title: NL replicate2

city: bethesda

first: Efsun

last: Arda

address: 41 medlars drive

institute: National Institutes of Health

description:
10x Genomics
M1077-3

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger-arc v2.0.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger-arc v2.0.1 (BWA 0.7.17-r1188). Sequenced reads were aligned to a 10x Genomics provided mouse reference sequence (refdata-cellranger-arc-mm10-2020-A-2.0.0). The subsequent analysis was performed using Seurat v.5.0.1 in R software v.4.2.0. A quality control step was performed in merged control and mutant samples to remove low quality cells, including possible cell debris (nFeature < 200), cell doublets (nFeature > 10,000), and cells with excessive cellular stress ( > 5% mitochondrial gene expression).
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 file for each sample was provided

source_name: pancreas

extract_protocol:
Mouse embryos were flash frozen in liquid nitrogen and minced to smaller chunks on ice with sterile micro-dissection scissors. The finely minced tissue were transferred to a pre-chilled 2 mL Dounce homogenizer containing 2 mL cold 1x Homogenization Buffer (HB) buffer which contained 0.26 M Sucrose, 0.03 M KCl, 0.01M Mg2Cl, 0.02M Tricine-KOH pH 7.8, and Ultra-Pure Water (Thermo-Fisher), with the following added on the day of tissue processing— 1mM DTT, 0.5 mM Spermidine (Sigma Aldrich), 0.15mM Spermine (Sigma Aldrich), 0.3% NP40, 1x Roche Complete Protease Inhibitor Cocktail, 1U/μl RNase Inhibitor (Fisher Scientific). The tissue was homogenized on ice by moving a ‘loose’ pestle up and down 10-15 times to disrupt tissue structure, followed with a ‘tight’ pestle to achieve a final homogenate. This homogenate was then strained through a 70μm Flowmi strainer into a 2 mL DNA/RNA LoBind tube and centrifuged at 4°C at 350 rcf for 5 minutes. After the centrifugation, the supernatant was discarded, and the pellet was washed with 1 mL cold PBS, passed through a 40μm Flowmi strainer, and centrifuged again. For density gradient separation, the isolated nuclei were resuspended in 400μl of 1x HB and combined with an equal volume of 50% chilled Iodixanol solution. Subsequent layers of 30% and 40% Iodixanol solutions, diluted in 1x HB, were gently layered under the initial mixture to create a gradient. In the final step, the tube with the nuclei was centrifuged using a pre-cooled bucket-rotor centrifuge at 3,000 rcf for 20 minutes at 4°C. After centrifugation, the top layer was carefully removed, without disrupting the “fuzzy” white ring of nuclei. A narrow-bore pipette tip was used to collect no more than 200μL of the nuclei, which were then mixed with an equal volume of 1x HB. Nuclei concentration was determined using a Countess II FL automated cell counter (Thermo Fisher Scientific), adjusting to a final concentration optimal for 10x Genomics Chromium library preparation.
Transposed nuclei are combined with GEL beads that contain barcodes and partiotioned on a Chromium Next GEM chip to form Gel Beads in emulsion (GEMs). The Gel Bead contains an Illumina TruSeq Read 1 primer, 16 nt 10x Barcode, 12 nt UMI, and a 30 nt poly-dT sequence which are released upon GEM formation. Incubation of the GEMs leads to barcoded cDNA production from the mRNA to create the gene expression library.

value: pancreas

value: Lats1&2 deletion in NGN3+ cells (NL mice)


title: IRF8cKO_rep2_RNA

status: Public on Jul 01 2024

type: SRA

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

country: USA

institute: NIH/NICHD

library_source: transcriptomic single cell

data_processing:
The fastq files were processed with Cellranger-arc v2.0.2 pipeline to make gene expression matrices.
The filtered matrix files (barcodes.tsv.gz/features.tsv.gz/matrix.mtx.gz) have been compressed into a tar file for each sample.
Assembly: mm10
Supplementary files format and content: Cellranger filtered matrices, ATAC fragment files, and h5 files

molecule: polyA RNA

organism: Mus musculus

source_name: FACS-sorted microglia

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

extract_protocol:
Microglia were FACS-sorted, immediately lysed according to the standard 10x procedures (ref. CG000365).
Isolated nuclei were then subjected to the libraries as the protocols that 10x Genomics provides (ref. CG000338).
single nuclei RNA-Seq and ATAC-seq

tag: Sex

value: male

tag: age

tag: cell type

value: FACS-sorted microglia

tag: genotype

tag: treatment

value: Tamoxifen for 5 days


title: WT control

description:
10x Genomics
M1077-2

molecule: nuclear RNA

tag: tissue

value: Wild type


title: NL replicate1

description:
10x Genomics
M1077-5


title: sham operation-2

city: Shanghai

first: Haihan

last: Gao

address: Xuhui District

department: Department of Orthopaedic Surgery

country: China

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
DESeq2 Version 1.24.0
Assembly: GRCm39
Supplementary files format and content: xlsx inculdes log2fc and p values

molecule: total RNA

source_name: rotator cuff enthesis injury

extract_protocol:
RNA was harvested and 1 ug of total RNA was used for the construction of seuencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacture's protocols.

value: rotator cuff enthesis injury

value: wild type

value: sham operation


title: sham operation-3


title: enthesis injury day3-2

value: enthesis injury and repair


title: enthesis injury day3-1


title: PBMC PBS CLP

city: xiamen

first: Qingxiang

address: Xiang'an south way

institute: Xiamen University

description: 10x Genomic

data_processing:
cellranger version 7.2
Assembly: GRCm38.p6

source_name: PBMC

growth_protocol: All animal protocols were reviewed and approved by the Institutional Animal Care and Use Committee of Xiamen University.

extract_protocol:
PBS or Py-TI mice were anesthetized by intraperitoneal injection of 1 % pentobarbital sodium [volume (μl): mouse weight (g) × 10 - 50]. After midline laparotomy, the cecum was exposed and stretched
The scRNA-seq library was prepared utilizing the Microwell-seq platform, with all procedures conducted as reported in the corresponding method.

treatment_protocol: For Plasmodium yoelii 17XNL (Py) infection model, mice were infected by intraperitoneal injection with 105 infected red blood cells (IRBC).

value: PBMC

value: WT

value: PBS CLP


title: Bone marrow PBS

description: 10x Genomic

source_name: Bone marrow

value: Bone marrow

value: PBS


title: PBMC Py CLP

description: 10x Genomic

value: Py CLP


title: tubular specific ROCK2 knockout mice

city: Minato City

first: Kensuke

last: Sekiguchi

state: Please Select

address: 3-19-18 Nishishinbashi

country: Japan

institute: Jikei University

data_processing:
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads. This process provides information of known transcripts, novel transcripts, and alternative splicing transcripts.
Assembly: mm10

source_name: kidney

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (TaKaRa Bio). 1.0 ug of total  RNA was used for the construction of RNA-seq libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following the manufacturer's protocol

value: kidney


title: Bone marrow Plasmodium

description: 10x Genomic

value: Plasmodium


title: PBMC PBS

description: 10x Genomic


title: PBMC Py

description: 10x Genomic


title: WT Medium

first: Qihang

last: Zhao

address: 800 xiangyin road

institute: National laboratory of medical immunology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and trimming low qulity base with Trimmomatic. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: mm39
Supplementary files format and content: txt files inculde FPKM for each sample

source_name: Macrophage

extract_protocol:
Total RNA was extracted by TriZOL.Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) was used to determine the concentration and evaluate the purity of RNA samples. Agilent 2100 Bioanalyzer and 2100 RNA nano 6000 assay kit (Agilent Technologies) were used to evaluate the integrity of RNA samples.
After the QC procedure, the RNA with poly-A in eukaryotic total RNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN). Then, using the captured RNA as the starting sample, TIANSeq Fast RNA Library Kit (Illumina) was used to construct the transcriptome sequencing libraries. Briefly, the transcriptome sequencing library was constructed through RNA randomly fragmentation, cDNA strand 1 / strand 2 synthesis, end repair, A-tailing, ligation of sequencing adapters, size selection and library PCR enrichment.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina sequencing platform and 150 bp paired-end reads were generated.

value: Macrophage

value: control


title: KO VSV

value: KO

value: VSV(MOI=1) for 12 hours


title: Wild type mice


title: Negative control, biol replicate 4, V(D)J

city: Nashville

first: Ivelin

last: Georgiev

state: TN

address: 11475 MRB IV 2213 Garland Ave

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

data_processing:
V(D)J-seq was processed using Cell Ranger v7.0.1, then annotated with IMGT/HighV-QUEST.
Assembly: vdj_GRCm38_alts_ensembl-7.0.0
Supplementary files format and content: Processed V(D)J sequences data provided as .csv files with sequence annotations for paired heavy and light chains.
Library strategy: scVDJ-seq

source_name: Lymph node

extract_protocol:
Twelve days after immunization animals were euthanized, and draining inguinal and popliteal lymph nodes harvested and pooled for each mouse for cell sorting.
B cell suspensions were processed for single cell sequencing following Chromium Next GEM Single Cell 5’ Version 2 protocol.
single-cell V(D)J

treatment_protocol: Mice were immunized intramuscularly with one dose (5 µg) of either U-mRNA or m1Ψ-mRNA formulated with LNP. Positive control constituted 20 µg of recombinant GnH/Gc antigen. formulated with Alhydrogel (2%) in a 1:1 ratio (total volume 50 µl)

value: Lymph node

value: B lymphocyte

value: Negative control empty LNP


title: WT VSV


title: Negative control, biol replicate 3, V(D)J


title: Negative control, biol replicate 2, V(D)J


title: Y2  Young with CDA-HFD diet

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to mice genome reference combining the GRCm38.  STAR v2.7.5 was used to align reads to reference genome.  Gene count was quantified by featureCounts v2.0.1.
Assembly: GRCm38
Supplementary files format and content: DK_featurecount_rawcount.txt: Reads mapped to mice GRCm38, featurecount was used to count reads per gene per sample, tab-delimited txt file

source_name: Young mice with CDA-HFD diet

growth_protocol: Young and old mice were fed with a chow diet or CDA-HFD diet for 6 weeks. Old mice were intraperitoneally injected with Fer1 or its vehicle every other day during the last 8 days of feeding .

extract_protocol:
Total RNA was extracted using an RNAeasy kit (Qiagen) and dissolved in RNase-free water. RNA samples were sequenced by Novogene Corporation. In brief, RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer Spectrophotometer (IMPLEN). RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Clustering of index-coded samples was performed on an Illumina NovaSeq sequencer

treatment_protocol: all mice were fed with CDA-HFD diet for 6 week, for Ofer group, mice were intraperitoneally injected with Fer1 every other day during last 8 days of feeding.

value: whole liver

value: Young

tag: diet

value: CDA-HFD diet

value: No


title: sham operation-1

value: rotator cuff enthesis injury

value: wild type

value: sham operation


title: Pseudouridine vaccine, biol replicate 3,  V(D)J

value: Pseudouridine mRNA vaccine


title: Uridine vaccine, biol replicate 3, V(D)J

value: Uridine mRNA vaccine


title: Pseudouridine vaccine, biol replicate 4, V(D)J


title: Uridine vaccine, biol replicate 1,  V(D)J


title: Negative control, biol replicate 1, V(D)J


title: Uridine vaccine biol replicate 2, V(D)J


title: Pseudouridine vaccine, biol replicate 1, V(D)J


title: enthesis injury day3-3

value: enthesis injury and repair


title: Positive control, biol replicate 3,  V(D)J

value: Positive control GPC


title: KO Medium

value: Macrophage

value: control


title: Negative control, biol replicate 3, scRNA-seq

description:
Sample tags included in meta data of AnnData (adata.obs layer)
processed_concatenated_adata.h5ad

data_processing:
scRNA-seq data was processed using Cell Ranger v7.0.1, then further analyzed using Scanpy v1.91.
Assembly: mm10-2020-A
Supplementary files format and content: scRNA-seq data provided in h5ad (AnnData) format with filtering, dimensionality reduction, and clustering included in the meta data (.obs layer). This format can be opened in Scanpy or converted to a Seurat object (https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html).

extract_protocol:
Twelve days after immunization animals were euthanized, and draining inguinal and popliteal lymph nodes harvested and pooled for each mouse for cell sorting.
B cell suspensions were processed for single cell sequencing following Chromium Next GEM Single Cell 5’ Version 2 protocol.


title: Positive control, biol replicate 1,  V(D)J


title: Positive control, biol replicate 2,  V(D)J


title: Negative control, biol replicate 4, scRNA-seq


title: Negative control, biol replicate 1, scRNA-seq


title: Positive control, biol replicate 4,  V(D)J


title: Uridine vaccine, biol replicate 4, scRNA-seq


title: Negative control, biol replicate 2, scRNA-seq


title: Uridine vaccine, biol replicate 3, scRNA-seq


title: Pseudouridine vaccine, biol replicate 2, scRNA-seq


title: Uridine vaccine biol replicate 2, scRNA-seq


title: Positive control, biol replicate 4, scRNA-seq


title: Pseudouridine vaccine, biol replicate 1, scRNA-seq


title: Pseudouridine vaccine, biol replicate 3, scRNA-seq


title: Uridine vaccine, biol replicate 1, scRNA-seq


title: Pseudouridine vaccine, biol replicate 2,  V(D)J


title: Positive control, biol replicate 3, scRNA-seq


title: Uridine vaccine, biol replicate 4, V(D)J


title: Positive control, biol replicate 1, scRNA-seq


title: AD.WEP.KO.CM.2.raw

city: Rehovot

first: Anat

last: Gershoni

address: 234 Herzl street

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute

data_processing:
Reads were trimmed using cutadapt. After trimming the reads were mapped to the mm10 genome. Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI (read 2 had the UMI). Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count. Normalization and differential expression was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Excel file includes DESeq2 analysis using umi counts

growth_protocol: undifferentiated 3T3-L1 cells were maintained in DMEM supplemented with 10% calf serum (CS), 1% sodium pyruvate, and 1% penicillin/streptomycin (P/S). Differentiated 3T3-L1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate, and 1% penicillin/streptomycin.

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel)
30ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourt AMPure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT and PCR.
MARS-seq

treatment_protocol: Adipocyte differentiation was induced by treatment of 2-day post confluent 3T3-L1 cells with DMEM supplemented with 10% FBS, 1% sodium pyruvate, 1% P/S, 0.5 mM 3-isobutyl-1-methylxanthine, 1 μg/mL insulin, 1 μM dexamethasone, and 2 μM rosiglitazone. After 2 days, the medium was replaced with DMEM medium containing 10% FBS, 1% sodium pyruvate, 1% P/S, and 1 μg/mL insulin. After an additional 2 days, the cells were switched to differentiated 3T3-L1 maintenance medium. For 3T3-L1 cells differentiated in the presence of cancer cell CM, filtered CM from WEP cells was added to the 3T3-L1 cells during each step of differentiation in a 1:1 ratio with the mediums previously listed.

tag: cell line

value: WT

value: adipogenic differentiation with WEP p53 KO cell CM


title: AD.WEP.KO.CM.1.raw


title: AD.WEP.WT.CM.3.raw

value: adipogenic differentiation with WEP p53 WT cell CM


title: AD.WEP.KO.CM.3.raw


title: AD.WEP.WT.CM.2.raw


title: Positive control, biol replicate 2, scRNA-seq

value: Lymph node

value: B lymphocyte


title: AD.Regdif.3.raw

value: differentiated, white adipocyte

value: adipogenic differentiation


title: AD.Regdif.2.raw


title: Pseudouridine vaccine, biol replicate 4, scRNA-seq


title: AD.WEP.WT.CM.1.raw


title: AD.3T3L1.2.raw

value: undifferentiated, preadipocyte


title: AD.WEA.KO.CM.3.raw

treatment_protocol: Adipocyte differentiation was induced by treatment of 2-day post confluent 3T3-L1 cells with DMEM supplemented with 10% FBS, 1% sodium pyruvate, 1% P/S, 0.5 mM 3-isobutyl-1-methylxanthine, 1 μg/mL insulin, 1 μM dexamethasone, and 2 μM rosiglitazone. After 2 days, the medium was replaced with DMEM medium containing 10% FBS, 1% sodium pyruvate, 1% P/S, and 1 μg/mL insulin. After an additional 2 days, the cells were switched to differentiated 3T3-L1 maintenance medium. For 3T3-L1 cells differentiated in the presence of cancer cell CM, filtered CM from WEA cells was added to the 3T3-L1 cells during each step of differentiation in a 1:1 ratio with the mediums previously listed.

value: adipogenic differentiation with WEA p53 KO cell CM


title: AD.3T3L1.3.raw


title: AD.WEA.KO.CM.2.raw


title: AD.Regdiff.1.raw


title: AD.3T3L1.1.raw


title: AD.WEA.WT.CM.2.raw

value: adipogenic differentiation with WEA p53 WT cell CM


title: AD.Regdif.6.raw (WEA)


title: AD.WEA.KO.CM.1.raw


title: AD.WEA.WT.CM.3.raw


title: AD.3T3L1.6.raw (WEA)


title: AD.Regdiff.4.raw (WEA)


title: AD.Regdif.5.raw (WEA)


title: AD.3T3L1.5.raw (WEA)


title: AD.3T3L1.4.raw (WEA)


title: EBD10b amplicon-seq

city: Guangzhou

first: Cheng

last: Chen

state: Guangdong

address: Kaiyuan Ave 190

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science

description: Amplicon-seq

data_processing:
library strategy:Amplicon-seq
Barcoding processing, read alignment, and gene counting were made using MGI-provided DNBelab_C_Series_HT_scRNA-analysis-software v1.0.
Normalization in Seurat ("LogNormalize")
Assembly: mm10
Supplementary files format and content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); molecular table containing filtered lineage tracer calls.
Supplementary files format and content: Comma-separated value files and matrix files

source_name: in vitro embryoid body

growth_protocol: HEK293T cells were cultured in DMEM basic media supplemented with 10% FBS. mESCs were cultured on plates coated with 0.1% gelatin in DMEM high-glucose media containing 15% FBS, 1 mM sodium pyruvate, 1 mM non-essential amino acids (NEAA), 1% GlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF), 3 μM CHIR99021, and 1 μM PD0325901. All the cell lines were cultured in humidified incubators at 37℃ in 5% (v/v) CO2.

extract_protocol:
Embryoid bodies were dissociated by the Papain dissociation kit (Worthington). In brief, embryoid bodies were incubated in 1 ml Enzyme A along with 20 μl DnaseI at 37℃ for 20-25 min, followed by gentle blowing every 5 minutes with wide-bore tips.  HEK293T cells were dissociated using trypsin according to the user’s guide. After washing and filtering, a suitable volume of PBS with 0.04% BSA was added to resuspend the cells to achieve a cell concentration of 2x106 /ml.
Single-cell RNA libraries were prepared using DNBelab C4 kit (BGI-MGI) according to the user’s guide. The main steps of library preparation include droplet formation, demulsification, reverse transcription, second-strand synthesis, cDNA and oligo product amplification following size selection. Each obtained cDNA pool was divided into two parts. One part of cDNA was prepared by Single-cell RNA libraries were prepared using DNBelab C4 kit (BGI-MGI) according to the user’s guide. The main steps of library preparation include droplet formation, demulsification, reverse transcription, second-strand synthesis, cDNA and oligo product amplification following size selection. Each obtained cDNA pool was divided into two parts. One part of cDNA was prepared by fragmentation, end repair, adaptor ligation and PCR to get a cDNA library for scRNA-seq. Another part of cDNA was used for amplicon sequencing. Corresponding oligo libraries were generated by PCR amplification from oligo products.In order to better capture information on target site, we divided the obtained  cDNA into two portions. One portion was used for normal transcriptome sequencing, while the other portion was used for amplicon sequencing.fragmentation, end repair, adaptor ligation and PCR to get a cDNA library for scRNA-seq. Another part of cDNA was used for amplicon sequencing. Corresponding oligo libraries were generated by PCR amplification from oligo products.In order to better capture information on target site, we divided the obtained  cDNA into two portions. One portion was used for normal transcriptome sequencing, while the other portion was used for amplicon sequencing.

value: in vitro embryoid body

value: organoid


title: EBD8b amplicon-seq

description: Amplicon-seq


title: EBD10a amplicon-seq

description: Amplicon-seq


title: EBD8a amplicon-seq

description: Amplicon-seq


title: IP2_Mouse_2_BMDM_WT_R1 [m6A-eCLIP]

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

description: Mouse2_BMDM_NTC_IP_vs_Input_eCLIP_peak_info.csv

data_processing:
library strategy: m6A-eCLIP
3′-adapters were trimmed from reads using cutadapt (v2.7) 34, and reads shorter than 18 bp in length were removed. Reads were then mapped to a database of human or mouse repetitive elements and rRNA sequences compiled from Dfam 35 and Genbank 36.
All non-repeat mapped reads were mapped to the human genome (hg38) or mouse genome (mm10) using STAR (v2.6.0c). PCR duplicates were removed using umi_tools (v0.5.1) by utilizing UMI sequences from the read names and mapping positions. Peaks were identified within m6A-eCLIP samples using the peak caller CLIPper
Assembly: mm10
Supplementary files format and content: peak_info.csv

source_name: BMDM

extract_protocol:
Total RNA was isolated from 20 x 106 cells using Quick-RNA MiniPrep (Zymo) followed by a poly(A) selection using oligo (dT) beads (ThermoFisher) from 50 µg of total RNA
After dephosphorylation with FastAP (ThermoFisher) and T4 PNK (NEB), a barcoded RNA adapter was ligated to the 3′ end (T4 RNA Ligase, NEB).

value: BMDM

value: macrophages


title: AAA, scRNAseq

city: Hangzhou

first: Xihao

address: Gudun road,num.1229

institute: Zhejiang Hospital

description: 10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Abdominal aorta

extract_protocol:
After removing the perivascular adipose and connective tissues, the isolated carotid arteries were cut into 0.5 mm2 pieces. Then, the diced vascular tissues were digested in enzyme solution (2 mg/mL collagenase II, 1mg/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum (FBS) and pipetted for 5 - 10 times. The cell suspension was filtered by passing through 30 μm stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100 μl 1× PBS (0.04% BSA), and added with 1× red blood cell lysis buffer (MACS 130 - 094 - 183, 10×) and incubated for 2 - 10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads (MACS 130 - 090 - 101) and remove dead cells using Miltenyi® Dead Cell Removal Kit (MACS 130 - 090 - 101). Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C. The cell pellet was resuspended in 1× PBS (0.04% BSA). The overall cell viability was more than 90% confirmed by trypan blue exclusion. The single cell suspensions were counted using Countess II Automated Cell Counter and the concentration was adjusted to 700 - 1200 cells / μl.
Single-cell suspensions were loaded to 10× Chromium to capture 10,000 single cells using a 10× Genomics Chromium Single-Cell 3′ reagent kit (V3) according to the manufacturer′s instructions (10× Genomics, CA). The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) by LC-Bio Technology Co., Ltd (Hangzhou, China) at a minimum depth of 20,000 reads per cell.

value: Abdominal aorta

value: Abdominal aorta cell

value: Abdominal aortic aneurysm (AAA)


title: CTR, scRNAseq

description: 10× Genomics

value: Control


title: IP1_Mouse_1_BMDM_WT_R1 [m6A-eCLIP]

description: Mouse1_BMBM_NTC_IP_vs_Input_eCLIP_peak_info.csv


title: Input2_Mouse_2_BMDM_WT_R1 [m6A-eCLIP]


title: Input1_Mouse_1_BMDM_WT_R1 [m6A-eCLIP]


title: CD8priming_RNA

first: Jianhua

last: Li

address: NO.131 DONGAN RD., FUXING BUILDING 306

institute: Fudan University

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
CD8priming_barcodes.tsv.gz
CD8priming_features.tsv.gz
CD8priming_matrix.mtx.gz

data_processing:
Raw gene expression matrices were generated by the Cell Ranger(v5.0) pipeline, as described above, coupled with mouse reference version mm10.
The output filtered gene expression matrices were analyzed by R software (v4.0.3) with the Seurat package (v.4.0.2). Low-quality cells or potential doublets were filtered out. Hashtag labeled cells were demultiplexed with HTODemux function to identify their original organs or time points.
Low-quality cells or potential doublets were filtered out. Hashtag labeled cells were demultiplexed with HTODemux function to identify their original organs or time points. UMI counts were then normalized with SCTransform function. PCA was calculated and used to construct a SNN network. A graph-based clustering approach was applied to identify cell clusters with the resolution = 0.6. Clusters were then classified and annotated based on expressions of canonical markers of particular cell types.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: liver

extract_protocol:
Single-cells were captured using the 10x Chromium (10x Genomics).
Libraries were prepared using Chromium Next GEM Single Cell 5’ Reagent Kits v2 or Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10 x Genomics) according to the manufacturer’s instructions.

value: liver

value: APC, hepatocyte, T cell

tag: library type

value: mRNA

tag: antibodies/tags


title: CD8priming_HTO

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
CD8priming_barcodes.tsv.gz
CD8priming_features.tsv.gz
CD8priming_matrix.mtx.gz

library_source: other

molecule: protein

value: HTO

value: Anti CD45 + Anti MHC class I :Day 0--/TotalSeq-B0303 ; Day 2.5--/TotalSeq-B0304


title: Day7_OTII_HTO

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Day7_OTII_barcodes.tsv.gz
Day7_OTII_features.tsv.gz
Day7_OTII_matrix.mtx.gz

source_name: spleen, dLN, liver

value: spleen, dLN, liver

value: T cell

value: Anti CD45 + Anti MHC class I :liver--/TotalSeq-C0301 ; spleen--/TotalSeq-C0302 ; dLN--/TotalSeq-C0303


title: AD.WEA.WT.CM.1.raw

value: WT

value: adipogenic differentiation with WEA p53 WT cell CM


title: OTII_day2_5_biol_rep_3

data_processing:
The raw data was handled by Skewer (v0.2.2) and data quality was checked by FastQC (v0.11.5).
Clean reads were aligned to the mm10 mouse genome with STAR (v2.7.9a) and counted with featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for genes for each library

source_name: Spleen

extract_protocol:
Sorted cells were snap frozen and then RNA was extracted with the RNeasy Mini Kit (QIAGEN). RNA was checked by gel electrophoresis and quantified with a Qubit Fluorometer (Invitrogen).
Barcoded sequencing libraries were constructed using the TruSeq Stranded mRNA kit (Illumina).

tag: time point

value: Spleen

value: OTII


title: OTII_day1_biol_rep_2


title: OTII_day2_5_biol_rep_1


title: OTII_day2_5_biol_rep_2


title: OTII_0h_biol_rep_3

value: Unimmune


title: OTII_0h_biol_rep_1


title: WT_rep2_RNA

value: male

value: FACS-sorted microglia

value: Tamoxifen for 5 days


title: S129G1_day2_5_biol_rep_2

value: B cell


title: OTII_0h_biol_rep_2


title: S129G1_day1_biol_rep_2


title: S129G1_day2_5_biol_rep_3


title: S129G1_day1_biol_rep_1


title: S129G1_18h_biol_rep_2


title: S129G1_0h_biol_rep_3


title: S129G1_18h_biol_rep_1


title: S129G1_0h_biol_rep_2


title: S129G1_0h_biol_rep_1


title: Polr1cpeaks_treatment_repeat_1

city: Melbourne

first: Diji

last: Kuriakose

state: Victoria

address: Wellington road

country: Australia

institute: Monash University

library_source: genomic

data_processing:
Basecalls were performed using fastq for Illumina output.
ChIP-seq reads were trimmed with a cut-off quality score > 30, using the Trim galore software
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.3.5.
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.01
Assembly: Bedgraph files were generated using bdgpeakcall of MACS3. narrowPeak and broadPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: Bedgraph files, narrowPeak /broadPeak (except for Input sample)

molecule: genomic DNA

source_name: Hippocampus

growth_protocol: DMEM, 8mM HEPES, B27 supplement, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus sonication (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using  AMPure XP beads from Beckman Coulter. Libraries were validated using the Qubit High Sensitivity DNA Kit.

value: Hippocampus

value: primary cells

value: Neural progenitor cells

tag: strain

value: Male


title: Day7_OTII_RNA

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
Day7_OTII_barcodes.tsv.gz
Day7_OTII_features.tsv.gz
Day7_OTII_matrix.mtx.gz

value: mRNA


title: Panx2peaks_treatment_repeat_1


title: Polr1cpeaks_treatment_repeat_2


title: Mgea5peaks_treatment_repeat_1


title: Panx2peaks_treatment_repeat_2


title: OTII_day1_biol_rep_1


title: Input_repeat_1


title: Input_repeat_2


title: sh-Prmt1-rep2

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

data_processing:
Transcript abundances were quantified using salmon65 with parameters --gcBias --seqBias –validateMappings. Transcript abundances were imported into DESeq266 using tximport67 to perform differential expression analyses. Fold changes were calculated with DESeq2 with default settings and fold changes and p-values corrected with the bioconductor packages apglm68 and IHW69, respectively. Genes with an absolute log2 fold change >= 1 and FDR < 5% were considered as differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: differential expression
Supplementary_files_format_and_content: salmon quant
Supplementary_files_format_and_content: raw counts

source_name: intestinal organoids

growth_protocol: Mouse organoids were obtained from small intestines as previously described61. A detailed description can be found in supplementary information. Wild-type organoids were cultured in presence of recombinant Wnt3a (homemade), R-spondin1 (homemade), 0.1 μg/ml Noggin, 0.05 μg/ml EGF.  Apc-/- and CtnnB1-ex3 organoids were only supplemented with 0.1 μg/ml Noggin and 0.05 μg/ml EGF.

extract_protocol: RNA-seq libraries were prepared using a custom Smart-seq2 procedure that was previously described65. A detailed description of the library preparation procedure is available in supplementary information.


title: sh-scramble-rep1

value: sh-scramble


title: sh-scramble-rep2


title: sh-Prmt1-rep1


title: livers, Alc UA, rep5

city: Xian yang

first: Hongbo

last: Zhang

state: Shannxi

address: Xi nong road

department: College of Food Science and Engineering

institute: Northwest A&F University

data_processing:
Data filtering:The raw data was filtered with SOAPnuke (v1.5.2)  by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping：The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping:The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5). The expression level of genes was calculated by RSEM (v1.2.8).
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
Differential Gene Expression: Within-group differential gene analysis was performed using DESeq under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001. Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and classifications, the differentially expressed genes were functionally classified, the phyper in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis (https://metacpan.org/pod/GO::TermFinder). With a Q value of ≤ 0.05 as the threshold, candidate genes that met this condition were defined as significantly enriched.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .
Assembly: The clean data were mapped to the reference genome by HISAT (v2.1.0)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard MGISEQ-2002RS protocols

value: liver

value: alcohol diet / UA


title: livers, Alc UA, rep1

value: WT


title: livers, Alc UA, rep4


title: S129G1_day2_5_biol_rep_1


title: livers, Alc, rep5

value: alcohol diet


title: livers, Alc, rep4


title: livers, Alc, rep1


title: livers, Alc UA, rep2


title: livers, Alc, rep2


title: livers, Ctrl, rep5

value: control diet


title: livers, Alc, rep3


title: livers, Ctrl, rep2


title: livers, Ctrl, rep4


title: livers, Ctrl, rep1


title: EBD14 amplicon-seq

description: Amplicon-seq

value: in vitro embryoid body

value: organoid


title: Mgea5peaks_treatment_repeat_2


title: EBD12 amplicon-seq

description: Amplicon-seq


title: livers, Ctrl, rep3


title: EBD8b scRNA-seq

description: DNBelab C4

data_processing:
Barcoding processing, read alignment, and gene counting were made using MGI-provided DNBelab_C_Series_HT_scRNA-analysis-software v1.0.
Normalization in Seurat ("LogNormalize")
Assembly: mm10
Supplementary files format and content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); molecular table containing filtered lineage tracer calls.
Supplementary files format and content: Comma-separated value files and matrix files


title: EBD10b scRNA-seq

description: DNBelab C4


title: livers, Alc UA, rep3


title: IonCode_0124

city: Chicago

first: Juan

middle: L

last: Mendoza

state: IL

address: 920 E 58th Street

institute: The University of Chicago

description: biol rep2

data_processing:
Ion Torrent S5 with ampliSeqRNA plugin v 5.16.1
Trimed sequence reads were mapped to hg19 AmpliSeq Transcriptome ERCC v1 using Ion Torrent S5 software
Read count extraction and normalization were performed using Ion Torrent S5 software
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads

organism: Homo sapiens

growth_protocol: HEK293 cells were maintained in Free-style Media supplemented with antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Monarch Total RNA miniprep kit (NEB). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ion Torrent Ion 540 or 550 Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with 100nM of indicated interferons for 15 minutes in humidified atomosphere with 5% CO2 at 37C

value: Embryonic Kidney Cells

value: Optimized receptors

value: IFNL3 treated

tag: time


title: EBD8a scRNA-seq

description: DNBelab C4


title: IonCode_0122

description: biol rep2

value: High-affinity INFL3 (H11) treated


title: EBD10a scRNA-seq

description: DNBelab C4


title: EBD14 scRNA-seq

description: DNBelab C4


title: IonCode_0120

description: biol rep2

value: IFNw treated


title: IonCode_0123

description: biol rep2

value: Wild-type receptors


title: IonCode_0119

description: biol rep2


title: IonCode_0117

description: biol rep2

value: Untreated


title: IonCode_0121

description: biol rep2


title: IonCode_0118

description: biol rep2


title: IonCode_0108

description: biol rep1


title: IonCode_0107

description: biol rep1


title: IonCode_0106

description: biol rep1


title: IonCode_0105

description: biol rep1


title: IonCode_0104

description: biol rep1


title: IonCode_0101

description: biol rep1


title: IonCode_0102

description: biol rep1


title: IonCode_0103

description: biol rep1


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 3 Day 6

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
cDNA amplified from total RNA using oligo(d)T primer
rep3_D6

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --twopassMode Basic --outSAMstrandField intronMotif --alignIntronMin 60 --alignIntronMax 2500 --outFilterIntronMotifs RemoveNoncanonical --alignEndsType EndToEnd
Only uniquely mapped reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
Standard normalized count Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated, except gene length in the formula is replaced with mapped length
Assembly: Plasmodium falciparum 3D7 geneDB version 3
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

organism: Plasmodium falciparum 3D7

source_name: infected erythorcytes culture in vitro

growth_protocol: P. falciparum strain 3D7 was obtained from BEI Resources (MRA-102) and cultured under standard conditions described before (William Trager, James B. Jensen, Human malaria parasites in continuous culture, Science, 193, 4254, 1976). Prior to the experiment, parasites were synchronized with 5% sorbitol solution to achieve a synchrony of +/- 6 hours.

extract_protocol:
500 cells infected with dormant parasites were sorted into 3μL of Lysis buffer (final concentration of RNAseOut 2U/μL and 1mg/mL BSA, Molecular Biology Grade (NEB)) by FACSAria II (BD) into 0.2mL PCR strip tubes and these samples were considered as total RNA.
Reverse transcription and cDNA synthesis were done following modifed Smart-Seq2 protocol (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014)). Purified amplicon (cDNA) was used to generate sequencing libraries using Illumina Nextera XT kit as described in manufacturer’s protocol. Libraries were analyzed on the Bioanalyser High-Sensitivity DNA chips (Agilent, Cat. No.: 5067-4626) and sequenced on Illumina NovaSeq6000 platform generating 150 bp paired end reads with 8 Gb data output per sample.

treatment_protocol: Parasites were treated by 700nm Dihydroartemisinin (DHA) for 6 hours on Day 0 and 500 cells were sorted on following days (corresponding to the Sample name, D1 = Day 1 etc.) by flow cytometry sorter (staining used: Hoechst 333342 and Dihydroethidium). Cultures were supplemented with fresh RPMI media every day and blood was added on Day 5 to prevent the lysis of the culture. Culture was monitored by making Giemsa smears and flow cytometry every day of the experiment.

value: infected erythorcytes culture in vitro

value: intraerythorcytic P.falciparum

value: 700nm DHA treatment for 6 hours

tag: post-treatment day

value: Day 6


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 3 Day 5

description:
cDNA amplified from total RNA using oligo(d)T primer
rep3_D5

value: Day 5


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 3 Day 7

description:
cDNA amplified from total RNA using oligo(d)T primer
rep3_D7

value: Day 7


title: EBD12 scRNA-seq

description: DNBelab C4


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 2 Day 7

description:
cDNA amplified from total RNA using oligo(d)T primer
rep2_D7


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 2 Day 6

description:
cDNA amplified from total RNA using oligo(d)T primer
rep2_D6


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 2 Day 5

description:
cDNA amplified from total RNA using oligo(d)T primer
rep2_D5


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 1 Day 12

description:
cDNA amplified from total RNA using oligo(d)T primer
rep1_D12

value: Day 12


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 1 Day 5

description:
cDNA amplified from total RNA using oligo(d)T primer
rep1_D5


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 1 Day 6

description:
cDNA amplified from total RNA using oligo(d)T primer
rep1_D6


title: P.falciparum 3D7 transcriptome DHA-treated persistance stage replicate 1 Day 7

description:
cDNA amplified from total RNA using oligo(d)T primer
rep1_D7


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 12

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D12


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 10

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D10

value: Day 10


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 9

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D9

value: Day 9


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 11

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D11

value: Day 11


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 8

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D8

value: Day 8


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 2

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D2

value: Day 2


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 4

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D4

value: Day 4


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 1

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D1

value: Day 1


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 5

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D5


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 12

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D12


title: P.falciparum 3D7 transcriptome untreated rings Biorep C

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_Rings

value: untreated


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 11

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D11


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 10

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D10


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 8

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D8


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 5

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D5


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 3

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D3

value: Day 3


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 9

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D9


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 4

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D4


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 2

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D2


title: P.falciparum 3D7 transcriptome DHA-treated Biorep B Day 1

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_D1


title: P.falciparum 3D7 transcriptome untreated rings Biorep B

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_B_Rings


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 10

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D10


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 9

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D9


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 4

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D4


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 8

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D8


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 11

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D11


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 3

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D3


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 2

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D2


title: P.falciparum 3D7 transcriptome DHA-treated Biorep C Day 3

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_C_D3


title: P.falciparum 3D7 transcriptome untreated rings Biorep A

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_Rings


title: A2780 cells,BPP2

city: Hefei

first: 丛蓉

last: 李

address: 安徽医科大学东校区弘毅楼1202室

institute: Nanjing Medical university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36)
low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Homo sapiens  using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: mm10
Supplementary files format and content: tab-delimited textefile includes raw counts for each sample
Supplementary files format and content: tab-delimited textefile includes RPKM values for each sample

growth_protocol: A2780 human ovary carcinoma cells were cultured in DMEM with 10% FBS and antibiotics in humidified atmosphere with 5%CO2 at 37°C

extract_protocol:
Total RNAs were extracted from A2780 cells using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: human ovary carcinoma cells


title: A2780 cells,Control 3

address: 安徽医科大学东校区弘毅楼1202室


title: A2780 cells,BPP1

address: 安徽医科大学东校区弘毅楼1202室


title: A2780 cells,Control 1

address: 安徽医科大学东校区弘毅楼1202室


title: MSC3, KDM4D knockdown

city: Shenzhen

first: Yunshu

last: Che

address: NO.3025 shennan road

institute: Sun Yat-sen University

data_processing:
The sequencing data were filtered with SOAPnuke (v1.5.2)11 by (1) removing reads containing sequencing adaptors; (2) removing reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20%; and (3) removing reads whose unknown base ('N' base) ratio was more than 5%
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5)13 was used to align the clean reads to the reference coding gene set, and then the expression level of the gene was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using DESeq2 (v1.4.5)15 with a Q value ≤ 0.05
Assembly: Grch38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

growth_protocol: MSCs were seeded in 6-well plates at a density of 1×105/well and cultured with DMEM (1000 mg/L glucose) without FBS to induce quiescence

extract_protocol:
Total RNA was extracted from MSCs using TRIzol (Invitrogen), and 1 μg of isolated RNA was the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: quiescent MSC was mobilized

value: bone marrow

value: Mesenchymal stem cells

value: KDM4D knockdown

tag: growth state

value: quiescent MSC mobilization


title: MSC1, KDM4D knockdown


title: MSC2, DFO treatment

value: DFO treatment


title: MSC3, DFO treatment


title: MSC2, KDM4D knockdown


title: MSC2, untreated


title: MSC3, untreated


title: MSC1, untreated


title: Chicken preadipocytes - input DNA_rep1

city: Harbin

first: Xinyang

state: Heilongjiang

address: No.600 Changjiang street

department: Animal Science and Technology

institute: Northeast Agricultural University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of chicken (Gallus_gallus-5.0) using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling.
The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test. The Homer（version 4.10）was used for motifs analysis.
Genome_build: Gallus_gallus-5.0

organism: Gallus gallus

source_name: Chicken preadipocyte stably overexpressing TCF21 (LV-TCF21)

growth_protocol: The preadipocytes were initially grown in DMEM (Gibco, NY, USA) with 10% FBS (Biological Industries) in a standard humidified incubator. At >90% confluency, the cells were either passaged or plated for follow-up experiments at 1×105 cells/ml.

extract_protocol:
Cells were then collected, treated with nuclear lysis buffer, and sonicated to mediate DNA fragmentation. The sonicated chromatin was used in each immunoprecipitation reactions with the anti-HA antibody (Abcam) or with control rabbit IgG (Cell Signaling Technology).
Libraries were prepared according to Illumina's instructions. The brief procedures are end repair, adding 3' A tail, ligating adaptors and enriching/linearizing with PCR.

treatment_protocol: At 50% confluency of the plated cells, differentiation was induced by replacing fresh differentiation media (DMEM with 10% FBS and 300 μM oleic acid) for 24h.

value: Adipose derived-chicken preadipocyte stably overexpressing TCF21 (LV-TCF21)

tag: chip antibody

value: Treatment with oleic acid for 24h


title: Chicken preadipocytes - input DNA_rep2


title: Chicken preadipocytes - TCF21_IP_rep3

value: anti-HA antibody, Abcam, ab9110


title: Chicken preadipocytes - TCF21_IP_rep1


title: EGFR-WT wild type 1

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

data_processing:
raw reads obtained from RNA-Seq were aligned and quantified using Illumina DRAGEN Bio-IT Platform RNA Pipeline (Illumina, USA) with the NCBI mouse mm39 transcriptome. Expression counts for each gene in all samples were normalized by a modified trimmed mean of the M-values normalization method and the unsupervised PC analysis (PCA) was performed with DESeq2 Bioconductor package version 1.40.2 in R version 4.3.1. Each gene was fitted into a negative binomial generalized linear model, and the Wald test was applied to assess the differential expressions between two sample groups by DESeq2. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing, and differential expression gene candidates were selected with a false discovery rate less than 0.05.
Assembly: mm39
Supplementary files format and content: Tab-separated values files and metric files

source_name: Bone marrow CD34-KSL cells

extract_protocol:
RNA was extracted using the SMART-Seq V4 Ultra Low RNA Input Kit for subsequent library preparation using the Nextera XT Library Preparation kit
For mRNA-Seq Library prep, the SMART-Seq V4 Ultra Low RNA Input Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription and generation of double stranded cDNA for subsequent library preparation using the Nextera XT Library Preparation kit (Illumina, San Diego, CA).  An input of 10 ng RNA was used for oligo(dT)-primed reverse transcription, followed by cDNA amplification and cleanup.  Quantification of cDNA was performed using Qubit (Thermo Fisher Scientific).  cDNA normalized to 80 pg/µl was fragmented and sequencing primers added simultaneously.  A limiting-cycle PCR added Index 1 (i7) adapters, Index 2 (i5) adapters, and sequences required for cluster formation on the sequencing flow cell.  Indexed libraries were pooled and cleaned up, and the pooled library size was verified on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and quantified via Qubit.  Libraries were sequenced on a NovaSeq 6000 (Illumina) using with a 1x75 bp read length and coverage of over 30M reads/sample.

treatment_protocol: WT genotype was maintained in drinking water with 0.2 g/L doxycycline

value: Bone marrow CD34-KSL cells

value: CD34- KSL

value: EGFR-WT

value: 0.2 g/L doxycycline


title: EGFR-DN dominant negative 3

value: EGFR-DN


title: EGFR-WT wild type 2


title: P.falciparum 3D7 transcriptome DHA-treated Biorep A Day 1

description:
cDNA amplified from total RNA using oligo(d)T primer
BR_A_D1

value: infected erythorcytes culture in vitro

value: intraerythorcytic P.falciparum

value: 700nm DHA treatment for 6 hours

value: Day 1


title: Chicken preadipocytes - TCF21_IP_rep2


title: A2780 cells,BPP3

address: 安徽医科大学东校区弘毅楼1202室

value: human ovary carcinoma cells


title: EGFR-DN dominant negative 1


title: A2780 cells,Control 2

address: 安徽医科大学东校区弘毅楼1202室


title: EGFR-DN dominant negative 2


title: MSC1, DFO treatment

value: bone marrow

value: Mesenchymal stem cells


title: 3xTgADPolB_F_UA_4

type: RNA

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
ADP_UA_6
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

hyb_protocol: Briefly, the purified RNA was diluted in nuclease-free water to 20 ng/uL. Total RNA, ~100ng, samples were used for hybridization assay. The purified RNA was hybridized using a thermal cycler at 65°C for 16 to 24 hours in nCounter 15 µL of hybridization buffer containing NanoString Reporter and Capture probes. Samples contained 8 μL of Master Mix, 5 µL and 2 µL of Capture ProbeSet to each tube. Maximum hybridization time should not exceed 48 hours.

scan_protocol: Per manufacturer, the nCounter Digital Analyzer, which is a multi-channel epifluorescence scanner, collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a .csv file.

data_processing: RCC format files containing the raw data were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform. Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR).

label: NanoString barcodes

source_name: hippocampus

label_protocol: According to manufacturer, https://nanostring.com/products/ncounter-assays-panels/neuroscience/mouse-and-human-ad/ .

extract_protocol: Hippocampal tissue (5 mg) from the mice were prepared for the extraction of total RNA using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, #12183018A) according to the manufacturer’s protocol.

treatment_protocol: Study was conducted in accordance with animal study protocol, 361-OSD-2023. Mice were group housed and fed ad libitum. WT (C57BL6/J), 3xTgAD, 3xTgAD/PolB +/- transgenic mice were treated with Urolithin A (200 mg/kg per day) by oral gavage for 5 months.

value: hippocampus

tag: strain/background

value: Female

value: 18 months

value: Urolithin A

value: 5 months


title: Chicken preadipocytes - input DNA_rep3

value: Adipose derived-chicken preadipocyte stably overexpressing TCF21 (LV-TCF21)

value: Treatment with oleic acid for 24h


title: 3xTgADPolB_F_UA_3

description:
ADP_UA_5
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

tag: Sex


title: 3xTgADPolB_F_UA_2

description:
ADP_UA_4
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

tag: age


title: 3xTgADPolB_M_UA_2

description:
ADP_UA_2
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

value: Male


title: 3xTgADPolB_M_UA_1

description:
ADP_UA_1
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_F_UA_2

description:
AD_UA_6
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

value: Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm


title: 3xTgAD_M_UA_4

description:
AD_UA_8
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_M_UA_2

description:
AD_UA_2
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_M_UA_3

description:
AD_UA_3
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgADPolB_F_VEH_2

description:
ADP_Veh_5
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

value: Vehicle


title: 3xTgADPolB_F_VEH_1

description:
ADP_Veh_4
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgADPolB_M_VEH_4

description:
ADP_Veh_7
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgADPolB_M_VEH_2

description:
ADP_Veh_2
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgADPolB_M_VEH_1

description:
ADP_Veh_1
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgADPolB_M_VEH_3

description:
ADP_Veh_3
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgADPolB_F_UA_1

description:
ADP_UA_3
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: EGFR-WT wild type 3

value: Bone marrow CD34-KSL cells

tag: cell type

value: CD34- KSL

value: EGFR-WT

value: 0.2 g/L doxycycline


title: 3xTgAD_F_VEH_2

description:
AD_Veh_4
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

tag: genotype


title: 3xTgAD_F_VEH_1

description:
AD_Veh_3
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

tag: treatment


title: 3xTgAD_F_VEH_4

description:
AD_Veh_6
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

tag: tissue


title: 3xTgAD_F_VEH_3

description:
AD_Veh_5
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_M_VEH_3

description:
AD_Veh_7
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_F_UA_3

description:
AD_UA_7
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_M_VEH_2

description:
AD_Veh_2
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_F_UA_1

description:
AD_UA_5
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: 3xTgAD_M_VEH_1

description:
AD_Veh_1
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: WT_F_VEH_4

value: WT


title: WT_F_VEH_3


title: 3xTgAD_M_UA_1

description:
AD_UA_1
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: WT_F_VEH_1


title: WT_F_VEH_2


title: 3xTgADPolB_F_VEH_3

description:
ADP_Veh_6
Heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.


title: WT_M_VEH_3


title: WT_M_VEH_1


title: WT_M_VEH_2


title: Alizarin Sample A at 30 hpf

city: Boston

first: Cynthia

last: Bradham

state: Massachusetts

address: 24 Cummington Mall

institute: Boston University

data_processing:
SOAPnuke developed by BGI.
Sequence Reads were trimmed for Adater Sequence/Low Quality Sequence using Soapnuke.
Trimmed Reads were mapped to the Lvar Genome using STAR 2.7.1a (default paarmeters)
Verse 0.1.5 was used to extarct the counts from the aligned BAM files
Assembly: Lvar Genome 3.0
Supplementary files format and content: comma delimited files having raw counts for all the samples

organism: Lytechinus variegatus

source_name: Whole embryo

extract_protocol:
RNA was harvested using the TRIzol Reagent kit. One microgram of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using the DNBSEQ mRNA-Seq Prep Kit.

value: Whole embryo

tag: developmental stage

value: 30 hpf

value: Alizarin


title: Alizarin Sample B at 30 hpf


title: Alizarin Sample C at 30 hpf


title: Alizarin Sample C at 24 hpf

value: 24 hpf


title: Alizarin Sample A at 24 hpf


title: Alizarin Sample B at 24 hpf


title: 3xTgAD_M_VEH_4

description:
AD_Veh_8
Tg(APPSwe,tauP301)L1Lfa Psen1tm1Mpm on C57BL6/J background.

value: hippocampus

value: 18 months


title: Alizarin Sample C at 18 hpf

value: 18 hpf


title: Alizarin Sample A at 12 hpf

value: 12 hpf


title: Alizarin Sample C at 12 hpf


title: Alizarin Sample B at 18 hpf


title: Control Sample A at 30 hpf

value: Control


title: Control Sample B at 30 hpf


title: Control Sample C at 18 hpf


title: Control Sample C at 24 hpf


title: Control Sample B at 24 hpf


title: Control Sample C at 30 hpf


title: Control Sample A at 18 hpf


title: Control Sample A at 24 hpf


title: Control Sample B at 18 hpf


title: Control Sample C at 12 hpf


title: Control Sample A at 12 hpf


title: Exhausted_rep2

city: Kuala Lumpur

first: Won Fen

last: Wong

address: Lembah Pantai

department: Medical Microbiology

country: Malaysia

institute: Universiti Malaya

description: A total of 366 genes was detected following exclusion of 20 internal reference genes and 382 genes which RNA count is below 20 copies.

hyb_protocol: Total of 100 ng RNA was hybridised in the CodeSet mixture of hybridization buffer, Reporter Probe and Capture Probe at 65ᵒC for overnight following manufacturer protocols. Hybridised samples were transferred to nCounter PrepStation for excess probes washing and sample immobilisation on a sample cartridge for 3 hours.

scan_protocol: The sample cartridge was further processed for 2 hours in the nCounter Digital Analyzer where hydridised complexes were scanned and read as direct RNA count in the nCounter MAX/FLEX. 555 fields of view (FOV) were collected per cartridge lane which corresponds to the number of reporters counted.

data_processing: Raw data were normalised using internal positive and negative controls as well as reference genes. Digital gene expression with RNA count below 20 copies in all comparison groups were removed from the analysis.

label: 6-spots of flourescence barcode

source_name: HIV infection

label_protocol: RNA was labelled with CodeSet that hybridised directly to the RNA target. Each probe pair consists of a colour-coded reporter probe and a capture probe that immobilises the hybridised complexfor data collection.

extract_protocol: Total PBMCs were pooled from five different samples of high viremic PLWH. RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA), and quantified using Nanodrop.

tag: viremia status

value: High viremic

tag: final rna concentration


title: Effector_rep1


title: Effector_rep2


title: PD1-Effector_rep2


title: PD1-Effector_rep1


title: Exhausted_rep1


title: Late_rep1


title: Intermediate_rep1


title: Intermediate_rep2


title: Late_rep2


title: LN, SMNP, replicate 1

city: Cambridge

first: Darrell

middle: J.

last: Irvine

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v7.1.0
Assembly: Mmul_10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: Lymph node

extract_protocol:
The inguinal LNs of vaccinated macaques were isolated 48 hours post-immunization. The collected lymph nodes were mechanically dissociated into a single cell suspension. Cells were filtered, counted, and resuspended in freezing medium before storage in liquid nitrogen and at -120C for subsequent analysis by single cell RNA sequencing.
Library construction was perfomed according to the manufacture's instruction (single cell 5` v2 protocol, 10x Genomics).

value: Lymph node

value: Live CD3lowCD8lowCD20low single cells

value: MD39 + SMNP

value: 3 - 4 years old

value: female


title: LN, SMNP, replicate 3

description: 10x Genomics


title: Naïve_rep1

value: Healthy control


title: LN, alum, replicate 3

description: 10x Genomics

value: MD39 + alum


title: Early_rep1


title: LN, alum, replicate 2

description: 10x Genomics


title: LN, control, replicate 1

description: 10x Genomics

value: control, nothing


title: Naïve_rep2


title: LN, alum, replicate 1

description: 10x Genomics


title: Alizarin Sample B at 12 hpf

value: Whole embryo


title: Input

city: Toronto

first: Matthew

last: Eroglu

state: ON

address: 686 Bay St

department: DSCB

country: Canada

institute: Hospital for Sick Children

data_processing:
adaptor removal with Cutadapt (https://github.com/marcelm/cutadapt) on Galaxy (https://usegalaxy.eu/)
UMI extraction with UMI-tools (https://github.com/CGATOxford/UMI-tools) on Galaxy
alignment with RNA STAR (https://github.com/alexdobin/STAR) on Galaxy
deduplication with UMI-tools on Galaxy
peak calling with PEAKachu (https://github.com/tbischler/PEAKachu) on Galaxy
coverage calculated with bamcoverage deepTools2 (https://github.com/deeptools/deepTools) on Galaxy
Genome_build: WS253
Supplementary_files_format_and_content: peak files, tabular; coverage plots, bigwig

organism: Caenorhabditis elegans

source_name: Whole worm lysate

growth_protocol: Standard NGM

extract_protocol:
RNA crosslinked to affinity purified MSTR-1::FLAG
eCLIP
CLIP-seq

treatment_protocol: UV 1.2mJ/cm2

tag: Stage

value: Young adult

tag: temperature


title: MSTR-1::FLAG CLIP2


title: N2 CLIP


title: Control Sample B at 12 hpf


title: Human aortic endothelial cells, 48h DF, rep1

city: Los Angeles

first: Soon-Gook

last: Hong

state: California

address: 630 Charles E Young Dr S

department: Medicine

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
The alignment was performed using Spliced Transcripts Alignment to a Reference (STAR) using the human reference genome assembly GRCh38.
The Ensembl Transcripts release GRCh38.107 GTF was used for gene feature annotation.
For normalization of transcripts counts, counts per million (CPM) normalized counts were generated by adding 1.0E-4 followed by CPM normalization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: HAECs

growth_protocol: Primary HAECs (Cell Applications #S304-05a) were used from P4-P12. For cell culture experiments, MCDB-131 complete media (VEC Technologies #MCDB-131 Complete) was supplemented with 10% FBS (Omega USDA certified FBS #FB-11). For plating cells on cell culture dishes, 0.1% gelatin (Stemcell #07903) coating was first applied. Cells were cultured in a 37 °C incubator with 5% CO2.

extract_protocol:
After 48 h flow application, cells were washed with 1X PBS (Gibco #14190-144) and then lysed using RLT lysis buffer (QIAGEN #79216) plus 1% 2-Mercaptoethanol (Sigma Aldrich #M6250). For each condition, four µ-Slides were combined as one flow-exposed sample for a total of 12 slides for n = 3 samples.
Libraries for RNA sequencing were prepared using KAPA Stranded mRNA-Seq Kit (KAPA Biosystems #KK8421).

treatment_protocol: HAECs were seeded in ibidi µ-Slide 0.2 (ibidi #80166) or 0.6 (ibidi #80186) Luer ibiTreat. Unidirectional laminar flow (20 dynes/cm2) or disturbed flow (±4 dynes/cm2, 2 Hz) was applied to confluent monolayers using the ibidi pump system (ibidi #10902) for 48 hrs.

tag: cell line

value: HAECs

value: Human aortic endothelial cells

value: WT

value: 48h DF


title: Human aortic endothelial cells, 48h DF, rep3


title: Human aortic endothelial cells, 48h DF, rep2


title: Human aortic endothelial cells, 48h UF, rep3

value: 48h UF


title: Human aortic endothelial cells, 48h UF, rep2


title: Human aortic endothelial cells, 48h UF, rep1


title: (+Glc) KO2 RNAseq exp2

first: Cunyu

last: Wang

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

description: High glucose condition

data_processing:
FASTQ sequences were mapped to human genome hg38(GRCh38) by Hisat2.
For the uniquely mapped reads, FeatureCounts were used to count the reads mapped to each gene
Supplementary files format and content: raw gene count

source_name: SCC23 HNSCC cells

growth_protocol: Human HNSCC cell line SCC23 was obtained from the University of Michigan, SCC46 and SCC74A cells were from Dr. Zhong Chen’s lab (National Institutes of Health) with permission from Dr. Thomas E. Carey (University of Michigan). These cell lines were maintained in high glucose DMEM (Thermo Fisher Scientific, Cat#11995065) containing 10% FBS and 1% antibiotics at 37°C in a 5% CO2 atmosphere.

extract_protocol:
RNA was extracted by RNAeasy kit(Thermo)
Neb UTRL2 RNAseq with PolyA mRNA

treatment_protocol: To generate KMT2D knockout cell lines, SCC23 and SCC1 cells were transfected with pSpCas9(BB)-2A-GFP plasmid (Addgene, Cat#48138) containing sgRNA targeting either LacZ or KMT2D for 24 hours.

value: SCC23 HNSCC cells

value: HNSCC

value: KMT2D Knockout

value: KO


title: (+Glc) WT2 RNAseq exp2

description: High glucose condition

value: control


title: LN, SMNP, replicate 2

description: 10x Genomics

value: Lymph node

value: Live CD3lowCD8lowCD20low single cells

value: MD39 + SMNP

value: 3 - 4 years old


title: Early_rep2

value: High viremic


title: (+Glc) KO1 RNAseq exp2

description: High glucose condition


title: NGWT-H3K9me3

data_processing:
ChIP-Seq reads were mapped to human genome hg19(GRCh37) by bowtie2
MACS2 was used for calling KMT2D peak with P value less than 0.01
Deeptools were used to generating bigwig file for each sample
Supplementary files format and content: Bigwig for genome covering reads
Supplementary files format and content: Peak files generated by MACS2

extract_protocol:
Briefly, cells were incubated in 1% formaldehyde for 10 minutes at RT for cross-linking. A final concentration of 1×glycine solution was added to the medium to stop cross-linking. The crosslinked cells were rinsed with ice-cold PBS and lysed with membrane extraction buffer containing protease/phosphatase inhibitors. Nuclei were extracted and sonicated to generate 200-500 bp chromatin fragments.
ChIP assays were performed using Pierce™ Magnetic ChIP Kit (Thermo Fisher Scientific, Cat#26157) following the manufacturer’s instructions.

value: HNSCC cells

value: Wild Type

value: Anti H3K9me3

value: Low Glucose condition


title: MSTR-1::FLAG CLIP1

value: Young adult


title: NGKO-H3K4me3

value: KMT2D Knock out

value: Anti H3K4me3


title: NGKO-H3

value: Anti H3


title: PDX-KMT2D mutation

data_processing:
Clean reads were obtained by TrimGalore
Clean reads were mapped to human genome hg19(GRCh37) by bowtie2
BCFTOOLs were used to call SNP with the sorted bam as input
Assembly: hg19
Supplementary files format and content: BCF file generated by bcftools with SNP information
Library strategy: Exome-seq

source_name: HNSCC pdx

extract_protocol:
DNA was extracted by Qiagen DNA Extraction Kits
Whole Exome Sequencing Library Prep with NimbleGen Seqcap Kit

value: HNSCC pdx


title: NGWT-H3


title: NGKO-H3K9me3


title: NGWT-H3K4me3


title: Kin_ct

value: Input


title: NGKO-H3K27me3

value: Anti H3K27me3


title: NGWT-H3K27ac

value: Anti H3K27ac


title: NGWT-H3K4me1

value: Anti H3K4me1


title: KD_ct

value: Anti KMT2D


title: NGKO-H3K4me1


title: 5G2

first: Lili

last: Yang

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

data_processing:
The reads were mapped with STAR 2.5.3a to the human genome (hg38). The counts for each gene were obtained by using –quantMode GeneCounts in STAR commands, and the other parameters during alignment were set to default. Differential expression analyses were carried out using DESeq2. Counts normalized by sequencing depth were obtained using DESeq2 estimateSizeFactors function with default parameters. Principle component analysis (PCA) was performed on the log10 normalized counts using the R function prcomp. Genes with adjusted p value < 0.05 were considered significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes normalized raw counts

source_name: PBMC

extract_protocol:
T cells were activated and expanded from PBMCs with either Beads3/28 (αCD3 and αCD28 on commercial beads) with external IL-2 (30U/ml) or GO-APP3/28 (αCD3 and αCD28 on graphene oxide antigen presenting platform) in absence of external IL-2. T cells were collected 7 days after activation. RNA was extracted subsequently with miRNeasy Micro Kit (Qiagen).
RNA libraries were prepared by the Technology Center for Genomics & Bioinformatics at UCLA using TruSeq Stranded Total RNA Sample Prep kit (Illumina) and sequenced with 50bp single end reads on an Illumina HiSeq3000.

value: PBMC-derived T cells

value: PBMC

tag: agent

value: with IL2

tag: donor


title: 5G

value: without


title: 4G2


title: NGKO-H3K27ac

value: HNSCC cells


title: 4G


title: 3G2


title: (+Glc) WT1 RNAseq exp2

description: High glucose condition

value: SCC23 HNSCC cells

value: HNSCC

value: WT

value: control


title: 3G


title: 2G


title: 4B2

value: Beads


title: 3B


title: 5B


title: 3B2


title: 4B


title: 2B2


title: 3T3, LTAlpha1Beta2, 24hr

city: Beijing

first: Hanqiu

last: Zheng

address: Haidian District

institute: Tsinghua university

data_processing:
Quality control, sequence mapping, and counts for each gene were performed following similar protocols as in scRNA-Seq. Gene expression matrix was normalized by using EdgeR (v3.30.0) package (Robinson et al., 2010) and carried out as counts per million (CPM) form.
Assembly: not provided
Supplementary files format and content: Comma-separated text file includes CPM values for each Sample.

extract_protocol:
Total RNA was isolated from cells using RNAiso Plus Regent (Takara, Cat# 9108) following the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat# E7765) was used to generate sequencing libraires from 1 μg of total RNA. All library preparations were conducted according to the manufacturer’s instructions. Paired-end 150bp sequencing was performed using an Illumina NovaSeq platform.

value: pre-osteoblast cell line

tag: time point


title: 3T3, LTAlpha1Beta2, 48hr


title: 3T3, NC, 24hr


title: 3T3, NC, 48hr


title: 4T1.2, Cell, Line, single cell 53

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)

tag: host

value: Female BALB/c mice

value: metastatic tumor cells


title: 4T1.2, Cell, Line, single cell 51


title: 4T1.2, Cell, Line, single cell 49


title: 4T1.2, Cell, Line, single cell 54


title: 4T1.2, Cell, Line, single cell 52


title: 4T1.2, Cell, Line, single cell 47


title: 4T1.2, Cell, Line, single cell 50


title: 4T1.2, Cell, Line, single cell 48


title: 2G2


title: 4T1.2, Cell, Line, single cell 45


title: 5B2


title: 4T1.2, Cell, Line, single cell 44


title: BCWM-1 WM cell line-untreated-replicate 1

city: Milan

first: Antonino

middle: of

last: Neri

address: Via Festa del Perdono 7

institute: University of Milan

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hr 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The Gene 1.0 ST arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: The raw intensity expression values were processed by Robust Multi-array Average procedure (RMA), with the re-annotated Chip Deﬁnition Files from BrainArray libraries version 19.0.0, available at http://brainarray.mbni.med.umich.edu.

label: biotin

source_name: BCWM-1 WM

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: BCWM-1 cells  were provided by DFCI (Boston, MA) and cultured as 5-x105 cells/ml in RPMI supplemented with 20% FBS.

extract_protocol: Cell pellets were resuspended in TRIzol Reagent (Life Technologies, Inc., Rockville, MD, USA), total RNA was then purified using the RNeasy® total RNA Isolation Kit (Qiagen, Valencia, CA).

treatment_protocol: BCWM-1 cells were treated with G-1  1microM for 48hours before undergoing GEP microarray analysis

value: BCWM-1 WM

value: untreated


title: 2B


title: 4T1.2, Cell, Line, single cell 41


title: 4T1.2, Cell, Line, single cell 42


title: 4T1.2, Cell, Line, single cell 46


title: 4T1.2, Cell, Line, single cell 38


title: 4T1.2, Cell, Line, single cell 43


title: 4T1.2, Cell, Line, single cell 40


title: 4T1.2, Cell, Line, single cell 36


title: 4T1.2, Cell, Line, single cell 35


title: BCWM-1 WM cell line-untreated-replicate 2


title: 4T1.2, Cell, Line, single cell 34


title: 4T1.2, Cell, Line, single cell 33


title: 4T1.2, Cell, Line, single cell 32


title: 4T1.2, Cell, Line, single cell 31


title: 4T1.2, Cell, Line, single cell 30


title: 4T1.2, Cell, Line, single cell 28


title: 4T1.2, Cell, Line, single cell 29


title: 4T1.2, Cell, Line, single cell 26


title: BCWM-1 WM cell line-treated with GPER1 selective agonist (G-1)-replicate 1

value: GPER1 selective agonist (G-1)


title: 4T1.2, Cell, Line, single cell 27


title: 4T1.2, Cell, Line, single cell 24


title: 4T1.2, Cell, Line, single cell 25


title: BCWM-1 WM cell line-treated with GPER1 selective agonist (G-1)-replicate 2


title: 4T1.2, Cell, Line, single cell 23


title: 4T1.2, Cell, Line, single cell 22


title: 4T1.2, Cell, Line, single cell 21


title: 4T1.2, Cell, Line, single cell 20


title: 4T1.2, Cell, Line, single cell 19


title: 4T1.2, Cell, Line, single cell 17


title: 4T1.2, Cell, Line, single cell 18


title: 4T1.2, Cell, Line, single cell 13


title: 4T1.2, Cell, Line, single cell 14


title: 4T1.2, Cell, Line, single cell 12


title: 4T1.2, Cell, Line, single cell 11


title: 4T1.2, Cell, Line, single cell 16


title: 4T1.2, Cell, Line, single cell 15


title: 4T1.2, Cell, Line, single cell 10


title: 4T1.2, Cell, Line, single cell 9


title: 4T1.2, Cell, Line, single cell 6


title: 4T1.2, Cell, Line, single cell 5


title: 4T1.2, Cell, Line, single cell 7


title: 4T1.2, Cell, Line, single cell 4


title: 4T1.2, Cell, Line, single cell 3


title: 4T1.2, Cell, Line, single cell 1


title: 4T1.2, Day4, single cell 242


title: 4T1.2, Cell, Line, single cell 2


title: 4T1.2, Day4, single cell 239


title: 4T1.2, Day4, single cell 243


title: 4T1.2, Day4, single cell 241


title: 4T1.2, Day4, single cell 240


title: 4T1.2, Day4, single cell 238


title: 4T1.2, Cell, Line, single cell 39


title: 4T1.2, Day4, single cell 235


title: 4T1.2, Day4, single cell 236


title: 4T1.2, Day4, single cell 234


title: 4T1.2, Day4, single cell 232


title: 4T1.2, Day4, single cell 233


title: 4T1.2, Cell, Line, single cell 8


title: 4T1.2, Day4, single cell 230


title: 4T1.2, Day4, single cell 228


title: 4T1.2, Day4, single cell 227


title: 4T1.2, Day4, single cell 229


title: 4T1.2, Day4, single cell 225


title: 4T1.2, Day4, single cell 222


title: 4T1.2, Day4, single cell 223


title: 4T1.2, Day4, single cell 224


title: 4T1.2, Day4, single cell 218


title: 4T1.2, Day4, single cell 217


title: 4T1.2, Day4, single cell 219


title: 4T1.2, Day4, single cell 220


title: 4T1.2, Day4, single cell 237


title: 4T1.2, Day4, single cell 216


title: 4T1.2, Day4, single cell 215


title: 4T1.2, Day4, single cell 214


title: 4T1.2, Day4, single cell 213


title: 4T1.2, Day4, single cell 212


title: 4T1.2, Day4, single cell 211


title: 4T1.2, Day4, single cell 231


title: 4T1.2, Day4, single cell 210


title: 4T1.2, Day4, single cell 209


title: NGWT-H3K27me3

value: Wild Type

value: Anti H3K27me3

value: Low Glucose condition


title: 4T1.2, Day4, single cell 208


title: 4T1.2, Day4, single cell 202


title: 4T1.2, Day4, single cell 207


title: 4T1.2, Day4, single cell 226


title: 4T1.2, Day4, single cell 205


title: 4T1.2, Day4, single cell 204


title: 4T1.2, Day4, single cell 203


title: 4T1.2, Day4, single cell 201


title: 4T1.2, Day4, single cell 200


title: 4T1.2, Day4, single cell 221


title: 4T1.2, Day4, single cell 199


title: 4T1.2, Day4, single cell 198


title: 4T1.2, Day4, single cell 197


title: 4T1.2, Day4, single cell 196


title: 4T1.2, Day4, single cell 195


title: 4T1.2, Day4, single cell 193


title: 4T1.2, Day4, single cell 194


title: 4T1.2, Day4, single cell 191


title: 4T1.2, Day4, single cell 189


title: 4T1.2, Day4, single cell 192


title: 4T1.2, Day4, single cell 188


title: 4T1.2, Day4, single cell 190


title: 4T1.2, Day4, single cell 187


title: 4T1.2, Day4, single cell 186


title: 4T1.2, Day4, single cell 206


title: 4T1.2, Day4, single cell 184


title: 4T1.2, Day4, single cell 182


title: 4T1.2, Day4, single cell 185


title: 4T1.2, Day4, single cell 181


title: 4T1.2, Day4, single cell 179


title: 4T1.2, Day4, single cell 180


title: 4T1.2, Day4, single cell 177


title: 4T1.2, Day4, single cell 178


title: 4T1.2, Day4, single cell 175


title: 4T1.2, Day4, single cell 173


title: 4T1.2, Day4, single cell 174


title: 4T1.2, Day4, single cell 168


title: 4T1.2, Day4, single cell 171


title: 4T1.2, Day4, single cell 167


title: 4T1.2, Day4, single cell 165


title: 4T1.2, Cell, Line, single cell 37


title: 4T1.2, Day4, single cell 172


title: 4T1.2, Day4, single cell 169


title: 4T1.2, Day4, single cell 166


title: 4T1.2, Day4, single cell 164


title: 4T1.2, Day4, single cell 163


title: 4T1.2, Day4, single cell 160


title: 4T1.2, Day4, single cell 158


title: 4T1.2, Day4, single cell 159


title: 4T1.2, Day4, single cell 183


title: 4T1.2, Day4, single cell 157


title: 4T1.2, Day4, single cell 176


title: 4T1.2, Day4, single cell 156


title: 4T1.2, Day4, single cell 155


title: 4T1.2, Day4, single cell 153


title: 4T1.2, Day4, single cell 170


title: 4T1.2, Day4, single cell 152


title: 4T1.2, Day4, single cell 151


title: 4T1.2, Day4, single cell 150


title: 4T1.2, Day4, single cell 149


title: 4T1.2, Day4, single cell 154


title: 4T1.2, Day4, single cell 147


title: 4T1.2, Day4, single cell 145


title: 4T1.2, Day4, single cell 143


title: 4T1.2, Day4, single cell 140


title: 4T1.2, Day4, single cell 141


title: 4T1.2, Day4, single cell 138


title: 4T1.2, Day4, single cell 142


title: 4T1.2, Day4, single cell 137


title: 4T1.2, Day4, single cell 135


title: 4T1.2, Day4, single cell 134


title: 4T1.2, Day4, single cell 133


title: 4T1.2, Day4, single cell 131


title: 4T1.2, Day4, single cell 132


title: 4T1.2, Day4, single cell 127


title: 4T1.2, Day4, single cell 130


title: 4T1.2, Day4, single cell 129


title: 4T1.2, Day4, single cell 126


title: 4T1.2, Day4, single cell 148


title: 4T1.2, Day4, single cell 124


title: 4T1.2, Day4, single cell 123


title: 4T1.2, Day4, single cell 146


title: 4T1.2, Day4, single cell 128


title: 4T1.2, Day4, single cell 121


title: 4T1.2, Day4, single cell 125


title: 4T1.2, Day4, single cell 144


title: 4T1.2, Day4, single cell 122


title: 4T1.2, Day4, single cell 120


title: 4T1.2, Day4, single cell 119


title: 4T1.2, Day4, single cell 117


title: 4T1.2, Day4, single cell 118


title: 4T1.2, Day4, single cell 116


title: 4T1.2, Day4, single cell 136


title: 4T1.2, Day4, single cell 114


title: 4T1.2, Day4, single cell 115


title: 4T1.2, Day4, single cell 139


title: 4T1.2, Day4, single cell 110


title: 4T1.2, Day4, single cell 113


title: 4T1.2, Day4, single cell 108


title: 4T1.2, Day4, single cell 107


title: 4T1.2, Day4, single cell 111


title: 4T1.2, Day4, single cell 109


title: 4T1.2, Day4, single cell 102


title: 4T1.2, Day4, single cell 101


title: 4T1.2, Day4, single cell 99


title: 4T1.2, Day4, single cell 105


title: 4T1.2, Day4, single cell 100


title: 4T1.2, Day4, single cell 103


title: 4T1.2, Day4, single cell 98


title: 4T1.2, Day4, single cell 95


title: 4T1.2, Day4, single cell 96


title: 4T1.2, Day4, single cell 93


title: 4T1.2, Day4, single cell 112


title: 4T1.2, Day4, single cell 86


title: 4T1.2, Day4, single cell 91


title: 4T1.2, Day4, single cell 89


title: 4T1.2, Day4, single cell 88


title: 4T1.2, Day4, single cell 106


title: 4T1.2, Day4, single cell 92


title: 4T1.2, Day4, single cell 85


title: 4T1.2, Day4, single cell 90


title: 4T1.2, Day4, single cell 104


title: 4T1.2, Day4, single cell 83


title: 4T1.2, Day4, single cell 84


title: 4T1.2, Day4, single cell 82


title: 4T1.2, Day4, single cell 78


title: 4T1.2, Day4, single cell 94


title: 4T1.2, Day4, single cell 97


title: 4T1.2, Day4, single cell 81


title: 4T1.2, Day4, single cell 76


title: 4T1.2, Day4, single cell 80


title: 4T1.2, Day4, single cell 79


title: 4T1.2, Day4, single cell 73


title: 4T1.2, Day4, single cell 75


title: 4T1.2, Day4, single cell 77


title: 4T1.2, Day4, single cell 74


title: 4T1.2, Day4, single cell 71


title: 4T1.2, Day4, single cell 69


title: 4T1.2, Day4, single cell 72


title: 4T1.2, Day4, single cell 70


title: 4T1.2, Day4, single cell 87


title: 4T1.2, Day4, single cell 68


title: 4T1.2, Day4, single cell 65


title: 4T1.2, Day4, single cell 66


title: 4T1.2, Day4, single cell 64


title: 4T1.2, Day4, single cell 60


title: 4T1.2, Day4, single cell 63


title: 4T1.2, Day4, single cell 61


title: 4T1.2, Day4, single cell 62


title: 4T1.2, Day4, single cell 58


title: 4T1.2, Day4, single cell 54


title: 4T1.2, Day4, single cell 56


title: 4T1.2, Day4, single cell 55


title: 4T1.2, Day4, single cell 59


title: 4T1.2, Day4, single cell 51


title: 4T1.2, Day4, single cell 52


title: 4T1.2, Day4, single cell 53


title: 4T1.2, Day4, single cell 45


title: 4T1.2, Day4, single cell 47


title: 4T1.2, Day4, single cell 48


title: 4T1.2, Day4, single cell 46


title: 4T1.2, Day4, single cell 49


title: 4T1.2, Day4, single cell 67


title: 4T1.2, Day4, single cell 44


title: 4T1.2, Day4, single cell 42


title: 4T1.2, Day4, single cell 43


title: 4T1.2, Day4, single cell 39


title: 4T1.2, Day4, single cell 57