feeding for 10 weeks, experimental peridontitis for 2weeks


title: BxPC-3_miR-4711-5p_1

description: Library name: GA28801


title: s40W1

description: Library name: Sample 13

value: 40%HFD feeding for 10 weeks


title: NKL3

description: Library name: Sample 12


title: Vehicle-treated I/R mouse brain, replicate 4

description:
Library name: P4
Ischemic hemisphere from I/R + Vehicle mouse, replicate 4

value: I/R + Vehicle


title: NKL1

description: Library name: Sample 10


title: NK3

description: Library name: Sample 9

value: ND feeding for 10 weeks


title: Vehicle-treated I/R mouse brain, replicate 3

description:
Library name: P3
Ischemic hemisphere from I/R + Vehicle mouse, replicate 3


title: Stag2KO_rep4

description: Library name: Sample 16

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: BxPC-3_Parent_2

description: Library name: GA28798

value: no treatment


title: Vehicle-treated I/R mouse brain, replicate 2

description:
Library name: P2
Ischemic hemisphere from I/R + Vehicle mouse, replicate 2


title: CTCF-Nm_rep3

description: Library name: Sample 15


title: BxPC-3_NC-1_1

description: Library name: GA28799


title: BxPC-3_Parent_1

description: Library name: GA28797


title: Stag2KO_rep5

description: Library name: Sample 17


title: CTCF-Nm_rep2

description: Library name: Sample 14


title: Vehicle-treated I/R mouse brain, replicate 1

description:
Library name: P1
Ischemic hemisphere from I/R + Vehicle mouse, replicate 1


title: NK2

description: Library name: Sample 8

value: Epididymal adipose tissue


title: CTCF-Nm_rep1

description: Library name: Sample 13