title: TCB, sample5, TCR

value: term cord blood

value: blood

value: primary cells

value: immune cells

value: TCR


title: TCB, sample5, BCR

status: Public on Feb 05 2025

type: SRA

city: New Haven

first: Liza

last: Konnikova

state: CT

address: 375 Congress Ave

country: USA

institute: Yale University

library_source: transcriptomic

data_processing:
Raw sequence reads were aligned to the human reference dataset GRCh38 to generate gene expression using Cell Ranger v6.1.2 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Cryopreserved samples are thawed slightly, and cells with a viability of >70% were used 10X single cell RNA sequencing.
Single-cell cDNA with matched TCR and BCR VDJ libraries were prepared using the 10x Chromium Next GEM 5′ reagent kit (v2) according to the manufacturer’s instructions. Sequencing was performed on the NovaSeq 6000 sequencer (Illumina) to obtain paired end reads.
scRNA-seq, scTCR-seq, scBCR-seq

tag: Stage

tag: tissue

tag: cell line

tag: cell type

tag: library type

value: BCR


title: Replicate 3, AsGM1+ Group 1 ILCs

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive
quality control report (Ewels et al., 2016).
Assembly: GRCm38 (ENSEMBL 102)
Supplementary files format and content: Tabular count table

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was isolated from AsGM1+ and AsGM1- ILC subsets using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s procedure. RNA samples were treated with the DNA-free kit (Ambion) to remove any traces of genomic DNA.
According to the manufacturer’s protocol (Illumina NovaSeq).

value: Liver

value: NK cell

tag: genotype

value: B6.Cg-Rag2tm1.1Cgn/J (RAG2 KO)


title: Replicate 2, AsGM1- Group 1 ILCs


title: Calu-3/2B4, Mock, 24 hpi, Rep 3

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: Mock, 24 hpi, Rep 3

data_processing:
STAR v. 2.7.10a was used to map filtered/trimmed reads to GRCh38 and generated gene reads counts.
sequencing reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v.1.15
Assembly: GRCh38
Supplementary files format and content: tab delimited text file containg raw gene level read counts

growth_protocol: Calu-3/2B4 cells were maintained in 1X MEM supplemented with 20% fetal bovine serum (FBS), 0.01% L-Glutamine, and 0.01% Penicillin-Streptomycin in an incubator with 5% CO2 at 37 degrees Celsius.

extract_protocol:
RNA was harvested following the Invitrogen TRIzol™ Reagent Protocol at 12-, 24-, and 48-hours post-infection.
RNA libraries were prepared using NEBNext polyA mRNA Magnetic Isolation Module and NEB Ultra II RNA library preparation kit for illumina following manufacturer's protocol

treatment_protocol: Calu-3/2B4 cells were infected with the Urbani strain of SARS-CoV-1 or the USA-WA1/2020 strain of SARS-CoV-2 at a MOI of 1.0. Uninfected cells served as controls.

value: bronchial epithelial cells

tag: infection status

value: Mock

tag: time

value: 24 hpi


title: retina, aged, sham, animal 14

city: Atlanta

first: Andrew

middle: J

last: Feola

address: 1365B Clifton Road NE

institute: Emory University

data_processing:
Transcript abundance estimates were calculated internally to the STAR aligner using the htseq-count algorithm. Gene counts were normalized using DESeq2 in R.
Assembly: Alignment was performed using STAR version 2.7.3a and transcripts were annotated using Rnor_6.0 Ensembl release 95.
Supplementary files format and content: Raw count values in csv

organism: Rattus norvegicus

source_name: Retina

extract_protocol:
All samples were stored at 25°C and processed within 48 hours of dissection. Tissues were homogenized in 700 µL of QIAzol and extracted using the miRNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent) and 10 ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding 30 million reads per sample on average.
RNA quality was assessed using a TapeStation 4200 (Agilent) and 10 ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding 30 million reads per sample on average.

value: Retina

value: Female

tag: treatment

value: Aged, Sham


title: TCB, sample5, GEX

library_source: transcriptomic single cell

value: GEX


title: TCB, sample4, BCR


title: Calu-3/2B4, Mock, 24 hpi, Rep 2

description: Mock, 24 hpi, Rep 2


title: TCB, sample4, TCR


title: retina, aged, sham, animal 13


title: Replicate 2, AsGM1+ Group 1 ILCs


title: Replicate 1, AsGM1- Group 1 ILCs


title: retina, young, ovx, animal 12

value: Young, OVX


title: TCB, sample4, GEX

value: term cord blood


title: retina, young, ovx, animal 11


title: Replicate 1, AsGM1+ Group 1 ILCs


title: TCB, sample3, BCR

value: blood


title: Calu-3/2B4, Mock, 12 hpi, Rep 2

description: Mock, 12 hpi, Rep 2

value: 12 hpi


title: Calu-3/2B4, Mock, 48 hpi, Rep 1

description: Mock, 48 hpi, Rep 1

value: 48 hpi


title: Gastric tissue, Smox-infected 5

city: Nashville

first: Keith

last: Wilson

state: Tennessee

address: 2215 Garland Ave

institute: Vanderbilt University

description: 5888-CS-20 (SmoxHp)

data_processing:
Reads were trimmed of the adapter sequences and read quality was checked using fastp
Reads were mapped to the indexed transcriptome of the GRCm38 assembly and quantified using Salmon
Transcript-level quantification was summarized to the gene-level using tximeta
Raw transcript counts were determined using the R package DESeq2. Genes that had a sinlge count or less across samples were excluded
An outlier mouse 17 was removed from the data
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts of each gene for each sample

source_name: Gastric tissue

growth_protocol: Littermates FVB/N INS-GAS WT and Smox male mices(6 to 12 weeks old)

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (Qiagen).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs)

treatment_protocol: Mice were gavaged on day 0 and day 2 with 1x10^9 H. pylori strain PMSS1. Stomachs were harvested after 8 weeks and gastric tissues used for RNA isolation

value: Gastric tissue

tag: infection

value: Yes

value: Smox

value: 8 weeks


title: Calu-3/2B4, Mock, 12 hpi, Rep 1

description: Mock, 12 hpi, Rep 1


title: retina, young, ovx, animal 10


title: retina, young, ovx, animal 9


title: retina, aged, sham, animal 15


title: Calu-3/2B4, SARS-2, 48 hpi, Rep 3

description: SARS-2, 48 hpi, Rep 3


title: TCB, sample3, GEX

value: primary cells

value: immune cells


title: retina, young, ovx, animal 8


title: Calu-3/2B4, SARS-2, 48 hpi, Rep 2

description: SARS-2, 48 hpi, Rep 2

value: bronchial epithelial cells


title: retina, young, ovx, animal 7


title: S3, sample1, BCR

value: 1 month

value: BCR


title: Calu-3/2B4, Mock, 24 hpi, Rep 1

description: Mock, 24 hpi, Rep 1

value: Mock

value: 24 hpi


title: S3, sample1, TCR

value: TCR


title: Gastric tissue, Smox-infected 1

description: 5888-CS-16 (SmoxHp)


title: Calu-3/2B4, SARS-2, 48 hpi, Rep 1

description: SARS-2, 48 hpi, Rep 1


title: Calu-3/2B4, Mock, 12 hpi, Rep 3

description: Mock, 12 hpi, Rep 3


title: retina, young, sham, animal 6

value: Retina

value: Female

value: Young, Sham


title: S3, sample1, GEX

value: blood

value: GEX


title: Calu-3/2B4, SARS-2, 24 hpi, Rep 3

description: SARS-2, 24 hpi, Rep 3


title: TCB, sample3, TCR

value: term cord blood


title: Gastric tissue, Smox-infected 4

description: 5888-CS-19 (SmoxHp)

value: Gastric tissue

value: Yes


title: adult, sample3, BCR

value: adult


title: adult, sample3, TCR

value: primary cells


title: retina, young, sham, animal 4


title: Calu-3/2B4, SARS-2, 24 hpi, Rep 2

description: SARS-2, 24 hpi, Rep 2


title: Gastric tissue, WT-infected 4

description: 5888-CS-14 (WTHp)

value: WT

value: 8 weeks


title: Calu-3/2B4, SARS-2, 24 hpi, Rep 1

description: SARS-2, 24 hpi, Rep 1

value: bronchial epithelial cells


title: retina, young, sham, animal 3


title: Gastric tissue, Smox-infected 3

description: 5888-CS-18 (SmoxHp)

value: Smox


title: Gastric tissue, WT-infected 3

description: 5888-CS-13 (WTHp)


title: Gastric tissue, WT-infected 2

description: 5888-CS-12 (WTHp)


title: Calu-3/2B4, SARS-2, 12 hpi, Rep 3

description: SARS-2, 12 hpi, Rep 3

value: 12 hpi


title: adult, sample2, BCR

value: immune cells

value: BCR


title: adult, sample3, GEX


title: Gastric tissue, Smox-infected 2

description:
5888-CS-17 (SmoxHp)
An outlier mouse 17 was removed from the data


title: retina, young, sham, animal 2

value: Retina


title: retina, young, sham, animal 1

value: Female


title: Calu-3/2B4, SARS-2, 12 hpi, Rep 1

description: SARS-2, 12 hpi, Rep 1


title: adult, sample2, TCR

value: TCR


title: Gastric tissue, Smox-uninfected 5

description: 5888-CS-10 (Smox)

value: No


title: retina, young, sham, animal 5

value: Young, Sham


title: S133A/R314A-CREB cells,TGFβ, RNA-seq

city: Guangzhou

first: Lan

last: Zhang

address: Jinsui Road 7#

country: China

institute: 中山眼科中心

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR 2.7.6a and paired-end clean reads were aligned to the reference genome using STAR 2.7.6a.
Stringtie v2.0.4 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length  for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010)
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq2 R package (1.26.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package(3.14.0), in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package(3.14.0) to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: NCBI GRCm39 genome
Supplementary files format and content: Stringtie v2.0.4 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: Lens

growth_protocol: Mouse lens epithelial cells (αTN4-1) overexpressing Vector, WT-CREB, S133A-CREB, R314A-CREB and S133A/R314A -CREB were cultured in monolayer in a 37°C incubator with 5% CO2 in Dulbecco’s modiﬁed Eagle’s medium (DMEM) supplemented  with 10% fetal bovine serum (FBS) , 50 Units/ml penicillin and streptomycin and 600 ug/ml neomycin.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen),RNA purity and quantification were evaluated using the Qubit4.0(Thermo Scientific, USA); RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA);
The RNA-seq libraries were constructed using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit for Illumina® ( Yeasen Biotechnology ,Shanghai). RNA-seq was performed on DNBSEQ-T7 platform (Geneplus-Shenzhen, Shenzhen, China).

treatment_protocol: Cells were passaged with 0.25% trypsin, seeded in six-well plates at a density of 1×105 cells/well, and treated with 20 ng/mL TGFβ (Syd Labs, Sigma) in DMEM without FBS for 24 h.

value: Lens

value: lens epithelial cells

value: S133A/R314A-CREB ovexexpressing


title: Gastric tissue, WT-infected 5

description: 5888-CS-15 (WTHp)

value: Gastric tissue

value: Yes


title: Gastric tissue, Smox-uninfected 4

description: 5888-CS-9 (Smox)


title: S133A/R314A-CREB cells, control, RNA-seq


title: adult, sample2, GEX

value: adult

value: blood

value: primary cells

value: GEX


title: PTCB, sample1, BCR

value: preterm cord blood


title: Calu-3/2B4, SARS-1, 48 hpi, Rep 2

description: SARS-1, 48 hpi, Rep 2

value: bronchial epithelial cells

value: 48 hpi


title: S133A-KCREB cells, TGFβ, RNA-seq

value: S133A-KCREB ovexexpressing


title: Calu-3/2B4, SARS-1, 48 hpi, Rep 1

description: SARS-1, 48 hpi, Rep 1


title: Gastric tissue, Smox-uninfected 2

description: 5888-CS-7 (Smox)

value: Smox

value: 8 weeks


title: PTCB, sample1, TCR

value: immune cells

value: TCR


title: Calu-3/2B4, SARS-2, 12 hpi, Rep 2

description: SARS-2, 12 hpi, Rep 2

value: 12 hpi


title: PTCB, sample1, GEX


title: Gastric tissue, Smox-uninfected 1

description: 5888-CS-6 (Smox)

value: No


title: Calu-3/2B4, SARS-1, 24 hpi, Rep 3

description: SARS-1, 24 hpi, Rep 3

value: 24 hpi


title: S133A-KCREB cells, control, RNA-seq

value: Lens

value: lens epithelial cells


title: S133A-CREB cells, TGFβ, RNA-seq

value: S133A-CREB ovexexpressing


title: Gastric tissue, WT-infected 1

description: 5888-CS-11 (WTHp)

value: Gastric tissue

value: Yes

value: WT


title: Calu-3/2B4, SARS-1, 24 hpi, Rep 2

description: SARS-1, 24 hpi, Rep 2


title: adult, sample1, BCR

value: adult

value: blood

value: primary cells

value: BCR


title: Gastric tissue, WT-uninfected 5

description: 5888-CS-5 (WT)


title: adult, sample1, TCR


title: S133A-CREB cells, control, RNA-seq


title: Gastric tissue, WT-uninfected 4

description: 5888-CS-4 (WT)


title: Calu-3/2B4, SARS-1, 24 hpi, Rep 1

description: SARS-1, 24 hpi, Rep 1

value: bronchial epithelial cells


title: R314A-CREB cells, TGFβ, RNA-seq

value: R314A-CREB ovexexpressing


title: Calu-3/2B4, SARS-1, 48 hpi, Rep 3

description: SARS-1, 48 hpi, Rep 3

value: 48 hpi


title: adult, sample1, GEX

value: immune cells

value: GEX


title: Calu-3/2B4, SARS-1, 12 hpi, Rep 3

description: SARS-1, 12 hpi, Rep 3

value: 12 hpi


title: R314A-CREB cells, control, RNA-seq


title: Gastric tissue, WT-uninfected 3

description: 5888-CS-3 (WT)

value: No

value: 8 weeks


title: Calu-3/2B4, SARS-1, 12 hpi, Rep 2

description: SARS-1, 12 hpi, Rep 2


title: Gastric tissue, Smox-uninfected 3

description: 5888-CS-8 (Smox)

value: Smox


title: Gastric tissue, WT-uninfected 2

description: 5888-CS-2 (WT)


title: KCREB cells, TGFβ, RNA-seq

value: Lens

value: lens epithelial cells

value: KCREB ovexexpressing


title: TCB, sample2, TCR

value: term cord blood

value: TCR


title: Calu-3/2B4, SARS-1, 12 hpi, Rep 1

description: SARS-1, 12 hpi, Rep 1


title: TCB, sample2, GEX

value: blood


title: KCREB cells, control, RNA-seq


title: Gastric tissue, WT-uninfected 1

description: 5888-CS-1 (WT)

value: Gastric tissue

value: WT


title: b7_nega_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

source_name: spleen

extract_protocol:
Total RNA was extracted from cells with QIAzol reagent and a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. An Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: spleen

value: plasma cells, integrin b7lo

value: B1-8hi k/w R26-creERT2 Klf2 +/+ CD45.1


title: Steer 4

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 175 W Campus Dr

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
The raw RNA-seq reads were filtered using Trimmomatic v0.39 to remove low-quality reads and reads containing adapters
Clean reads were aligned to the bovine reference genome ARS-UCD 2.0 using STAR v2.7.11a
Gffread v0.12.18 was used to convert the genomic annotation files from gff to gtf format
FeatureCounts (v2.0.2) was used to estimate the read counts
Differential expression analysis was performed using the DESeq2 (v1.42.0) R package
Genes with Benjamini–Hochberg approach adjusted P value < 0.05 and |log2fold change| ≥ 1 were designated as differentially expressed genes (DEGs)
Assembly: ARS-UCD 2.0
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: comma separated file contains gene expression profile that includes list of all genes that are differentially expressed

organism: Bos taurus

source_name: Adult Steer

extract_protocol:
Total RNA was extracted using TRIzol reagent (Zymo Research, Irvine, CA) and the Direct-zol RNA MiniPrep Plus Kit (Zymo Research)
Total RNA was extracted and fragmented, followed by first-strand cDNA synthesis using random hexamer primers. Second-strand cDNA synthesis was performed using a dUTP mix. The resulting double-stranded cDNA was purified using the AMPure XP system. After end repair and adaptor ligation, the adaptor-linked cDNA was again purified with the AMPure XP system and enriched through 10 cycles of PCR. The final cDNA library was purified using the AMPure XP system, pooled, and paired-end sequenced on an Illumina platform.

treatment_protocol: Rumen tissue was collected from four neonatal male calves and four adult steers, all of which were angus cross breed.

value: Rumen

tag: Sex

value: male

value: Adult Steer


title: WT-CREB cells, control, RNA-seq

value: WT-CREB ovexexpressing


title: S1, sample1, GEX

value: 1 week

value: primary cells

value: immune cells

value: GEX


title: Steer 3


title: Steer 2


title: WT-CREB cells, TGFβ, RNA-seq

value: Lens

value: lens epithelial cells


title: b7_nega_1


title: TCB, sample1, GEX

value: term cord blood


title: TCB, sample2, BCR

value: blood

value: BCR


title: Calf 4

source_name: Newborn Calf

value: Neonatal Calf


title: HLA02-T1, CD45+ skin biopsy cells from pt with gamma/delta mycosis fungoides, scRNA-seq VDJ-T library

city: Palo Alto

first: Michael

last: Khodadoust

state: CA

address: 1701 Page Mill Rd

department: Medicine (Oncology)

institute: Stanford University School of Medicine

data_processing:
Demultiplexing of bulk sequencing FASTQs was performed using internal pipelines.
Barcode processing, gene counting, and aggregation were accomplished using Cell Ranger 6.1.2 and 7.0.1 (10x Genomics).
Assembly: hg38
Supplementary files format and content: Tab-delimited gzipped value files (*barcodes.tsv.gz, *features.tsv.gz), comma-delimited value files (*filtered_contig_annotations.csv, *cell_barcodes.json), and gzipped matrix files (*matrix.mtx.gz)

source_name: Skin

extract_protocol:
Fresh peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using Ficoll-Paque density-gradient centrifugation and cryopreserved in a solution of 50% fetal bovine serum, 40% RPMI 1640 media, and 10% dimethyl sulfoxide. At a later time, PBMCs were thawed. Skin biopsies were dissociated into single cell suspensions using either the Tumor Dissociation Reagent (BD Biosciences) or gentleMACS Tumor Dissociation Kit (Miltenyi Biotec). For both PBMC and skin samples, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec). Cells from skin samples additionally underwent CD45+ enrichment using CD45 (TIL) MicroBeads (Miltenyi Biotec). Remaining viable cells were resuspended in 0.04% BSA in DPBS (no Ca2+/Mg2+).
Library construction was performed according to the manufacturer's instructions (Single Cell Next GEM 5' v2 protocol, 10x Genomics). Briefly, PBMCs were resuspended in the master mix and loaded 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 contained an Illumina R1 primer sequence, 10x barcode, and unique molecular identifier (UMI). The pooled barcoded DNA was then cleaned up using Silane Dynabeads, amplified by PCR, and then the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequences, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: Skin

value: CD45+ cells from skin biopsy


title: b7_posi_3

value: spleen

value: plasma cells, integrin b7hi

value: B1-8hi k/w R26-creERT2 Klf2 +/+ CD45.1


title: b7_posi_2


title: Vector cells, control, RNA-seq

value: WT


title: HLA08-T3, CD45+ skin biopsy cells from pt with Sézary syndrome, reaction 2, scRNA-seq VDJ-T library


title: Input DNA

library_source: genomic

data_processing:
ChIP-seq reads were trimmed polyX (except polyG) from 3' with length of polyX > 10 bp, using fastp v0.23.4, discarding reads with number of N base is > 5 bp, length of reads < 100 bp, and percents of bases is unqualified > 40%. A base phred quality >= Q15 is qualified.
ChIP-seq reads were aligned to the NCBI GRCm39 genome using bwa-mem2 v2.2.1. Only uniquely mapping reads were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were renormalized，that reads per genomic content (1x normalization) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: NCBI GRCm39 genome
Supplementary files format and content: bigWig files were generated using the bigwigCompare v3.5.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.

molecule: genomic DNA

growth_protocol: Mouse lens epithelial cells (αTN4-1) overexpressing Vector, WT-CREB, S133A-CREB, R314A-CREB and S133A/R314A –CREB were cultured in monolayer in a 37°C incubator with 5% CO2 in Dulbecco’s modiﬁed Eagle’s medium (DMEM) supplemented  with 10% fetal bovine serum (FBS) , 50 Units/ml penicillin and streptomycin and 600 ug/ml neomycin.

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. After micrococcal nuclease digestion, chromatin was sonicated into 150-900 bp DNA fragments.
NGS libraries were prepared using VAHTS Universal DNA Library Prep Kit for MGI (Vazyme Biotech, Nanjing ,China) according to the manufacturer’s protocol. All DNA libraries were quantified by Qubit Fluorescence Quantification/Enzyme Labeling Instrument, and the length distribution range of the products was quantified, which required that the total amount meets the requirements and there was no contamination of adaptors and large fragments. After library construction was completed, Qubit was used for quantitative quality control, and sequencing was performed after the quality of the library passed.

value: S133A/R314A-CREB ovexexpressing


title: Vector cells, TGFβ, RNA-seq


title: Calf 2

value: Rumen

value: male


title: b7_posi_1


title: Klf2_cKO_3

value: plasma cells

value: B1-8hi k/w R26-creERT2 Klf2 fl/fl CD45.1


title: S133A/R314A-CREB cells, CREB, ChIP

value: Lens


title: b7_nega_2

value: plasma cells, integrin b7lo


title: HLA08-T3, CD45+ skin biopsy cells from pt with Sézary syndrome, reaction 1, scRNA-seq VDJ-T library


title: Calf 1


title: R314A-CREB cells, CREB, ChIP

value: lens epithelial cells

value: R314A-CREB ovexexpressing


title: HLA08-T3, CD45+ skin biopsy cells from pt with Sézary syndrome, reaction 1, scRNA-seq GEX library


title: HLA08-T3, CD45+ skin biopsy cells from pt with Sézary syndrome, reaction 2, scRNA-seq GEX library


title: HLA02-T2, CD45+ skin biopsy cells from pt with gamma/delta mycosis fungoides, scRNA-seq GEX library


title: Klf2_cKO_2


title: HLA02-T2, CD45+ skin biopsy cells from pt with gamma/delta mycosis fungoides, scRNA-seq VDJ-T library


title: Steer 1

value: Adult Steer


title: HLA22-T1, peripheral blood mononuclear cells from pt with Sézary syndrome, scRNA-seq VDJ-T library

source_name: Blood

value: Blood

value: Peripheral blood mononuclear cells


title: Klf2_cKO_1


title: Vector cells, CREB, ChIP


title: Control_3


title: WT-CREB cells, CREB, ChIP

value: WT-CREB ovexexpressing


title: Calf 3

value: Neonatal Calf


title: HLA22-T1, peripheral blood mononuclear cells from pt with Sézary syndrome, scRNA-seq GEX library


title: B16-OVA Mice 4 immunized with NLC-Ova mRNA (4_ttt1)

city: La Tronche

first: Carole

last: Fournier

address: Site Santé - Allée des Alpes

country: France

institute: Institute for Advanced Biosciences

data_processing:
Clean reads were aligned against Mus musculus mm39 reference genome (source: UCSC) using HISAT
Data analysis were performed with Dr. Tom online system (BGI genomices, Hong Kong, China)
Assembly: mm39
Supplementary files format and content: Exel file containing a table which summarizes TPM across samples for targeted sequencing of 18045 protein-coding genes

source_name: Subcutaneous tumor

extract_protocol:
Total RNA was extracted from frozen B16-OVA tumors lysed by TissueLyser II (QIAGEN) using phenol-chloroform extraction method with Trizol (Invitrogen) and Isopropanol (XILONG). The quality of the total RNA and the sample RNA concentration were determined by using the Bioanalyzer 2100 (Agilent).
1 µg of total RNA was used to build mRNA libraries using MGIEasy RNA Library Prep kit (MGI, China) following the manufacturers’ instructions.

value: Subcutaneous tumor

value: Melanoma cell line

value: NLC Ova mRNA


title: Control_1

value: spleen

value: B1-8hi k/w R26-creERT2 Klf2 +/+ CD45.1


title: S133A-CREB cells, CREB, ChIP

value: S133A-CREB ovexexpressing


title: HLA02-T1, CD45+ skin biopsy cells from pt with gamma/delta mycosis fungoides, scRNA-seq GEX library

value: Skin

value: CD45+ cells from skin biopsy


title: P005_post/P003_post_TCR [Batch8]

first: Yanjuan

last: Chen

state: Guangdong

address: Guangzhou

department: Department of Geriatrics and Division of Rheumatology and Research

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

data_processing:
Library strategy: TCR-Seq
10X Genomics CellRanger version 3.0.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 3.0.1) with default mapping arguments.
Split the samples in one batch datesets according to the HTO barcodes. The HTO data were normalized using “NormalizeData” functions with "CLR" normalization method and were assigned sample-of-origin for each cell, annotate doublets by the “HTODemux” functions in Seurat package1-3(version 3.2.2, implemented in R software) following the tutorial at https://satijalab.org/.
After quality control, UMI data was subjected to Seurat (version 3.2.2) for analyses.
Differentially expressed genes were identified using the Wilcox method implemented by ‘FindMarkers’ or ‘FindAllMarkers’ functions in Seurat (version 3.2.2).
Scirpy (version 0.3) package was used to analyze our TCR sequencing data.
Genome_build: hg19 human reference genome
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: Peripheral blood

extract_protocol: Chromium Single cell 5' Library and Gel Bead Kit V3 (10X Genomics) was used for scRNA-seq and TCR sequences libraries construction. Cell-hashing antibody (HTO)-labeled cells from 2 samples were pooled together and washed with RPMI-1640 immediately before loading on the 10X controller.Then library was constructed following the manufacturer’s protocol, with some additional steps for the amplification of HTO barcodes.

value: T cells

tag: facs antibody

tag: state

value: Non-small cell lung cancer patient post radiotherapy


title: Control_2

value: plasma cells


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 1000 ng/ml, sample 3

city: New York

first: Nicholas

last: Arpaia

state: NY

department: Microbiology & Immunology

institute: Columbia University

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000, yielding paired-end 100bp reads
RTA (Illumina) for base calling and bcl2fastq2 (v2.19) for converting BCL to fastq (with adaptor trimming)
Pseudoalignment using kallisto (0.44.0) from transcriptomic data (Ensembl v96, Mouse GRCm38 p6)
DESeq2 for analysis
Assembly: Ensembl v96, Mouse GRCm38.p6
Supplementary files format and content: tab delimited .txt file with raw estimated counts for each gene/sample
Supplementary files format and content: tab delimited .txt file with transcript per million (TPM) values for each gene/sample

source_name: lung

extract_protocol:
Cells were lysed in wells with Trizol Reagent, and RNA was extracted using a Qiagen kit
PolyA pulldown of RNA, then cDNA library synthesis with NexteraXT Kit
Bulk RNA-Seq

treatment_protocol: Col14-LMC were sorted, plated, and allowed to adhere for 24h, then washed/media replaced, then treated with NaClO3 and incubated overnight (16-18h), then treated with Areg and incubated 4h, then lysed

value: lung

value: Lung Col14-LMC

value: male

value: NaClO3/Areg 1000 ng/ml


title: Doxy-D22

city: Lyon

first: Hermes

last: Paraqindes

address: 28 rue Laennec

institute: CRCL

data_processing:
We used the pipeline: RiboMethSeq-nf. fastQC was used to verify sequencing quality and adapter removal was performed using Trimmomatic. The trimmed reads were aligned by Bowtie2 on the 7.2 kb-long rRNA sequence of reference (NR_046235) and the 5’ read-ends were computed using bedtool genomcov utility
The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window using rRMSAnalyzer
Assembly: NR_046235
Supplementary files format and content: Raw counts of 5' end reads on each position of each rRNA
Supplementary files format and content: The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window (Marcel et al, NAR Cancer 2020)
Library strategy: RiboMethSeq

source_name: hMEC

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) according to manufacturer’s instructions.
Illumina

value: hMEC

tag: sequencing library

value: -Doxy


title: P005_post/P003_post_RNA [Batch8]

data_processing:
10X Genomics CellRanger version 3.0.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 3.0.1) with default mapping arguments.
Split the samples in one batch datesets according to the HTO barcodes. The HTO data were normalized using “NormalizeData” functions with "CLR" normalization method and were assigned sample-of-origin for each cell, annotate doublets by the “HTODemux” functions in Seurat package1-3(version 3.2.2, implemented in R software) following the tutorial at https://satijalab.org/.
After quality control, UMI data was subjected to Seurat (version 3.2.2) for analyses.
Differentially expressed genes were identified using the Wilcox method implemented by ‘FindMarkers’ or ‘FindAllMarkers’ functions in Seurat (version 3.2.2).
Scirpy (version 0.3) package was used to analyze our TCR sequencing data.
Genome_build: hg19 human reference genome
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell


title: Doxy-D10


title: P004_post/P002_post_RNA [Batch7]


title: B16-OVA Mice 3 immunized with NLC-Ova mRNA (3_ttt1)

value: Subcutaneous tumor


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 1000 ng/ml, sample 2


title: B16-OVA Mice 1 immunized with NLC-Ova mRNA (1_ttt1)

value: Melanoma cell line


title: P006_post_RNA [Batch6]


title: B16-OVA Mice 2 immunized with NLC-Ova mRNA (2_ttt1)

value: NLC Ova mRNA


title: Doxy-D4

value: Doxy


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 500 ng/ml, sample 3

value: NaClO3/Areg 500 ng/ml


title: P004_post/P002_post_TCR [Batch7]


title: Doxy-D3


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 500 ng/ml, sample 2


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 1000 ng/ml, sample 1


title: B16-OVA Mice 2 immunized with NLC-Egfp mRNA (2_CTL)

value: NLC Egfp mRNA


title: P003_pre_RNA [Batch5]

value: Non-small cell lung cancer patient pre radiotherapy


title: Doxy-D2


title: B16-OVA Mice 3 immunized with NLC-Egfp mRNA (3_CTL)


title: B16-OVA Mice 1 immunized with NLC-Egfp mRNA (1_CTL)


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 500 ng/ml, sample 1


title: Doxy-D14


title: Doxy-D1


title: P001_post_TCR [Batch4]


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 200 ng/ml, sample 3

value: NaClO3/Areg 200 ng/ml


title: Doxy-H6


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 200 ng/ml, sample 2


title: NT-D22

value: NT


title: CDX2P-CreERT2Apcfl/fl Hmga1+/+ mouse 279M and 269F

city: Baltimore

first: LI

last: LUO

state: MD

address: 720 Rutland Ave, Ross Build

department: Hematology

institute: Johns Hopskins University

data_processing:
Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) and Chromium instrument (10X Genomics) were used following the manufacturer’s protocol.
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5 for all 3 genotypes

source_name: colon crypt cells

extract_protocol:
After flushing the mouse colons with phosphate-buffered saline (PBS), the colon was incised longitudinally after which colon epithelium was collected.  Sections (~ 2-3 cm) were incubated in EDTA (3 mM) for 1 hour at 4oC with vigorous shaking, after which remaining tissue was placed in a new tube for consecutive collection.  This process was repeated 4-5 times and fractions were observed under a light microscope to monitor for crypt isolation.  After isolation, crypt cells were pelleted and passed through a cell strainer (70 µm). Crypt cells were fixed in cold methanol for sequencing via the 10x Chromium platform.
Libraries were sequenced using the Illumina NovaSeq platform.
Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 6.1.2 (10X Genomics).

value: colon crypt cells

value: CDX2P-CreERT2Apcfl/fl Hmga1+/+

value: tamoxifen induction at 12 weeks


title: P004_pre/P002_pre_TCR [Batch3]

value: T cells


title: Lung Col14-LMC, HS inhibition (NaClO3), Areg 200 ng/ml, sample 1

value: lung

value: Lung Col14-LMC

value: male


title: P004_pre/P002_pre_RNA [Batch3]


title: NT-D14

value: hMEC


title: Lung Col14-LMC, HS inhibition (NaClO3), vehicle treatment (no Areg), sample 3


title: B16-OVA Mice 4 immunized with NLC-Egfp mRNA (4_CTL)

value: Subcutaneous tumor


title: NT-D10


title: P005_pre/P006_pre_TCR [Batch2]


title: P005_pre/P006_pre_RNA [Batch2]


title: NT-D7


title: Lung Col14-LMC, HS inhibition (NaClO3), vehicle treatment (no Areg), sample 1


title: P001_pre_TCR [Batch1]


title: NT-D4


title: Lung Col14-LMC, no HS inhibition, Areg 1000 ng/ml, sample 3

value: control (no HS inhibition)/Areg 1000 ng/ml


title: P001_post_RNA [Batch4]

value: Non-small cell lung cancer patient post radiotherapy


title: P001_pre_RNA [Batch1]


title: Lung Col14-LMC, no HS inhibition, Areg 1000 ng/ml, sample 2


title: H087

type: RNA

city: Durham

last: DeVito

state: NC

address: 308 Research Drive

institute: Duke University

hyb_protocol: Nanostring

data_processing: Samples were analyzed on a NanoString nCounter Max system using the nCounter Vantage 3D Human Wnt Pathways Panel (N2_WNT_Pth_v1.0), which is comprised of Wnt ligands, receptors, regulators, gene targets, and other pathway components with the addition of a custom gene panel composed of cytolytic T cell markers and IDO1.  Analysis was performed using the nSolver software.

source_name: metastatic melanoma

label_protocol: de-identified patient samples were labeled according to response and time of sample acquisition

extract_protocol: RNA from FFPE tumor samples from metastatic melanoma patients were extracted and a Nanostring Wnt Pathway panel was performed

treatment_protocol: Sample acquisition: Archival melanoma specimens of patients treated with anti-PD-1 (either pembrolizumab or nivolumab) monotherapy were obtained via an ongoing clinical trial (NCT02694965). After verification by a board-certified pathologist, microdissection was performed if deemed necessary.

tag: group

value: Nonresponder

value: metastatic melanoma


title: H093


title: H0851


title: H079


title: NT-D2


title: Lung Col14-LMC, no HS inhibition, Areg 1000 ng/ml, sample 1


title: Lung Col14-LMC, HS inhibition (NaClO3), vehicle treatment (no Areg), sample 2


title: HF + 2% Mix 33

city: Aberdeen

first: Morven

last: Cruickshank

state: Aberdeenshire

address: Ashgrove Road West

department: Rowett Institute

country: United Kingdom

institute: University of Aberdeen

description:
Library name: Colon 33
Column name in Combined_Counts_and_Genes.xlsx:C33

data_processing:
Sequencing and base calling were performed on an Illumina NextSeq500 with v2.5 chemistry.
Following sequencing, quality control analysis was performed on the sequence reads using FastQC   [v.0.11.9] and the quality reports combined with MultiQC [v1.1]. Quality trimming was carried out using cutadapt [v.4.1]  and trim-galore [v.0.6.6] with a quality threshold of Q30.
Trimmed reads were aligned to the GRCm39 reference genome using hisat2 [v.2.2.0], followed by the aligned reads being sorted and filtered using samtools [v.1.14]. Aligned read counts were subsequently assigned to genes using the associated annotation file for GRCm39 and the featureCounts program of the subread package [v.2.0.2].
Assembly: GRCm39
Supplementary files format and content: Excel file: Combined_Counts_and_Genes.xlsx contains raw counts for each sample

source_name: colon

extract_protocol:
Total RNA was extracted from colon mucosal scrapings using RNeasy Mini Kit (QAIGEN, Crawley, UK) and following the manufacturer’s protocol.
Unique dual indexed Illumina libraries were prepared from 500ng total RNA using the Stranded TruSeq mRNAseq kit according to the manufacturer’s instructions (Illumina, CA).

treatment_protocol: Mice were randomly weight matched as pairs into 8 groups of 10 mice using the rand feature in Excel, then continuing in paired housing, were fed a low fat (LF) refined + 10% cellulose diet (LF + 10% cellulose) during a 2-week acclimation period, after which groups of 10 mice were randomly assigned to one of 8 treatments. One group of mice was maintained on the LF + 10% cellulose diet for the 8-week intervention period while the remaining groups of mice were transferred onto one of the following diet treatments: High fat (HF) refined 10% cellulose diet (HF + 10% cellulose) or High Fat refined diets where the cellulose was replaced with either high (10%) or low (2%) levels of pectin (HF + Pectin), or Fructo-oligosaccharide (FOS) (HF + FOS), or Mixed Fiber (HF + Mixed Fiber).

value: colon

tag: strain

value: epithelial cells

value: WT


title: GB27


title: NT-D1

value: NT


title: Lung Col14-LMC, no HS inhibition, Areg 500 ng/ml, sample 3

value: control (no HS inhibition)/Areg 500 ng/ml


title: GB16


title: NT-H6


title: GB08


title: Lung Col14-LMC, no HS inhibition, Areg 500 ng/ml, sample 2


title: NT-D3


title: NT-J0


title: LF Control 15

description:
Library name: Colon 15
Column name in Combined_Counts_and_Genes.xlsx:C15


title: Lung Col14-LMC, no HS inhibition, Areg 500 ng/ml, sample 1


title: GB3


title: ZEB1-polysomes 5


title: HF + 10% Mix 27

description:
Library name: Colon 27
Column name in Combined_Counts_and_Genes.xlsx:C27


title: Lung Col14-LMC, no HS inhibition, Areg 200 ng/ml, sample 3

value: control (no HS inhibition)/Areg 200 ng/ml


title: DM03


title: H039


title: HF + 10% Mix 41

description:
Library name: Colon 41
Column name in Combined_Counts_and_Genes.xlsx:C41


title: Polysomes 5


title: Lung Col14-LMC, no HS inhibition, Areg 200 ng/ml, sample 2


title: HF + 10% Pec 19

description:
Library name: Colon 19
Column name in Combined_Counts_and_Genes.xlsx:C19


title: ZEB1-polysomes 4


title: HF + 10% Mix 28

description:
Library name: Colon 28
Column name in Combined_Counts_and_Genes.xlsx:C28


title: Lung Col14-LMC, no HS inhibition, Areg 200 ng/ml, sample 1


title: Polysomes 4


title: HF + 10% Cel 23

description:
Library name: Colon 23
Column name in Combined_Counts_and_Genes.xlsx:C23


title: H076


title: HF + 2% Mix 34

description:
Library name: Colon 34
Column name in Combined_Counts_and_Genes.xlsx:C34


title: ZEB1-polysomes 3


title: P006_post_TCR [Batch6]


title: Lung Col14-LMC, no HS inhibition, vehicle treatment (no Areg), sample 3

value: control (no HS inhibition)/vehicle


title: Lung Col14-LMC, no HS inhibition, vehicle treatment (no Areg), sample 2


title: H061


title: H059


title: HF + 2% Mix 73

description:
Library name: Colon 73
Column name in Combined_Counts_and_Genes.xlsx:C73


title: Doxy-D7

value: Doxy


title: Polysomes 3


title: Lung Col14-LMC, no HS inhibition, vehicle treatment (no Areg), sample 1

value: lung


title: ZEB1-polysomes 2


title: CDX2P-CreERT2Apcfl/fl Hmga1-/- mouse 266M and 284F

value: colon crypt cells

value: CDX2P-CreERT2Apcfl/fl Hmga1-/-

value: tamoxifen induction at 12 weeks


title: HF + 10% Pec 12

description:
Library name: Colon 12
Column name in Combined_Counts_and_Genes.xlsx:C12


title: GB25-SP15


title: 3T3-L1-AD, Pnpla2-En5_7D, rep3

city: Sichuan

first: Sha

last: Zeng

address: 211 Huimin Road

institute: Sichuan Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
We used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Sequence reads were aligned to the mouse reference genome (GRCm38/mm10) by STAR alignment tool (version 2.5.3a).
Sequence reads were quantified by featureCounts from Rsubread package (v2.8.1).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

source_name: Mouse embryo

growth_protocol: 3T3-L1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin-streptomycin (Invitrogen) at 37°C in 5% CO2. Adipocyte differentiation of 3T3-L1 cells was induced using a standard adipogenic cocktail (MDI: IBMX, dexamethasone, and insulin). Upon reaching confluence, the medium was replaced, and the cells were cultured for 48 hours. Subsequently, differentiation was initiated by culturing the cells for another 48 hours in DMEM supplemented with the MDI cocktail (2 μg/mL dexamethasone, 0.5 mM IBMX, and 10 μg/mL insulin) and 10% FBS. Thereafter, the medium was replaced with DMEM containing 10 µg/mL insulin and 10% FBS every two days until adipocyte-like morphology was observed at day 7 post-induction.

extract_protocol:
Total RNA was isolated from cells with TRIzol reagent (Invitrogen).  1 μg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L) following manufacturer's protocols.

treatment_protocol: 3T3-L1 cells were plated in 12-well plates overnight. When confluence reaches about 50-60%, cells were infected with 1 mL lentiviruses medium containing dCas9-KRAB-sgRNAs (Experimental group) or dCas9-KRAB-Control (Control group) at the multiplicity of infection (MOI) of 100 for 12 h. The medium was then replaced after 24 h post-infection. At 48 h post-infection, cells were selected with 2 μg/mL puromycin (Sigma). Untreated 3T3-L1 and 3T3-L1 stably expressing dCas9-KRAB-sgRNAs or dCas9-KRAB-Control were induced to adipogenic differentiation using a standard MDI cocktail.

value: Mouse embryo

value: Adipocyte

value: Lentiviral transduction of the dCas9-KRAB-Pnpla2-En5 system

value: Adipogenic induced differentiation day 7


title: Polysomes 2

value: hMEC


title: HF + 10% Pec 53

description:
Library name: Colon 53
Column name in Combined_Counts_and_Genes.xlsx:C53

value: colon


title: H012

value: Nonresponder

value: metastatic melanoma


title: 3T3-L1-AD, Pnpla2-En5_7D, rep2


title: H045


title: ZEB1-polysomes 1


title: GB18-SP17


title: 3T3-L1-AD, Pnpla2-En5_7D, rep1


title: H102 Pre


title: NT-3

value: NT


title: 3T3-L1-AD, Dgat2-En4_7D, rep2

value: Lentiviral transduction of the dCas9-KRAB-Dgat2-En4 system


title: LF Control 32

description:
Library name: Colon 32
Column name in Combined_Counts_and_Genes.xlsx:C32

value: epithelial cells

value: WT


title: 3T3-L1-AD, Dgat2-En4_7D, rep3


title: HF + 10% Cel 3

description:
Library name: Colon 3
Column name in Combined_Counts_and_Genes.xlsx:C3


title: Polysomes 1


title: H013


title: HF + 10% Fos 40

description:
Library name: Colon 40
Column name in Combined_Counts_and_Genes.xlsx:C40


title: 3T3-L1-AD, Dgat2-En4_7D, rep1


title: LF Control 60

description:
Library name: Colon 60
Column name in Combined_Counts_and_Genes.xlsx:C60


title: TGFb-3

value: TGFb


title: GB21


title: HF + 10% Mix 36

description:
Library name: Colon 36
Column name in Combined_Counts_and_Genes.xlsx:C36


title: 3T3-L1-AD, dCas9-KRAB-Control_7D, rep3

value: Lentiviral transduction of the dCas9-KRAB system


title: GB20


title: TGFb-2


title: 3T3-L1-AD, dCas9-KRAB-Control_7D, rep2


title: NT-2


title: HF + 10% Mix 35

description:
Library name: Colon 35
Column name in Combined_Counts_and_Genes.xlsx:C35


title: NT-1


title: H069


title: H073


title: HF + 2% Mix 8

description:
Library name: Colon 8
Column name in Combined_Counts_and_Genes.xlsx:C8


title: HF + 10% Fos 29

description:
Library name: Colon 29
Column name in Combined_Counts_and_Genes.xlsx:C29


title: HF + 10% Cel 4

description:
Library name: Colon 4
Column name in Combined_Counts_and_Genes.xlsx:C4


title: TGFb-1


title: ChIP-Seq_mES_RPB1_CTDP1_dCDK9_rep2

city: Beijing

first: Xiong

last: Ji

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

department: School of Life Sciences

institute: Peking University

data_processing:
Raw ChIP-Seq reads with spike-in were firstly trimmed by Cutadapt software (v3.4) and then mapped to mm10 and hg19 genome by Bowtie2 software (v2.3.5.1) in end-to-end mode.
Only uniquely and concordantly mapped reads were kept for further analysis.
The bigwig files were generated using bamCoverage from Deeptools software (v3.5.1) normalized by the reads mapped to hg19 genome.
Assembly: mm10, hg19
Supplementary files format and content: bigwig

source_name: CTDP1-degron mES

growth_protocol: The cell were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, D5796) with 15 % fetal bovine serum (FBS) (GeminiBio, 900-108), also supplemented with 1 mM L-glutamine (Gibco, 25030081), 1× nucleosides (Millipore, ES-008-D), 1× nonessential amino acids (Gibco, 11140050), 1× penicillin/ streptomycin (Gibco, 15140122), 1 mM Sodium Pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107). All the cells were cultured in 0.2 % gelatin-coated plates at 37°C and 5% CO2 under humid environment.

extract_protocol:
The 1%(wt/vol) formaldehyde crosslinked, MNase digested and Qsonica sonicated chromatin fraction were incubated with indicated antibody overnight and Protein G magnetic beads (Thermo Fisher, 10004D) for another 3 h. After sufficient washing, elution and incubation at 65 °C overnight, DNA was purified through the DNA Extraction Reagent (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0), Solarbio, P1012).
DNA library was constructed by NEB DNA Library Prep Kit for Illumina (NEB, E7645S), according to the manufacturer's instructions.

treatment_protocol: For RPB7 degradation, cells were treated with 2 μg/ml Dox for 12 h, then with 500 μM auxin for 3 h.  For transcription elongation inhibition, cells were pretreated with 0.5 μM CDK9 degrader THAL-SNS-032 (dCDK9, Selleck, S8979) for 2 h. Each sample was combiend with 10 % HEK293T cells for spike-in normalization.

value: CTDP1-degron mES


title: HF + 10% Fos 39

description:
Library name: Colon 39
Column name in Combined_Counts_and_Genes.xlsx:C39


title: ChIP-Seq_mES_RPB1_CTDP1_untreated_rep1

value: untreated


title: oscc5

city: Wuhu City

first: wenjie

last: wen

address: No.22 Wenchang West Road

institute: wannan medical college

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Matching genomes to obtain expression profiling data
Analysis of variances
GO, KEGG analysis
Assembly: UCSC HG19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Oral squamous cell carcinoma

extract_protocol:
Oral squamous cell carcinoma were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Oral squamous cell carcinoma


title: HF + 10% Pec 72

description:
Library name: Colon 72
Column name in Combined_Counts_and_Genes.xlsx:C72


title: DM02

value: Late Relapse


title: oscc3


title: HF + 2% Mix 74

description:
Library name: Colon 74
Column name in Combined_Counts_and_Genes.xlsx:C74


title: HF + 10% Pec 69

description:
Library name: Colon 69
Column name in Combined_Counts_and_Genes.xlsx:C69


title: ChIP-Seq_mES_RPB1_CTDP1_untreated_rep2


title: H050


title: ChIP-Seq_mES_RPB1_CTDP1_input

value: no


title: oscc4


title: oscc1


title: HF + 10% Cel 58

description:
Library name: Colon 58
Column name in Combined_Counts_and_Genes.xlsx:C58


title: P003_pre_TCR [Batch5]

value: T cells

value: Non-small cell lung cancer patient pre radiotherapy


title: H048

value: Responder


title: H055


title: DM04


title: ChIP-Seq_mES_RPB1_CTDP1_degron_3h_rep2

value: CTDP1 degron for 3h


title: oscc2


title: control5

source_name: precancerous tissue

value: precancerous tissue


title: H044

value: metastatic melanoma


title: 3T3-L1-AD, dCas9-KRAB-Control_7D, rep1

value: Mouse embryo

value: Adipocyte

value: Adipogenic induced differentiation day 7


title: ChIP-Seq_mES_RPB1_CTDP1_dCDK9_rep1


title: HF + 10% Cel 61

description:
Library name: Colon 61
Column name in Combined_Counts_and_Genes.xlsx:C61

value: colon

value: epithelial cells

value: WT


title: H036-SP17


title: ChIP-Seq_mES_RPB1_CTDP1_degron_3h_rep1

value: CTDP1-degron mES


title: H042


title: ChIP-Seq_mES_RPB1_both_dCDK9_CTDP1_degron_3h_rep2

value: dCDK9 and CTDP1 degron for 3h


title: LF Control 48

description:
Library name: Colon 48
Column name in Combined_Counts_and_Genes.xlsx:C48


title: control3


title: ChIP-Seq_mES_RPB1_both_dCDK9_CTDP1_degron_3h_rep1


title: Tc_3

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
Sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt- 4.6. Trimmed reads were mapped to the mouse reference genome (mm10) using STAR v2.7.11ac with GENCODE vM23 (mouse). Uniquely mapped reads were summarized at the gene level using HTSeq-count v2.0.5, and the expression level of each gene and differentially expressed genes were determined using DESeq2 v1.42.0.
Assembly: mm10
Supplementary files format and content: Tab separated file. Normalized counts.

source_name: Liver

extract_protocol:
Freshly collected livers were frozen in liquid nitrogen and ground into powder using a mortar. Total RNA was isolated from livers using an RNeasy Fibrous Tissue Mini Kit (QIAGEN).
RNA-seq libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB), and the number of PCR cycles was minimized to avoid skewing the representation of the libraries. RNA-seq libraries were subjected to single-end sequencing (86 bp) with NextSeq500 (Illumina).

treatment_protocol: Four-week-old mice received Dox hyclate (2mg/mL, Sigma) in drinking water supplemented with 10 mg/mL sucrose (Nacalai Tesque) for 7 days. Tc hydrochloride (Wako) was administered to mice in the same manner and concentration as Dox.

value: Liver

value: Tamoxifen and tetracycline


title: LF Control 31

description:
Library name: Colon 31
Column name in Combined_Counts_and_Genes.xlsx:C31


title: control1


title: control2


title: H052


title: Tc_1


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_40min_rep2

value: untreated and 40min after washing out DRB


title: H031


title: Tc_2


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_20min_rep2

value: untreated and 20min after washing out DRB


title: GB13


title: D30 ZNF-G2 ZNF292 Sample 4

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were processed using AIAP (v1.1) for trimming, alignment, bigWig generation and peak calling
Assembly: hg38
Supplementary files format and content: bigWig density file
Supplementary files format and content: narrowPeak file containing output from MACS2 peakcalling

source_name: Immature Cortical Interneurons

growth_protocol: Embryonic stem cells were mainatined in mTeSR media on Matrigel coated cultureware.

extract_protocol:
Genomic DNA was processed using CUT&Tag (Epicypher) and isolated using phenol-chloroform follow by the NucleoSpin® Gel and PCR Clean-Up kit (Macherey-Nagel).
After PCR amplification samples with unique dual-end indexes were pooled in equimolar concentrations.

value: Immature Cortical Interneurons

tag: stem cell_source

value: H9 hESC

tag: passage

tag: timepoint

tag: antibody


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_20min_rep1

tag: cell type


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_40min_rep1


title: H115

value: Responder


title: GB12


title: D30 ZNF-G2 ZNF292 Sample 2


title: H113-SR21


title: control4

tag: tissue

value: precancerous tissue


title: Dox_2

value: Tamoxifen and doxycycline


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_10min_rep2

value: untreated and 10min after washing out DRB


title: Dox_3


title: Dox_1


title: H100-SP20

value: metastatic melanoma


title: Control_3

value: Tamoxifen


title: D30 ZNF-G2 IgG Sample 1

value: IgG


title: CDX2P-CreERT2Apcfl/fl Hmga1+/- mouse 262M and 278F

value: colon crypt cells

value: CDX2P-CreERT2Apcfl/fl Hmga1+/-

tag: genotype

value: tamoxifen induction at 12 weeks


title: D30 ZNF-G2 ZNF292 Sample 3


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_0min_rep2

value: CTDP1-degron mES

value: untreated and 0min after washing out DRB


title: D30 ZNF-G1 ZNF292 Sample 4


title: D30 ZNF-G2 ZNF292 Sample 1


title: H098 Pre


title: D30 ZNF-G1 ZNF292 Sample 3


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_0min_rep1


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_40min_rep2

value: CTDP1 degron for 2h and 40min after washing out DRB


title: Control_1

value: Liver


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 9 hpi, H-NS, ChIP-mini, replicate 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

description: ChIP-mini_14028s_HNS_J774A1_9hr_rep2 (macrophage intracellular)

data_processing:
Sequenced reads of E.coli K-12 MG1655 samples were mapped onto NC_000913.3 reference genome sequence using bowtie v1.0.0 with parameters -p 8 -S. Sequenced reads of S. Typhimurium 14028s samples were mapped onto NC_016856.1 and NC_016855.1 reference genome sequence using bowtie v1.0.0 with parameters -p 8 -S
RpoD and RpoH binding sites were identified using DEOCSU(DEep-learning Optimized ChIP-exo peak calling SUite). sites were identified using DEOCSU(DEep-learning Optimized ChIP-exo peak calling SUite).
Assembly: NC_000913.3, NC_016856.1, NC_016855.1
Supplementary files format and content: Binding sites and their intensities of ChIP-exo and ChIP-mini datasets were included.
Library strategy: ChIP-exo

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: E. coli K-12 MG1655 WT and rpoH-8myc tagged cells were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. S. Typhimurium 14028s WT or hns-8myc tagged strains were aerobically cultured at 37°C overnight with agitation in LB media. Mouse macrophage-like cells (J774A.1, RAW 264.7) and human epithelial cells (HeLa, INT407) were infected with S. Typhimurium 14028s hns-8myc tagged strains (MOI of 1:10) in DMEM for 30 minutes. Following infection, extracellular bacteria were isolated and utilized for ChIP-mini (Extracellular Chip-mini). Subsequently, the remaining extracellular bacteria were removed by washing process and gentamycin treatment. At 6 hours post-infection (hpi), the S. Typhimurium-infected host cells  were co-crosslinked using formaldehyde. Additionally, at 2, 4, 9 and 21 hpi, the S. Typhimurium-infected J774A.1 cells were co-crosslinked using formaldehyde. Crosslinked intracellular bacteria were used for ChIP-mini method (Intracellular Chip-mini)

extract_protocol:
Chromatin Immunoprecipitation (ChIP) and, for immunomagnetic separation ChIP-mini, an antibody-magnetic bead complex, comprising an anti-Salmonella antibody (ab35156, Abcam) and Dynabeads M-280 Sheep Anti-Rabbit IgG magnetic beads (Invitrogen), was used to isolate intracellular S. Typhimurium from co-crosslinked host intracellular S. Typhimurium samples.
KAPA HiFi HotStart ReadyMix

tag: chip antibody

value: Anti-c-myc


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 21 hpi, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_J774A1_21hr_rep2 (macrophage intracellular)


title: D30 ZNF-G1 ZNF292 Sample 2

value: Immature Cortical Interneurons


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_40min_rep1


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 9 hpi, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_J774A1_9hr_rep1 (macrophage intracellular)


title: D30 ZNF-G1 ZNF292 Sample 1

value: H9 hESC


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_20min_rep2

value: CTDP1 degron for 2h and 20min after washing out DRB


title: DB05005

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

data_processing:
Illumina bcl2fastq command line tool (v2.19.1.403)
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403), incl. trimming of the sequencing adapters.
Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Raw reads per gene were counted by STAR. Batch correction was performed using ComBat from sva version 3.35.2.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: ProcessedDataMatrix.txt.gz contains a matrix with raw gene counts, gene symbols and gene types for each sample

source_name: blood

growth_protocol: Primary white blood cells were maintained in CellGro serum-free medium (CellGenix, Freiburg, Germany; 25 × 106 cells/ml).

extract_protocol:
Total RNA was isolated from approximately 25 × 106 PBMCs using Trizol® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. Total RNA was quantified using a NanoDrop-1000 spectrophotometer (Peglab, Erlangen, Germany), and RNA quality was monitored by an Agilent 2100 Bioanalyzer (Agilent, Böblingen, Germany).
Sequencing libraries were prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocols (New England Biolabs, Ipswich, MA) with unique dual indices (UDI).

treatment_protocol: PBMCs from the three donors were incubated for 20 hours without or with 300 µg/mL of enamel derivative matrix (EMD; Straumann AG, Basel, Switzerland) or a 30% solution of a PRF lysate.

value: blood

value: primary white blood cells

value: Enamel Matrix Derivatives (EMD)


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 4 hpi, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_J774A1_4hr_rep2 (macrophage intracellular)


title: DB05004

value: Platelet-rich fibrin (PRF)


title: D30 ZNF-G1 IgG Sample 1


title: ChIP-Seq_mES_pSer2_CTDP1_untreated_DRB_10min_rep1

value: untreated and 10min after washing out DRB


title: Control_2

value: Tamoxifen


title: D30 KRAB ZNF292 Sample 4


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 21 hpi, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_J774A1_21hr_rep1 (macrophage intracellular)


title: D30 KRAB ZNF292 Sample 3


title: DB05002

value: untreated


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_10min_rep1

value: CTDP1 degron for 2h and 10min after washing out DRB


title: DB05003


title: DB05006


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 2 hpi, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_J774A1_2hr_rep1 (macrophage intracellular)


title: DB05001


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 2 hpi, H-NS, IMS ChIP-mini, replicate 2

description: IMS_ChIP-mini_14028s_HNS_J774A1_2hr_rep2 (macrophage intracellular)


title: D30 KRAB ZNF292 Sample 2


title: DB03003


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_0min_rep1

value: CTDP1 degron for 2h and 0min after washing out DRB


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 2 hpi, H-NS, IMS ChIP-mini, replicate 1

description: IMS_ChIP-mini_14028s_HNS_J774A1_2hr_rep1 (macrophage intracellular)


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_0min_rep2

value: CTDP1-degron mES


title: D30 KRAB ZNF292 Sample 1


title: DB03002


title: DB03001


title: ChIP-Seq_mES_pSer2_CTDP1_degron_90min_rep2

value: CTDP1 degron for 90min


title: D15 ZNF-G2 ZNF292 Sample 4

source_name: Ventrally Patterned Neuronal Progenitors


title: ChIP-Seq_mES_pSer2_CTDP1_degron_90min_rep1


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 4 hpi, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_J774A1_4hr_rep1 (macrophage intracellular)


title: D15 ZNF-G2 ZNF292 Sample 3

value: Ventrally Patterned Neuronal Progenitors


title: Mouse macrophage cell (RAW264.7) extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_RAW264.7_extra_rep1 (macrophage extracellular)


title: Mouse macrophage cell (RAW264.7) extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_RAW264.7_extra_rep2 (macrophage extracellular)


title: Mouse macrophage cell (J774A.1) intracellular S. Typhimurium 14028s, 2 hpi, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_J774A1_2hr_rep2 (macrophage intracellular)


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_10min_rep2


title: ChIP-Seq_mES_pSer2_CTDP1_dergon_2h_DRB_20min_rep1


title: D30 KRAB IgG Sample 1

value: IgG


title: ChIP-Seq_mES_pSer2_CTDP1_degron_60min_rep2

value: CTDP1 degron for 60min


title: Human epithelial cell (HeLa) extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_HeLa_extra_rep2 (epithelial cell extracellular)

value: Anti-c-myc


title: ChIP-Seq_mES_pSer2_CTDP1_degron_60min_rep1


title: D15 ZNF-G2 ZNF292 Sample 2

value: H9 hESC


title: D15 ZNF-G2 ZNF292 Sample 1


title: Human epithelial cell (INT407) extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_INT407_extra_rep2 (epithelial cell extracellular)


title: Human epithelial cell (INT407) extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_INT407_extra_rep1 (epithelial cell extracellular)


title: ChIP-Seq_mES_pSer2_CTDP1_degron_40min_rep1

value: CTDP1 degron for 40min


title: D15 ZNF-G1 ZNF292 Sample 3


title: Granulosa cells treated with LY294002 replicate2

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

country: Germany

institute: Leibniz institute for farm animal biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the TAC 4.0 software (Affymetrix) and RMA method was used for normalization.

label: Biotin

source_name: Granulosa cells treated with LY294002

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: granulosa cells were collected from <6mm ovarian follicles and cultured in the presence of FSH and IGF1 to induce the AKT phosphorilation.

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: RNA from cultured granulosa cells after treatment with either DMSO or 50 µM LY294002 were used for the microarray

value: Primary granulosa cells


title: Granulosa cells treated with LY294002 replicate3


title: D15 ZNF-G1 ZNF292 Sample 2


title: Granulosa cells treated with LY294002 replicate1


title: D15 ZNF-G1 ZNF292 Sample 1


title: G63_FMT_149_ABXPRE

city: Dallas

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_149_D7_FMT

data_processing:
Base calling and demultiplexing were performed by MiSeq Controller Software. Nextera XT Indices were used for sample level demultiplexing.
DADA2 (v1.16.0) R package was used for reads filtering, mergein forward/reserve reads, construct sequence table, and remove remove chimeras.
Divisive Amplicon Denoising Algorithm version 2 (DADA2) R package was used to analyze the 16S amplicon reads and construct the operational taxonomic units (OTUs).
Assembly: silva_nr99_v138_train_set.fa.gz and silva_species_assignment_v138.fa.gz
Supplementary files format and content: tab-delimited text files

source_name: fecal pellet bacterial DNA

extract_protocol:
Mouse fecal DNA extraction was performed using the ZymoBIOMICS DNA Miniprep Kit (Cat# D4300)
Libraries were constructed following the the Illumina 16S Metagenomic Sequencing Library Preparation protocol (PN 15044223 Rev. B).
Libraries were normalized and multiplexed into a single pool prior to validation by Qubit High-Sensitivity dsDNA, Agilent Bioanalyzer DNA 7500 Chip, and Kapa Illumina Library Quantification qPCR analyses. Libraries were sequenced on the MiSeq System using MiSeq V2 500 cycle kit (250-PE with 8-bp dual indexing) and MiSeq 300 PE.

treatment_protocol: fecel pellets were collected from young-adult (12 weeks old) wild type C57Bl/6 mice after 21 days of vehicle or antibiotics treatment (to induce gut microbiota depletion). In one sequencing round, we sequenced a total of 6 different fecal samples (3 control, 3 depleted gut microbiota (ABX)). To evaluate fecal matter transplant (FMT) efficacy, ~12 weeks old C57BL/6 mice were first pre-treated for 14 days with vehicle or ABX. Following the 14-day pre-treatment, all mice were switched to regular water and received PBS via oral gavage for a 2-day washout period. Next, mice from vehicle and ABX pre-treatment groups were randomized and cohoused. For FMT, fresh fecal pellets were collected from mice in the vehicle pre-treatment group. 2-3 pellets were placed in 1 mL of sterile PBS in a 1.5 mL tube and vortexed into a homogenate. The homogenates were then centrifuged at 500 g for 5 minutes and supernatant was collected. All mice received 200 uL of fecal matter supernatant by oral gavage. This procedure was repeated every other day for a seven-day period.

value: fecal pellet bacterial DNA

tag: mouse strain

value: ABXPre+FMT


title: ChIP-Seq_mES_pSer2_CTDP1_degron_40min_rep2

tag: treatment


title: ChIP-Seq_mES_pSer2_CTDP1_degron_20min_rep1

value: CTDP1 degron for 20min


title: Human epithelial cell (HeLa) intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_HeLa_intra_rep2 (epithelial cell intracellular)


title: Mouse macrophage cell (RAW264.7) intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_RAW264.7_intra_rep1 (macrophage intracellular)


title: Mouse macrophage cell (RAW264.7) intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_RAW264.7_intra_rep2 (macrophage intracellular)


title: D15 KRAB ZNF292 Sample 4


title: Human epithelial cell (HeLa) intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_HeLa_intra_rep1 (epithelial cell intracellular)


title: ChIP-Seq_mES_pSer2_CTDP1_degron_180min_rep2

value: CTDP1 degron for 180min


title: G63_FMT_146_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_146_D7_FMT


title: ChIP-Seq_mES_pSer2_CTDP1_degron_180min_rep1


title: Human epithelial cell (INT407) intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description: ChIP-mini_14028s_HNS_INT407_intra_rep2 (epithelial cell intracellular)


title: ChIP-Seq_mES_pSer2_CTDP1_degron_0min_rep2

value: CTDP1 degron for 0min


title: D15 KRAB ZNF292 Sample 3


title: Human epithelial cell (HeLa) extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_HeLa_extra_rep1 (epithelial cell extracellular)


title: D15 ZNF-G1 ZNF292 Sample 4


title: G63_FMT_159_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_159_D7_FMT


title: Granulosa cells treated with DMSO replicate1

source_name: Granulosa cells treated with DMSO


title: D15 KRAB ZNF292 Sample 2


title: Human epithelial cell (INT407) intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description: ChIP-mini_14028s_HNS_INT407_intra_rep1 (epithelial cell intracellular)


title: ChIP-Seq_mES_pSer2_CTDP1_degron_20min_rep2


title: Granulosa cells treated with DMSO replicate3


title: D15 KRAB ZNF292 Sample 1


title: ChIP-Seq_mES_CTDP1_RPB7_untreated_rep2

source_name: RPB7-degron mES

value: RPB7-degron mES

value: untreated


title: G63_FMT_141_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_141_D7_FMT


title: S. Typhimurium 14028s, H-NS, ChIP-exo, LB media, overnight-grown, replicate 2


title: ChIP-Seq_mES_CTDP1_RPB7_untreated_rep1


title: Granulosa cells treated with DMSO replicate2


title: G63_D14_146_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_146_D14

value: ABX


title: G63_D14_149_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_149_D13


title: D15 KRAB IgG Sample 4


title: ChIP-Seq_mES_CTDP1_RPB7_degron_3h_rep2

value: RPB7 degron for 3h


title: S. Typhimurium 14028s, H-NS, ChIP-exo, LB media, overnight-grown, replicate 1


title: D15 KRAB IgG Sample 3


title: S. Typhimurium 14028s, RpoD, ChIP-exo, LB media, overnight-grown, replicate 2

value: Anti-RpoD

value: WT


title: G63_FMT_139_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_139_D7_FMT


title: D15 KRAB IgG Sample 2

value: Ventrally Patterned Neuronal Progenitors

value: IgG


title: ChIP-Seq_mES_CTDP1_RPB7_degron_3h_rep1


title: G63_D14_139_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_139_D12


title: G63_D14_159_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_159_D14


title: ChIP-Seq_mES_CTDP1_input

value: no


title: D15 KRAB IgG Sample 1

value: H9 hESC


title: Macrophage extracellular S. Typhimurium 14028s, RNA-seq, replicate 2

data_processing:
Sequenced reads of S. Typhimurium 14028s samples were mapped onto NC_016856.1 and NC_016855.1 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S.
Transcript Per Million (TPM) were calculated using featureCounts in R. Differentially expressed genes were identifiec using DEseq2 in R.
Assembly: NC_016856.1, NC_016855.1
Supplementary files format and content: Tab-delimited text files (.tsv) include TPM values and DEGs for samples.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

growth_protocol: Macrophage-like cells (J774A.1) were infected with S. Typhimurium 14028s WT strain (MOI of 1:10) in DMEM for a duration of 30 minutes. Following infection, extracellular bacteria were isolated and utilized for in vitro RNA-seq. Subsequently, the remaining extracellular bacteria were removed by washing process and gentamycin treatment. At 6 hours post-infection (hpi), the S. Typhimurium-infected macrophages were utilized for in vivo RNA-seq.

extract_protocol:
The cell cultures were treated with the RNAprotect reagent (Qiagen). Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a Qubit 4.0 (Thermo Scientific Inc., Wilmington, DE, USA). The ribosomal RNAs (rRNAs) were depleted with the Ribo-Zero Plus rRNA Depletion Kit (Illumina, USA).
KAPA Stranded RNA-seq Library Preparation Kit


title: ChIP-Seq_mES_pSer2_CTDP1_degron_0min_rep1

value: CTDP1-degron mES


title: S. Typhimurium 14028s, RpoD, ChIP-exo, LB media, overnight-grown, replicate 1


title: D30 ZNF-G2 Sample 4

data_processing:
Raw reads for RNAseq samples were quality trimmed using cutadapt (v3.4) and aligned using STAR (v2.5.4b).
Assembly: Aligned reads were quantified using featureCounts (v1.4.6-p4) from the subreads package.
Supplementary files format and content: hg38
Supplementary files format and content: tab-deliminated text file containing raw counts for each sample

growth_protocol: Embryonic stem cells were mainatined in mTeSR media on Vitronectin coated cultureware.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (Takara Bio)
RNA-seq library preparation was performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche) per the manufacturer’s instructions.

value: Immature Cortical Interneurons


title: PRO-Seq_mES_CTDP1_degron_60min_rep2

data_processing:
library strategy: PRO-seq
Raw PRO-Seq reads with spike-in were firstly trimmed by Cutadapt software (v3.4) and then mapped to mm10 and dm6 genome by Bowtie2 software (v2.3.5.1) in end-to-end mode.
Only uniquely and concordantly mapped reads were kept for further analysis. rRNA reads were discarded.
Genes shorter than 1kb were firstly removed, then reads that mapped to gene body regions (+300 to TES) of each gene were counted by featureCounts software (v2.0.1).
Assembly: mm10, dm6
Supplementary files format and content: excel file include raw read counts for each Sample

molecule: nuclear RNA

extract_protocol:
10 million cells were collected by trypsinization and mixed with 10% S2 cells, then resuspended in permeabilization buffer (10 mM Tris-HCl (pH 7.4), 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP-40, 0.5 mM DTT, 4 U/ml RNase inhibitor, 1 × proteinase inhibitor cocktail) and incubated on ice for 5 min. After centrifugation, nuclei pellet was washed twice with permeabilization buffer, then resuspended in 100 μl storage buffer (10 mM Tris-HCl (pH 8.0), 25% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 5 mM DTT), and stored at -80°C. For 1-Biotin run-on, 100 μl 2 × mix (10 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 50 μM biotin-11-CTP, 0.5 μM CTP, 250 μM ATP/GTP/UTP, 80 U RNase inhibitor, and 1% Sarkosyl) were made freshly and mixed with thawed sample, then incubated at 37°C for 3 min. TRIzol LS reagent was added immediately to extract the RNA. After following the manufacturer’s instructions, the RNA pellet was dissolved in 200 μl RNase-free water and fragmented by sonication in Diagenode Bioruptor plus (30 s on/30 s off, 10 cycles, high). In order to enrich biotin-labeled RNA, the fragmented RNA was denatured at 65°C for 40 sec and incubated with prewashed streptavidin Dynabeads which is in 200 μl binding buffer (10 mM Tris-HCl (pH 7.4), 300 mM NaCl, 0.1% Triton X-100). After 20 min incubation at 25°C, the beads were washed three times with high-salt wash buffer (50 mM Tris-HCl (pH 7.4), 2 M NaCl, and 0.5% Triton X-100), once with low-salt wash buffer (5 mM Tris-HCl (pH 7.4) and 0.1% Triton X-100) and vortexed with 300 μl TRIzol reagent twice to elude the RNA.
The RNA pellets were dissolved in 8 μl RNase-free water followed by library preparation with VAHTS Universal V8 RNA-seq Library Prep Kit according to the manufacturer’s manual.

treatment_protocol: For CTDP1 degradation, cells were treated with 2 μg/ml Dox for 12 h, then with 500 μM auxin for indicated time points.

tag: cell line

value: CTDP1 degron for 60min


title: D30 ZNF-G2 Sample 3


title: G63_D14_141_ABXPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_141_D12

value: fecal pellet bacterial DNA


title: G63_FMT_156_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_156_D7_FMT

value: VehiclePre+FMT


title: PRO-Seq_mES_CTDP1_degron_60min_rep1


title: Macrophage intracellular S. Typhimurium 14028s, RNA-seq, replicate 2


title: D30 ZNF-G2 Sample 2


title: G63_FMT_140_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_140_D7_FMT


title: G63_FMT_161_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_161_D7_FNT


title: Macrophage intracellular S. Typhimurium 14028s, RNA-seq, replicate 1


title: PRO-Seq_mES_CTDP1_degron_40min_rep2

value: CTDP1 degron for 40min


title: D30 ZNF-G2 Sample 1


title: G63_FMT_155_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_155_D7_FMT


title: PRO-Seq_mES_CTDP1_degron_40min_rep1


title: D30 ZNF-G1 Sample4


title: PRO-Seq_mES_CTDP1_degron_0min_rep2

value: CTDP1 degron for 0min


title: G63_FMT_151_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_151_D7_FMT


title: D30 ZNF-G1 Sample3


title: PRO-Seq_mES_CTDP1_degron_0min_rep1


title: Macrophage extracellular S. Typhimurium 14028s, RNA-seq, replicate 1


title: Micro-C_mES_CTDP1_untreated_rep2

data_processing:
library strategy: Micro-C
The linkers of raw reads were firstly trimmed using trimLinker command from ChIA-PET2 software.
The trimmed reads were then mapped to mm10 genome using HiC-Pro pipeline.
Uniquely mapped read pairs without PCR duplicates were filtered as valid interaction pairs.
The valid read pairs in each sample were randomly sampled to the same depth (n=51M) and converted to hic format using hicpro2juicebox in HiC-Pro software
Assembly: mm10
Supplementary files format and content: hic

extract_protocol:
1% formaldehyde-fixed cells were further crosslinked by DSG. After being lysed in MB#1 buffer (50 mM NaCl, 10 mM Tris, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1 x Protease inhibitor cocktail) for 20 min on ice, nuclei pellet was digested by MNase (2,500 U MNase for 6 million cells) for 20 min at 37°C with shaking at 1,000 rpm, then 4 mM EGTA was added to stop the reaction. To repair fragment ends for linker ligation, nuclei pellet was treated firstly with T4 PNK in Buffer A (50 mM NaCl, 10 mM Tris-HCl (pH 7.5), 10 mM MgCl2, 100 μg/mL BSA, 2 mM ATP, 5 mM DTT) for 15 min at 37°C, then with Klenow Fragment in Buffer B (23 mM Tris-HCl (pH 7.5), 10 mM MgCl2, 0.33 mM ATP, 6.67 mM DTT, 66 μM dNTPs, 100 μg/mL BSA) for 45 minutes at 25°C with interval shaking. 30 mM EDTA was added to stop the reaction. For A-Tailing, the DNA overhangs were tailed with dATP by Klenow (3’-5’ exo-) enzyme in 400 μl Buffer C (40 μl NEB buffer 2, 8 μl 10 mM dATP, 40 μl 10% Triton X-100, 304 μl H2O) for 1 hr at 37°C at 700 rpm, followed by ligated with a biotin-labeled bridge linker by T4 DNA ligase at room temperature for 6 hr. Then the chromatin DNA was digested by lambda exonuclease and exonuclease I. After being reverse crosslinked at 65°C, the ligated DNA was purified through biotin-streptavidin pulldown.
The DNA library for Micro-C was constructed on beads capturing ligated-DNA by using NEBNext Ultra II DNA library prep kit.


title: D30 ZNF-G1 Sample1


title: D30 ZNF-G1 Sample2


title: Micro-C_mES_CTDP1_untreated_rep1


title: G63_D14_140_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_140_D12

value: Vehicle


title: G63_D14_156_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_156_D14


title: Treatment-SAHA, biological rep3

city: Linkoping

first: Sallam Hasan Saleem Abdallah

last: Abdallah

state: SWEDEN

address: Linköping

country: Sweden

institute: Linköping University

hyb_protocol: We followed the manufacturer instructions for GeneChip™ Expression Wash and Stain

scan_protocol: GeneChip Scanner 3000 7G were used for the scanning process

data_processing: R; The log2 fold change values of probe sets mapped on the same gene were averaged to calculate its expression alteration

label: biotin

source_name: ASC52 cell line

label_protocol: The arrays were washed and stained using GeneChip Fluidics Station 450.

growth_protocol: ASC52telo cells (ASC52), adipose-derived mesenchymal stem cells immortalized with hTERT, was maintained in a humidified chamber set at 37°C with 5% CO2, using Dulbecco's Modified Eagle’s Medium enriched with 10% fetal bovine serum albumin (FBS).

extract_protocol: Total cellular RNAs were extracted using RNeasy Kit following the manufacturer’s instructions.

treatment_protocol: ADSCs were initially seeded at 50% confluency, subjected to 24 hours of serum deprivation, followed by treatment with SAHA at concentrations 1000nM. SAHA was dissolved in EtOH, and the latter was considered as a control vehicle. The treatment was applied sequentially for 72 hours.

value: Adipose derived stem cells

value: Treatment-SAHA


title: Micro-C_mES_CTDP1_degron_3h_rep2

value: CTDP1 degron for 3h


title: G63_D14_161_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_161_D14


title: Treatment-SAHA, biological rep2


title: D30 KRAB Sample 3


title: Vehicle-EtOH, biological rep1

value: Vehicle-EtOH


title: Vehicle-EtOH, biological rep3


title: Micro-C_mES_CTDP1_degron_3h_rep1


title: Treatment-SAHA, biological rep1


title: D30 KRAB Sample 2


title: Control-Ctrl, biological rep3

value: Control-Ctrl


title: D30 KRAB Sample 1


title: ABXEND_YA2_R

description:
V3/V4 Amplicons
seqtab.nochim_CtrlABX.csv
YA2-R_END

value: ABX


title: D15 ZNF-G2 Sample 4

value: Ventrally Patterned Neuronal Progenitors


title: Gill, Standing Stone, heatwave 2, recovery, sample ID 66

city: University Park

first: Justin

last: Waraniak

state: PA

address: 421 Forestry Resources Building

department: Ecosystem Sciences and Management

institute: Penn State University

data_processing:
Reads were aligned to a decoy-aware Salvelinus fontinalis transcriptome, constructed from the Salvelinus fontinalis transcriptome available from Phylofish (Pasquier et al. 2016), and the full Salvelinus fontinalis genome (NCBI RefSeq: GCF_029448725.1). Reads that aligned to the decoy-aware transcriptome were counted for each sample using the Salmon aligner tool v.1.10.0 (Patro et al. 2017).
Assembly: GCF_029448725.1 (genome)
Supplementary files format and content: quant.sf: tab-delimited text file with 5 columns: 1) Name - transcript names from the Phylofish transcriptome, 2) Length - the total length in base pairs of the transcript, 3) Effective Length - the computed effective length of the transcript based on the probability of sampling fragments and taking GC-bias into account, 4) TPM - the estimated number of transcripts per million reads, and 5) NumReads - the expected number of reads from the library that aligned to each transcript taking into account reads that mapped to multiple transcripts

organism: Salvelinus fontinalis

source_name: gill

extract_protocol:
RNA and DNA were both extracted as part of the same reactions using the Macherey-Nage Nucleospin RNA kit with RNA/DNA buffer using the manufacturer's recommendations with an additional repeat of the final RNA elution step to increase the total amount of RNA extracted.
RNA libraries were constructed using the improved TagSeq library construction procedure as described in Lohman et al. (2016)

value: gill

tag: location

value: Standing Stone Creek

tag: date

tag: Sex

value: F

tag: water temp_at_time_of_sampling_(c)


title: NASHTofo3 (miRNA-Seq)

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

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

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 101-base single-end mode.
Before analysis of the small RNA-Seq data, reads were trimmed the 3' adapter sequence (AGATCGGAAGAGCACACGTCT) using the software Cutadapt 1.14.
Trimmed reads were mapped to the mouse genome sequence (mm10) and quantified using the miRBase mouse miRNA dataset and the softwere StrandNGS ver.4.0 (Strand Life Sciences Pvt. Ltd.).
Assembly: mm10 and miRBase mouse miRNA dataset
Supplementary files format and content: tab-delimited text files include count data for each sample

source_name: renal cortex

extract_protocol:
Total RNA was isolated using the NucleoSpin miRNA (Cat.No.740971, Takara Bio, Shiga, Japan).
Each library was prepared using NEBNext Multiplex Small RNA Library Prep Set for illumina (New England Biolabs).

value: renal cortex

value: HF/HC/HS/BA+tofogliflozin, 8weeks


title: D30 KRAB Sample 4

value: Immature Cortical Interneurons

value: H9 hESC


title: ABXEND_YA1_R

description:
V3/V4 Amplicons
seqtab.nochim_CtrlABX.csv
YA1-R_END

value: fecal pellet bacterial DNA


title: D15 ZNF-G2 Sample 3


title: NASHTofo1 (miRNA-Seq)


title: Gill, Standing Stone, heatwave 2, recovery, sample ID 64


title: D15 ZNF-G2 Sample 2


title: Gill, Standing Stone, heatwave 2, recovery, sample ID 63


title: NASH3 (miRNA-Seq)

value: HF/HC/HS/BA diet, 8weeks


title: ABXEND_YA2_LL

description:
V3/V4 Amplicons
seqtab.nochim_CtrlABX.csv
YA2-LL_END


title: G63_D14_155_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_155_D14

value: Vehicle


title: D15 ZNF-G2 Sample 1


title: NASH2 (miRNA-Seq)


title: Control-Ctrl, biological rep2

value: Adipose derived stem cells


title: G63_D14_151_CTLPRE

description:
V3/V4 Amplicons
seqtab.nochim_FMT.csv
G63_151_D13


title: NASH1 (miRNA-Seq)


title: D15 ZNF-G1 Sample 4


title: CtrlEND_YC1_L

description:
V3/V4 Amplicons
seqtab.nochim_CtrlABX.csv
YC1-L_END


title: Control-Ctrl, biological rep1


title: NASHTofo3 (RNA-Seq)

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Cat.No.74106, QIAGEN, Hilden, Germany).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).


title: Gill, Standing Stone, heatwave 2, post-peak, sample ID 53

value: M


title: Gill, Standing Stone, heatwave 2, post-peak, sample ID 54


title: NASHTofo2 (miRNA-Seq)


title: BM-PC-4

first: Katsuyuki

last: Shiroguchi

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

institute: RIKEN

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assembly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of clusters for each gene was counted, which provides the number of molecules detected for each gene
The number of RNA molecules for each gene and index was listed
Assembly: mm10
Supplementary files format and content: The copy number of detected RNA molecules for genes and indexes (tubes) are summarized

source_name: bone marrow

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction.
Libraries were prepared by using molecular barcoding technique. First, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

value: bone marrow

value: plasma cells

value: B1-8germ k/w S1pr2-creERT2-Tg Ai14 k/w CD45.1


title: NASHTofo2 (RNA-Seq)


title: D15 ZNF-G1 Sample 2


title: Gill, Standing Stone, heatwave 2, post-peak, sample ID 52


title: D15 ZNF-G1 Sample 3


title: D15 ZNF-G1 Sample 1


title: Gill, Standing Stone, heatwave 2, post-peak, sample ID 51


title: Gill, Standing Stone, heatwave 2, recovery, sample ID 60


title: BM-PC-2


title: BM-PC-3


title: CtrlEND_YC2_R

description:
V3/V4 Amplicons
seqtab.nochim_CtrlABX.csv
YC2-R_END


title: NASHTofo1 (RNA-Seq)


title: NASH3 (RNA-Seq)


title: D15 KRAB Sample 4


title: NASH2 (RNA-Seq)


title: BM-PC-1


title: CtrlEND_YC1_R

description:
V3/V4 Amplicons
seqtab.nochim_CtrlABX.csv
YC1-R_END


title: Gill, Standing Stone, heatwave 2, peak, sample ID 48


title: D15 KRAB Sample 3


title: integrin-b7nega-spl-PC-5

source_name: spleen

value: spleen


title: NASH1 (RNA-Seq)


title: D15 KRAB Sample 2

value: Ventrally Patterned Neuronal Progenitors


title: Gill, Standing Stone, heatwave 2, peak, sample ID 47

value: gill


title: integrin-b7nega-spl-PC-3


title: D15 KRAB Sample 1


title: integrin-b7nega-spl-PC-2


title: 18mo CD45+ RAG2GFP- thymic cells - day 7 after SL-TBI biological rep2 [single cell]

city: Duarte

first: Anastasia

middle: I

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

description:
Chromium - Single Cell 3’ Reagent Kit (v2)
CD45pos_thymic_RAG2-CD45+cells_all+annotation.h5ad

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.01).
Assembly: GRCm38.p5 (mm10)
Supplementary files format and content: CD45pos_thymic_RAG2-CD45+cells_all+annotation.h5ad: H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format
Supplementary files format and content: molecule_info.h5: contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or Feature Barcode; this file is a required input to run cellranger aggr

source_name: thymus

extract_protocol:
All steps were performed at 4 C unless indicated. 10-15 thymi of 2-month-old or 18-month-old female RAG2GFP.C57BL/6 mice were injected with 3 μg of conjugated CD45 antibody and sacrificed 3 min later. The thymic tissue was excised and enzymatically digested. Briefly, thymi were mechanically dissociated into ca. 2 mm pieces. Tissue pieces were incubated with a digestion buffer (RPMI, 10% FCS, 62.5 um/mL liberase TM, 0.4 mg/ml DNase I) twice for 30 min at 37 C. Between incubation steps, supernatant containing dissociated cells was transferred to 50 mL conical tubes equipped with 100 um filter. Cells were pelleted by centrifugation at 400g for 5 min. The fraction of CD45+ peripheral i.v.-labeled cells where removed and cells where sorted for RAG2-GFP- cells after removal of  TER119 and DAPI+ cells. Cells were sorted into tubes containing RPMI supplemented with 2% BSA. FACS-purified cells were spun down at 1200 RPM for 5 min and resuspended in PBS supplemented with 0.04 % BSA for generation of single-cell suspensions. Viability of cells was confirmed to be above 80%.
The single-cell RNA-seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual (CG00052 Rev E) and using Single Cell 3’ Reagent Kit (v2). The viability of cells prior to loading onto the encapsulation chip was 73-98%, as confirmed with 0.2% (w/v) Trypan Blue stain. Each sample, containing approximately 8000 cells, was encapsulated in microfluidic droplets at a final dilution of 66–70 cells/µl (a multiplet rate ~3.9%). Following reverse transcription step the emulsion droplets were broken, barcoded-cDNA purified with DynaBeads and amplified by 12-cycles of PCR: 98 ̊C for 180 s, 12x (98 ̊C for 15 s, 67 ̊ C for 20 s, 72 ̊C for 60 s), and 72 ̊C for 60 s. The 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit, purified with SPRI beads and resulting DNA library was ligated to the sequencing adapter followed by indexing PCR: 98 ̊C for 45 s; 12x 98 ̊C for 20 s, 54 ̊C for 30 s, 72 ̊C for 20 s), and 72 ̊C for 60 s. The final DNA library was double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina Nova-Seq platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) at depth of 200-270 million reads per sample.

value: thymus

value: RAG2-CD45+ thymic cells

tag: age

value: 18-month old

value: SL-TBI

tag: time point

value: day 7


title: integrin-b7nega-spl-PC-1