title: OSCC 190Ad

description:
Library name: Strain 190Ad
A190

source_name: Strain 190Ad

value: Strain 190Ad

value: OSCC


title: KO-EBF2,rep2,Day 0,Cut&Tag Hdac1

status: Public on Mar 11 2026

type: SRA

city: Guangzhou

first: Li

last: Chen

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description: Library name: pre-Hdac1-KO-EBF2-2

library_source: genomic

data_processing:
For RNA-seq data analysis, transcript quantification was performed using Salmon (v1.2.28) with a pre-built mm39 mouse genome index. Transcript-to-gene mapping was based on Ensembl release 104 genome annotations.  For ATAC-seq data analysis, all sequencing reads were aligned to the mm39 mouse genome assembly using Bowtie2 (v2.5.4) with the following parameters: -p 20 --very-sensitive -k 10. Duplicate reads were removed using Sambamba (v1.0.1) based on the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Alignment BAM files were converted into read coverage files (bigWig format) using deepTools (v3.5.5) with RPKM normalization.  For CUT&Tag and data analysis, Sequencing reads were aligned to the mm39 mouse reference genome using Bowtie2, with the parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Sambamba was used for sorting and duplicate removal with the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Reads mapped to mitochondrial DNA or unassigned sequences were discarded. Alignment BAM files were converted into bigWig format using deepTools, with RPKM normalization.
Assembly: mm39
Supplementary files format and content: Bigwig, CSV file(raw count for each smaple in RNAseq)
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Immortalized brown preadipocytes line-LGT cells were maintained in complete DMEM/F12 medium (Gibco™, C11330500BT) supplemented with 10% FBS and 1% P/S. All these cells were grown at a humidified atmosphere at 37°C with 5% CO₂.

extract_protocol:
Total RNA from cells were extracted using RN28-EASYspin Plus RNA Mini Kit (Aidlab, RN2801) according to manufacturer’s protocol.
RNA libraries were constructed with Fast RNA-seq Lib Prep Kit V2 (Cat. No. RK2030) and sequenced using Illumina Novaseq X PLUS.  ATAC-seq libraries were generated using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, Cat# TD711-02) following the manufacturer’s instructions and the protocol as previously described (Buenrostro et al., 2013). Briefly, 50,000 cells were washed twice with cold PBS and pelleted by centrifugation at 300 × g for 5 minutes at 4°C. Cells were then resuspended in 50 μL of ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.2% IGEPAL CA-630) and incubated on ice for 15 minutes to release nuclei. Nuclei were pelleted by centrifugation at 300 × g for 10 minutes at 4°C. Tagmentation and library construction were performed using the TruePrep™ DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD501–503). Libraries were purified using the QIAquick PCR Purification Kit (Qiagen) and quantified for quality control. Sequencing was performed on the Illumina NovaSeq X PLUS platform.  A total of 2 × 10⁵ LGT preadipocytes or differentiated adipocytes were processed using the NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit for Illumina (Novoprotein Scientific, Cat# N259-YH01-01A), following the manufacturer’s protocol. The library preparations were sequenced on Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: For LGT differentiation, LGT cells were cultured to 100% confluence and subsequently induced with differentiation medium which contains 20 nM insulin (Sigma, I9278), 1 nM triiodothyronine (T3; Sigma, T2877), 1 μM dexamethasone (Sigma, D4902), 500 μM 3-isobutyl-1-methylxanthine (IBMX; Sigma, I5879), 125 μM indomethacin (Sigma, I7378), and 1 μM rosiglitazone (Selleck, S2556) for 48 hours. The differentiation medium was then replaced with maintenance medium containing 20 nM insulin and 1 nM T3 for an additional 5 days.

tag: cell line

tag: genotype

value: EBF2 CTD

tag: time

value: Day 0

tag: treatment

value: preadipocyte differentiation

tag: batch


title: CGND-HRA-02805

city: New York

first: Hemali

last: Phatnani

state: NY

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

description: Library name: CGND-HRA-02805

library_source: transcriptomic

data_processing:
Raw sequencing files was demultiplexed with bcl2fastq
Samples were uniformly processed using RAPiD-nf, an efficient RNA-Seq processing pipeline implemented in the NextFlow framework(Di Tommaso et al. 2017). Following adapter trimming with Trimmomatic (version 0.36)(Bolduc, n.d.), all samples were aligned to the hg38 build (GRCh38.primary_assembly) of the human reference genome using STAR (2.7.2a)(Dobin et al. 2013), with indexes created from GENCODE, version 30(Harrow et al. 2012). Gene expression was quantified using RSEM (1.3.1)(B. Li and Dewey 2011). Quality control was performed using SAMtools(H. Li et al. 2009) and Picard, and the results were collated using MultiQC(Ewels et al. 2016).
Assembly: hg38
Supplementary files format and content: csv files contatining count and tpm data

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA extraction from fresh frozen tissue or cells – starting material is homogenized in TRIzol reagent using a series of needles for trituration. The homogenized sample undergoes phase separation with the addition of chloroform,  the upper aqueous phase of the mixture then follows the RNeasy Mini procedure (Qiagen, 74106). A series of washes will purify the final eluted total RNA. The RNeasy Mini portion of the protocol is processed on the QIAcube Connect automated platform (Qiagen, 9002864) for higher throughput.
RNA sequencing libraries are prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche 07962304001) in accordance with the manufacturer’s instructions. Samples are normalized to 500ng and undergo rRNA depletion through oligo hybridization and RNase H treatment. DNase treatment removes DNA oligos. Samples are fragmented to 350bp inserts and undergo cDNA generation. Samples undergo A-tailing and are ligated to Illumina sequencing adapters and amplified. Final libraries are quantified using the Qubit Fluorometer (Life Technologies) or Spectramax M2 (Molecular Devices) and Fragment Analyzer (Agilent). Libraries are sequenced on an Illumina sequencer.

tag: tissue

value: ALS

tag: subject id

tag: gender

value: female

tag: age


title: WB_2_invivo

city: Storrs

first: Elsio

middle: Augusto

last: Wunder

state: CT

address: 61 N Eagleville

department: Pathobiology and Veterinary Sciences

institute: University of Connecticut

description:
Library name: WB_2
collum name in Leptospira_raw_counts:WB_2

data_processing:
terminal linux
Trimmed raw reads were aligned to the reference genome of L. interrogans serovar Copenhageni strain Fiocruz L1-130 from NCBI (267671) using HISAT2 v2.1
Alignments with a quality score below 20 were excluded from further analysis. Reads were counted for each gene with StringTie v1.3.3
differentially expression analysis was performed in DESeq2
Assembly: NCBI:txid267671
Supplementary files format and content: csv files includes raw counts for each sample

organism: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

source_name: Spirochaete cells

extract_protocol:
RNA for two biological replicates of each culture condition and hamster blood. A volume of 20 mL of leptospires cultured on different media at late-logarithmic phase and EDTA tubes containing ∼3 mL of whole blood from each hamster were centrifuged at 6000 x g for 15 minutes. Trizol (Invitrogen) was added to the pellets for RNA stabilization (3:1 v/v). RNA isolation was performed on 400 mL of the mix using Direct-zol RNA MiniPrep (Zymo Research), following manufacturer’s instructions.
Only samples with RIN > 7 were chosen for mRNA library construction using TruSeq standard mRNA Library Prep kit (Illumina) following manufacture's protocol

value: Spirochaete cells

value: Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130

value: WB


title: EMJH_2_invitro

description:
Library name: EMJH_2
collum name in Leptospira_raw_counts:EMJH_2

value: EMJH


title: KO-P>A,rep4,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-P2A-4

source_name: Immortalized brown preadipocytes line-LGT cells


title: WB_1_invivo

description:
Library name: WB_1
collum name in Leptospira_raw_counts:WB_1


title: CGND-HRA-02803

description: Library name: CGND-HRA-02803


title: EMJH_1_invitro

description:
Library name: EMJH_1
collum name in Leptospira_raw_counts:EMJH_1


title: KO-EBF2,rep1,Day 0,Cut&Tag Hdac1

description: Library name: pre-Hdac1-KO-EBF2-1

value: Immortalized brown preadipocytes line-LGT cells


title: HAN_1_invitro

description:
Library name: HAN_1
collum name in Leptospira_raw_counts:HAN_1

value: HAN


title: HAN_2_invitro

description:
Library name: HAN_2
collum name in Leptospira_raw_counts:HAN_2


title: Moderate dysplasia 185A1d

city: Philadelphia

first: Nezar

last: Al-hebshi

state: PA

address: 3223 N Broad Street, Office L213

institute: Temple University

description:
Library name: Strain 185A1d
A185

data_processing:
Novogene pipeline for analysis of prokaryote RNA-seq data
Assembly: NCTC10562
Supplementary files format and content: fpkm normalized gene counts for each sample

organism: Fusobacterium polymorphum

source_name: Strain 185A1d

extract_protocol:
Pelleted cells were processed for total RNA extraction using the PureLink™ RNA Mini Kit (Thermo Fisher Scientific, USA) according to the bacterial RNA workflow
Novogene pipeline for directional library preparation from prokaryote RNA seq

tag: strain

value: Strain 185A1d

tag: source subject_status

value: Moderate dysplasia


title: KO-P>A,rep3,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-P2A-3


title: KO-FUS,rep5,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-FUS-5


title: CGND-HRA-02794

description: Library name: CGND-HRA-02794

value: CTL


title: Mild dysplasia 139A

description:
Library name: Strain 139A
A139

source_name: Strain 139A

value: Strain 139A

value: Mild dysplasia


title: CGND-HRA-02796

description: Library name: CGND-HRA-02796


title: KO-EBF2,rep4,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-EBF2-4


title: DMEM_1_invitro

description:
Library name: DMEM_1
collum name in Leptospira_raw_counts:DMEM_1

value: DMEM


title: EMEM_1_invitro

description:
Library name: EMEM_1
collum name in Leptospira_raw_counts:EMEM_1

value: EMEM


title: DMEM_2_invitro

description:
Library name: DMEM_2
collum name in Leptospira_raw_counts:DMEM_2


title: EMEM_2_invitro

description:
Library name: EMEM_2
collum name in Leptospira_raw_counts:EMEM_2


title: CGND-HRA-02797

description: Library name: CGND-HRA-02797

source_name: Cerebellum

value: Cerebellum


title: CGND-HRA-02764

description: Library name: CGND-HRA-02764


title: KO-EBF2,rep3,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-EBF2-3

value: EBF2 CTD

value: Day 0

value: preadipocyte differentiation


title: 5 month old mouse brain hippocampus - APP<NLGF/NLGF>P16<KO/KO> genotype - sample 23

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

country: France

institute: IGBMC/PHENOMIN-ICS

description: Library name: NNHT43

data_processing:
Raw sequencing reads were preprocessed to remove adapter sequences, polyA tails, and low-quality reads (defined as those with a Phred score < 20). Reads shorter than 40 bases after trimming were excluded from downstream analysis. Preprocessing was performed using the R package cutadapt (v4.2) (26). Reads were first aligned to ribosomal RNA (rRNA) reference sequences from RefSeq (27) and GenBank (28) using bowtie (v2.3.5) (29), and rRNA-matching reads were discarded. Remaining reads were then aligned to the Mus musculus GRCm38 genome assembly using STAR (v2.7.10b) (30). Gene body coverage was assessed across all samples using the geneBodyCoverage function from RSeQC (v5.0.1) (31), and transcript integrity number (TIN) values were calculated for transcripts with at least 10 uniquely aligned reads. In cases of overlapping genomic annotations, priority was assigned as follows: exonic > intronic > antisense genic > intergenic regions. Strand specificity was also evaluated using RSeQC (v5.0.1) (31).
Gene expression levels were quantified using uniquely aligned reads with STAR (v2.7.10b) (30), based on Ensembl annotation version 102. Only reads unambiguously assigned to a gene were retained for downstream analysis. To reduce noise from lowly expressed genes, those with fewer than 15 reads in more than 10% of the samples were excluded, yielding a final set of 18,768 genes.
Outlier samples were identified using Principal Component Analysis (PCA) on variance-stabilized expression data (VST)-normalized using DESeq2 (v1.45.3) (32). The number of PCs retained was determined using the Elbow Method, automated with the FindPC package (v1.0) (33), which identifies the point of maximal deviation from a straight line between the first and last PC. Mahalanobis distances were then calculated based on the selected PCs to detect statistical outliers. Squared Mahalanobis distances were compared to the 95th percentile of the Chi-squared distribution; samples exceeding this threshold were classified as outliers.
Assembly: mm39
Supplementary files format and content: CSV

molecule: polyA RNA

source_name: Brain

extract_protocol:
mice were sacrificed via cervical dislocation at ~5 months of age. For transcriptomic analysis, both hippocampi were collected from a subset of randomly selected animals and stored at −80°C. Tissue homogenization was performed using the Precellys 24 Touch (Bertin Instruments, Montigny-le-Bretonneux, France) at 4500 rpm for 20 seconds. RNA extraction was carried out using the RNeasy Lipid Tissue Mini Kit (74804, Qiagen), following the manufacturer’s instructions. RNA concentration was measured using the Qubit RNA Assay Kit (Thermo Fisher Scientific), and RNA integrity was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Les Ulis, France).
Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Reference Guide – PN 1000000124518). RNA-Seq libraries were generated from 350 ng of total RNA following the manufacturer’s instructions (Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes, Illumina, San Diego, USA). After polyA selection, mRNA was fragmented at 94 °C for 8 minutes. DNA libraries were then amplified using 12 PCR cycles, and excess primers were removed by two rounds of purification using SPRIselect beads (Beckman-Coulter, Villepinte, France). Library quality and concentration were assessed using the Bioanalyzer 2100 system (Agilent Technologies, Les Ulis, France). Sequencing was performed on an Illumina NextSeq 2000 platform using single-end 50 base reads. Image analysis and base calling were conducted using RTA (v2.7.7) and BCL Convert (v3.8.4).

value: Brain


title: CGND-HRA-02762

description: Library name: CGND-HRA-02762

value: ALS

value: female


title: KO-EBF2,rep2,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-EBF2-2


title: 5 month old mouse brain hippocampus - APP<NLGF/NLGF>P16<KO/KO> genotype - sample 21

description: Library name: NNHT41


title: 5 month old mouse brain hippocampus - APP<NLGF/NLGF>P16<KO/KO> genotype - sample 18

description: Library name: NNHT38


title: CGND-HRA-02757

description: Library name: CGND-HRA-02757


title: 5 month old mouse brain hippocampus - APP<NLGF/NLGF>P16<KO/KO> genotype - sample 22

description: Library name: NNHT42


title: CGND-HRA-02756

description: Library name: CGND-HRA-02756


title: KO-CTD,rep2,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-CTD-2


title: 5 month old mouse brain hippocampus - APP<NLGF/NLGF>P16<KO/KO> genotype - sample 20

description: Library name: NNHT40


title: KO-CTD,rep1,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-CTD-1


title: 5 month old mouse brain hippocampus - APP<NLGF/NLGF>P16<KO/KO> genotype - sample 19

description: Library name: NNHT39


title: 5 month old mouse brain hippocampus - APP NLGF genotype - sample 15

description: Library name: NNHT35

value: APP<NLGF/NLGF>


title: CGND-HRA-02755

description: Library name: CGND-HRA-02755


title: 5 month old mouse brain hippocampus - APP NLGF genotype - sample 16

description: Library name: NNHT36


title: 5 month old mouse brain hippocampus - APP NLGF genotype - sample 13

description: Library name: NNHT33


title: 5 month old mouse brain hippocampus - APP NLGF genotype - sample 14

description: Library name: NNHT34


title: 5 month old mouse brain hippocampus - APP NLGF genotype - sample 17

description: Library name: NNHT37


title: CGND-HRA-02748

description: Library name: CGND-HRA-02748


title: KO-P>A,rep2,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-P2A-2

value: Immortalized brown preadipocytes line-LGT cells


title: CGND-HRA-02741

description: Library name: CGND-HRA-02741

value: male


title: CGND-HRA-02754

description: Library name: CGND-HRA-02754


title: 5 month old mouse brain hippocampus - P16 KO genotype - sample 12

description: Library name: NNHT32


title: KO-EBF2,rep1,Day 0,Cut&Tag EBF2

description: Library name: pre-HA-KO-EBF2-1


title: KO-P>A,rep1,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-P2A-1


title: 5 month old mouse brain hippocampus - P16 KO genotype - sample 11

description: Library name: NNHT31


title: 5 month old mouse brain hippocampus - P16 KO genotype - sample 10

description: Library name: NNHT30


title: 5 month old mouse brain hippocampus - P16 KO genotype - sample 9

description: Library name: NNHT29


title: 5 month old mouse brain hippocampus - P16 KO genotype - sample 7

description: Library name: NNHT27


title: CGND-HRA-02714

description: Library name: CGND-HRA-02714

source_name: Hippocampus

value: Hippocampus


title: KO-FUS,rep2,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-FUS-2


title: 5 month old mouse brain hippocampus - P16 KO genotype - sample 8

description: Library name: NNHT28


title: 5 month old mouse brain hippocampus - WT genotype - sample 5

description: Library name: NNHT25

value: WT


title: CGND-HRA-02709

description: Library name: CGND-HRA-02709


title: KO-EV,rep2,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-EV-2


title: 5 month old mouse brain hippocampus - WT genotype - sample 6

description: Library name: NNHT26


title: KO-FUS,rep1,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-FUS-1


title: KO-EBF2,rep2,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-EBF2-2


title: 5 month old mouse brain hippocampus - WT genotype - sample 2

description: Library name: NNHT22


title: HPV-16 specific CD4+ T cells

city: Seattle

first: Rongyu

last: Zhang

state: WA

address: 401 Terry Ave N

institute: ISB

description: Library name: HPV

data_processing:
Illumina bcl2fastq2 was used to generate fastq files from bcl files. Raw data were processed using the Cell Ranger Single-Cell Software Suite (v3.1.0, 10X Genomics) with GRCh38 as the reference genome. Gene expression data (GEX) were quality-controlled to eliminate low quality cells: cells with less than 200 or above 5,000 unique genes or a mitochondrial content above 15%. Any genes detected in less than three cells were also removed. Gene expression counts for each cell were normalized by the total expression, scaled by a factor of 10,000, and transformed to a log scale. All cells that pass the quality control were clustered through PCA and KNN graphs based on the highly variable genes and projected onto UMAPs. Phenotypes were defined based on enrichment of signature gene sets and assigned to single cells based on clusters identified using the Leiden algorithm.
Assembly: Raw data were alighed against GRCh38 which served as the reference genome.
Supplementary files format and content: A matrix file (.h5ad) that contains processed transcription information.

source_name: PBMC

growth_protocol: PBMCs were processed immediately after thawing and were not cultured.

extract_protocol:
PBMC samples were stained with hashtag antibodies (Biolegend, custom TotalSeq anti-CD298, clone LNH-94) based on patients and/or timepoints. After two washes, PBMCs were pooled for MACS-based CD4+ T cell enrichment through negative selection (Miltenyi, 130-096-533). Isolated CD4+ T cells were incubated in 50 nM PKI solution at 37C for 20-30 min, followed by dextramer pool staining in 50 nM PKI for 20-25 min at 4C. After 2-3 washes, the cells were stained with live dye (Biolegend, 427402), CD4-BV421 (Biolegend, 317434, clone OKT4), and TCR-APC (Biolegend, 306718, clone IP26) for 10 min at 4C. The cells were then FACS sorted, washed and loaded onto Chromium Next GEM chips for single cell sequencing (10x Genomics).
Library was constructed according to standard library prep manuals from 10x Genomics.

value: PBMC

tag: cell type

value: CD4+ T cell


title: 5 month old mouse brain hippocampus - WT genotype - sample 4

description: Library name: NNHT24


title: 5 month old mouse brain hippocampus - WT genotype - sample 3

description: Library name: NNHT23


title: 5 month old mouse brain hippocampus - WT genotype - sample 1

description: Library name: NNHT21


title: Patient 3C

city: London

first: Kritarth

last: Singh

state: England

address: Biosciences Stores, Anatomy Building, Gower street

department: Cell and Developmental Biology

country: United Kingdom

institute: University College London

description:
Library name: Sample 9
Column name in raw_counts_all_samples: Patient 3C

data_processing:
DRAGEN (version 3.9.5)
Sequence reads were trimmed for adaptor sequence/ low quality sequence using DRAGEN (version 3.9.5).
Trimmed sequence reads were mapped to GRCh37 (hg19).
RNA count extraction and normalization was performed using DRAGEN (version 3.9.5)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file included raw count for each sample
Supplementary files format and content: A csv file contains raw counts of all the samples

source_name: Skin tissue

growth_protocol: All cell lines were cultured and maintained in Dulbecco’s modified Eagle’s medium (10566016, Gibco) supplemented with 10% fetal bovine serum (16140071, Gibco), and 1% Antibiotic-Antimycotic (15240096, Gibco) and incubated at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using Mag-Bind® Total RNA 96 Kit.
RNA library for RNA-seq was prepared using Kapa mRNA HyperPrep with IDT xGen UDI-UMI adaptors.

treatment_protocol: No treatment conditions were involved in the experiment design.

value: Skin tissue

value: Primary cells

value: Human dermal fibroblasts

value: Untreated


title: SARS-CoV-2 specific CD4+ T cells

description: Library name: COVID


title: CGND-HRA-02699

description: Library name: CGND-HRA-02699


title: CGND-HRA-02695

description: Library name: CGND-HRA-02695


title: KO-EBF2,rep1,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-EBF2-1

value: EBF2 CTD


title: CGND-HRA-02690-2

description: Library name: CGND-HRA-02690-2


title: KO-EV,rep2,Day 7,H3K27ac

description: Library name: post-H3K27ac-KO-EV-2

value: Day 7


title: KO-EV,rep1,Day 7,H3K27ac

description: Library name: post-H3K27ac-KO-EV-1

value: preadipocyte differentiation


title: CGND-HRA-02677

description: Library name: CGND-HRA-02677


title: Patient 3B

description:
Library name: Sample 8
Column name in raw_counts_all_samples: Patient 3B


title: CGND-HRA-02704

description: Library name: CGND-HRA-02704


title: CGND-HRA-02646

description: Library name: CGND-HRA-02646


title: KO-EV,rep1,Day 0,H3K27ac

description: Library name: pre-H3K27ac-KO-EV-1

value: Day 0


title: Patient 1A

description:
Library name: Sample 4
Column name in raw_counts_all_samples: Patient 1A


title: Patient 3A

description:
Library name: Sample 7
Column name in raw_counts_all_samples: Patient 3A


title: KO-EBF2,rep2,Day 7,H3K27ac

description: Library name: post-H3K27ac-KO-EBF2-2


title: CGND-HRA-02642

description: Library name: CGND-HRA-02642

value: Cerebellum

value: ALS


title: Patient 1B

description:
Library name: Sample 5
Column name in raw_counts_all_samples: Patient 1B


title: CGND-HRA-02634

description: Library name: CGND-HRA-02634

value: CTL


title: Control 1B

description:
Library name: Sample 2
Column name in raw_counts_all_samples: Control 1B

value: wild-type


title: CGND-HRA-02635

description: Library name: CGND-HRA-02635

value: male


title: Neutrophils, Donor Siglec14-NULL, Bf-stimulated

city: Trento

first: Fulvio

last: Chiacchiera

address: Via Sommarive  9

department: Department of Cellular, Computational and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

description: Library name: Sample 6

library_source: transcriptomic single cell

data_processing:
Raw FASTQ data were processed using the BD Rhapsody™ Sequence Analysis Pipeline (v2.2.1), with the pre-built RhapRef_Human_WTA_2025-03 reference. All parameters were left at their default settings.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood neutrophils

extract_protocol:
Peripheral blood neutrophils (PBNs) from the healthy donor and Siglec14-NULL donor were isolated by negative sorting with magnetic beads. Freshly isolated PBNs were resuspended into phenol red- and serum-free RPMI and plated at a 0.5x106/ml concentration. They were then cocultured alone or in the presence of live bacteria at a 50:1 bacteria: neutrophil ratio.
Reverse transcription was performed on mRNA captured by BD Rhapsody™ Cell Capture Beads usingthe BD Rhapsody™ cDNA Kit, following the manufacturer’s instructions. This step generatedbead-bound cDNA via oligo(dT)-primed reverse transcription. Whole transcriptomeamplification (WTA) was then carried out using the BD Rhapsody™ WTA Amplification Kit,which amplifies 3ʹ end transcript fragments through targeted PCR to produce whole-transcriptome libraries. Purification steps were conducted using SPRIselect magnetic beadsaccording to the recommended ratios for each step of the protocol. Final libraries werequantified using the Qubit™ dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific), and39size distribution was assessed on an Agilent 2100 Bioanalyzer using the High Sensitivity DNAkit (Agilent Technologies).

value: Peripheral blood neutrophils

value: Donor Siglec14-NULL


title: Patient 1C

description:
Library name: Sample 6
Column name in raw_counts_all_samples: Patient 1C


title: Control 1A

description:
Library name: Sample 1
Column name in raw_counts_all_samples: Control 1A


title: KO-CTD,rep2,Day 7,H3K27ac

description: Library name: post-H3K27ac-KO-CTD-2

value: Immortalized brown preadipocytes line-LGT cells


title: KO-P>A,rep4,Day 0,ATAC

description: Library name: pre-ATAC-KO-P2A-4

data_processing:
For RNA-seq data analysis, transcript quantification was performed using Salmon (v1.2.28) with a pre-built mm39 mouse genome index. Transcript-to-gene mapping was based on Ensembl release 104 genome annotations.  For ATAC-seq data analysis, all sequencing reads were aligned to the mm39 mouse genome assembly using Bowtie2 (v2.5.4) with the following parameters: -p 20 --very-sensitive -k 10. Duplicate reads were removed using Sambamba (v1.0.1) based on the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Alignment BAM files were converted into read coverage files (bigWig format) using deepTools (v3.5.5) with RPKM normalization.  For CUT&Tag and data analysis, Sequencing reads were aligned to the mm39 mouse reference genome using Bowtie2, with the parameters: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Sambamba was used for sorting and duplicate removal with the filtering criteria: [XS] == null AND NOT unmapped AND NOT duplicate. Reads mapped to mitochondrial DNA or unassigned sequences were discarded. Alignment BAM files were converted into bigWig format using deepTools, with RPKM normalization.
Assembly: mm39
Supplementary files format and content: Bigwig, CSV file(raw count for each smaple in RNAseq)


title: Neutrophils, Donor WT, Fn-stimulated

description: Library name: Sample 2

value: Donor WT


title: Neutrophils, Donor Siglec14-NULL, Fn-stimulated

description: Library name: Sample 5


title: KO-CTD,rep1,Day 7,H3K27ac

description: Library name: post-H3K27ac-KO-CTD-1


title: CGND-HRA-02631

description: Library name: CGND-HRA-02631

value: Hippocampus


title: Neutrophils, Donor Siglec14-NULL, unstimulated

description: Library name: Sample 4


title: Control 1C

description:
Library name: Sample 3
Column name in raw_counts_all_samples: Control 1C

value: Skin tissue

value: Primary cells


title: Neutrophils, Donor WT, unstimulated

description: Library name: Sample 1


title: KO-EBF2,rep1,Day 7,H3K27ac

description: Library name: post-H3K27ac-KO-EBF2-1


title: DLX3-KO isAM organoids, C3-DLL4 treated, biol rep 1

first: Hannele

last: Ruohola-Baker

address: UW Medicine at South Lake Union, 850 Republican Street

department: Department of Biochemistry

institute: University of Washington

description: Library name: DLX3KO_C3DLL4_isAM_1

data_processing:
Quality Control: Raw FASTQ files were quality-checked using FastQC (v0.11.9).
Alignment: Reads were aligned to the human reference genome GRCh38 using HISAT2 (v2.2.1) with default parameters.
Quantification: Gene-level counts were obtained using FeatureCounts (Subread v2.0.1) based on GENCODE GRCh38 annotations.
Normalization & Differential Expression: Data normalization and differential expression analysis were performed using the DESeq2 R package (v1.34.0).
Downstream Analysis: Gene Ontology and pathway enrichment analyses were performed using TopGO (v2.48.0) and DAVID 6.8.
Assembly: Human reference genome GRCh38 (Ensembl release 104).
Supplementary files format and content: Gene-level raw counts (CSV).

growth_protocol: WTC-11 human induced pluripotent stem cells (hiPSCs) were maintained on growth factor-reduced Matrigel (Corning #356231) and cultured in mTeSR medium (StemCell Technologies #85850) under standard conditions at 37 °C, 5% CO₂, with daily medium changes until cells reached confluency.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) following the manufacturer’s instructions. RNA was treated with Turbo DNase (Thermo Fisher) to remove genomic DNA and quantified using the Qubit RNA HS Assay Kit and Agilent High Sensitivity D5000 ScreenTape.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep, Ligation Kit (Illumina #20040532), according to the manufacturer’s instructions. Libraries were size-selected using AMPure XP beads (Beckman Coulter #A63880), quality checked on the Agilent D5000 ScreenTape system, and indexed with Illumina adapters. Sequencing was performed on the Illumina NextSeq 2000 platform (paired-end, 100 bp).

treatment_protocol: On day 24 of ameloblast differentiation, C3-DLL4 (50 nM) — a computationally designed trimeric scaffold conjugated to DLL4 — was added to induce Notch activation for 24 h. For control samples, no treatment was applied. DLX3 knockout organoids followed the same treatment protocol.

value: induced secretory ameloblast organoids (isAM)

value: DLX3 knockout


title: KO-P>A,rep3,Day 0,ATAC

description: Library name: pre-ATAC-KO-P2A-3

value: EBF2 CTD


title: WT isAM organoids, C3-DLL4 treated, biol rep 2

description: Library name: WT_C3DLL4_isAM_2

value: WT


title: CGND-HRA-02623-2

description: Library name: CGND-HRA-02623-2


title: WT isAM organoids, C3-DLL4 treated, biol rep 1

description: Library name: WT_C3DLL4_isAM_1


title: CGND-HRA-02621

description: Library name: CGND-HRA-02621

value: female


title: KO-FUS,rep6,Day 0,ATAC

description: Library name: pre-ATAC-KO-FUS-6

value: Day 0

value: preadipocyte differentiation


title: KO-FUS,rep5,Day 0,ATAC

description: Library name: pre-ATAC-KO-FUS-5


title: Neutrophils, Donor WT, Bf-stimulated

description: Library name: Sample 3


title: WT isAM organoids, untreated, biol rep 2

description: Library name: WT_isAM_2


title: WT isAM organoids, untreated, biol rep 1

description: Library name: WT_isAM_1


title: CGND-HRA-02611

description: Library name: CGND-HRA-02611

value: ALS


title: CGND-HRA-02632

description: Library name: CGND-HRA-02632

value: Cerebellum

value: CTL


title: CGND-HRA-02609

description: Library name: CGND-HRA-02609

value: male


title: KO-EV,rep6,Day 0,ATAC

description: Library name: pre-ATAC-KO-EV-6


title: DLX3-KO isAM organoids, C3-DLL4 treated, biol rep 2

description: Library name: DLX3KO_C3DLL4_isAM_2


title: KO-EBF2,rep4,Day 0,ATAC

description: Library name: pre-ATAC-KO-EBF2-4


title: CGND-HRA-02605

description: Library name: CGND-HRA-02605


title: WT_48h_rep1

type: RNA

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

description: Gene expression 48h after shift to a light intensity of 250 μmol photons m-2 s-1

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Here, the raw data are submitted. For further analysis, raw data were normexp background corrected (Ritchie et al., 2014) and quantile normalized using the limma R package (Ritchie et al., 2007). The transcriptome differences were calculated between WT and ∆sliP4 mutant for the two different light conditions and time points.

organism: Synechocystis sp. PCC 6803

source_name: liquid culture

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: The Synechocystis 6803 substrain M (Trautmann et al., 2012) was used throughout. The generation of the ∆sliP4 mutant was described in detail by Alvarenga-Lucius et al. (2023). The wild-type (WT) and ∆sliP4 mutant strains were grown in glass Erlenmeyer flasks (125 mL) filled with 40 mL of BG-11 buffered medium (pH 8.0) without sodium carbonate (Rippka et al., 1979) under the following conditions: 28 ± 2°C, continuous light of 50 μmol photons m-2 s-1. Growth experiments were performed for 48 h in a Multi-Cultivator MC1000-OD at 30°C (Photon Systems Instruments, Czech Republic) with continuous illumination of 250 μmol photons m-2 s-1 and bubbling with 5% (v/v) CO2 supplemented. The ∆sliP4 mutant was grown in the presence of 50 µg mL-1 kanamycin during pre-culture and without antibiotics during the experiments for accurate comparison with the WT.

extract_protocol: Cells were collected by centrifugation at 7000 g for 5 min at 4°C and the pellet was frozen in liquid nitrogen. Total RNA was prepared using the hot-phenol method.

treatment_protocol: Gene expression analyses were performed for cultures precultivated under continuous light of 50 μmol photons m-2 s-1 and after shifts to high light conditions of 250 μmol photons m-2 s-1 for 30 min or for 48 h.

value: PCC-M

value: wild type


title: KO-EV,rep2,Day 7,ATAC

description: Library name: post-ATAC-KO-EV-2

value: Immortalized brown preadipocytes line-LGT cells

value: Day 7


title: CGND-HRA-02593

description: Library name: CGND-HRA-02593

value: Hippocampus


title: slip4_0min_rep1b

description: Gene expression at a light intensity of 50 μmol photons m-2 s-1

value: {delta}sliP4 mutant


title: WT_0min_rep2b

value: a light intensity of 50 μmol photons m-2 s-1


title: CGND-HRA-02583

description: Library name: CGND-HRA-02583


title: CGND-HRA-02588

description: Library name: CGND-HRA-02588


title: CGND-HRA-02606

description: Library name: CGND-HRA-02606


title: CGND-HRA-02578

description: Library name: CGND-HRA-02578


title: KO-EBF2,rep3,Day 0,ATAC

description: Library name: pre-ATAC-KO-EBF2-3


title: KO-EV,rep5,Day 0,ATAC

description: Library name: pre-ATAC-KO-EV-5


title: KO-EV,rep1,Day 7,ATAC

description: Library name: post-ATAC-KO-EV-1


title: KO-EBF2,rep1,Day 7,ATAC

description: Library name: post-ATAC-KO-EBF2-1


title: KO-EBF2,rep2,Day 7,ATAC

description: Library name: post-ATAC-KO-EBF2-2


title: slip4_48h_rep2

value: 48h after shift to a light intensity of 250 μmol photons m-2 s-1


title: WT_0.5h_rep2

description: Gene expression 30 min after shift to a light intensity of 250 μmol photons m-2 s-1


title: slip4_48h_rep1


title: WT_48h_rep2


title: CGND-HRA-02574

description: Library name: CGND-HRA-02574


title: WT_0min_rep1b


title: WT_0.5h_rep1

value: 30 min after shift to a light intensity of 250 μmol photons m-2 s-1


title: slip4_0.5h_rep1


title: KO-CTD,rep2,Day 7,ATAC

description: Library name: post-ATAC-KO-CTD-2

value: EBF2 CTD


title: HEK293FT, RNA, Replicate 3

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: HEK_MPRA3_RNA
label in metadata files is RNA_Neurons_3

data_processing:
DNA and RNA Counts as well as DNA and RNA annotations were generated using the MPRAflow count utility as specified in Gordon et al. 2020 using the --mpranalyze flag
Barcode association dictionary and design file with illegal characters removed were generated using the MPRAflow association utility as specified in Gordon et al. 2020
Assembly: hg38
Supplementary files format and content: DNA and RNA counts are total barcode counts in csv format
Supplementary files format and content: DNA and RNA annotations are label files for use with mpranalyze in tsv format
Supplementary files format and content: Design File contains MPRA sequences and lables for input into MPRAflow's association utility in fasta format
Supplementary files format and content: Barcode association dictionary is used for MPRAflow's count utility and is a python pickle file

extract_protocol:
Qiagen Allprep RNA/DNA mini kit for MPRA output sequencing, Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

value: human embryonic kidney cells


title: HEK293FT, DNA, Replicate 2

description:
Library name: HEK_MPRA2_DNA
label in metadata files is DNA_Neurons_2


title: HEK293FT, DNA, Replicate 3

description:
Library name: HEK_MPRA3_DNA
label in metadata files is DNA_Neurons_3


title: HEK293FT, RNA, Replicate 2

description:
Library name: HEK_MPRA2_RNA
label in metadata files is RNA_Neurons_2


title: A2929_Rel_pAY15_5phIAA_3D_rep2

city: Chicago

first: Harun

last: Ozturk

state: Illinois

address: 303. E. Superior, Lurie cancer center

institute: Northwestern University

description: Library name: Sample12

data_processing:
Data were quality checked using FASTQC.
Reads were aligned to mm39 genome assembly using STAR (settings: --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard)
The DESeq2 package was used with default settings to determine differentially expressed genes.
Assembly: mm39
Supplementary files format and content: The CSV file contains raw count numbers for each sample.

source_name: pancreas

growth_protocol: Cells are cultured in ultra low attachment plates to form non-adherent spheroids. Spheroid medium contains 0.5 L of DMEM/F12 (1:1) (Gibco, 21331--020), 5 mL of Pen/Strep (Gibco, 1500--063), 2 mL of amphotericin B (R&D Systems, B23192), 5 mL of L-glutamine (Gibco, 25030--024), 10 mL of B-27 supplement (Gibco, 17504--044), and 10 μg of FGF (R&D Systems, 3718-FB or BioLegend, 579602).

extract_protocol:
RNA extraction made with the Maxwell® 16 LEV simple RNA Purification Kit (Promega, AS1280) and the Maxwell® 16 instrument (AS2000).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Rel-pAY15 stable transfectants are treated with 1uM 5phIAA during the entire spheroid formation time.

value: pancreas

value: pancreatic cancer cell line


title: Neurons, DNA, Replicate 3

description:
Library name: Neuron_MPRA3_DNA
label in metadata files is DNA_Neurons_3

value: Neurons


title: Neurons, RNA, Replicate 2

description:
Library name: Neuron_MPRA2_RNA
label in metadata files is RNA_Neurons_2


title: KO-CTD,rep1,Day 7,ATAC

description: Library name: post-ATAC-KO-CTD-1

value: preadipocyte differentiation


title: CGND-HRA-02559

description: Library name: CGND-HRA-02559

value: ALS

value: female


title: Neurons, RNA, Replicate 3

description:
Library name: Neuron_MPRA3_RNA
label in metadata files is RNA_Neurons_3


title: A2929_Rel_pAY15_3D_rep2

description: Library name: Sample10


title: CGND-HRA-02554

description: Library name: CGND-HRA-02554


title: WT_0min_rep1a

value: PCC-M


title: slip4_0min_rep2b


title: CGND-HRA-02564

description: Library name: CGND-HRA-02564


title: Neurons, DNA, Replicate 2

description:
Library name: Neuron_MPRA2_DNA
label in metadata files is DNA_Neurons_2


title: CGND-HRA-02521-2

description: Library name: CGND-HRA-02521-2

value: male


title: CGND-HRA-02569

description: Library name: CGND-HRA-02569


title: A2929_Rel_pAY15_5phIAA_3D_rep1

description: Library name: Sample11


title: slip4_0.5h_rep2


title: DOK_uninfected_control_R2

description:
Library name: DOK*uninfected_2
N2

data_processing:
Novogene pipeline for analysis of human RNA-seq data
Assembly: GRCh38, Ensembl v94
Supplementary files format and content: fpkm normalized gene counts for each sample

source_name: dysplastic oral keratinocytes (DOK)

extract_protocol:
Total RNA was extracted using the PureLink™ RNA Mini Kit (Thermo Fisher Scientific, USA)
Novogene pipeline for  library preparation from human RNA

value: dysplastic oral keratinocytes (DOK)

tag: sample group


title: DOK_uninfected_control_R3

description:
Library name: DOK*uninfected_3
N3


title: slip4_0min_rep2a


title: DOK_uninfected_control_R1

description:
Library name: DOK*uninfected_1
N1


title: slip4_0min_rep1a


title: CGND-HRA-02516-2

description: Library name: CGND-HRA-02516-2


title: DOK infected, Healthy_derived C55Bd

description:
Library name: DOK*C55Bd
C55

value: DOK infected, Healthy_derived


title: WT_0min_rep2a

value: wild type


title: DOK infected, Healthy_derived C75Bd

description:
Library name: DOK*C75Bd
C75


title: DOK infected, Healthy_derived C65Bd

description:
Library name: DOK*C65Bd
C65


title: A2929_pAY15_3D_rep2

description: Library name: Sample8


title: CGND-HRA-02509

description: Library name: CGND-HRA-02509


title: DOK infected, Healthy_derived C44Ad

description:
Library name: DOK*C44Ad
C44


title: A2929_pAY15_3D_rep1

description: Library name: Sample7


title: CGND-HRA-02518

description: Library name: CGND-HRA-02518


title: DOK infected, Healthy_derived C47A

description:
Library name: DOK*C47A
C47


title: DOK infected, Healthy_derived C48Bd

description:
Library name: DOK*C48Bd
C48


title: CGND-HRA-02502

description: Library name: CGND-HRA-02502

value: CTL


title: DOK infected, Mild dysplasia_derived 60A2

description:
Library name: DOK*60A2
A60

value: DOK infected, Mild dysplasia_derived


title: A2770_Rel_pAY15_5phIAA_3D_rep1

description: Library name: Sample5


title: A2929_Rel_pAY15_3D_rep1

description: Library name: Sample9


title: A2770_Rel_pAY15_5phIAA_3D_rep2

description: Library name: Sample6


title: DOK infected, Severe dysplasia_derived 43A3

description:
Library name: DOK*43A3
A43

value: DOK infected, Severe dysplasia_derived


title: DOK infected, Severe dysplasia_derived 41A

description:
Library name: DOK*41A_
A41


title: A2770_Rel_pAY15_3D_rep2

description: Library name: Sample4


title: DOK infected, Moderate dysplasia_derived 40A2

description:
Library name: DOK*40A2
A40


title: A2770_pAY15_3D_rep2

description: Library name: Sample2


title: CGND-HRA-02500

description: Library name: CGND-HRA-02500

value: Cerebellum


title: DOK infected, OSCC_derived 190Ad

description:
Library name: DOK*190Ad
A190

value: DOK infected, OSCC_derived


title: DOK infected, Mild dysplasia_derived 199A2d

description:
Library name: DOK*199A2d
A199


title: DOK infected, Severe dysplasia_derived 141A

description:
Library name: DOK*141A
A141


title: DOK infected, Moderate dysplasia_derived 185A1d

description:
Library name: DOK*185A1d
A185


title: DOK infected, Moderate dysplasia_derived 161A

description:
Library name: DOK*161A
A161


title: A2770_pAY15_3D_rep1

description: Library name: Sample1


title: CGND-HRA-02495

description: Library name: CGND-HRA-02495


title: A2770_Rel_pAY15_3D_rep1

description: Library name: Sample3


title: CD8+ CAR-T cell, TM28, Donor 24

city: Barcelona

first: David

middle: F.

last: Moreno

state: Barcelona

address: Villarroel 170

department: Hematology

country: Spain

institute: IDIBAPS - Hospital Clínic de Barcelona

description: Library name: D24_TM28

data_processing:
FastQC (v. 0.11.9) was used to analyze quality control of paired-end reads.
Kallisto (v. 0.46.1) was used to map reads to human genome (GRCh38).
DESeq2 (v. 1.44.0) was used for differential expression analyses.
Assembly: GRCh38
Supplementary files format and content: Raw read counts for each sample and gene are included in a tab-delimited text file.

source_name: Peripheral blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats obtained from healthy donors through the Blood and Tissue Bank of Barcelona (Banc de Sang i Teixits) using Ficoll density gradient centrifugation. T cells were purified from PBMCs by magnetic-activated cell sorting (MACS) using the Pan T-cell Isolation Kit (Miltenyi Biotec) in accordance with the manufacturer's protocol. For activation, the isolated T cells were cultured with CD3/CD28 Dynabeads (Life Technologies). Lentiviral transduction of T cells was performed 48 hours after activation. At day 7 after activation, Dynabeads were removed, and T cells were expanded in complete T-cell medium comprising RPMI and Click's medium (50%/50%), supplemented with 5% AB human serum (Sigma, H4522), penicillin-streptomycin (100 µg/mL), and 100 IU of IL-2 added every 2-3 days. CAR expression on T cells was analyzed via flow cytometry following 8-10 days of expansion.

extract_protocol:
Post-rechallenge, CD8+ CAR-T cells were isolated using a magnetic bead-based CD8 Positive Selection Kit (EasySep). RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries for RNA-seq were prepared according to Illumina instructions.

treatment_protocol: CAR-T cells were co-cultured with ARP-1 GFP+ target cells at a 1:2 E:T for 48 hours, after which the remaining CAR-T cells were rechallenged with fresh target cells under identical conditions. This process was repeated for up to four rounds.

value: Peripheral blood

value: CD8+ T cells

value: CD28 domain

value: ARP-1 stimulated

value: September 11th 2024


title: DOK infected, Mild dysplasia_derived 139A

description:
Library name: DOK*139A
A139


title: CGND-HRA-02493-2

description: Library name: CGND-HRA-02493-2

value: ALS


title: CGND-HRA-02507-2

description: Library name: CGND-HRA-02507-2

value: female


title: CD8+ CAR-T cell, ARI2, Donor 24

description: Library name: D24_ARI2

value: CD8 alpha domain


title: CGND-HRA-02486

description: Library name: CGND-HRA-02486

value: male


title: CD8+ CAR-T cell, ARI2, Donor 22

description: Library name: D22_ARI2


title: CD8+ CAR-T cell, TM28, Donor 22

description: Library name: D22_TM28


title: CGND-HRA-02474

description: Library name: CGND-HRA-02474


title: CD8+ CAR-T cell, TM28, Donor 23

description: Library name: D23_TM28


title: CD8+ CAR-T cell, TM28, Donor 07

description: Library name: D07_TM28


title: A2929_Rel_pAY15_ c-Rel C&R

description: Library name: Sample1

data_processing:
Data were quality checked using FASTQC.
Reads were aligned to mm39 genome assembly using Bowtie2 software (settings: --local --very-sensitive).
PCR duplicates and blacklisted regions were removed using Picard and Bedtools, respectively.
Peak calling was performed using MACS2 (settings: -f BAMPE --call-summits --keep-dup all).
BigWig files were generated using deeptools (settings: --binSize 1 --normalizeUsing RPGC).
Assembly: mm39
Supplementary files format and content: BigWig file
Library strategy: CUT&Run

growth_protocol: The cells were routinely cultured under standard 5% CO2, 37C conditions,The cell culture medium consisted of Dulbecco's modified Eagle medium (DMEM)+ GlutaMAX (#10566016; Gibco) supplemented with 10% FBS (#10082147; Gibco), NEAA (#11140050; Gibco) and 1% PenStrep (#1500--063; Gibco).

extract_protocol:
The cells were treated with 1.5 μL of pA/G-MNase (#40366, Cell Signaling) and incubated on ice for 1 h. The samples were subsequently washed and resuspended in 50 μL of calcium buffer for targeted digestion. 1 μL of 0.1X Epicypher E. coli spike in DNA (#40366, Cell Signaling) was added. The final mixture subsequently purified according to the manufacturer's protocol (MinElute, Qiagen). Finally, 11 μL of each sample was eluted for analysis for sample quality and sequencing by Novogene.
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

treatment_protocol: the cells were treated for 30 minutes with leptomycin-B (20 ng/mL, L2913, Sigma) in full medium. Before subsequent steps, c-Rel nuclear localization was assessed via visual GFP inspection.

value: pancreas

value: pancreatic cancer cell line

value: AF2699 R&D anti-cRel


title: CGND-HRA-02488

description: Library name: CGND-HRA-02488


title: CD8+ CAR-T cell, ARI2, Donor 23

description: Library name: D23_ARI2


title: CGND-HRA-02471

description: Library name: CGND-HRA-02471


title: ESRRB_KO_E6.5_EXE_H3K27ac_2

city: Boston

first: Yi

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

description: Library name: ESRRB_KO_E65_EXE_H3K27ac_2

data_processing:
RNA-seq data analysis: The raw paired-end sequencing reads of RNA-seq were first processed with the Trimmomatic (v0.39) to remove sequencing adaptors if present. After adaptor trimming, reads with length less than 35 bp were discarded. The trimmed reads were mapped to GRCm38 mouse reference genome using STAR (v2.7.8a). The gene annotations were downloaded from GENCODE (https://www.gencodegenes.org) with version vM24.  The read counts mapped to each gene were calculated using RSEM (v1.3.1) with the transcriptome alignments generated by STAR as input. To calculate differentially expressed genes (DEGs) between conditions, R package DESeq2 (v1.46.0) was employed. Genes with adjusted p-value < 0.05, fold change ≥ 2 and mean FPKM ≥ 1 were identified as DEGs. The Gene Ontology (GO) enrichment of DEGs was calculated with R package clusterProfiler (v4.14.3).  CUT&RUN data analysis: The raw paired-end reads of CUT&RUN were trimmed with Trimmomatic (v0.39) to remove sequencing adaptors and the trimmed reads with length at least 35 bp were kept. The cleaned reads were mapped to GRCm38 mouse reference genome using bowtie2 (v2.4.2) with parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 --soft-clipped-unmapped-tlen. Picard MarkDuplicates (v2.23.4) were used to remove PCR duplicates. The aligned reads were further filtered to retain proper paired reads with a minimum mapping quality of 30. For histone modifications CUT&RUN data, the FPKM (fragments per kilobase region per million mapped fragments) signal tracks were generated with bamCoverage in deeptools (v3.5.1) with 100 bp bin size. For TF CUT&RUN data, the CPM (counts per million) signal tracks were generated with bamCoverage in deeptools (v3.5.1) with 1 bp bin size. To call peaks for H3K4me3 ChIP-seq data and ESRRB CUT&RUN data, the MACS2 (v2.2.7.1) was used. The reproducible peaks between two replicates were calculated with the irreproducible discovery rate (IDR) framework, with the IDR cutoff of 0.05. For ESRRB binding peaks, we further filtered them with q-value cutoff of 10−30 to remove weak binding peaks. The heatmaps of CUT&RUN signals around TSS or peak center were calculated with computeMatrix in deeptools (v3.5.1) with bin sizes of 10, and plotted with R packages profileplyr (v1.22.0) and EnrichedHeatmap (v1.36.0). The promoter (±1 kb around TSS) average levels of H3K27me3 or H3K4me3 were calculated with multiBigwigSummary in deeptools (v3.5.1). For genes with multiple TSSs, the highest value among all the TSSs was used as the signal level of that gene.  ATAC-seq data analysis: The signal tracks of ATAC–seq were calculated with the ENCODE ATAC–seq pipeline using default parameters (v2.1.2, https://github.com/ENCODE-DCC/atac-seq-pipeline), and the fold change signal tracks were used.
Assembly: mm10
Supplementary files format and content: bigwig files contain CUT&RUN signals and ATAC-seq fold changes; txt files contain gene-level reads counts of RNA-seq
Library strategy: CUT&Run

source_name: E6.5 EXE

growth_protocol: All experiments were conducted in accordance with the National Institute of Health Guide for Care and Use of Laboratory Animals and approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital and Harvard Medical School (protocol number IS00000270-9). Mice were housed in specific pathogen-free facilities with regulated temperature (20-22°C) and humidity (40-70%), and maintained on a 12-hour light/dark cycle. To generate knock-in mice, the mixture of Eed donor DNA (30 ng/μl), sgRNA (40 ng/μl) and Cas9 mRNA (100 ng/μl) were injected into early 2-cell stage embryos with a Piezo-driven micromanipulator (Primer Tech, Ibaraki, Japan). Following injection, embryos were cultured in KSOM medium for 6 hours, and then transferred into the oviducts of pseudo-pregnant ICR females (Charles River) (**). The F0 chimeras were backcrossed to C57BL/6J wild-type mice for a minimum of two generations to achieve stable genetic inheritance.

extract_protocol:
For RNA-seq, intact or isolated embryos were collected and immediate freeze at -80 °C until use. SMART-Seq™ v4 Kit (Clontech, 634890) was used to constructed cDNA libraries.  For CUT&RUN, intact or isolated embryos were mixed with activated Concanavalin A Magnetic Beads (Polysciences, 86057-3) for 10 mins at RT, followed the incubation with primary antibodies overnight at 4°C. After three washes, samples were included with 3 ng/μl pA-MNase (home-made) for 2 hours with rotation at 4 °C. Subsequently, pA-MNase was activated by incubating with 200 μl pre-cooled 0.5 μM CaCl2 for 20 mins at 4 °C, and quench by adding 23 μl 10×stop buffer. To release DNA, samples were first incubated at 37 °C for 15 minutes, followed by addition 2.5 μl 10% SDS and 2.5 μl Proteinase K (20 mg/ml; Thermo Fisher, AM2546), and then incubated at 55 °C for 1 hour. DNA was subsequently purified using phenol-chloroform extraction.  For ATAC-seq, isolated embryos were incubated with Tn5 (Diagenode, C01070012-30) for 15 mins at 37°C. Subsequently, DNA fragments were released by dissecting with Proteinase overnight at 55°C.
Nextera® XT DNA Sample Preparation Kit kit (Illumina, FC-131-1024) was used for the RNA-seq libraries construction. For CUT&RUN, libraries were constructed using NEBNext Ultra II DNA library preparation kit (New England Biolabs, E7645S). ATAC-seq ibraries were constructed with NEBNext High-Fidelity 2×PCR Master Mix (NEB, M0541S).

treatment_protocol: To degrade EED in pre-implantation embryos, EeddTAG/dTAG embryos were cultured in KSOM with 1 μM dTAG13 (Tocris, 6605). To degrade EED in ESCs, EeddTAG/dTAG ESCs were cultured in 2i/LIF medium with 0.5 μM dTAG13. For EED degradation in post-implantation embryos in vitro, EeddTAG/dTAG embryos were maintained in culture medium (75% pregnant rat serum, 2 mM GlutaMAX, 11 mM HEPES and 1x MEM NEAA) containing 2 μM dTAGV-1. For EED degradation in post-implantation embryos in vivo, intraperitoneal (IP) injections were employed. 1 mg dTAGV-1 was initially dissolved in 25 μl DMSO and subsequently diluted with 475 μl 10% castor oil (Sigma, C5135) to prepare the injection solution. Mice (~28 g each) were injected with 1 mg dTAGV-1 every 12 hours to maintain sustained EED degradation.

value: E6.5 EXE

value: Esrrb KO

value: no treatment


title: CGND-HRA-02473

description: Library name: CGND-HRA-02473


title: CGND-HRA-02462

description: Library name: CGND-HRA-02462

value: Cerebellum


title: ESRRB_CUTrun_E7_EXE_2

description: Library name: ESRRB_CUTrun_E7_EXE_2

source_name: E7.0 EXE

value: E7.0 EXE

value: WT


title: WT_E6.5_EXE_H3K27ac_2

description: Library name: WT_E65_EXE_H3K27ac_2


title: CGND-HRA-02468

description: Library name: CGND-HRA-02468


title: CD8+ CAR-T cell, ARI2, Donor 07

description: Library name: D07_ARI2

value: Peripheral blood

value: CD8+ T cells


title: ESRRB_CUTrun_E6.5_EXE_2

description: Library name: ESRRB_CUTrun_E65_EXE_2


title: ESRRB_CUTrun_E7_EXE_1

description: Library name: ESRRB_CUTrun_E7_EXE_1


title: WT_E6.5_EXE_H3K27ac_1

description: Library name: WT_E65_EXE_H3K27ac_1


title: ESRRB_CUTrun_E6.5_EXE_1

description: Library name: ESRRB_CUTrun_E65_EXE_1


title: CGND-HRA-02450

description: Library name: CGND-HRA-02450


title: ESRRB_KO_E6.5_EXE_H3K27ac_1

description: Library name: ESRRB_KO_E65_EXE_H3K27ac_1


title: RNA_EED_dTAG_Esrrb_KO_E6.5_EXE_2

description: Library name: RNA_EED_dTAG_Esrrb_KO_E65_EXE_2

data_processing:
RNA-seq data analysis: The raw paired-end sequencing reads of RNA-seq were first processed with the Trimmomatic (v0.39) to remove sequencing adaptors if present. After adaptor trimming, reads with length less than 35 bp were discarded. The trimmed reads were mapped to GRCm38 mouse reference genome using STAR (v2.7.8a). The gene annotations were downloaded from GENCODE (https://www.gencodegenes.org) with version vM24.  The read counts mapped to each gene were calculated using RSEM (v1.3.1) with the transcriptome alignments generated by STAR as input. To calculate differentially expressed genes (DEGs) between conditions, R package DESeq2 (v1.46.0) was employed. Genes with adjusted p-value < 0.05, fold change ≥ 2 and mean FPKM ≥ 1 were identified as DEGs. The Gene Ontology (GO) enrichment of DEGs was calculated with R package clusterProfiler (v4.14.3).  CUT&RUN data analysis: The raw paired-end reads of CUT&RUN were trimmed with Trimmomatic (v0.39) to remove sequencing adaptors and the trimmed reads with length at least 35 bp were kept. The cleaned reads were mapped to GRCm38 mouse reference genome using bowtie2 (v2.4.2) with parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 --soft-clipped-unmapped-tlen. Picard MarkDuplicates (v2.23.4) were used to remove PCR duplicates. The aligned reads were further filtered to retain proper paired reads with a minimum mapping quality of 30. For histone modifications CUT&RUN data, the FPKM (fragments per kilobase region per million mapped fragments) signal tracks were generated with bamCoverage in deeptools (v3.5.1) with 100 bp bin size. For TF CUT&RUN data, the CPM (counts per million) signal tracks were generated with bamCoverage in deeptools (v3.5.1) with 1 bp bin size. To call peaks for H3K4me3 ChIP-seq data and ESRRB CUT&RUN data, the MACS2 (v2.2.7.1) was used. The reproducible peaks between two replicates were calculated with the irreproducible discovery rate (IDR) framework, with the IDR cutoff of 0.05. For ESRRB binding peaks, we further filtered them with q-value cutoff of 10−30 to remove weak binding peaks. The heatmaps of CUT&RUN signals around TSS or peak center were calculated with computeMatrix in deeptools (v3.5.1) with bin sizes of 10, and plotted with R packages profileplyr (v1.22.0) and EnrichedHeatmap (v1.36.0). The promoter (±1 kb around TSS) average levels of H3K27me3 or H3K4me3 were calculated with multiBigwigSummary in deeptools (v3.5.1). For genes with multiple TSSs, the highest value among all the TSSs was used as the signal level of that gene.  ATAC-seq data analysis: The signal tracks of ATAC–seq were calculated with the ENCODE ATAC–seq pipeline using default parameters (v2.1.2, https://github.com/ENCODE-DCC/atac-seq-pipeline), and the fold change signal tracks were used.
Assembly: mm10
Supplementary files format and content: bigwig files contain CUT&RUN signals and ATAC-seq fold changes; txt files contain gene-level reads counts of RNA-seq

value: EED-dTAG/dTAG Esrrb KO

value: dTAG


title: CGND-HRA-02444

description: Library name: CGND-HRA-02444

data_processing:
Raw sequencing files was demultiplexed with bcl2fastq
Samples were uniformly processed using RAPiD-nf, an efficient RNA-Seq processing pipeline implemented in the NextFlow framework(Di Tommaso et al. 2017). Following adapter trimming with Trimmomatic (version 0.36)(Bolduc, n.d.), all samples were aligned to the hg38 build (GRCh38.primary_assembly) of the human reference genome using STAR (2.7.2a)(Dobin et al. 2013), with indexes created from GENCODE, version 30(Harrow et al. 2012). Gene expression was quantified using RSEM (1.3.1)(B. Li and Dewey 2011). Quality control was performed using SAMtools(H. Li et al. 2009) and Picard, and the results were collated using MultiQC(Ewels et al. 2016).
Assembly: hg38
Supplementary files format and content: csv files contatining count and tpm data

value: ALS


title: RNA_EED_dTAG_Esrrb_KO_E6.5_EXE_1

description: Library name: RNA_EED_dTAG_Esrrb_KO_E65_EXE_1


title: CGND-HRA-02438

description: Library name: CGND-HRA-02438


title: RNA_Esrrb_KO_E6.5_EXE_2

description: Library name: RNA_Esrrb_KO_E65_EXE_2


title: CGND-HRA-02434

description: Library name: CGND-HRA-02434


title: RNA_Esrrb_WT_E6.5_EXE_2

description: Library name: RNA_Esrrb_WT_E65_EXE_2


title: RNA_Esrrb_WT_E6.5_EXE_1

description: Library name: RNA_Esrrb_WT_E65_EXE_1


title: CGND-HRA-02432

description: Library name: CGND-HRA-02432


title: E6.5_VE_H3K27me3_2

description: Library name: E65_VE_H3K27me3_2

source_name: E6.5 VE

value: E6.5 VE


title: CGND-HRA-02412

description: Library name: CGND-HRA-02412


title: E6.5_EXE_H3K27me3_2

description: Library name: E65_EXE_H3K27me3_2


title: RNA_Esrrb_KO_E6.5_EXE_1

description: Library name: RNA_Esrrb_KO_E65_EXE_1


title: E6.5_VE_H3K27me3_1

description: Library name: E65_VE_H3K27me3_1


title: E6.5_EXE_H3K27me3_1

description: Library name: E65_EXE_H3K27me3_1


title: CGND-HRA-02411

description: Library name: CGND-HRA-02411


title: E6.5_EPI_H3K27me3_2

description: Library name: E65_EPI_H3K27me3_2

source_name: E6.5 EPI

value: E6.5 EPI


title: CGND-HRA-02407

description: Library name: CGND-HRA-02407

value: male


title: RNA_E6.5_VE_EED_dTAG_2

description: Library name: RNA_E65_VE_EED_dTAG_2

value: EED-dTAG/dTAG


title: CGND-HRA-02405

description: Library name: CGND-HRA-02405


title: RNA_E6.5_VE_EED_dTAG_1

description: Library name: RNA_E65_VE_EED_dTAG_1


title: RNA_E6.5_EXE_EED_dTAG_2

description: Library name: RNA_E65_EXE_EED_dTAG_2


title: RNA_E6.5_EPI_EED_dTAG_2

description: Library name: RNA_E65_EPI_EED_dTAG_2


title: RNA_E6.5_EXE_EED_dTAG_1

description: Library name: RNA_E65_EXE_EED_dTAG_1


title: CGND-HRA-02404

description: Library name: CGND-HRA-02404


title: CGND-HRA-02394

description: Library name: CGND-HRA-02394

value: Hippocampus

value: CTL


title: RNA_E6.5_EPI_EED_dTAG_1

description: Library name: RNA_E65_EPI_EED_dTAG_1


title: RNA_E6.5_EXE_EED_DMSO_2

description: Library name: RNA_E65_EXE_EED_DMSO_2

value: E6.5 EXE

value: DMSO


title: RNA_E6.5_VE_EED_DMSO_2

description: Library name: RNA_E65_VE_EED_DMSO_2


title: CGND-HRA-02373

description: Library name: CGND-HRA-02373


title: RNA_E6.5_VE_EED_DMSO_1

description: Library name: RNA_E65_VE_EED_DMSO_1


title: CGND-HRA-02359

description: Library name: CGND-HRA-02359


title: RNA_E6.5_EXE_EED_DMSO_1

description: Library name: RNA_E65_EXE_EED_DMSO_1


title: RNA_E6.5_EPI_EED_DMSO_2

description: Library name: RNA_E65_EPI_EED_DMSO_2


title: RNA_E6.5_EPI_EED_DMSO_1

description: Library name: RNA_E65_EPI_EED_DMSO_1


title: E6.5_EPI_H3K27me3_1

description: Library name: E65_EPI_H3K27me3_1

value: no treatment


title: ATAC_E4.5_ICM_EED_dTAG_2

description: Library name: ATAC_E45_ICM_EED_dTAG_2

source_name: E4.5 ICM

value: E4.5 ICM


title: ATAC_E4.5_ICM_EED_dTAG_1

description: Library name: ATAC_E45_ICM_EED_dTAG_1


title: CGND-HRA-02317

description: Library name: CGND-HRA-02317

value: female


title: ATAC_E4.5_ICM_EED_DMSO_2

description: Library name: ATAC_E45_ICM_EED_DMSO_2


title: ATAC_E4.5_ICM_EED_DMSO_1

description: Library name: ATAC_E45_ICM_EED_DMSO_1


title: Older women with normal weight_26

type: genomic

city: Ribeirão Preto

first: Ana

middle: Claudia

last: Rossini Venturini

state: São Paulo

address: Av. Bandeirantes, 3900 - Vila Monte Alegre, Ribeirão Preto - SP,

department: EEFERP

country: Brazil

institute: USP

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation Beadchip EPIC using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Champ package for Rstudio was used to process data.

label: biotin

source_name: peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: Peripheral blood samples were collected in EDTA tubes. DNA extraction was performed using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following the manufacturer's instructions. Genomic DNA was quantified (NanoDrop ND1000, Thermo Scientific) and its integrity was assessed by agarose gel electrophoresis. A total of 500 ng of DNA per sample was subjected to bisulfite conversion using the EZ-96 DNA Methylation Kit (Zymo Research Corp., CA, USA), according to the manufacturer’s instructions for Infinium assays. Samples were amplified and hybridized to Illumina HumanMethylation850k v2.0 BeadChips (Illumina, Inc., San Diego, CA, and USA). This array covers both genic and intergenic regions (Pidsley, Zotenko et al. 2016), and all target sites are documented by the manufacturer.

tag: altura

tag: Sex

value: Female

tag: disease state

value: Normal weight

tag: peso(kg)

value: peripheral blood

value: Older women with normal weight


title: CGND-HRA-02354

description: Library name: CGND-HRA-02354


title: EED_dTAG_E4.5_ICM_H3K4me3_2

description: Library name: EED_dTAG_E45_ICM_H3K4me3_2

value: dTAG


title: EED_dTAG_E4.5_ICM_H3K4me3_1

description: Library name: EED_dTAG_E45_ICM_H3K4me3_1


title: CGND-HRA-02312

description: Library name: CGND-HRA-02312

value: ALS


title: CGND-HRA-02316

description: Library name: CGND-HRA-02316


title: EED_DMSO_E4.5_ICM_H3K4me3_2

description: Library name: EED_DMSO_E45_ICM_H3K4me3_2


title: EED_DMSO_E4.5_ICM_H3K4me3_1

description: Library name: EED_DMSO_E45_ICM_H3K4me3_1


title: EED_dTAG_E4.5_ICM_H2Aub_2

description: Library name: EED_dTAG_E45_ICM_H2Aub_2


title: EED_dTAG_E4.5_ICM_H2Aub_1

description: Library name: EED_dTAG_E45_ICM_H2Aub_1


title: CGND-HRA-02311

description: Library name: CGND-HRA-02311


title: CGND-HRA-02310

description: Library name: CGND-HRA-02310


title: Older women with sarcopenic obesity_15 OS

value: Sarcopenic obesity

value: Older women with sarcopenic obesity


title: Older women with sarcopenic obesity_13 OS


title: Older women with sarcopenic obesity_41 OS


title: Older women with sarcopenic obesity_21 OS


title: Older women with sarcopenic obesity_2 OS


title: EED_DMSO_E4.5_ICM_H2Aub_1

description: Library name: EED_DMSO_E45_ICM_H2Aub_1


title: E4.5_ICM_H3K27me3_2

description: Library name: E45_ICM_H3K27me3_2

value: WT


title: CGND-HRA-02309

description: Library name: CGND-HRA-02309

value: male


title: Older women with sarcopenia_27

value: Sarcopenia

value: Older women with sarcopenia


title: E4.5_ICM_H3K27me3_1

description: Library name: E45_ICM_H3K27me3_1


title: CGND-HRA-02308

description: Library name: CGND-HRA-02308


title: EED_DMSO_E4.5_ICM_H2Aub_2

description: Library name: EED_DMSO_E45_ICM_H2Aub_2

value: EED-dTAG/dTAG


title: RNA_E4.5_ICM_EED_dTAG_2

description: Library name: RNA_E45_ICM_EED_dTAG_2


title: Older women with sarcopenia_20


title: Older women with sarcopenic obesity_12 OS


title: CGND-HRA-02302

description: Library name: CGND-HRA-02302


title: RNA_E4.5_ICM_EED_DMSO_2

description: Library name: RNA_E45_ICM_EED_DMSO_2

value: DMSO


title: RNA_E4.5_ICM_EED_DMSO_1

description: Library name: RNA_E45_ICM_EED_DMSO_1


title: CGND-HRA-02300

description: Library name: CGND-HRA-02300


title: Older women with sarcopenia_23


title: Older women with sarcopenia_25


title: RNA_Morula_EED_dTAG_2

description: Library name: RNA_Morula_EED_dTAG_2

source_name: morula

value: morula


title: CGND-HRA-02294-2

description: Library name: CGND-HRA-02294-2


title: RNA_Morula_EED_dTAG_1

description: Library name: RNA_Morula_EED_dTAG_1


title: RNA_Morula_EED_DMSO_2

description: Library name: RNA_Morula_EED_DMSO_2


title: CGND-HRA-02290

description: Library name: CGND-HRA-02290


title: RNA_Morula_EED_DMSO_1

description: Library name: RNA_Morula_EED_DMSO_1


title: RNA_L2C_EED_dTAG_2

description: Library name: RNA_L2C_EED_dTAG_2

source_name: late 2-cell

value: late 2-cell


title: Older women with obesity_19

value: Obesity

value: Older women with obesity


title: CGND-HRA-02289

description: Library name: CGND-HRA-02289


title: RNA_L2C_EED_DMSO_2

description: Library name: RNA_L2C_EED_DMSO_2


title: RNA_L2C_EED_dTAG_1

description: Library name: RNA_L2C_EED_dTAG_1


title: Older women with normal weight_21

value: Female

value: Normal weight


title: RNA_E4.5_ICM_EED_dTAG_1

description: Library name: RNA_E45_ICM_EED_dTAG_1

value: E4.5 ICM


title: Older women with sarcopenia_15

value: peripheral blood


title: Older women with sarcopenia_24


title: RNA_E2C_EED_dTAG_2

description: Library name: RNA_E2C_EED_dTAG_2

source_name: early 2-cell

value: early 2-cell

value: dTAG


title: RNA_E2C_EED_dTAG_1

description: Library name: RNA_E2C_EED_dTAG_1


title: CGND-HRA-02276

description: Library name: CGND-HRA-02276

value: ALS


title: RNA_L2C_EED_DMSO_1

description: Library name: RNA_L2C_EED_DMSO_1


title: rCDX2 OE in RMES RNA-seq

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description:
rCDX2 OE in RMES RNA-seq
RMES_mm10_CDX2_rnaseq_featureCounts_4samples.txt
RMES_rn6_CDX2_rnaseq_featureCounts_4samples.txt
RMES_RD

data_processing:
STAR (v2.7.0d) was used to align the RNA-seq reads to mouse genome (mm10) with gene annotation. FeatuerCounts (v1.5.3) was used to count the read number of each gene (with parameters -T 12 -s 2 -p -g gene_name).
Fastp (v0.19.5) was first used to trimmed and removed low quality ATAC-seq reads and adapter sequences (-a CTGTCTCTTATA --detect_adapter_for_pe -w 12 --length_required 20 -q 30). Reads were aligned to mouse reference genome (hg38) using Bowtie2 v2.3.4.3 with parameters (-p 12 -X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom scripts. Sambamba (v0.7.0) was then used to sort the reads and remove duplicates. MACS2 was used to call peaks
paired-end ChIP-seq reads were first trimmed to remove adapter sequences using cutadapt v2.6 (-a AGATCGGAAGAG -A AGATCGGAAGAG -m 20 -q 30). Reads were aligned to mouse reference genome (mm10) using Bowtie2 v2.3.4.3 with parameters (-X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom script. Picard (v2.6.0, http://broadinstitute.github.io/picard/) was then used to sort the reads and remove duplicates.  MACS2 was used to call peaks (-g mm --keep-dup all -q 0.05 -B).
Genome_build: mm10 or rn6
Supplementary_files_format_and_content: txt, read count

organism:
Mus musculus
Rattus norvegicus

source_name: RMES

extract_protocol:
(a) Total RNA were extracted from all the treated cells using TRIzol reagent according to the manufacturer’s protocol (Life Technologies).; (b) For ATAC-seq, samples were washed and then lysed in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501).; (c) The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST, 56383)
(a) Truseq Stranded mRNA sequencing libraries were prepared with 2 μg total RNA according to the manufacturer’s protocol (Yeasen  12300ES24). (b) For ATAC-seq, PCR was then performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411). (c) ChIP-seq libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, ND607)

value: RMES

tag: genotype/variation

value: rCDX2 OE


title: RNA_E2C_EED_DMSO_2

description: Library name: RNA_E2C_EED_DMSO_2

tag: genotype


title: CGND-HRA-02278

description: Library name: CGND-HRA-02278

extract_protocol:
Total RNA extraction from fresh frozen tissue or cells – starting material is homogenized in TRIzol reagent using a series of needles for trituration. The homogenized sample undergoes phase separation with the addition of chloroform,  the upper aqueous phase of the mixture then follows the RNeasy Mini procedure (Qiagen, 74106). A series of washes will purify the final eluted total RNA. The RNeasy Mini portion of the protocol is processed on the QIAcube Connect automated platform (Qiagen, 9002864) for higher throughput.
RNA sequencing libraries are prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche 07962304001) in accordance with the manufacturer’s instructions. Samples are normalized to 500ng and undergo rRNA depletion through oligo hybridization and RNase H treatment. DNase treatment removes DNA oligos. Samples are fragmented to 350bp inserts and undergo cDNA generation. Samples undergo A-tailing and are ligated to Illumina sequencing adapters and amplified. Final libraries are quantified using the Qubit Fluorometer (Life Technologies) or Spectramax M2 (Molecular Devices) and Fragment Analyzer (Agilent). Libraries are sequenced on an Illumina sequencer.

value: male


title: mCDX2 OE in RMES RNA-seq

description:
mCDX2 OE in RMES RNA-seq
RMES_mm10_CDX2_rnaseq_featureCounts_4samples.txt
RMES_rn6_CDX2_rnaseq_featureCounts_4samples.txt
RMES_MD

value: mCDX2 OE


title: Older women with sarcopenia_22

value: Sarcopenia

value: Older women with sarcopenia


title: CGND-HRA-02256

description: Library name: CGND-HRA-02256

source_name: Cerebellum

value: Cerebellum

value: female


title: RNA_E2C_EED_DMSO_1

description: Library name: RNA_E2C_EED_DMSO_1

value: EED-dTAG/dTAG

value: DMSO


title: WT RMES RNA-seq rep2

description:
WT RMES RNA-seq rep2
RMES_mm10_CDX2_rnaseq_featureCounts_4samples.txt
RMES_rn6_CDX2_rnaseq_featureCounts_4samples.txt
RMES_WT2

value: WT


title: Older women with normal weight_16

value: Female

value: Normal weight

value: Older women with normal weight


title: S-1076_J_std_0.3_perc_meoh rep1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description: Library name: d1326.S-1076_J_std_0.3_perc_meoh

data_processing:
Sequencing using v3 chemistry. Software: Control v2.2.1.1645, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Komagataella phaffi transcripts and exogenous transgenes were quantified using salmon 1.6.0
Gene-level summaries created with tximport 1.24.0
Assembly: Komagataella phaffi WT (strain Y11430) with transcriptome phaffi_plus_240125Lov_transgenes
Supplementary files format and content: phaffi_plus_240125Lov_transgenes.fa.gz is fasta format transcriptome used in salmon quantitation
Supplementary files format and content: 240125Lov_transcript2gene.txt.gz is a tab-delimited file that associates transcript and gene identifiers
Supplementary files format and content: 240125Lov_annotation.txt.gz is a tab-delimited annotation file associating gene names with gene IDs.
Supplementary files format and content: 240125Lov_intCt.txt.gz is a tab delimited file of integrer count data
Supplementary files format and content: 240125Lov_l2tpm.txt.gz is a tab-delimited file of log2 TPM data with a +1 offset.

organism: Komagataella phaffii

source_name: K. phaffii S-1076

growth_protocol: Strains were grown in 3 mL cultures in 24-deep well plates (toom temperature, 600 RPM, 3 mm orbit). Cells were cultivated in complex media (potassium phosphate buffer pH 6.5, 1.34% nitrogen base w/o amino acids, 1% yeast extract, 2% peptone). Cultures were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and cells resuspended in fresh media with the described quantity of methanol and corresponding co-feed. Supernatant samples were collected after 18 hrs and 24 hrs of production for the co-feed screen and the knockout screen respectively, and analyzed.

extract_protocol:
Qiagen RNeasy 96 kit
Nextera XT DNA Library Preparation Kit with the Illumina DNA/RNA UD Indexes

tag: carbon cofeed

value: Xylose

tag: cofeed concentration_(m)

tag: meoh concentration_(v/v_%)


title: S-1076_J_std_0.3_perc_meoh rep2

description: Library name: d1327.S-1076_J_std_0.3_perc_meoh


title: CGND-HRA-02244

description: Library name: CGND-HRA-02244

tag: tissue


title: CGND-HRA-02250

description: Library name: CGND-HRA-02250

tag: subject id

value: Unknown


title: Older women with obesity_11

value: Obesity

value: peripheral blood

value: Older women with obesity


title: rCDX2 OE in RMES ChIP-seq

description:
rCDX2 OE in RMES ChIP-seq
merge_FSC_MFO_RFO_cdx2_mm10.flt5.SAF.featureCounts.txt
merge_FSC_MFO_RFO_cdx2_rn6.flt5.SAF.featureCounts.txt

value: RMES

value: rCDX2 OE


title: Older women with obesity_14


title: Older women with normal weight_13


title: S-1076_H_0.1_0.3_perc_meoh rep1

description: Library name: d1323.S-1076_H_0.1_0.3_perc_meoh

value: Sorbitol


title: Older women with sarcopenia_18

value: Sarcopenia

value: Older women with sarcopenia


title: S-1076_H_0.1_0.3_perc_meoh rep2

description: Library name: d1324.S-1076_H_0.1_0.3_perc_meoh


title: CGND-HRA-02242

description: Library name: CGND-HRA-02242

value: ALS

tag: gender

value: male


title: S-1076_H_0.5_0.3_perc_meoh rep3

description: Library name: d1322.S-1076_H_0.5_0.3_perc_meoh


title: Older women with normal weight_17

tag: age


title: S-1076_J_std_0.3_perc_meoh rep3

description: Library name: d1328.S-1076_J_std_0.3_perc_meoh

tag: strain


title: Older women with obesity_7


title: Older women with obesity_9


title: mCDX2 OE in RMES ChIP-seq

description:
mCDX2 OE in RMES ChIP-seq
merge_FSC_MFO_RFO_cdx2_mm10.flt5.SAF.featureCounts.txt
merge_FSC_MFO_RFO_cdx2_rn6.flt5.SAF.featureCounts.txt

value: mCDX2 OE


title: S-1076_H_0.5_0.3_perc_meoh rep2

description: Library name: d1321.S-1076_H_0.5_0.3_perc_meoh


title: CGND-HRA-02238

description: Library name: CGND-HRA-02238

value: Cerebellum


title: sepsis patient 30

city: Beijing

first: Haiyan

last: Xue

address: 11th Xizhimen South Street

institute: Peking University People's Hospital

description: Library name: Sep30

data_processing:
The data generated from BGI platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology.
Assembly: Homo_sapiens_Ensembl_104
Supplementary files format and content: csv files include FPKM values for each sample

source_name: whole blood cells

extract_protocol:
Total RNA was extracted from the whole blood cell using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina MGISEQ-T7 instrument.

value: whole blood cells


title: Older women with normal weight_12

value: Female

value: Normal weight


title: S-1076_H_std_0.3_perc_meoh rep3

description: Library name: d1319.S-1076_H_std_0.3_perc_meoh


title: CGND-HRA-02232

first: Hemali

institute: New York Genome Center

description: Library name: CGND-HRA-02232


title: S-1076_H_0.5_0.3_perc_meoh rep1

description: Library name: d1320.S-1076_H_0.5_0.3_perc_meoh


title: S-1076_H_std_0.3_perc_meoh rep2

description: Library name: d1318.S-1076_H_std_0.3_perc_meoh


title: sepsis patient 29

description: Library name: Sep29


title: S-1076_H_std_0.3_perc_meoh rep1

description: Library name: d1317.S-1076_H_std_0.3_perc_meoh


title: CGND-HRA-02228

description: Library name: CGND-HRA-02228


title: S-1076_G_0.1_0.3_perc_meoh rep3

description: Library name: d1316.S-1076_G_0.1_0.3_perc_meoh

value: D-Arabinose


title: CGND-HRA-02226-2

description: Library name: CGND-HRA-02226-2


title: S-1076_G_0.1_0.3_perc_meoh rep1

description: Library name: d1314.S-1076_G_0.1_0.3_perc_meoh


title: WT RMES RNA-seq rep1

description:
WT RMES RNA-seq rep1
RMES_mm10_CDX2_rnaseq_featureCounts_4samples.txt
RMES_rn6_CDX2_rnaseq_featureCounts_4samples.txt
RMES_WT1

value: WT


title: Older women with normal weight_3

value: Older women with normal weight


title: S-1076_G_0.1_0.3_perc_meoh rep2

description: Library name: d1315.S-1076_G_0.1_0.3_perc_meoh


title: S-1076_H_0.1_0.3_perc_meoh rep3

description: Library name: d1325.S-1076_H_0.1_0.3_perc_meoh


title: sepsis patient 28

description: Library name: Sep28


title: CGND-HRA-02175

description: Library name: CGND-HRA-02175

value: female


title: sepsis patient 27

description: Library name: Sep27


title: S-1076_G_0.5_0.3_perc_meoh rep2

description: Library name: d1312.S-1076_G_0.5_0.3_perc_meoh


title: sepsis patient 26

description: Library name: Sep26


title: S-1076_G_0.5_0.3_perc_meoh rep3

description: Library name: d1313.S-1076_G_0.5_0.3_perc_meoh


title: Older women with sarcopenic obesity_8

value: Sarcopenic obesity

value: peripheral blood

value: Older women with sarcopenic obesity


title: S-1076_G_0.5_0.3_perc_meoh rep1

description: Library name: d1311.S-1076_G_0.5_0.3_perc_meoh


title: CGND-HRA-02149

description: Library name: CGND-HRA-02149


title: S-1076_G_std_0.3_perc_meoh rep3

description: Library name: d1310.S-1076_G_std_0.3_perc_meoh


title: sepsis patient 25

description: Library name: Sep25


title: S-1076_G_std_0.3_perc_meoh rep2

description: Library name: d1309.S-1076_G_std_0.3_perc_meoh


title: S-1076_F_0.1_0.3_perc_meoh rep3

description: Library name: d1307.S-1076_F_0.1_0.3_perc_meoh

value: Rhamnose


title: sepsis patient 24

description: Library name: Sep24


title: CGND-HRA-01975

description: Library name: CGND-HRA-01975

value: CTL


title: CGND-HRA-01634

description: Library name: CGND-HRA-01634


title: CGND-HRA-01591-2

description: Library name: CGND-HRA-01591-2


title: sepsis patient 23

description: Library name: Sep23


title: S-1076_F_0.1_0.3_perc_meoh rep2

description: Library name: d1306.S-1076_F_0.1_0.3_perc_meoh


title: S-1076_F_0.5_0.3_perc_meoh rep3

description: Library name: d1304.S-1076_F_0.5_0.3_perc_meoh


title: CGND-HRA-01510-2

description: Library name: CGND-HRA-01510-2


title: S-1076_F_0.5_0.3_perc_meoh rep2

description: Library name: d1303.S-1076_F_0.5_0.3_perc_meoh


title: S-1076_G_std_0.3_perc_meoh rep1

description: Library name: d1308.S-1076_G_std_0.3_perc_meoh


title: S-1076_F_0.5_0.3_perc_meoh rep1

description: Library name: d1302.S-1076_F_0.5_0.3_perc_meoh


title: sepsis patient 22

description: Library name: Sep22


title: sepsis patient 21

description: Library name: Sep21


title: Older women with obesity_1

value: Obesity

value: Older women with obesity


title: CGND-HRA-01504

description: Library name: CGND-HRA-01504

value: ALS


title: Older women with sarcopenic obesity_2


title: S-1076_F_0.1_0.3_perc_meoh rep1

description: Library name: d1305.S-1076_F_0.1_0.3_perc_meoh


title: sepsis patient 20

description: Library name: Sep20


title: Older women with normal weight_6


title: Older women with obesity_4


title: S-1076_E_0.1_0.3_perc_meoh rep2

description: Library name: d1297.S-1076_E_0.1_0.3_perc_meoh

value: Sucrose


title: sepsis patient 19

description: Library name: Sep19


title: S-1076_E_0.1_0.3_perc_meoh rep3

description: Library name: d1298.S-1076_E_0.1_0.3_perc_meoh


title: CGND-HRA-01492-2

description: Library name: CGND-HRA-01492-2

value: Cerebellum


title: CGND-HRA-00639-2

description: Library name: CGND-HRA-00639-2

value: male


title: S-1076_E_0.5_0.3_perc_meoh rep3

description: Library name: d1295.S-1076_E_0.5_0.3_perc_meoh


title: Older women with obesity_5

value: Female


title: S-1076_E_0.1_0.3_perc_meoh rep1

description: Library name: d1296.S-1076_E_0.1_0.3_perc_meoh


title: CGND-HRA-00522

description: Library name: CGND-HRA-00522


title: S-1076_F_std_0.3_perc_meoh rep2

description: Library name: d1300.S-1076_F_std_0.3_perc_meoh


title: sepsis patient 17

description: Library name: Sep17

value: whole blood cells


title: sepsis patient 18

description: Library name: Sep18


title: S-1076_E_0.5_0.3_perc_meoh rep1

description: Library name: d1293.S-1076_E_0.5_0.3_perc_meoh


title: S-1076_E_std_0.3_perc_meoh rep1

description: Library name: d1290.S-1076_E_std_0.3_perc_meoh


title: sepsis patient 16

description: Library name: Sep16


title: sepsis patient 15

description: Library name: Sep15


title: S-1076_E_std_0.3_perc_meoh rep2

description: Library name: d1291.S-1076_E_std_0.3_perc_meoh


title: CGND-HRA-00521

description: Library name: CGND-HRA-00521


title: S-1076_F_std_0.3_perc_meoh rep1

description: Library name: d1299.S-1076_F_std_0.3_perc_meoh


title: S-1076_F_std_0.3_perc_meoh rep3

description: Library name: d1301.S-1076_F_std_0.3_perc_meoh


title: CGND-HRA-00515

description: Library name: CGND-HRA-00515


title: S-1076_E_std_0.3_perc_meoh rep3

description: Library name: d1292.S-1076_E_std_0.3_perc_meoh


title: S-1076_D_std_0.3_perc_meoh rep2

description: Library name: d1288.S-1076_D_std_0.3_perc_meoh

value: NoCofeed


title: CGND-HRA-00520

description: Library name: CGND-HRA-00520


title: S-1076_D_std_0.3_perc_meoh rep3

description: Library name: d1289.S-1076_D_std_0.3_perc_meoh


title: S-1076_D_std_0.3_perc_meoh rep1

description: Library name: d1287.S-1076_D_std_0.3_perc_meoh


title: sepsis patient 14

description: Library name: Sep14


title: sepsis patient 13

description: Library name: Sep13


title: S-1076_C_0.1_0.3_perc_meoh rep3

description: Library name: d1286.S-1076_C_0.1_0.3_perc_meoh

value: Citrate


title: CGND-HRA-00513

description: Library name: CGND-HRA-00513


title: S-1076_C_0.1_0.3_perc_meoh rep1

description: Library name: d1284.S-1076_C_0.1_0.3_perc_meoh


title: S-1076_C_0.1_0.3_perc_meoh rep2

description: Library name: d1285.S-1076_C_0.1_0.3_perc_meoh


title: CGND-HRA-00514

description: Library name: CGND-HRA-00514


title: sepsis patient 12

description: Library name: Sep12


title: S-1076_C_0.5_0.3_perc_meoh rep2

description: Library name: d1282.S-1076_C_0.5_0.3_perc_meoh


title: S-1076_E_0.5_0.3_perc_meoh rep2

description: Library name: d1294.S-1076_E_0.5_0.3_perc_meoh


title: CGND-HRA-00512

description: Library name: CGND-HRA-00512


title: S-1076_C_0.5_0.3_perc_meoh rep1

description: Library name: d1281.S-1076_C_0.5_0.3_perc_meoh


title: S-1076_C_0.5_0.3_perc_meoh rep3

description: Library name: d1283.S-1076_C_0.5_0.3_perc_meoh


title: CGND-HRA-00511

description: Library name: CGND-HRA-00511


title: CGND-HRA-00510

description: Library name: CGND-HRA-00510


title: sepsis patient 11

description: Library name: Sep11


title: S-1076_C_std_0.3_perc_meoh rep2

description: Library name: d1279.S-1076_C_std_0.3_perc_meoh


title: S-1076_C_std_0.3_perc_meoh rep3

description: Library name: d1280.S-1076_C_std_0.3_perc_meoh


title: S-1076_B_0.1_0.3_perc_meoh rep2

description: Library name: d1276.S-1076_B_0.1_0.3_perc_meoh

value: Galactose


title: sepsis patient 8

description: Library name: Sep8


title: S-1076_B_0.1_0.3_perc_meoh rep1

description: Library name: d1275.S-1076_B_0.1_0.3_perc_meoh


title: sepsis patient 10

description: Library name: Sep10


title: S-1076_C_std_0.3_perc_meoh rep1

description: Library name: d1278.S-1076_C_std_0.3_perc_meoh


title: sepsis patient 7

description: Library name: Sep7


title: sepsis patient 9

description: Library name: Sep9


title: S-1076_B_0.1_0.3_perc_meoh rep3

description: Library name: d1277.S-1076_B_0.1_0.3_perc_meoh


title: S-1076_B_0.5_0.3_perc_meoh rep3

description: Library name: d1274.S-1076_B_0.5_0.3_perc_meoh


title: CGND-HRA-00506

description: Library name: CGND-HRA-00506


title: S-1076_B_0.5_0.3_perc_meoh rep2

description: Library name: d1273.S-1076_B_0.5_0.3_perc_meoh


title: S-1076_B_0.5_0.3_perc_meoh rep1

description: Library name: d1272.S-1076_B_0.5_0.3_perc_meoh


title: CGND-HRA-00509

description: Library name: CGND-HRA-00509

value: female


title: sepsis patient 6

description: Library name: Sep6


title: CGND-HRA-00505

description: Library name: CGND-HRA-00505


title: sepsis patient 5

description: Library name: Sep5


title: S-1076_B_std_0.3_perc_meoh rep3

description: Library name: d1271.S-1076_B_std_0.3_perc_meoh


title: S-1076_B_std_0.3_perc_meoh rep2

description: Library name: d1270.S-1076_B_std_0.3_perc_meoh


title: S-1076_J_0.1_0.7_perc_meoh rep3

description: Library name: d1268.S-1076_J_0.1_0.7_perc_meoh

value: Xylose


title: S-1076_J_0.1_0.7_perc_meoh rep2

description: Library name: d1267.S-1076_J_0.1_0.7_perc_meoh


title: S-1076_B_std_0.3_perc_meoh rep1

description: Library name: d1269.S-1076_B_std_0.3_perc_meoh


title: S-1076_J_0.1_0.7_perc_meoh rep1

description: Library name: d1266.S-1076_J_0.1_0.7_perc_meoh


title: S-1076_J_0.5_0.7_perc_meoh rep2

description: Library name: d1264.S-1076_J_0.5_0.7_perc_meoh


title: S-1076_J_0.5_0.7_perc_meoh rep1

description: Library name: d1263.S-1076_J_0.5_0.7_perc_meoh


title: CGND-HRA-00503

description: Library name: CGND-HRA-00503


title: CGND-HRA-00507

description: Library name: CGND-HRA-00507


title: sepsis patient 4

description: Library name: Sep4


title: S-1076_J_std_0.7_perc_meoh rep3

description: Library name: d1262.S-1076_J_std_0.7_perc_meoh


title: sepsis patient 1

description: Library name: Sep1


title: CGND-HRA-00495

description: Library name: CGND-HRA-00495


title: CGND-HRA-00504

description: Library name: CGND-HRA-00504


title: CGND-HRA-00500

description: Library name: CGND-HRA-00500


title: S-1076_J_std_0.7_perc_meoh rep2

description: Library name: d1261.S-1076_J_std_0.7_perc_meoh


title: sepsis patient 3

description: Library name: Sep3


title: CGND-HRA-00494

description: Library name: CGND-HRA-00494


title: S-1076_J_0.5_0.7_perc_meoh rep3

description: Library name: d1265.S-1076_J_0.5_0.7_perc_meoh


title: S-1076_H_0.1_0.7_perc_meoh rep2

description: Library name: d1258.S-1076_H_0.1_0.7_perc_meoh

value: Sorbitol


title: healthy control 9

description: Library name: ctrl9


title: S-1076_H_0.1_0.7_perc_meoh rep1

description: Library name: d1257.S-1076_H_0.1_0.7_perc_meoh


title: CGND-HRA-00117-2

description: Library name: CGND-HRA-00117-2


title: healthy control 10

description: Library name: ctrl10


title: S-1076_H_0.1_0.7_perc_meoh rep3

description: Library name: d1259.S-1076_H_0.1_0.7_perc_meoh


title: S-1076_H_0.5_0.7_perc_meoh rep3

description: Library name: d1256.S-1076_H_0.5_0.7_perc_meoh


title: sepsis patient 2

description: Library name: Sep2


title: S-1076_H_0.5_0.7_perc_meoh rep1

description: Library name: d1254.S-1076_H_0.5_0.7_perc_meoh


title: S-1076_H_0.5_0.7_perc_meoh rep2

description: Library name: d1255.S-1076_H_0.5_0.7_perc_meoh


title: S-1076_H_std_0.7_perc_meoh rep3

description: Library name: d1253.S-1076_H_std_0.7_perc_meoh


title: ABS-CSF-C09

description: Library name: ABS-CSF-C09

value: Not Applicable


title: S-1076_H_std_0.7_perc_meoh rep1

description: Library name: d1251.S-1076_H_std_0.7_perc_meoh


title: CGND-HRA-00498

description: Library name: CGND-HRA-00498


title: healthy control 7

description: Library name: ctrl7


title: NEUZW597-KX3

description: Library name: NEUZW597-KX3


title: ABS-CSF-C02

description: Library name: ABS-CSF-C02


title: healthy control 6

description: Library name: ctrl6


title: S-1076_G_0.1_0.7_perc_meoh rep1

description: Library name: d1248.S-1076_G_0.1_0.7_perc_meoh

value: D-Arabinose


title: healthy control 4

description: Library name: ctrl4


title: S-1076_G_0.1_0.7_perc_meoh rep3

description: Library name: d1250.S-1076_G_0.1_0.7_perc_meoh


title: S-1076_H_std_0.7_perc_meoh rep2

description: Library name: d1252.S-1076_H_std_0.7_perc_meoh


title: NEURY438-LMU

description: Library name: NEURY438-LMU


title: S-1076_G_0.1_0.7_perc_meoh rep2

description: Library name: d1249.S-1076_G_0.1_0.7_perc_meoh


title: S-1076_G_0.5_0.7_perc_meoh rep3

description: Library name: d1247.S-1076_G_0.5_0.7_perc_meoh


title: ABS-CSF-C08

description: Library name: ABS-CSF-C08

value: CTL


title: healthy control 5

description: Library name: ctrl5


title: healthy control 8

description: Library name: ctrl8


title: healthy control 3

description: Library name: ctrl3


title: ABS-CSF-C01

description: Library name: ABS-CSF-C01


title: S-1076_G_0.5_0.7_perc_meoh rep1

description: Library name: d1245.S-1076_G_0.5_0.7_perc_meoh


title: S-1076_G_std_0.7_perc_meoh rep3

description: Library name: d1244.S-1076_G_std_0.7_perc_meoh


title: SBU-ABS-002

description: Library name: SBU-ABS-002


title: healthy control 2

description: Library name: ctrl2


title: S-1076_G_std_0.7_perc_meoh rep1

description: Library name: d1242.S-1076_G_std_0.7_perc_meoh


title: healthy control 1

description: Library name: ctrl1


title: S-1076_G_0.5_0.7_perc_meoh rep2

description: Library name: d1246.S-1076_G_0.5_0.7_perc_meoh


title: S-1076_F_0.1_0.7_perc_meoh rep3

description: Library name: d1241.S-1076_F_0.1_0.7_perc_meoh

value: Rhamnose


title: S-1076_F_0.5_0.7_perc_meoh rep3

description: Library name: d1238.S-1076_F_0.5_0.7_perc_meoh


title: MT_rep3

city: Jatai

first: Bruna

middle: Tereza Thomazini

last: Zanella

state: Goias

institute: Federal University of Jatai (UFJ)

description: Library name: MT3

data_processing:
Transcriptome was obtained through the NovaSeq 6000 platform (Illumina) with 150 base pairs, paired-end, and 6 GB data per sample
Quality of the sequencing was evaluated through the software FastQC version 0.11.8
Adapters were removed, and the reads were filtered using the software Trimmomatic using a phred score >33
De novo transcriptome assembly was performed using Trinity software
Contigs were mapped and annotated based on the proteome data of Danio rerio (GRcz11), Pygocentrus nattereri (Pygocentrus_nattereri-1.0.2), and Astyanax mexicanus (Astyanax_mexicanus-2.0) using the Bowtie2 aligner
Counts were normalized by the median of ratios method, with the counts divided by sample-specific size factors, using DESeq2 package in R environment. Only genes with counts mean >10 between samples were maintained.
Assembly: A. mexicanus (Astyanax_mexicanus-2.0), D. rerio (GRcz11) and P. nattereri (Pygocentrus_nattereri-1.0.2)
Supplementary files format and content: tab-delimited file with normalized gene counts for every gene and every sample

organism: Piaractus mesopotamicus

source_name: Fast-twitch muscle

growth_protocol: Fish were fed ad libitum once a day with commercial food. Cells were cultured in completed growth medium (DMEM supplemented with 10% fetal bovine serum and 1% antiobiotics)

extract_protocol:
The total RNA was extracted using TRIzol® Reagent (Thermo Fisher Scientific), following the manufacturer's protocol guidelines.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol

value: Fast-twitch muscle

value: WT

tag: treatment

value: Ad libitum feeding with commercial food


title: S-1076_F_0.1_0.7_perc_meoh rep2

description: Library name: d1240.S-1076_F_0.1_0.7_perc_meoh


title: MT_rep2

description: Library name: MT2


title: S-1076_F_0.5_0.7_perc_meoh rep2

description: Library name: d1237.S-1076_F_0.5_0.7_perc_meoh


title: NEUPN640-MFG

city: New York

last: Phatnani

description: Library name: NEUPN640-MFG

value: ALS


title: S-1076_J_std_0.7_perc_meoh rep1

description: Library name: d1260.S-1076_J_std_0.7_perc_meoh


title: ABS-CSF-C11

description: Library name: ABS-CSF-C11

value: male


title: S-1076_F_0.5_0.7_perc_meoh rep1

description: Library name: d1236.S-1076_F_0.5_0.7_perc_meoh


title: ABS-CSF-C07

description: Library name: ABS-CSF-C07