title: ChIP-Seq_HEK293T_ZBTB7B_GFP_rep2

value: GFP


title: ChIP-Seq_HEK293T_ZBTB7B_GFP_rep1

status: Public on Jun 02 2023

type: SRA

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

country: China

institute: Peking University

library_source: genomic

data_processing:
Raw ChIP-Seq reads were firstly trimmed using Cutadapt (v2.6) software and then mapped to the mm10 or hg19 genome using Bowtie2 (v2.3.5.1) software in ‘--very-sensitive-local’ mode.
RCR duplicates and discordant reads were filtered for further analysis.
Peaks were called by MACS2 (v2.1.1) software using a q threshold of 0.05. The two replicates were filtered by IDR (v.2.0.3) software using an idr threshold of 0.05 to obtain repeatable peaks.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Bigwig files were generated by deepTools2 (v.3.5.0)  software in 10 bp bins with normalized methods using RPGC.

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol:
The mouse embryonic stem cells (mESCs) (obtained from Richard Young’s lab, MIT) were cultured in Knock out DMEM (Gibco, #10829018-018), supplemented with 10% FBS,1x PenStrep (Gibco, #15140-122),1x nucleoside (Sigma, #ES-008),1x L-glutamine (Gibco, #25030-149),1x NEAA (non-essential amino acids, Milipore, #TMS-001-C), 3 μM CHIR99021 (Selleck, #S1036), 0.5 μM PD0325901 (Selleck, #S1263), 143 μM β-mercaptoethanol (Sigma, #M3148),1000 U/ml mLIF (Milipore, #ESG1107) at 37 ℃ with 5% CO2 in a humidified incubator.
HEK293T (ATCC, CRL-3216) cells were cultured in DMEM (Gibco, #11995-065) supplemented with 10% FCS (FBS, Gibco, #10099-141) and 1% PenStrep (Gibco, #15140-122) at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
The soluble chromatin fractions were extracted as previously reported (Ji et al., 2015).
DNA library was constructed by previous publication TELP library construction protocol (Peng et al., 2015) and NEBNext®UltraTMII DNA Library Prep Kit for Illumina (NEB, #E765S).

treatment_protocol: We treated the degron-mESCs with 1 μg/ml Doxycycline  (Sigma Aldrich,#D9891) for 24 hours, then added 500 μM IAA (Sigma Aldrich, #115148) for indicated time points for different analyses.

tag: cell line

tag: treatment

value: untreated

tag: sample type

value: GFP tagged HEK293T

tag: chip antibody


title: HiC_ZBTB21_degron_6h_rep2

data_processing:
The bridge linkers of raw Hi-C reads were firstly trimmed using trimLinker of ChIA-PET2 (v0.9.3) software.
The processed reads were then mapped to the mm10 genome by Bowtie2 (v2.2.3) in '--very-sentitive-local' mode and filtered to obtain valid contact pairs using HiC-Pro pipeline (v2.11.4).
RCP duplicated, dangling ended, re-ligated and self-circled read pairs were discarded for further analysis.
Long-range (>20 kb) intra-chromosomal valid pairs of all the samples were randomly sampled to the same depth (n = 34 M) and merged together (n = 68 M) between the two replicates to obtain higher resolution.
Genome_build: mm10
Supplementary_files_format_and_content: HIC format files were generated by hicpro2juicebox of Hic-Pro pipline (v2.11.4)

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: The mouse embryonic stem cells (mESCs) (obtained from Richard Young’s lab, MIT) were cultured in Knock out DMEM (Gibco, #10829018-018), supplemented with 10% FBS,1x PenStrep (Gibco, #15140-122),1x nucleoside (Sigma, #ES-008),1x L-glutamine (Gibco, #25030-149),1x NEAA (non-essential amino acids, Milipore, #TMS-001-C), 3 μM CHIR99021 (Selleck, #S1036), 0.5 μM PD0325901 (Selleck, #S1263), 143 μM β-mercaptoethanol (Sigma, #M3148),1000 U/ml mLIF (Milipore, #ESG1107) at 37 ℃ with 5% CO2 in a humidified incubator.

extract_protocol:
The BAT Hi-C experiment was conducted as previously reported (Huang et al., 2020).
DNA library was constructed by Illumina Nextera DNA Sample Preparation Kit (FC-121-1030).

tag: cell type

value: mouse embryonic stem cell (mESC)

value: ZBTB21 degron 6h

value: ZBTB21 degron 6h mES

tag: restriction enzyme

value: Alu I


title: NK92_Control_H3K27ac_rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
sequnced using Illumina HiSeq 2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.27.4
peaks were called using macs2 v2.2.7.1 with input reference bam file and the following setting: -f BAMPE -g hs (--broad for H3K27ac ChIP-seq peak calling, -q 0.1 for Runx3 ChIP-seq peak calling) and all peaks in blacklist regions were removed
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: hg19
Supplementary files format and content: narrowPeak, broadPeak, CPM normalized bigwig

growth_protocol: NK92 cells were cultured α-MEM medium supplemented with 20% FBS, 55μM 2-mercaptoethanoland 100U/ml IL-2, 100U/ml Penicillin and 100μg/ml Streptomycin.

extract_protocol:
ChIP-seq was performed using the protocol from Schmidl et al., 2015 with small modifications. Fixed cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq2500, NovaSeq6000, HiSeq 2500 platform.

treatment_protocol: NK92 was treated with 1000nM SAHA for 24 hours.

value: NK Cells

tag: passages

value: 12 passages

value: H3K27ac (Abcam #ab4729)


title: NK92_Control_H3K27ac_rep1


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 2 pre-treament

type: RNA

city: Pittsburgh

first: Anda

middle: M.

last: Vlad

state: PA

address: 204 Craft Avenue, B403

country: USA

institute: Magee-Womens Research Institute

description: Two probes were used to detect each transcript: a reporter probe that carries the fluorescent barcode, and a biotinylated capture probe that immobilizes the complex for data collection. The code set contained 770 probe pairs, each pair specific to a particular nucleic acid target

hyb_protocol: according to Nanostring instructions

scan_protocol: according to Nanostring instructions

data_processing: Used NanostringNorm function in NanostringNorm package to normalize the gene expression data to the 20 housekeeping genes, and then keep the endogenous genes.

label: Fluorescent barcode, unique to each probe

molecule: total RNA

source_name: ovarian cancer

label_protocol: according to Nanostring instructions

growth_protocol: Not applicable.

extract_protocol: RNA from peripheral blood mononuclear cells (PBMCs) was isolated using the Qiagen AllPrep DNA/RNA Kit. All RNA isolation was performed according to the manufacturer’s protocol. RNA concentration was measured with a NanoDrop 2000 UV-Vis Spectrophotometer (Thermo Scientific).

treatment_protocol: Samples were not pre-treated in vitro prior to RNA extraction. However, sample collection relative to the patient's treatment is specified in column L.

tag: gender

value: Female

tag: age at diagnosis

tag: tumor histology

value: Papillary Serous

tag: Stage

value: IIIC


title: IP fluid late-time-point for patient 7

extract_protocol: RNA was isolated from IP cells obtained from IP fluid using the AllPrep DNA/RNA/Protein Kit (Qiagen). All RNA isolation was performed according to the manufacturer’s protocol. RNA concentration was measured with a NanoDrop 2000 UV-Vis Spectrophotometer (Thermo Scientific).

value: Serous

value: IIB


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 5 pre-treament


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 9 pre-treament


title: RNA-Seq_mES_ZBTB21_untreated_rep1

library_source: transcriptomic

data_processing:
Raw RNA-Seq reads were firstly trimmed using Cutadapt (v.2.6) software and then mapped to the mm10 genome using STAR (v2.7.6a) software
Only uniquely mapped reads were kept for further analysis.
The raw counts of genes downloaded from GENECODE vM25 were obtained using featureCounts (v.1.6.3) software.
Genome_build: mm10
Supplementary_files_format_and_content: Table with raw counts for each sample

extract_protocol:
The total RNA was extracted with TRIzol by following manufacturer's instructions.
RNA library was constructed by Novogene with Illumina Poly (A) RNA-Seq library preparation kit.
Poly (A) RNA-Seq

value: ZBTB21 untreated mES


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 2 post-treament


title: NK92_input

value: Not applied


title: IP fluid late-time-point for patient 6

value: IIIA


title: HiC_ZBTB21_untreated_rep2

value: untreated


title: IP fluid late-time-point for patient 8

value: IV


title: ChIP-Seq_HEK293T_ZBTB7A_GFP_rep1

value: GFP tagged HEK293T

value: GFP


title: NK92_SAHA_RNA_rep3

data_processing:
sequnced using Illumina HiSeq 2500 platform
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR v2.6.0a with parameters--twopassMode Basic --chimSegmentMin 20 --quantMode TranscriptomeSAM
Fragments Per Kilobase Million (FPKM), Transcripts Per Kilobase Million(TPM) and raw counts were calculated using RSEM
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: hg19
Supplementary files format and content: RSEM output files including raw counts, FPKM, TPM values
Supplementary files format and content: normalized bigwig

molecule: polyA RNA

extract_protocol:
RNA was extracted from cells based on chloroform-phenol/guanidine. Total RNA prepared with rRNA depletion and PolyA RNA was isolated by oligo dT beads.
cDNA is amplified through 9 cycles of PCR amplification using the NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were paired-end sequenced on Illumina HiSeq 2500 platform.

value: SAHA treated


title: IP fluid late-time-point for patient 5


title: ChIP-Seq_mES_SMC1_ZBTB21_ZBTB7B_input

value: mouse embryonic stem cell (mESC)

value: ZBTB21 & ZBTB21 untreated mES


title: 20_MIBC_MACE

city: Frankfurt

first: Florestan

middle: Johannes

last: Koll

address: Theodor-Stern-Kai 7

department: Department of Urology

country: Germany

institute: University Hospital Frankfurt, Goethe University

description:
Massive Analysis of cDNA (MACE)
VH20

data_processing: median normalization, log2-transformed

source_name: bladder cancer

extract_protocol:
A 1mm punch was taken from FFPE blocks of a representative tumor area with at least 50% tumor content. RNA was isolated using the “truXTRAC FFPE total NA Kit – Column” (Covaris, Woburn, MA, USA)
The samples were prepared by GenXPro GmbH (Frankfurt, Germany) using the MACE-Kit V2 according to the manual of the manufacturers (GenXPro GmbH). Briefly, RNA was fragmented and polyadenylated mRNA was enriched by poly-A specific reverse transcription and, a specific adapter was integrated at the 5’ends and the products were amplified by competitive PCR and sequenced on an Illumina NextSeq 550 instrument.

tag: tissue

value: bladder cancer

tag: tissue preparation

value: FFPE

tag: Sex

value: f

tag: age

tag: protocol

value: MACE


title: ChIP-Seq_mES_SMC1_ZBTB21_ZBTB7B_double_degron_rep2

value: ZBTB21 & ZBTB7B degron 6h

value: ZBTB21 & ZBTB21 degroh 6h mES


title: NK92_SAHA_RNA_rep2

value: NK Cells

value: 12 passages


title: HiC_ZBTB21_degron_6h_rep1

value: ZBTB21 degron 6h

value: ZBTB21 degron 6h mES

value: Alu I


title: ChIP-Seq_HEK293T_ZBTB7A_GFP_rep2

value: untreated


title: NK92_SAHA_RNA_rep1


title: NK92_Control_RNA_rep3


title: IP fluid late-time-point for patient 4

value: Female

value: Papillary Serous


title: 17_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH17

value: m


title: ChIP-Seq_mES_SMC1_ZBTB21_ZBTB7B_double_degron_rep1

value: mouse embryonic stem cell (mESC)


title: 42_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH42


title: NK92_Control_RNA_rep2


title: ChIP-Seq_mES_SMC1_ZBTB21_ZBTB7B_ZBTB21_degron_rep2


title: IP fluid late-time-point for patient 2

value: IIIC


title: IP fluid late-time-point for patient 1

value: Endometrioid


title: HiC_ZBTB21_untreated_rep1

value: ZBTB21 untreated mES


title: ChIP-Seq_mES_SMC1_ZBTB21_ZBTB7B_ZBTB21_degron_rep1


title: NK92_Control_RNA_rep1


title: 08_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH8

value: bladder cancer

value: FFPE


title: Sample 25

city: RENNES

first: vonick

last: sibut

address: avenue du Prof Leon BERNARD

country: France

data_processing:
Illumina software used for basecalling.
FastQC control quality
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using STAR with parameters :                     --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using Subread
Differential gene expression analysis was performed for all conditions using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample ...

source_name: Healthy Donor Bone Marrow Mesenchymal Stem Cells

growth_protocol: BM-MSC were plated at 500 cells/cm2  in 175cm2 flasque up to confluency  in αMEM+10% SVF+100 IU/mL penicillin+100 μg/mL streptomycin + 1 ng/mL FGF2

extract_protocol:
Total RNA was extracted using Macherey-Nagel NucleoSpin RNA Columns with DNAse treatment, according to the manufacturer’s recommendations (Macherey-Nagel).
RNA libraries were prepared (with 10ng of total RNA)  for sequencing using standard Illumina protocols

treatment_protocol: αMEM+10% SVF+100 IU/mL penicillin+100 μg/mL streptomycin addition or not by 10 ng/mL TNFα and 100 ng/mL LTα1β2 or a ratio of  10.000 AnnexinV_Pos_Evs to 1 MSC, during 3 days at 37°C and 5% CO2

tag: passage

value: End P1

tag: donor number

value: EVs from DOHH2


title: 44_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH44

value: MACE


title: 46_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH46


title: IP fluid intermediate-time-point for patient 3

value: Clear Cell

value: IA


title: IP fluid intermediate-time-point for patient 2


title: 09_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH9


title: Sample 24

value: Healthy Donor Bone Marrow Mesenchymal Stem Cells

value: End P2

tag: treatment


title: ChIP-Seq_mES_NIPBL_ZBTB21_degron_input

value: untreated

tag: sample type


title: 48_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH48


title: IP fluid late-time-point for patient 3

value: Female


title: 45_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH45


title: Sample 23


title: Sample 22


title: ChIP-Seq_mES_NIPBL_ZBTB21_degron_1h_rep2

value: ZBTB21 degron 1h

value: ZBTB21 degron 1h mES

tag: chip antibody

value: Nipbl


title: 49_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH49

value: m


title: IP fluid intermediate-time-point for patient 1

value: Endometrioid


title: ChIP-Seq_mES_SMC1_ZBTB21_ZBTB7B_untreated_rep2

tag: cell type

value: mouse embryonic stem cell (mESC)

value: ZBTB21 & ZBTB21 untreated mES


title: IP fluid early-time-point for patient 8

value: Papillary Serous

value: IV


title: IP fluid early-time-point for patient 7

value: Serous

value: IIB


title: ChIP-Seq_mES_NIPBL_ZBTB21_degron_1h_rep1


title: Sample 21

value: EVs from DOHH2


title: 26_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH26

value: bladder cancer

value: FFPE

value: MACE


title: 32_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH32


title: Sample 20

value: Healthy Donor Bone Marrow Mesenchymal Stem Cells

value: End P1

value: EVs from SU_DHL4


title: ChIP-Seq_mES_NIPBL_ZBTB21_degron_0h_rep2

value: untreated

value: ZBTB21 untreated mES


title: IP fluid early-time-point for patient 5

value: Female

value: IIIC


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_input

value: mouse embryonic stem cell (mESC)


title: Sample 18

value: End P2


title: 07_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH7

value: m


title: IP fluid early-time-point for patient 4

value: Papillary Serous


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_6h_rep2

value: ZBTB21 degron 6h

value: ZBTB21 degron 6h mES


title: IP fluid intermediate-time-point for patient 5


title: Sample 17


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_6h_rep1


title: 41_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
1VH41

value: f


title: Sample 16


title: 21_MIBC_MACE

description:
Massive Analysis of cDNA (MACE)
VH21

value: bladder cancer


title: Sample 15

value: EVs from RL


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_1h_rep2

value: ZBTB21 degron 1h

value: ZBTB21 degron 1h mES


title: 20_MIBC_HTG

description:
HTG transcriptome panel
260-A039078

data_processing: The sequencing data on mRNA expression of target genes were imported into HTG EdgeSeq Parser software for alignment of FASTQ files to the to the probe list and quantification of the reads. The HTG EdgeSeq Reveal Application was utilized to quality check and normalize data. Gene counts were normalized using CPM and median normalization and log2-transformed for further analysis. Post-Sequencing QC:  Post-sequencing QC metrics (QC0, QC1, QC2, and QC3) detect four different sample failure modes. QC0 detects degraded RNA or poor quality / quantity samples, by assessing the percentage of overall reads being allocated to the positive process control probe for each sample. QC1 detects samples with insufficient read depth; this is evaluated by setting the cut-off at the minimum number of reads that can be allocated to each sample for the data set to be repeatable. QC2 detects samples with minimal expression variability, of which is determined by the median log2 (CPM) for negative control probes. QC3 detects samples with elevated gDNA background, which is caused by incomplete digestion of gDNA by the DNase enzyme.

extract_protocol:
A 1mm punch was taken from FFPE blocks of a representative tumor area with at least 50% tumor content. RNA was isolated using the “truXTRAC FFPE total NA Kit – Column” (Covaris, Woburn, MA, USA)
The mRNA expression was determined using the HTG Transcriptome Panel (HTG Molecular Diagnostics, Tuscon, AZ, USA) as describes before. Briefly, target capture was done by the HTG EdgeSeq chemistry with nuclease protection probes on a 96-well plate. Processed samples were used to set up PCR reactions with specially designed primers, referred to as “tags”. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode that is used for sample identification and multiplexing. The library was prepared using a PCR with OneTaq (New England Biolabs, Ipswich, MA, USA) and EdgeSeq PCR tag primers (HTG Molecular Diagnostics). Sequencing was performed on the Illumina NextSeq 550 system (Illumina, San Diego, CA, USA) in accordance with manufacturer’s recommendations but also including two HTG custom sequencing primers.

value: FFPE

value: HTG


title: IP fluid early-time-point for patient 2


title: IP fluid early-time-point for patient 1

value: Endometrioid


title: 46_MIBC_HTG

description:
HTG transcriptome panel
260-A039095


title: 09_MIBC_HTG

description:
HTG transcriptome panel
260-A039072


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_1h_rep1


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_0h_rep2

value: untreated

value: ZBTB21 untreated mES


title: Sample 14

value: Healthy Donor Bone Marrow Mesenchymal Stem Cells


title: Sample 13


title: FFPE tumor specimens for patient 7 post-treament

extract_protocol: RNA was also isolated from tumor tissue using the Qiagen AllPrep DNA/RNA FFPE Kit. Tissue was scrapped from 10 µm thick slices of FFPE tumor specimens using 2-5 slides per specimen. All RNA isolation was performed according to the manufacturer’s protocol. RNA concentration was measured with a NanoDrop 2000 UV-Vis Spectrophotometer (Thermo Scientific).

value: Female

value: Serous

value: IIB


title: IP fluid early-time-point for patient 3

value: Clear Cell

value: IA


title: 17_MIBC_HTG

description:
HTG transcriptome panel
260-A039075

value: m


title: Sample 12

value: End P2


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_0h_rep1

value: mouse embryonic stem cell (mESC)


title: FFPE tumor specimens for patient 7 pre-treament


title: ChIP-Seq_mES_CTCF_untreated_rep2

value: untreated mES

value: Ctcf


title: Sample 11

value: EVs from RL


title: FFPE tumor specimens for patient 3 post-treament


title: ChIP-Seq_mES_CTCF_untreated_rep1


title: 08_MIBC_HTG

description:
HTG transcriptome panel
260-A039071

value: bladder cancer

value: FFPE


title: FFPE tumor specimens for patient 3 pre-treament


title: 44_MIBC_HTG

description:
HTG transcriptome panel
260-A039093

value: HTG


title: FFPE tumor specimens for patient 9 post-treament

value: Papillary Serous


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_24h_rep2

value: ZBTB21 degron 24h

value: ZBTB21 degron 24h mES


title: 48_MIBC_HTG

description:
HTG transcriptome panel
260-A039096


title: 45_MIBC_HTG

description:
HTG transcriptome panel
260-A039094


title: FFPE tumor specimens for patient 5 post-treament

value: Female

value: IIIC


title: FFPE tumor specimens for patient 9 pre-treament


title: Sample 8

value: Healthy Donor Bone Marrow Mesenchymal Stem Cells

value: TNFaLTab


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_24h_rep1


title: 49_MIBC_HTG

description:
HTG transcriptome panel
260-A039097


title: FFPE tumor specimens for patient 5 pre-treament


title: 42_MIBC_HTG

description:
HTG transcriptome panel
260-A039092

value: f


title: Sample 6


title: FFPE tumor specimens for patient 4 post-treament


title: 26_MIBC_HTG

description:
HTG transcriptome panel
260-A039082

value: m


title: Sample 5

value: End P1

value: Untreated


title: 32_MIBC_HTG

description:
HTG transcriptome panel
260-A039084


title: ChIP-Seq_mES_ZBTB21_GFP_input

value: mouse embryonic stem cell (mESC)

value: untreated

value: GFP tagged mES


title: FFPE tumor specimens for patient 4 pre-treament


title: Sample 4

value: End P2


title: 07_MIBC_HTG

description:
HTG transcriptome panel
260-A039070

value: bladder cancer

value: FFPE


title: ChIP-Seq_mES_ZBTB21_GFP_rep2

value: GFP


title: Sample 3


title: 21_MIBC_HTG

description:
HTG transcriptome panel
260-A039069

value: HTG


title: ChIP-Seq_mES_ZBTB21_GFP_rep1


title: ChIP-Seq_mES_SMC1_ZBTB21_untreated_rep1

value: ZBTB21 untreated mES


title: ATAC-Seq_untreated_rep2

data_processing:
Raw ChIP-Seq reads were firstly trimmed using Cutadapt (v2.6) software and then mapped to the mm10 or hg19 genome using Bowtie2 (v2.3.5.1) software with default parameters.
RCR duplicates, discordant reads and reads mapped to chrM were discarded for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files were generated by MACS2 (v2.1.1) software using a q threshold of 0.05. Peaks between two replicates were merged together by IDR (v.2.0.3) using a idr threshold of 0.05 to obtain repeatable peaks.

source_name: V6.5 cells

growth_protocol: The V6.5 mouse ES (mES) cell line was cultured with irradiated mouse embryonic fibroblasts in DMEM-KO containing 15% FBS, leukaemia inhibiting factor (LIF), L-glutamine, β-mercaptoethanol, non-essential amino acids and penicillin/ streptomycin at 37 ℃ with 5% CO2, and passaged twice for experiments.

extract_protocol:
ATAC-seq were performed according to the protocol from (Corces M.R et al., 2017).
50,000 viable cells were used for library preparation using TruePrep DNA Library Prep Kit V2 for Illumina Kit (Vazyme #TD501), PCR amplified libraries were extracted with Megen gel purification kit (Megen # D2111-03) with size selection for mono and dinucleosome.

treatment_protocol: Degron mES cells were treated with 1 μg/ml Doxycycline for 24 hours

tag: cell line

value: V6.5 cells


title: FFPE tumor specimens for patient 2 pre-treament

value: Female

value: Papillary Serous

value: IIIC


title: 41_MIBC_HTG

description:
HTG transcriptome panel
260-A039091

data_processing:
The sequencing data on mRNA expression of target genes were imported into HTG EdgeSeq Parser software for alignment of FASTQ files to the to the probe list and quantification of the reads. The HTG EdgeSeq Reveal Application was utilized to quality check and normalize data. Gene counts were normalized using CPM and median normalization and log2-transformed for further analysis. Post-Sequencing QC:  Post-sequencing QC metrics (QC0, QC1, QC2, and QC3) detect four different sample failure modes. QC0 detects degraded RNA or poor quality / quantity samples, by assessing the percentage of overall reads being allocated to the positive process control probe for each sample. QC1 detects samples with insufficient read depth; this is evaluated by setting the cut-off at the minimum number of reads that can be allocated to each sample for the data set to be repeatable. QC2 detects samples with minimal expression variability, of which is determined by the median log2 (CPM) for negative control probes. QC3 detects samples with elevated gDNA background, which is caused by incomplete digestion of gDNA by the DNase enzyme.
median normalization, log2-transformed

value: f


title: Sample 1

value: Healthy Donor Bone Marrow Mesenchymal Stem Cells


title: ATAC-Seq_untreated_rep1


title: Macosko_HomoTrimerTSO_polyA

status: Public on Jun 01 2023

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: ONT MinION

library_source: transcriptomic single cell

data_processing:
We performed basecalling on the raw fast5 data using Guppy (v) (guppy_basecaller –compress-fastq -c dna_r104_450bps_hac.cfg -x “cuda:1”) in GPU mode from Oxford Nanopore Technologies running on a RTX 3090 graphics card.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: JJN3 and 5TGMG1

extract_protocol:
Samples were processed using the Drop-seq DolomiteBio Nadia encapsulator system.
ScCOLOR-seq protocol was used.
For nanopore sequencing, cDNA was amplified with 25 SMART PCR reactions and sequencing libraries were prepared using the Oxford Nanopore LSK-109 library preperation kit.

value: JJN3 and 5TGMG1

value: Myeloma cell lines (1000 cells)


title: FFPE tumor specimens for patient 6 post-treament

value: IIIA


title: polyAconst_LSK114_R1041_SUP

data_processing: The data was processed using a custom pipeline 'pipeline_count' written using cgatcore and included within the TallyNNN repository (https://github.com/cribbslab/TallyNNN). Briefly, the polyA associated UMI sequence by searching for the polyA region and reverse complementing the read if it does not appear in the correct orientation. The 30bp UMI is then identified upstream of the SMART primer by pattern matching for GTACTCTGCGTTGATACCACTGCTT. We then corrected for errors or remove the read based the number of UMI errors and then the UMI is added to the read name. Next, the TSO associated UMI is identified using the SMART primer sequence AAGCAGTGGTATCAACGCAGAGTAAT. The 30bp UMI sequence is then corrected for errors or remove the read based the number of UMI errors and then the UMI is added to the read name. Both the TSO and polyA associated UMIs and primer sequences are removed from the read sequence.  For transcrip0t level analysis, the fastq file is then mapped against the transcriptome using minimap2 (v2.22) with the following settings: -ax map-ont -p 0.9 --end-bonus 10 -N 3. The resulting sam file was then sorted and indexed using samtools18. A custom script was then used to add the transcript name to the XT tag of the samfile for downstream counting by homotrimer deduplication, UMI-tools or mclUMI. For gene level analysis, the fastq data was mapped using minimap2 using the following setting: -ax splice -k 14 --sam-hit-only --secondary=no --junc-bed. The resulting sam file was then sorted and indexed followed by feature annotation using featurecounts (v2.0.1) using the following settings to generate an annotated bam file: featureCounts -a (gtf) -o (output) -R BAM. This bam file was then used for downstream counting by UMI-tools or mclUMI. The reference transcriptome and genomes used for the analysis were hg38_ensembl98 and mm10_ensembl88. Downstream differential expression was performed using Deseq2.

source_name: JJN3 and 5TGM1 cells

growth_protocol: JJN3, 5TGM1 and RM82  cells were cultured in RPMI with 10% FBS and 1% Pen/Strep in a 37oC incubator with 5% CO2.

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: RM82 cells were treated with either DMSO control or SGC-CLK1 inhibitor

value: JJN3 and 5TGM1 cells


title: polyAconst_LSK114_R1041_R2


title: polyAconst_LSK114_R1041_R1


title: FFPE tumor specimens for patient 6 pre-treament


title: ChIP-Seq_mES_SMC1_ZBTB21_untreated_rep2

value: mouse embryonic stem cell (mESC)

value: untreated


title: polyAconst_LSK114_R1041_HAC


title: polyAconst_LSK112_R941_R3


title: polyAconst_LSK112_R941


title: FFPE tumor specimens for patient 2 post-treament


title: ChIP-Seq_mES_SMC1_ZBTB21_ZBTB7B_untreated_rep1

value: ZBTB21 & ZBTB21 untreated mES


title: Sample 7

value: End P2

value: TNFaLTab


title: Sample 9


title: polyAconst_LSK109_R941_R1


title: polyAconst_HiFi


title: polyAconst_LSK109_R411_R3


title: Sample 10

value: End P1


title: monomer_CMI


title: polyAconst_LSK109_R941_R2


title: homodimer_CMI


title: Sample 2

value: Untreated


title: polyAconst_LSK112_R941_R2


title: polyAconst_LSK114_R1041_R3


title: Ank_Mut48m AF

city: Philadelphia

first: Makarand

middle: V.

last: Risbud

address: 1025 Walnut Street, Suite 501 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson University

description: Total RNA from ank/ank AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75

hyb_protocol: Affymetrix Gene chips, Mouse Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix).

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the experiment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05. Inclusion cutoffs were defined at a 1.75-fold change and p-value < 0.05.

label: biotin

source_name: AF Mut

label_protocol: Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: ank/ank mice and littermate WT mice were aged until 13-week-old.

extract_protocol: NP and AF tissues were micro-dissected from caudal and lumbar intervertebral discs of 5 WT and 5 ank/ank animals and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

value: annulus fibrosus (AF)

value: male

tag: genotype

value: Ank mutant


title: Ank_Mut34f AF

value: female


title: Ank_Mut31m AF


title: MrC26_My_A

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

data_processing:
clipping of adapters and quality trimming with Trimmomatic, ver. 0.36, parameters: “ILLUMINACLIP:2:30:10 LEADING:7 TRAILING:7 SLIDINGWINDOW:10:20 MINLEN:36”
mapped using Bowtie2, ver. 2.3.4.1, parameters: “–non-deterministic -k 1 –very-sensitive -t”
Read counts with GenomicAlignments, ver 1.18.1
Assembly: Mror_plus_Cacao.CDS.reference.fasta
Supplementary files format and content: tabular text file, tab delimited
Supplementary files format and content: Fasta sequences

organism: Moniliophthora roreri

extract_protocol:
2–3 agar plugs were transferred from cultures grown on V8 agar plate to 250 ml conical flask containing 50 ml potato dextrose broth and grown at room temperature (22–25°C) while shaking at 100 rpm. Cultures were allowed to grow for 10–15 days. Mycelia were washed with sterile water and collected by centrifuging at 20,000 g for 10 min followed by flash freezing in liquid nitrogen and freeze drying. Freeze-dried mycelia were ground in a mortar and pestle in liquid nitrogen and transferred to a 50 mL centrifuge tube containing 15 mL of 65°C extraction buffer (Bailey et al., 2005)
Illumina TruSeq RNA sample preparation kit v.2, Illumina TruSeq RNA sample preparation kit v.1

value: mycelia

tag: replicate

value: A


title: Ank_Mut41f AF


title: Ank_WT59m NP

description: Total RNA from WT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75

source_name: NP WT

value: nucleus pulposus (NP)

value: WT


title: Ank_WT55f NP


title: Ank_WT55f AF

description: Total RNA from WT AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.78

source_name: AF WT


title: Ank_Mut41f NP

description: Total RNA from ank/ank NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75

source_name: NP Mut


title: Ank_WT33f NP


title: Ank_WT53f AF

description: Total RNA from WT AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.77


title: Ank_WT33f AF

description: Total RNA from WT AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.76


title: Ank_WT32m AF

description: Total RNA from WT AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.75


title: Ank_Mut34f NP


title: Mmp20+/+ Tg-AT4 (Tg)

city: Fukuoka

first: Masashi

last: Shin

state: Fukuoka

address: 2-15-1 Tamura, Sawara-ku

country: Japan

institute: Fukuoka Dental College

description: Test; SAMPLE 3

data_processing:
The normalization and all the data analysis were performed using excel manually.
Target gene signals normalized to housekeeping gene, Gapdh; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_Gapdh)]
We manually performs all deltadeltaCt based fold-change calculations from the raw threshold cycle data.

label: SYBR Green

source_name: Ameloblast

label_protocol: Reverse transcription was performed from 10 ng total RNA using the PrimeScript RT Master Mix (Takara Bio). Quantitative real-time PCR were performed (CFX96 Real-Time System, Bio-Rad) with 40 cycles at 95 oC for 10 seconds and 55 oC for 30 seconds.

extract_protocol: Total RNA was extracted with NucleoSpin RNA XS Kit followed by DNase I treatment.

value: Ameloblast

tag: strain

value: Mmp20+/+ Tg-AT4


title: Mmp20-/- -AT4 (KO)

description: Test; SAMPLE 2


title: Ank_Mut48m NP


title: MrC26_My_B

value: B


title: Ank_Mut39f NP


title: Ank_WT59m AF

description: Total RNA from WT AF tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.79


title: Mr60dpi_A

value: 60 dpi cacao pod


title: Ank_WT53f NP


title: Mr60dpi_C

value: C


title: Mr60dpi_B


title: Ank_Mut39f AF


title: Mr30dpi_B

value: 30 dpi cacao pod


title: Mr30dpi_C


title: MrC26-21dpi-C

value: 21 dpi cacao pod


title: Mr30dpi_A


title: ChIP-Seq_mES_NIPBL_ZBTB21_degron_0h_rep1

extract_protocol:
The soluble chromatin fractions were extracted as previously reported (Ji et al., 2015).
DNA library was constructed by previous publication TELP library construction protocol (Peng et al., 2015) and NEBNext®UltraTMII DNA Library Prep Kit for Illumina (NEB, #E765S).

value: mouse embryonic stem cell (mESC)

value: untreated

value: ZBTB21 untreated mES

value: Nipbl


title: MrC26-21dpi-B


title: Sample 19

value: Healthy Donor Bone Marrow Mesenchymal Stem Cells

value: End P2

value: EVs from SU_DHL4


title: MrC26-7dpi-C

value: 7 dpi cacao pod


title: MrC26-7dpi-A

value: A


title: MrC26-7dpi-B


title: Nc_20C

data_processing:
clipping of adapters and quality trimming with Trimmomatic, ver. 0.36, parameters: “ILLUMINACLIP:2:30:10 LEADING:7 TRAILING:7 SLIDINGWINDOW:10:20 MINLEN:36”
mapped using Bowtie2, ver. 2.3.4.1, parameters: “–non-deterministic -k 1 –very-sensitive -t”
Read counts with GenomicAlignments, ver 1.18.1
Assembly: Mper_plus_Cacao.CDS.reference.fasta
Supplementary files format and content: tabular text file, tab delimited
Supplementary files format and content: Fasta sequences

organism: Moniliophthora perniciosa

extract_protocol:
2–3 agar plugs were transferred from cultures grown on V8 agar plate to 250 ml conical flask containing 50 ml potato dextrose broth and grown at room temperature (22–25°C) while shaking at 100 rpm. Cultures were allowed to grow for 10–15 days. Mycelia were washed with sterile water and collected by centrifuging at 20,000 g for 10 min followed by flash freezing in liquid nitrogen and freeze drying. Freeze-dried mycelia were ground in a mortar and pestle in liquid nitrogen and transferred to a 50 mL centrifuge tube containing 15 mL of 65°C extraction buffer (Bailey et al., 2005)
Illumina TruSeq RNA sample preparation kit v.2

value: D


title: Nc_19C


title: Nc_17C


title: IP fluid early-time-point for patient 6

tag: gender

value: Female

tag: age at diagnosis

tag: tumor histology

value: Papillary Serous

value: IIIA


title: MrC26-21dpi-A


title: Ts_14C


title: Ts_13C

value: B


title: Ts_1C


title: Ank_Mut31m NP

tag: tissue

value: nucleus pulposus (NP)

value: male

value: Ank mutant


title: Gb_11C


title: Ank_WT32m NP

tag: Sex

value: WT


title: Nc_18C


title: Gb_6C


title: Gb_8C

value: C


title: Mp-Bs-3

value: basidiospores


title: Mp-Bs-2


title: Mp-Bc-3

value: basidiocarps


title: Mp-Bc-2


title: Mp-Bs-1


title: Mp_Myc-4

value: mycelia


title: Gb_4C


title: Mp_Myc-3


title: Mp-My-1


title: Mp-My-2


title: Liver, bear, rep 1

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample

organism: Ursus americanus

source_name: Liver

extract_protocol:
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)

treatment_protocol: The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).

value: Liver

tag: age

value: adult

value: wild type


title: Osteogenic differentiation, Nontreated

city: Chuncheon

first: Ju Hyun

last: Park

state: Gangwon-do

address: 1 Kangwondaehak-gil

department: Department of Biomedical Science

institute: Kangwon National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: #1 hUSCs

growth_protocol: The urine-derived stem cells were then cultured in growth medium, which consisted of a 1:1 mixture of renal epithelial proliferation medium (REGM basal media supplemented with 10% FBS, REGM SingleQuots Kit, and 100 μg/mL Primocin) and mesenchymal cell proliferation medium (DMEM high glucose supplemented with 10% FBS, 1× GlutaMax, 1× non-essential amino acids (Thermo Fisher Scientific), 5 ng/mL basic fibroblasts growth factor (bFGF, PeproTech, Seoul, Korea), 5 ng/mL platelet-derived growth factor-AB (PDGF-AB, PeproTech), and 5 ng/mL epithelial growth factor (EGF, R&D Systems, Minneapolis, MN, USA). Human osteoblasts (OBs) (#CC-2538, Lonza) were cultured in Osteoblasts Growth Medium (PromoCell, Heidelberg, Germany).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: To induce osteoblast differentiation, the growth medium was then replaced with DMEM supplemented with 10% FBS, 10 mM β‐glycerol phosphate, 50 μg/mL ascorbic acid, and 100 nM dexamethasone, and the cells were further cultured with medium changes every two days.

value: #1 hUSCs

value: urine-derived stem cells

value: osteogenic differentiation


title: Osteogenic differentiation, 30Kc19α-Lin28A treated


title: SH-SY5Y_24h MPP+_Rep1

city: Stockholm

last: Pfab

state: Stockholms län [SE-01]

address: Svante Arrhenius väg 20B

department: MBW

country: Sweden

institute: Stockholm University

data_processing:
library strategy: PRO-seq
Adapters were removed from single-end PRO-seq reads of two biological replicates from each condition using Cutadapt (Galaxy Version 1.16.5).
Reads with a quality score > 20 and a sequence length >20 bps were mapped to the human genome (hg38) using Bowtie2 (Galaxy Version 2.4.2).
PRO-seq coverage tracks with separate strands were generated by filtering + and – strands using BamTools (Galaxy Version 2.4.1), merging replicates using SamTools (Galaxy Version 1.13) and normalizing to reads per kilobase per million (RPKM) and formatting into bigwig file format using bamCoverage (Galaxy Version 3.5.1.0.0).
Differentially expressed genes of 0.5 h MPP+ versus control and 24 h MPP+ versus control were identified basing on PRO-seq reads over gene bodies using featureCounts (Galaxy Version 2.0.1, using gene annotation file from GENCODE v37 and filtering for GFF feature type “gene”) and DESeq2 (Galaxy Version 2.11.40.6).
Assembly: hg38
Supplementary files format and content: bigwig, tabular

molecule: nuclear RNA

growth_protocol: Human SH-SY5Y cells were cultured in high glucose Dulbecco’s modified Eagle’s Medium supplemented with 10% fetal bovine serum and 100 units/ml penicillin and 100 mg/ml streptomycin under a humidified atmosphere of 95% air and 5% CO2 at 37°C.

extract_protocol:
SH-SY5Y cell nuclei were isolated with buffer A (10 mM Tris–HCl pH 7.5, 300 mM sucrose, 3 mM CaCl2, 2 mM MgAc2, 0.1% Triton X-100, 0.5 mM DTT) and quick frozen and stored at -80°C in buffer D (10 mM Tris–HCl pH 8.0, 25% glycerol, 5 mM MgAc2, 0.1 mM EDTA, 5 mM DTT) as described in Mahat et al. 2016.
Nulcear run-on reaction was performed, Biotin RNA was fragmented in 0.2N NaOH, 3'RNA adapters (5'p-GAUCGUCGGACUGUAGAACUCUGAAC-/3InvertedT/) were ligated, 5'RNA adapters (5'-CCUUGGCACCCGAGAAUUCCA-3') were ligated to the 5' repaired RNA (RppH and PNK treated). Adaptor ligated nascent RNA was reverse transcribed using RP1 primer (5'-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3'). Final library was amplified using RP1 and barcoded RPIx (5#-CAAGCAGAAGACGGCATACGAGAT xxxxxx GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3') primers (As decribed in Mahat et al., 2016).

treatment_protocol: 10 million SH-SY5Y cells (70% confluent monolayer) were treated with 0.1 mM MPP+ for 0.5h and 24h.

value: Neuroblastoma

value: 0.1 mM MPP+ for 24h


title: SH-SY5Y_0.5h MPP+_Rep2

value: 0.1 mM MPP+ for 0.5h


title: Kidney, bear, rep 1

source_name: Kidney

value: Kidney


title: SH-SY5Y_0.5h MPP+_Rep1


title: Mmp20+/+ -AT4 (WT)

description: Control; SAMPLE 1

value: Ameloblast


title: SH-SY5Y_Control_Rep2

value: No treatment


title: BRI_249

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) was used to processing the single-cell expression data.
Assembly: GRCh38
Supplementary files format and content: h5 files containing transcript counts for each sample

source_name: Blood

extract_protocol:
Peripheral blood was collected in a blood collection tube containing ethylenediaminetetraacetic acid [EDTA] (Becton, Dickinson and Company). Plasma was isolated by centrifugation at 2,000 × g for 20 min and stored at -80ºC. Peripheral blood mononuclear cells (PBMC) were isolated using the density gradient centrifugation method (GE Healthcare, STEMCELL Technology).
Prepared using 10X Genomics protocols

tag: group

value: Healthy

tag: time


title: BRI_248


title: Human osteoblast

source_name: Human osteoblast

value: Human osteoblast


title: SH-SY5Y_24h MPP+_Rep2


title: BRI_244

value: Poor


title: BRI_242


title: BRI_241

value: Good


title: BRI_243


title: BRI_238


title: BRI_245


title: BRI_246


title: BRI_237


title: Mp-Bc-1

value: basidiocarps

value: A


title: BRI_235


title: BRI_234


title: 972_FFA05, 72 hpf

city: Jackson

first: Michael

middle: R.

last: Garrett

state: MISSISSIPPI

address: 2500 N State Street, Department of Pharmacology and Toxicology

department: Pharmacology and Toxicology

institute: University of Mississippi Medical Center

data_processing:
Sequenced reads were assessed for quality using the Illumina BaseSpace Cloud Computing Platform and FASTQ sequence files were used to align reads to the Danio Rerio genome [DANRER7 (REFSEQ)] using RNA-Seq Alignment Application (using STAR aligner).
Differential expression was determined using the RNA-Differential Expression Application (v1.0.1) and DESeq2. Gene expression differences are denoted as log2 (ratio) and q > 0.05.
Assembly: DANRER7 (REFSEQ)
Supplementary files format and content: Gene count ouput from Illumina  Basespace RNA-Seq Alignment Application

organism: Danio rerio

source_name: 72 hpf zebrafish embryos

extract_protocol:
RNA was extracted using TRIzol Reagent along with Pure Link RNA Mini Kit (Invitrogen) according to manufacturer instructions and assessed for quality control parameters of minimum concentration and fidelity (i.e. 18S and 28S bands, RIS >8).
Libraries were developed using the Illumina TruSeq mRNA Stranded Library Prep Kit (Set-A-indexes), quantified with a Qubit fluorimeter (Invitrogen), and assessed for quality and size using the QIAxcel Advanced System
Samples were pooled into a single library (n=17 pooled samples per library) and sequenced using the NextSeq 500 High Output Kit (150 cycles, paired end 75bp) on the  Illumina NextSeq 500 platform.

value: 72 hpf zebrafish embryos

value: whole embryo

value: AB line

value: 3% glucose 24-72 hpf


title: SH-SY5Y_Control_Rep1


title: 972_FFA06, 72 hpf


title: C70

city: Shenzhen

first: Zheng

last: Zhang

state: Guangdong

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

description: Single-cell RNAseq

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count

source_name: Liver biopsy

extract_protocol: Total 11 µl of single cell suspension and 40 µl barcoded Gel Beads were loaded to Chromium Chip A to generate single-cell gel bead-in-emulsion (GEM). The poly-adenylated transcripts were reverse-transcribed later. The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 3’ V3 (liver biopsy) and Chromium Single Cell 5’ (BALF) library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and sequencing libraries were prepared and normalized to 3 nM.

tag: organ

value: Liver

tag: diagnosis

value: chronic hepatitis B infection

tag: sars-ncov-2 status

value: negative

tag: cell subsets

value: Total cell


title: 972_FFA03, 72 hpf

tag: cell type

tag: treatment


title: BRI_247


title: 972_FFA01, 72 hpf

tag: genotype

value: FFA injected 24-72 hpf


title: 972_FFA04, 72 hpf


title: 972_Glucose05, 72 hpf


title: 972_Glucose06, 72 hpf


title: 972_FFA02, 72 hpf


title: 972_Glucose04, 72 hpf


title: 972_Glucose02, 72 hpf


title: 972_Control03_S3, 72 hpf

value: control 72 hpf


title: 972_Control02_S2, 72 hpf


title: 972_Glucose01, 72 hpf


title: BRI_236


title: 972_Control01_S1, 72 hpf


title: BRI_233


title: T1_rep2,treatment with erythritol,day 3

city: chongqiong

first: Lei

last: Li

address: central road daxuecheng

institute: CHONGQIONG NORMAL UNIVERSITY

data_processing:
Calculate the sequencing error rate distribution using Illumina Casava 1.8
Calculate GC base content distribution
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Reference genome alignment using HISAT2
Read count extraction and normalization
Assembly: Release 6 plus ISO1 MT
Supplementary files format and content: ALL_COMPARE.xlsx

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Standard extraction methods are used to extract RNA from tissues or cells, and then strict quality control is conducted on RNA samples, mainly through Agilent 2100 bioanalyzer: accurate detection of RNA integrity.
The mRNA with polyA tail was enriched by the Oligo(dT) magnetic beads, based on the structural feature that most mrnas in eukaryotes have polyA tail

value: whole body

tag: time point

value: day 3

value: erythritol


title: T1_rep3,treatment with erythritol,day 3


title: T1_rep1,treatment with erythritol,day 3


title: CK2_rep3,control,day 4

value: day 4

value: control


title: T2_rep1,treatment with erythritol,day 4


title: T2_rep2,treatment with erythritol,day 4


title: CK2_rep1,control,day 4


title: CK1_rep2,control,day 3


title: CK1_rep3,control,day 3


title: CK2_rep2,control,day 4


title: CK1_rep1,control,day 3


title: 972_Glucose03, 72 hpf


title: 972_Control06_S6, 72 hpf


title: 972_Control04_S4, 72 hpf


title: Myc knockin GEMM OS 1

city: Houston

first: Jason

middle: T

last: Yustein

state: TX

address: 1102 Bates Ave

department: Pediatrics-Oncology

institute: Texas Children's Hospital

data_processing:
Samples were trimmed using TrimGalore
Trimmed fastq were aligned to the mm10 genome using STAR
Features were quantified using featurecounts
Assembly: mm10
Supplementary files format and content: Matrix table with feature counscounts for every gene and every sample

source_name: tumor

extract_protocol:
RNA was extracted with Qiagen RNAeasy Plus Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor


title: Myc knockin GEMM OS 4


title: Myc knockin GEMM OS 2


title: Pooled mouse experiment (WT_Unstim, WT_PIM6, WT_H37Rv, TLR2KO_Unstim, TLR2KO_PIM6, TLR2KO_H37Rv) - HTO

city: Cambridge

first: Bryan

last: Bryson

state: MA

address: 400 Technology Square

department: Biological Engineering

institute: MIT

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Mice were euthanized by carbon-dioxide inhalation, and femurs and tibias were harvested for bone marrow isolation. Bone marrow cells were incubated at 37°C with 5% carbon dioxide in BMDM media (DMEM (Gibco) with 20% fetal bovine serum (Hyclone) and 25ng/ml recombinant mouse M-CSF (R and D Systems)) on petri dishes. After 6 days, adherent cells were washed and harvested for use as bone marrow-derived macrophages (BMDM).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Cells were then counted prior to proceeding with MULTI-seq barcoding. Samples were multiplexed as previously described. In brief, samples were barcoded with 2.5uM of the LMO anchor and barcode for 5 minutes on ice in PBS before adding 2.5 uM of the LMO co-anchor and incubating for an additional 5 minutes. Samples were quenched with 1% BSA in PBS and washed once. Barcoded cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: BMDM

value: bone marrow

tag: strain

value: 7-8 weeks old

value: Sample pool:WT_Unstim, WT_PIM6, WT_H37Rv, TLR2KO_Unstim, TLR2KO_PIM6, TLR2KO_H37Rv


title: T2_rep3,treatment with erythritol,day 4


title: Myc knockin GEMM OS 3


title: Myc knockin GEMM OS 5


title: Pooled mouse experiment (WT_Unstim, WT_PIM6, WT_H37Rv, TLR2KO_Unstim, TLR2KO_PIM6, TLR2KO_H37Rv) - GEX

description: 10x Genomics


title: p53-driven GEMM OS 3


title: p53-driven GEMM OS 2


title: p53-driven GEMM OS 4


title: IRF8cKO_Cre_3m_rep3 [RNA-seq]

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

description: 2x55 paired-end sequence reads

data_processing:
Basecalls performed using bcl2fastq without the acceptance of index mismatch
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.2b.
Sequence duplicates were removed using Picard v2.17.11. Aligned tags were counted with Subread featureCounts. All steps are packaged in CCBR/Pipeliner.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: FACS-sorted microglia

growth_protocol: In vivo microglia from each brain were non-enzymatically isolated.

extract_protocol:
Microglia were FACS-sorted directly in TRIzol and stored until usage. Total RNA was purified by phase extraction.
The cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA Kit (Takara bio USA, CA) with 15-cycle amplification. Adaptors were added to 1ng cDNA using the Nextera XT library prep kit (Illumina, CA).

tag: gender

value: female

value: 5 concecutive days of Tamoxifen injection since P12


title: Batf3KO_3m_rep3 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8cKO_Cre_3m_rep4 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8cKO_Cre_3m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8cKO_Cre_3m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8cKO_WT_3m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8cKO_WT_3m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8cKO_WT_3m_rep3 [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_3m_rep3_control_for_Batf3KO [RNA-seq]

description: 2x55 paired-end sequence reads

value: WT


title: Batf3KO_3m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_3m_rep2_control_for_Batf3KO [RNA-seq]

description: 2x55 paired-end sequence reads


title: 5xFAD/IRF8KO_9m_rep3 [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_3m_rep1_control_for_Batf3KO [RNA-seq]

description: 2x55 paired-end sequence reads


title: 5xFAD/IRF8KO_9m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: 5xFAD_9m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: 5xFAD/IRF8KO_9m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: 5xFAD_9m_rep3 [RNA-seq]

description: 2x55 paired-end sequence reads


title: p53-driven GEMM OS 1


title: 5xFAD_9m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8KO_9m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_9m_rep3 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8KO_3m_rep4 [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_9m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8KO_9m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_9m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8KO_3m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: Batf3KO_3m_rep1 [RNA-seq]

description: 2x55 paired-end sequence reads


title: Adult microglia - IgG control

description: 2x35 paired-end sequence reads

data_processing:
Basecalls performed using bcl2fastq without the acceptance of index mismatch
Sequenced reads were trimmed for the adaptor and low-quality sequences with TrimGalore, then mapped to mm10 whole genome using bowtie2 Bowtie2 with --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 --no-overlap --no-dovetail options
Bigwig files were generated using deeptools bamCoverage with -bs 10 --normalizeUsing RPGC --extendReads options after merging all bam files by each genotype.
Peaks were called using MACS2 with --keep-dup all -q 0.01 –max-gap 640 options
Assembly: mm10
Supplementary files format and content: Bigwig (.bw) files consist of RPGC-normalized average ChIP signal by genotype.
Supplementary files format and content: Peak files (.xls) contain peak regions and tag density generated by MACS2

growth_protocol: In vivo microglia were non-enzymatically isolated from a 3-month-old WT and IRF8KO brain and enriched by cell sorting.

extract_protocol:
The cells/nuclei were immobilized with Con-A beads and incubated with an antibody overnight. The immunocomplexes were further incubated with protein A-fused micrococcal nuclease (pA-MNase), then digested for 30 min in the presence of 3mM Ca2++ (Ref: PMID: 28079019).
If needed, the ChIPped DNA was de-crosslinked and purified by phase extraction. The DNA was filtered with 0.5x AMPure beads to remove unwanted large fragments. Purified ChIPed DNA was then processed to construct a library using SMARTer® ThruPLEX DNA-Seq Kit (TAKARA Bio USA, CA) as the manufacturer’s protocol except PCR cycles to avoid amplifying long fragments (13 cycles, 10s for extension).

treatment_protocol: Brain cells were crosslinked with 1% PFA/PBS for 10 min prior to sorting in case of transcription factor ChIP

value: Female

tag: chip antibody

value: IgG (Cell Signaling)


title: WT_3m_rep3_control_for_IRF8KO [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_3m_rep1_control_for_IRF8KO [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_3m_rep2_control_for_IRF8KO [RNA-seq]

description: 2x55 paired-end sequence reads


title: WT_3m_rep4_control_for_IRF8KO [RNA-seq]

description: 2x55 paired-end sequence reads


title: Adult microglia - IRF8KO_PU1_rep2

description: 2x35 paired-end sequence reads

value: PU.1 (Abcam, EPR22624)


title: Adult microglia - WT_PU1_rep1

description: 2x35 paired-end sequence reads


title: Adult microglia - IRF8KO_PU1_rep1

description: 2x35 paired-end sequence reads


title: Adult microglia - WT_PU1_rep2

description: 2x35 paired-end sequence reads


title: IRF8KO_9m_rep3 [RNA-seq]

description: 2x55 paired-end sequence reads


title: Adult microglia - IRF8KO_H3K4me1_rep2

description: 2x35 paired-end sequence reads

value: H3K4me1 (Abcam, ab8895)


title: Adult microglia - IRF8KO_H3K4me1_rep1

description: 2x35 paired-end sequence reads


title: Adult microglia - WT_H3K27ac_rep2

description: 2x35 paired-end sequence reads

value: H3K27ac (Abcam, ab4729)


title: IRF8KO_3m_rep2 [RNA-seq]

description: 2x55 paired-end sequence reads


title: IRF8KO_3m_rep3 [RNA-seq]

description: 2x55 paired-end sequence reads


title: Adult microglia - WT_H3K27ac_rep1

description: 2x35 paired-end sequence reads


title: Adult microglia - WT_H3K4me1_rep2

description: 2x35 paired-end sequence reads


title: Adult microglia - WT_H3K4me1_rep1

description: 2x35 paired-end sequence reads


title: peritoneal macrophages - IgG control

description: 2x35 paired-end sequence reads


title: peritoneal macrophages - IRF8_rep3_batch2

description: 2x35 paired-end sequence reads

value: GFP (Abcam, ab290)


title: peritoneal macrophages - IRF8_rep2_batch1

description: 2x35 paired-end sequence reads


title: Adult microglia - IRF8_rep3_batch2

description: 2x35 paired-end sequence reads


title: Adult microglia - IRF8_rep2_batch1

description: 2x35 paired-end sequence reads


title: P14 microglia - IgG control

description: 2x35 paired-end sequence reads


title: peritoneal macrophages - IRF8_rep1_batch1

description: 2x35 paired-end sequence reads


title: P14 microglia - IRF8_rep3

description: 2x35 paired-end sequence reads


title: P14 microglia - IRF8_rep2

description: 2x35 paired-end sequence reads


title: P9 microglia - IRF8_rep3

description: 2x35 paired-end sequence reads, 4/7 samples were provided


title: P9 microglia - IRF8_rep2


title: Adult microglia - IRF8KO_H3K27ac_rep1

description: 2x35 paired-end sequence reads, 2/3 samples were provided


title: P14 microglia - IRF8_rep1

description: 2x35 paired-end sequence reads


title: Adult microglia - IRF8KO_H3K27ac_rep2


title: P9 microglia - IRF8_rep1


title: WT microglia - ATAC_rep1

data_processing:
Basecalls performed using bcl2fastq without the acceptance of index mismatch
After removing the adapter and low-quality sequences, the data were aligned to the mm10 genome with Bowtie2.
Peaks were called on aligned sequences using MACS2 v2.1.1.20160309 with -p 0.01 --nomodel --shift -37 --extsize 73 -B --SPMR --keep-dup all options.
All peaks were further filtered with less than 0.01 irreversible differential rates.
The bigwig files were generated with Deeptools to visualize the RPGC-normalized, average peaks of each genotype.
Assembly: mm10
Supplementary files format and content: Peak files (.xlsx) consist of peak regions and tag density generated by MACS2
Supplementary files format and content: A bigwig file contains RPGC-normalized, average peaks of each genotype.

source_name: Microglia

growth_protocol: Microglia were non-enzymatically isolated from a 3-month-old WT and IRF8KO brain.

extract_protocol:
FACS-sorted microglia were lysed in NP-40 lysis buffer.
As manufacturer's protocol, the isolated nuclei were tagmented using the Nextera DNA library prep kit (Illumina). The library was amplified by 12-cycle PCR and size-selected.

value: FACS-sorted microglia

value: untreated


title: IRF8KO microglia - ATAC_rep1


title: EWAG-02729 DMM

city: Vienna

first: Kazuhiko

last: Matsuoka

address: Borschkegasse 8a

department: Cellular and Molecular Tumor biology

country: Austria

institute: CeCenter for Cancer research, Medical University of Vienna

data_processing:
fastq generation incl. demultiplexing and adapter trimming, bcl2fastq v2.19.1.403
alignment and extraction of counts/gene, STAR aligner v2.6.1a_08-27, command: STAR --runThreadN 16 --genomeDir GRCm38_RSEM_index --readFilesCommand zcat --readFilesIn $FASTQ --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:"$sample" SM:"$sample" CN:MUW_CF PG:STAR --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
count normalization and transformation, DESeq2 v1.22.2
Assembly: GRCm38
Supplementary files format and content: plain text, raw counts per gene, one file per sample

source_name: c-FosDCh DMM_1 articular cartilage

extract_protocol:
For bulk RNA-sequencing, mice were sacrificed 4 weeks after DMM and articular cartilage from DMM-treated and contralateral sides of knee joints was carefully dissected by a surgery scalpel using binocular and immediately processed for RNA isolation by TRI Reagent. Sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep and sequenced on an Illumina NextSeq500 platform in a 75–base pair single-read mode. Sequencing data were then mapped to the Mus musculus/mmc10 assembly of the mouse genome with the Spliced Transcripts Alignment to a Reference (STAR) aligner, and differential gene expression was analyzed using DESeq2. Differentially expressed genes were considered statistically significant with an adjusted P < 0.05.
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module, the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina and the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) according to manufacturer's protocols (New England Biolabs).
Single-end stranded mRNA-Seq. Pooled libraries were sequenced on a NextSeq500 instrument (Illumina) in 1x75bp single-end sequencing mode.

value: 14 weeks of age

value: DMMptreated isde from  c-FosDCh


title: EWAG-02126 DMM

source_name: c-FosDCh DMM_3 articular cartilage


title: EWAG-02724 DMM


title: EWAG-02731 DMM

source_name: c-FosDCh DMM_2 articular cartilage


title: EWAG-02728 Cont.

source_name: c-Fos_WT cont_4 articular cartilage

value: c-FosWT


title: EWAG-02728 DMM

source_name: c-Fos_WT DMM_3 articular cartilage

value: DMM-treated side from c-FosWT


title: EWAG-02722 DMM

source_name: c-Fos_WT DMM_1 articular cartilage


title: Adult microglia - IRF8_rep1_batch1

description: 2x35 paired-end sequence reads


title: EWAG-02723 Cont.

source_name: c-Fos_WT cont_2 articular cartilage


title: EWAG-02722 Cont.

source_name: c-Fos_WT cont_1 articular cartilage


title: EWAG-02723 DMM

source_name: c-Fos_WT DMM_2 articular cartilage


title: Lung from mice bearing KrasG12D, rep 1, scRNAseq

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output directories

source_name: Lung

extract_protocol:
Whole lungs from 3 to 4 animals were dissociated with fine scissors and then proteolytic digestion was performed with DMEM containing 2,5mg/mL collagenase D (Roche)  at 37°C for 30min. Single-cell suspension was submitted to red blood cell lysis. Single-cells  were encapsulated in droplets using 10X Genomics GemCode Technology and processed following manufacturer’s specifications
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lung cells

value: Lung

value: CCSP-CreERTM/+ x LSL-KrasG12D/+ +/- R26R-EYFP

value: 16-18 weeks old


title: EWAG-2726 Cont.

source_name: c-Fos_WT cont_3 articular cartilage


title: P9 microglia - IRF8_rep4


title: Lung control WT, rep 1, scRNAseq

description: 10x Genomics

value: CCSP-CreERTM/+


title: 5XFAD, replicate 4, scRNAseq

city: Pittsburgh

first: Hansruedi

last: Mathys

address: 3501 5th Avenue

institute: University of Pittsburgh

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Seurat object saved as .rds file

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: 6 months old


title: Lung from mice bearing KrasG12D with defective cholesterol efflux (i.e, Abca1 and Abcg1 deficiency), rep 2, scRNAseq

description: 10x Genomics

value: CCSP-CreERTM/+ x LSL-KrasG12D/+ x Abca1fl/flAbcg1fl/fl


title: WT microglia - ATAC_rep2

value: WT


title: IRF8KO microglia - ATAC_rep2


title: Wild type, replicate 3, scRNAseq

description: 10x Genomics


title: Wild type, replicate 1, scRNAseq

description: 10x Genomics

source_name: mammillary body

value: Brain cells (neuronal and non-neuronal)

value: mammillary body


title: 5XFAD, replicate 2, scRNAseq

description: 10x Genomics


title: P9 microglia - IgG control

description: 2x35 paired-end sequence reads

value: Female

value: IgG (Cell Signaling)


title: 5XFAD, replicate 3, scRNAseq

description: 10x Genomics


title: Wild type, replicate 2, scRNAseq

description: 10x Genomics


title: IL-17 neutralizing Ab CD8+CD44+PD1-Tim3- Tcells rep 3

first: Lawrence

middle: P.

last: Kane

address: 5051 Centre Ave.

department: Immunology

description: Well Number G7

data_processing:
STAR aligned RNA-seq data, using ENSEMBLE annotations
Read count extraction and normalization were performed using DESeq2
Assembly: mm10
Supplementary files format and content: CSV document containing raw read counts, with each sample contained in a separate column

source_name: Spleen

extract_protocol:
Spleens were removed from infected mice, single-cell suspensions were prepared by mechanically disrupting tissue using double frosted slide, followed by red blood cell lysis with RBC Lysis Buffer , and stained with fluorescently labeled CD8, CD44 and PD-1 and Tim-3 antibodies. Then different subsets of Live CD8+T cells were sorted with help of fluorescence assisted cell sorter directly into lysis buffer.
SmartSeq cDNA / Nextera XT libraries

value: Spleen

value: CD8+T cells

value: Day 12 post LCMV CL13 infection

value: IL-17 neutralizing Antibody


title: 5XFAD, replicate 1, scRNAseq

description: 10x Genomics


title: IL-17 neutralizing Ab CD8+PD1+Tim3- Tcells rep 3

description: Well Number E6


title: IL-17 neutralizing Ab CD8+CD44+PD1-Tim3- Tcells rep 2

description: Well Number E7


title: Isotype Ab CD8+CD44+PD1-Tim3- Tcells rep 1

description: Well Number A3

value: Isotype Antiboby


title: IL-17 neutralizing Ab CD8+PD1+Tim3- Tcells rep 2

description: Well Number C6


title: IL-17 neutralizing Ab CD8+PD1+Tim3- Tcells rep 4

description: Well Number G6


title: Isotype Ab CD8+CD44+PD1-Tim3- Tcells rep 4

description: Well Number G3


title: Isotype Ab CD8+PD1+Tim3- Tcells rep 2

description: Well Number C2


title: Isotype Ab CD8+CD44+PD1-Tim3- Tcells rep 2

description: Well Number C3


title: IL-17 neutralizing Ab CD8+PD1+Tim3+ Tcells rep 3

description: Well Number E5


title: IL-17 neutralizing Ab CD8+PD1+Tim3- Tcells rep 1

description: Well Number A6


title: IL-17 neutralizing Ab CD8+CD44+PD1-Tim3- Tcells rep 1

description: Well Number A7


title: Isotype Ab CD8+PD1+Tim3- Tcells rep 1

description: Well Number A2


title: Wild type, replicate 4, scRNAseq

description: 10x Genomics


title: Isotype Ab CD8+PD1+Tim3- Tcells rep 3

description: Well Number G2


title: Isotype Ab CD8+PD1+Tim3+ Tcells rep 2

description: Well Number C1


title: IL-17 neutralizing Ab CD8+PD1+Tim3+ Tcells rep 4

description: Well Number G5


title: IL-17 neutralizing Ab CD8+PD1+Tim3+ Tcells rep 2

description: Well Number C5


title: Isotype Ab CD8+PD1+Tim3+ Tcells rep 4

description: Well Number G1


title: Isotype Ab CD8+PD1+Tim3+ Tcells rep 3

description: Well Number E1


title: Isotype Ab CD8+PD1+Tim3+ Tcells rep 1

description: Well Number A1


title: Isotype Ab CD8+CD44+PD1-Tim3- Tcells rep 3

description: Well Number E3


title: jump-liver-795_S96_WD

city: Corvallis

first: Andrey

last: Morgun

state: Oregon

address: Pharmacy Building, 1601 SW Jefferson Way

institute: Oregon State University

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-795_S96

data_processing:
RNA libraries were prepared with the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System and sequenced using Illumina NextSeq.
The sequences were processed to remove the adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/) using bbduk parameters of k=13, ktrim=r, forcetrimleft=12, useshortkmers=t, mink=5, qtrim=r, trimq=15, minlength=20.
Then the reads were aligned to mouse genome and transcriptome (ENSEMBL NCBIM37) using Tophat (v2.1.1) with default parameters.
The number of reads per million for mouse liver genes were counted using HTSeq (v 0.6.0) 71 and quantile normalized.
Assembly: ENSEMBL NCBIM37
Supplementary files format and content: relativized per million reads log transformed and quantile normalized data

source_name: liver

growth_protocol: Briefly, male and female mice (B6;129S7- Ldlr Tm1Her/J mice, stock# 002207) were purchased from Jackson Labs and were group housed (5 mice/cage) and maintained on a 12-hour light/dark cycle. Mice were acclimatized to the Oregon State University Linus Pauling science center vivarium for 2 weeks before proceeding with the experiments.

extract_protocol:
RNA was extracted from cell lysates using the RNeasy Mini Kit and subjected to a DNase treatment according to manufacturer's protocols (Qiagen) then stored at -80 ºC until further use.
mRNA libraries were prepared for sequencing with the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) HT for Illumina Sequencing platforms (Kit#k15.384) and sequenced on the Illumina NextSeq.

treatment_protocol: Mice consumed the one of the following  diets, ad libitum for upto 40 weeks or as mention in the  duration column; each group consisted of 3-8 male and female mice. Research Diets: D12450K was used as the Reference diet (RD).  The western diet (WD) was obtained from Research Diets (12709B) and used to induce NASH.

tag: mouse id

value: Male

tag: diet

value: WD

tag: duration


title: jump-liver-793_S94_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-793_S94

tag: Sex


title: jump-liver-799_S87_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-799_S87


title: jump-liver-800_S88_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-800_S88


title: jump-liver-798_S86_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-798_S86


title: jump-liver-796_S84_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-796_S84


title: jump-liver-794_S95_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-794_S95


title: jump-liver-788_S90_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-788_S90


title: jump-liver-790_S92_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-790_S92


title: IL-17 neutralizing Ab CD8+PD1+Tim3+ Tcells rep 1

description: Well Number A5

tag: tissue


title: jump-liver-787_S89_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-787_S89


title: jump-liver-786_S83_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-786_S83


title: jump-liver-789_S91_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-789_S91


title: jump-liver-792_S93_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-792_S93


title: jump-liver-782_S80_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-782_S80


title: jump-liver-783_S81_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-783_S81


title: jump-liver-780_S78_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-780_S78


title: jump-liver-779_S77_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-779_S77


title: jump-liver-797_S85_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-797_S85


title: jump-liver-776_S74_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-776_S74


title: jump-liver-781_S79_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-781_S79


title: jump-liver-777_S75_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-777_S75


title: jump-liver-775_S73_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-775_S73


title: jump-liver-771_S69_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-771_S69


title: jump-liver-770_S68_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-770_S68


title: jump-liver-772_S70_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-772_S70


title: jump-liver-773_S71_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-773_S71


title: jump-liver-774_S72_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-774_S72


title: jump-liver-767_S65_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-767_S65


title: jump-liver-768_S66_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-768_S66


title: jump-liver-769_S67_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-769_S67


title: jump-liver-778_S76_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-778_S76


title: jump-liver-785_S82_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-785_S82


title: jump-liver-766_S64_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-766_S64


title: jump-liver-764_S62_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-764_S62


title: jump-liver-761_S59_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-761_S59


title: jump-liver-763_S61_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-763_S61


title: jump-liver-765_S63_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-765_S63


title: jump-liver-759_S57_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-759_S57


title: jump-liver-760_S58_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-760_S58


title: jump-liver-762_S60_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-762_S60


title: jump-liver-757_S55_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-757_S55

value: LFD


title: jump-liver-750_S32_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-750_S32


title: jump-liver-755_S53_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-755_S53


title: jump-liver-752_S50_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-752_S50


title: jump-liver-751_S49_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-751_S49


title: jump-liver-754_S52_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-754_S52


title: jump-liver-756_S54_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-756_S54


title: jump-liver-753_S51_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-753_S51


title: jump-liver-749_S31_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-749_S31


title: jump-liver-745_S40_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-745_S40


title: jump-liver-744_S39_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-744_S39


title: jump-liver-743_S38_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-743_S38


title: jump-liver-746_S28_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-746_S28


title: jump-liver-738_S46_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-738_S46


title: jump-liver-741_S36_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-741_S36


title: jump-liver-742_S37_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-742_S37


title: jump-liver-737_S45_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-737_S45


title: jump-liver-734_S34_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-734_S34


title: jump-liver-740_S48_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-740_S48


title: jump-liver-733_S33_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-733_S33


title: jump-liver-736_S35_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-736_S35


title: jump-liver-739_S47_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-739_S47


title: jump-liver-731_S44_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-731_S44


title: jump-liver-748_S30_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-748_S30


title: jump-liver-747_S29_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-747_S29


title: jump-liver-730_S43_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-730_S43


title: jump-liver-727_S27_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-727_S27


title: jump-liver-724_S24_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-724_S24


title: jump-liver-722_S22_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-722_S22


title: jump-liver-725_S25_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-725_S25


title: jump-liver-728_S41_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-728_S41


title: jump-liver-726_S26_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-726_S26


title: jump-liver-729_S42_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-729_S42


title: jump-liver-758_S56_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-758_S56


title: jump-liver-719_S19_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-719_S19


title: jump-liver-720_S20_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-720_S20


title: jump-liver-721_S21_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-721_S21


title: jump-liver-718_S18_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-718_S18


title: jump-liver-717_S17_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-717_S17


title: jump-liver-723_S23_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-723_S23


title: jump-liver-714_S14_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-714_S14


title: jump-liver-716_S16_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-716_S16


title: jump-liver-713_S13_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-713_S13


title: jump-liver-715_S15_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-715_S15


title: jump-liver-712_S12_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-712_S12


title: jump-liver-709_S9_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-709_S9


title: jump-liver-711_S11_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-711_S11


title: jump-liver-708_S8_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-708_S8


title: jump-liver-707_S7_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-707_S7


title: jump-liver-710_S10_WD

description:
Western diet (Research Diets: D12079B) baseline
jump-liver-710_S10


title: jump-liver-706_S6_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-706_S6


title: jump-liver-703_S3_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-703_S3


title: jump-liver-705_S5_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-705_S5


title: jump-liver-702_S2_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-702_S2


title: jump-liver-704_S4_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-704_S4


title: jump-liver-701_S1_LFD

description:
Reference Diet (Research Diets: D12450K)
jump-liver-701_S1


title: c57bl/6 mouse zygotes, miRNA-10b rep3

city: Washington

first: Sonia

last: de Assis

state: DC

address: 3970 Reservoir Rd. NW, New Research Building E408

department: Oncology

institute: Georgetown University

data_processing:
Paired end alignment using Hisat2 v2.0.5 to the mouse genome (GRCm38/mm10 reference genome)
Quantification using Stringtie-2.2.1 and Gencod vM25 gene annotation
Differential expression analysis using DEseq2
Assembly: GrCm38/mm10
Supplementary files format and content: tab delimited text file containing normalized abundance measurements output from DEseq2

source_name: blastocyst stage (E3.5)

extract_protocol:
Total RNA was isolated from snap frozen mouse tissues (mammary tumors and embryos at the blastocyst stage) using Qiagen’s RNeasy extraction kit
Transcript libraries were constructed using the TruSeq mRNA Library Prep Kit

value: blastocyst stage (E3.5)

value: wt


title: c57bl/6 mouse zygotes, miRNA-10b rep1


title: c57bl/6 mouse zygotes, control rep1

value: buffer


title: c57bl/6 mouse zygotes, miRNA-10b rep2


title: c57bl/6 mouse zygotes, control rep2


title: c57bl/6 mouse zygotes, control rep3


title: E14, dAT2, primed, replicate 3, PRO-seq

first: Junwoo

last: Lee

state: Texas

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

description:
sorted_D8_CDM_minus.30xrpm.bw
sorted_D8_CDM_plus.30xrpm.bw

data_processing:
Adaptor trimming and low-quality reads were removed by Cutadapt.
The filtered reads were aligned on mm10 genome by bowtie2 with “--very-sensitive” option to discard reads mapped to more than one region.
The mapped reads were compressed as binary form using samtools and rRNAs were removed from those reads by bedtools intersect.
The 3’ end of the filtered reads were captured and in strand-specific manner using bedtools genomecov.
After the validation of replicates, all replicates were merged and normalized to meet final 30 million reads
Assembly: mm10, M22
Supplementary files format and content: bw files with raw readcount numbers
Supplementary files format and content: bw files with 30xrpm normalized readcount numbers
Library strategy: PRO-seq

growth_protocol: Mouse embryonic stem cells (E14Tg2a, ATCC) were maintained on 1% gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). Embryonic stem cells (ESCs) were cultured on gelatin-coated plates in DMEM (Invitrogen) supplemented with 15% FBS, 1X-Gultamax (Gibco), Na-Pyruvate (Gibco), 10mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Gibco), 1U/ml of ESGRO mLIF (Millipore), and 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 – Stem Cell technology) in naïve (or +2i) condition. In epiblast stem cells (EpiSCs)  or primed condition, cells were cultured in chemically defined medium (IMDM and F12-Invitrogen) supplemented with 2%-BSA (Sigma), Insulin (Roche), Transferrin (Roche), CD-lipid concentrate (Gibco), FGF2 (R&D), and Activin-A (R&D).

extract_protocol:
Nuclei were isolated using Dounce homogenizer (1 million cells per mL) and nuclear run-on was performed with all four biotin-NTPs. RNAs were extracted by Trizol LS (Ambion) and fragmentated by base hydrolysis. From the fragmentated RNAs, biotin RNAs were enriched by streptavidin beads.
The biotin RNAs were enriched twice more in each 3’ and 5’ RNA adaptor ligation processes. Reverse transcription, PCR amplification, and library size selection were performed to obtain 140 ~ 350bp, 5ng/uL libraries.

tag: cell line

value: embryonic stem cells

value: dAT

value: FGF2 (R&D), and Activin-A (R&D)

tag: developmental stage

value: primed


title: E14, dAT2, naïve, replicate 2, PRO-seq

description:
sorted_D8_2i_minus.30xrpm.bw
sorted_D8_2i_plus.30xrpm.bw

value: 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 - Stem Cell technology))

value: naive


title: E14, dAT1, primed, replicate 3, PRO-seq

description:
sorted_A2_CDM_minus.30xrpm.bw
sorted_A2_CDM_plus.30xrpm.bw


title: E14, dAT2, naïve, replicate 1, PRO-seq


title: E14, dAT2, primed, replicate 1, PRO-seq


title: E14, dAT2, primed, replicate 2, PRO-seq


title: E14, dAT1, primed, replicate 1, PRO-seq


title: E14, dAT1, primed, replicate 2, PRO-seq


title: E14, WT, primed, replicate 4, PRO-seq

description:
sorted_WT_CDM_minus.30xrpm.bw
sorted_WT_CDM_plus.30xrpm.bw

value: WT


title: E14, WT, primed, replicate 3, PRO-seq


title: E14, dAT1, naïve, replicate 2, PRO-seq

description:
sorted_A2_2i_minus.30xrpm.bw
sorted_A2_2i_plus.30xrpm.bw


title: E14, dAT1, naïve, replicate 1, PRO-seq


title: E14, WT, primed, replicate 2, PRO-seq


title: E14, WT, naïve, replicate 1, PRO-seq

description:
sorted_WT_2i_minus.30xrpm.bw
sorted_WT_2i_plus.30xrpm.bw


title: E14, WT, primed, replicate 1, PRO-seq


title: E14, WT, naïve, replicate 2, PRO-seq


title: d13_Pparg_KO_Sp#1

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

extract_protocol:
1,000 Cells were double-sorted by Aria into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: Spleen

value: Primary cells from mouse

value: Regulatory T cells

value: Ppargf/f Foxp3-Cre


title: d13_Pparg_KO_skin#1

source_name: Skin

value: Skin


title: d13_Pparg_KO_skin#2


title: d13_Pparg_WT_Sp#1

value: Pparg+/+ Foxp3-Cre


title: d13_Pparg_KO_Sp#2


title: PD1 +/- MI, scRNAseq

city: Dallas

first: Miao

last: Cui

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome.
Further analyses for quality filtering was performed using the Seurat R package
For data quality filtering, we removed cells that had more than 6000 or fewer than 200 detected genes or cells that had a percent of mitochondrial genes > 10%.
We then normalized the data by the total expression, multiplied by a scale factor of 10,000 and log-transformed the result. IntegrateData function implemented in Seurat V4 was used to correct batch effects between samples and to merge samples into one Seurat object. Briefly, we performed standard preprocessing (log-normalization), and identified the top 2000 variable features for each individual dataset. We then identified integration anchors using the FindIntegrationAnchors function. We used default parameters and dimension 30 to find anchors. We then passed these anchors to the IntegrateData function to generate an integrated Seurat object
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Hearts were harvested with atria removed. The tissue was minced with dissecting scissors and digested at 37°C for 45 minutes in DMEM medium containing collagenase I (450 U/mL), hyaluronidase type I-S (60 U/mL) and DNase-I (60 U/mL). The digested material was then filtered, washed and red blood cells were lysed using RBC lysis buffer. Cells suspensions were blocked with TruStain FcX (anti-mouse CD16/32) antibody and True-Stain Monocyte Blocker and incubated with Zombie Fixable Dyes (all from Biolegend) to label dead cells for 15min at RT in dark. Cells were then stained in FACS buffer with monoclonal CD45 antibodies at 4°C for 20 min. Cd45+ immune cells were isolated using cell sorter BD FACSAria II.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, CD45+ immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Immune cells

value: Heart

value: PD1 Het

value: myocardial infarction

tag: age


title: PD1 -/- Sham, scRNAseq

description: 10x Genomics

value: PD1 KO

value: Sham


title: d13_Pparg_WT_skin#1


title: PD1 -/- MI, scRNAseq

description: 10x Genomics


title: PD1 +/- MI, visium

description:
10x Genomics
PD1Het

data_processing:
The Space Ranger Single-Cell Software Suit was used to perform sample demultiplexing, reads alignment, and to generate feature-spot matrices.
The cDNA reads were aligned to the mm10/GRCm38 mRNA reference genome. The H&E staining image was supplemented to Spatial Ranger for tissue detection, fiducial detection, and alignment of the spatial position of sequenced data points.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, and H&E tissue staining images

source_name: Heart, transverse section

extract_protocol:
Hearts at 7-day post the surgery were dissected and immediately embedded in a tissue embedding mold filled with OCT and placed in a bath of isopentane and liquid nitrogen. OCT embedded heart tissue blocks were cryosectioned in a cryostat to generate appropriately sized sections for Visium Spatial slides. 10 um sections at 200 um below the ligation suture were collected and placed on the Visum Spatial slides capture areas.
Heart sections were permeabilized for 18 min followed by RNA reverse transcription. The optimized permeabilization time was determined using the Visum Spatial Tissue Optimization Kit (10xGenomics) according to the manufacturer’s protocol. Second strand cDNA was subsequently synthesized on tissue sections and was transferred to an Eppendorf tube after denaturation. The cDNA from the tissue slide that was spatially barcoded was next amplified via PCR and enzymatically fragmentated. P5, P7, i7 and i5 sample indexes are added via End Repair, A-tailing, Adaptor ligation and PCR to make the final sequencing library.
Visium Spatial Transcriptome RNAseq

treatment_protocol: Myocardial infarction surgery was performed on 2-day-old mice by ligating the  left anterior descending artery

value: all cardiac cells

value: Heart, transverse section