title: DU19-01S0003492, MSSA, scATACseq

description:
DU19_01S0003492
Staph_scATAC_integration.tar


title: 12F_M_84

status: Public on May 19 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: hmC.ASDS.C.CX.1

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: Illumina Hiseq 2000

data_processing:
Data mapping and processing was performed as previously described [18]. Briefly, bowtie2 (v2.3.5.1) [351] was used to map pair-end reads to the mm9 reference genome followed by MACS2 peak calling (v 2.1.2) [352]. Technical replicates were combined using the bedtools (v2.28.0)   “window” function with a 300bp extension applied up and downstream of the peak. Only the common peaks in all the replicates were considered for further analysis. Peaks were then annotated to their corresponding genes using HOMER (Hypergeometric Optimization of Motif EnRichment) (v4.11.1) [353] and the flag “-annStat” was added to annotate these peaks to genomic features. Raw RNA-seq reads were aligned to the mouse mm9 genome using TopHat2 (v2.1.0) [354] and differential gene expression analysis was conducted using Cuffdiff (v2.2.1).
Assembly: mm9

source_name: Cortex

extract_protocol:
In brief, 5mg of genomic DNA was sonicated to 300-400 base pairs and 5hmC containing fragments were glucosylated (T4 phage ß-glucosyltransferase enzyme and UDP-6-N3-glucose). The glucosylated fragments were purified and then biotinylated (disulfide biotin linker) and pulled down with Dynabeads MyOne Streptavidin C1 beads. The 5hmC fragments were released from the beads using dithiothreitol and purified for a final time. DNA fragments were eluted in nuclease-free water and quantified by Qubit. 5mC: 3mg of genomic DNA was sonicated to 300-400 base pairs using a Covaris focused ultrasonicator. The DNA fragments were then subjected to end repair, A-tailing, adaptor ligation and USER digestion using the NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs, E7645S) according to the manufacturer’s protocol. Following USER digestion and purification, DNA was denatured for 10 minutes at 95°C and immunoprecipitated overnight at 4°C with 4mL of either 5mC antibody (Active Motif, 39649) or IgG antibody (Sigma 12-371) in IP buffer (500mM Tris-HCl, pH 7.4, 750mM NaCl and 0.25% TritonX). The mixture was then incubated with Protein G coated Dynabeads for at least 2 hours at 4°C, washed with ice cold IP buffer and finally washed in ice cold high salt (300mM NaCl) IP buffer. After the final washing, the beads were treated with 200mL digest buffer (1X TE Buffer, pH 7.4, 0.25% SDS, 0.25% Proteinase K (2.5mg/mL)) and shaken at 1000rpm for 2 hours at 55°C. The methylated DNA was recovered by phenol:chloform:isoamyl alcohol (25:24:1) extraction followed by precipitation in 3X volume of 100% ethanol supplemented with 3mL glycogen(5mg/mL) and 15mL NaAC pH 5.2 overnight at -20°C. The next day, the DNA was pelleted and washed with 75% ethanol and dissolved in nuclease-free water. Illumina indexes were added, PCR enriched and purified using the NEBNext Ultra II DNA Library Prep kit for Illumina following the manufacturer’s protocol.
The NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs, E7645S) was used per the manufacturer’s protocol for enriched and unenriched genomic DNA. An Agilent 2100 Bioanalyzer was used to confirm purity and fragmentation size of the final libraries. Libraries were sequenced pair-end (150bp) on an Illumina HiSeq platform by Admera Health, LLC.

tag: seq

value: ChIP

tag: genotype

value: WT


title: DU19-01S0003482, MSSA, scATACseq

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description:
DU19_01S0003482
Staph_scATAC_integration.tar

library_source: genomic single cell

data_processing:
Reads of scATAC-seq experiments were aligned to the GRCh38 (hg38) human reference genome using cellranger-atac software (10x Genomics; version 1.2 or 1.0). The resulting fragment files were processed using ArchR [PMID: 33633365].
Assembly: hg38
Supplementary files format and content: tar file contains the integrated data of all samples

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Thawed PBMCs were washed with PBS/0.04% BSA. Cells were counted and 100,000-1,000,000 cells were added to a 2 mL-microcentrifuge tube. Cells were centrifuged at 300xg for 5min at 4°C. The supernatant carefully completely removed, and 0.1X lysis buffer (1x: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 3 min incubation on ice, 1 ml of chilled wash buffer was added. The nuclei were pelted at 500 xg for 5 min at 4°C and resuspended in a chilled diluted nuclei buffer (10X Genomics) for scATAC-seq. Nuclei were counted and the concentration was adjusted to run the assay.
ScATAC-seq was performed immediately after nuclei isolation and following the Chromium Single Cell ATAC Reagent Kits V1.1 User Guide (10x Genomics, Pleasanton, CA). Transposition was performed in 10 ul at 37°C for 60 min on at least 1,000 nuclei, before loading of the Chromium Chip H (PN-2000180). Barcoding was performed in the emulsion (12 cycles) following the Chromium protocol. After post GEM cleanup, libraries were prepared following the protocol and were indexed for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000427). Each library was assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit).

tag: tissue

value: PBMC

tag: disease state

value: MSSA

tag: Sex

value: Male


title: 12F_M_85


title: 12F_M_88


title: hmC.6CSDS.SS.CX.2

description: Illumina Hiseq 2000


title: 12F_M_82


title: DU19-01S0003466, MSSA, scATACseq

description:
DU19_01S0003466
Staph_scATAC_integration.tar


title: DU19-01S0003464, MSSA, scATACseq

description:
DU19_01S0003464
Staph_scATAC_integration.tar

value: Female


title: hmC.6CSDS.SS.CX.1

description: Illumina Hiseq 2000


title: hmC.6CSDS.SR.CX.3

description: Illumina Hiseq 2000


title: 12F_M_81


title: OU_102

type: RNA

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

description: Training

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.

data_processing: Probe intensities were normalized with Robust Multichip Analysis

label: biotin

molecule: total RNA

source_name: Training with random primer

label_protocol: RNA (50 ng) was subjected to the generation of second-strand combinational DNA (cDNA), and cRNA was amplified with a random primer (WT-Ovation FFPE RNA Amplification System V2; NuGEN, Cincinnati, Ohio). Next, the amplified cRNA was biotinylated and fragmented with the FL-Ovation cDNA Biotin Module V2 (NuGEN).

extract_protocol: Trizol (Invitrogen, Carlsbad, Calif) was used to extract RNA from core-needle tumor biopsy samples that were obtained with the Mammotome.

treatment_protocol: Patients prospectively consented to a research biopsy by vacuum-assisted core-biopsy instrument (Mammotome 8G; HH Ethicon Endosurgery, Johnson and Johnson Company) under ultrasonographic guidance for histologic examination and gene expression analysis prior to any systemic therapy, and to the future assessment of pathologic response

value: greater than 50

tag: ct

tag: cn

value: Positive

tag: er

value: Negative

tag: hg

value: wP-FEC

value: Non-pCR

value: LumB


title: DU19-01S0003462, MSSA, scATACseq

description:
DU19_01S0003462
Staph_scATAC_integration.tar


title: OU_101

description: Training

value: less than or equal to 50

value: Basal


title: hmC.CSDS.SS.CX.4

description: Illumina Hiseq 2000


title: hmC.6CSDS.C.CX.2

description: Illumina Hiseq 2000


title: OU_100

description: Validation

source_name: Validation with random primer

value: LumA


title: DU19-01S0003453, MSSA, scATACseq

description:
DU19_01S0003453
Staph_scATAC_integration.tar


title: hmC.CSDS.SS.CX.3

description: Illumina Hiseq 2000


title: BWJ0023, Control, scATACseq

description:
BWJ0023
Staph_scATAC_integration.tar

value: Control


title: 12F_M_78


title: 12F_M_83


title: OU_099

description: Validation


title: 12F_M_79


title: 12F_M_80


title: OU_097

description: Training

value: pCR (ypT0/N0)


title: OU_098

description: Training


title: OU_095

description: Validation


title: OU_096

description: Validation


title: hmC.CSDS.SR.CX.4

description: Illumina Hiseq 2000

value: ChIP


title: hmC.6CSDS.C.CX.4

description: Illumina Hiseq 2000

value: WT


title: 12F_M_77


title: BMI0102, Control, scATACseq

description:
BMI0102
Staph_scATAC_integration.tar

value: PBMC


title: BMI0101, Control, scATACseq

description:
BMI0101
Staph_scATAC_integration.tar


title: OU_094

description: Training


title: OU_092

description: Validation


title: BMI0099, Control, scATACseq

description:
BMI0099
Staph_scATAC_integration.tar


title: hmC.CSDS.C.CX.3

description: Illumina Hiseq 2000


title: 12F_M_75


title: BMI0095, Control, scATACseq

description:
BMI0095
Staph_scATAC_integration.tar


title: 12F_M_74


title: OU_093

description: Validation


title: OU_090

description: Training


title: BMI0094, Control, scATACseq

description:
BMI0094
Staph_scATAC_integration.tar


title: Input.Stress.CX

description: Illumina Hiseq 2000

tag: chip antibody

value: IgG antibody (Sigma 12-371)


title: BMI0093, Control, scATACseq

description:
BMI0093
Staph_scATAC_integration.tar


title: SAM20862166

city: South San Francisco

first: James

last: Maksymetz

address: 1 DNA Way

department: Neuroscience

institute: Genentech, Inc

library_source: transcriptomic

data_processing:
The fastq sequence files for all RNA-seq samples were filtered for read quality and ribosomal RNA contamination. The remaining reads were then aligned to the mouse reference genome (GRCm38) using the GSNAP alignment tool (Wu and Nacu, 2010). Alignments were produced using the following GSNAP parameters: ‘-M 2 n 10 -B 2 -i 1 N 1 w 200000 -E 1 –pairmax-rna = 200000 –clip-overlap’. These steps, and the downstream processing of the resulting alignments to obtain read counts and normalized Reads Per Kilobase Million (nRPKMs) per gene (over all exons of RefSeq gene models), are implemented in the Bioconductor package, HTSeqGenie (v 3.12.0) (Pau and Reeder, 2014). Only uniquely mapped reads were used for further analysis.
Assembly: mm10
Supplementary files format and content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene counts, gene length, and RPKM values

source_name: Dorsal root ganglia

extract_protocol:
Lumbar DRGs L4, L5, L6  (6 DRGs) from one mouse were used per biological replicate. DRGs were isolated and total RNA was purified using a RNeasy-Lipid Tissue Kit (7400, Qiagen).
RNA samples passing a mRNA quality check were proceeded to sequencing on an Illumina Hiseq 2000.

value: Dorsal root ganglia

tag: animal id

value: 12-18 weeks old

value: Scn9a loxP/loxP, pCAAG.Cre.ER Pos


title: hmC.CSDS.SR.CX.2

description: Illumina Hiseq 2000


title: 12F_M_76


title: BMI0040, Control, scATACseq

description:
BMI0040
Staph_scATAC_integration.tar

value: Male


title: BMI0037, Control, scATACseq

description:
BMI0037
Staph_scATAC_integration.tar

value: Female


title: 12F_M_73


title: 12F_M_71


title: 12F_M_70


title: hmC.CSDS.C.CX.2

description: Illumina Hiseq 2000


title: AS18-00669, Control, scATACseq

description:
AS18_00669
Staph_scATAC_integration.tar


title: 12F_M_69


title: SAM20862164


title: 12F_M_72


title: SAM20862163

value: Scn9a loxP/loxP, pCAAG.Cre.ER Neg


title: Input.Control.CX

description: Illumina Hiseq 2000


title: OU_089

description: Validation

value: Positive

value: Negative

value: wP-FEC


title: OU_091

description: Training

value: greater than 50

value: Basal


title: AS17-02129, Control, scATACseq

description:
AS17_02129
Staph_scATAC_integration.tar

value: Control


title: OU_087

description: Validation

value: Non-pCR


title: OU_086

description: Training

value: less than or equal to 50

value: LumB


title: OU_085

description: Validation

value: LumA


title: SAM20862162


title: SAM20862165


title: AS17-00144, Control, scATACseq

description:
AS17_00144
Staph_scATAC_integration.tar

value: PBMC


title: OU_082

description: Validation


title: OU_083

description: Validation

value: pCR (ypT0/N0)


title: 12F_M_67


title: OU_084

description: Training


title: OU_088

description: Validation


title: SAM20862161

value: Dorsal root ganglia

value: 12-18 weeks old


title: mRNA, ndx1-4, rep2

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

description: ndx1.4_rep2_count, ndx1.4_rep2_fpkm

data_processing:
NGS libraries were sequenced (1x75 bp reads) using an Illumina NextSeq 500 instrument.
Reads were mapped to the A. thaliana reference transcriptome (Araport11, coding and noncoding genes) to quantify gene expression and reads were mapped to transposable elements (Araport11) themselves to quantify their expression using Salmon. Transcript quantities were corrected for GC bias to reduce isoform quantification errors.
Differentially expressed genes and differentially expressed transposable elements between Col-0 and ndx1-4 samples were identified by DESeq2 (FDR < 0.01 and FDR < 0.05 respectively).
For data visualisation, reads were aligned to the A. thaliana reference sequence (TAIR10) using HISAT2 allowing for reporting spliced alignments. We used deepTools bamCoverage to create RPKM (Reads per Kilobase per Million) normalized coverage files.
Assembly: A. thaliana (Araport11)
Supplementary files format and content: Coverage data (bigWig) files are RPKM normalized read coverage data of mapped reads.
Supplementary files format and content: Differentially expressed genes data (tab-delimited text) files are the results of DESeq2 analyses. Comparisons are: ndx1-4 vs Col-0 flower samples, Col-0 flower vs seedling (GSE207842) samples, ndx1-4 flower vs seedling (GSE207842) samples. Data table includes count, FPKM, log2(Fold Change), adjusted p-value of differentially expressed coding and noncoding genes.
Supplementary files format and content: Differentially expressed transposon data (tab-delimited text file) is a result of DESeq2 analysis between Col-0 and ndx1-4 samples. Data table includes count, FPKM, log2(Fold Change), adjusted p-value of differentially expressed transposable elements.

organism: Arabidopsis thaliana

source_name: flower

growth_protocol: Inflorescence tissues of 5-week-old Col-0 and ndx1-4 flowering plants were collected.

extract_protocol:
Total RNA was purified from Col-0 and ndx1-4 flowers using the phenol-chloroform extraction method. The quality of total RNA samples was checked by an Agilent bioanalyzer (RIN > 9).
cDNA libraries were prepared according to Illumina's TruSeq RNA Library Preparation Kit v2 protocol.

value: flower

tag: developmental stage

tag: ecotype

value: ndx1-4 mutant


title: AS13-08590, Control, scATACseq

description:
AS13_08590
Staph_scATAC_integration.tar

value: Male


title: 12F_M_65


title: 12F_M_66


title: mRNA, ndx1-4, rep1

description: ndx1.4_rep1_count, ndx1.4_rep1_fpkm


title: 12F_M_64


title: mRNA, Col-0, rep2

description: col0_rep2_count, col0_rep2_fpkm

value: wild type


title: 12F_M_68


title: AS13-13951, Control, scATACseq

description:
AS13_13951
Staph_scATAC_integration.tar


title: OU_078

description: Validation

value: Positive

value: Negative


title: OU_081

description: Validation

value: greater than 50

value: wP-FEC


title: OU_079

description: Validation


title: OU_080

description: Validation


title: 12F_M_63


title: mRNA, Col-0, rep1

description: col0_rep1_count, col0_rep1_fpkm


title: AS14-03700, Control, scATACseq

description:
AS14_03700
Staph_scATAC_integration.tar

value: Control


title: AS11-18755, Control, scATACseq

description:
AS11_18755
Staph_scATAC_integration.tar


title: 12F_M_62


title: AS11-12162, Control, scATACseq

description:
AS11_12162
Staph_scATAC_integration.tar


title: AS14-00902, Control, scATACseq

description:
AS14_00902
Staph_scATAC_integration.tar


title: Taiping_Ileum_FOS2

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

country: China

institute: Tianshui normal university

data_processing:
Raw reads were further filtered using fastp(version 0.18.0). After removal of reads containing adapters, containing more than 10% of unknown nucleotides (N) and low quality reads containing more than 50% of low quality (Q-value≤20) bases. The rRNA mapped reads were removed by using Short reads alignment tool Bowtie2
The remaining clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1in a reference-based approach.
The expression abundance and variations of each gene was estimated using abundance and variations by calculated FPKM （fragment per kilobase of transcript per million mapped reads）value. RNAs differential expression analysis was performed by DESeq2 between two different groups
The transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed transcripts.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: ileum of Taiping chicken

extract_protocol:
Total RNA of the six libraries  was extracted using the standard TRIzol™. Agarose gel electrophoresis, Nano Photometer® Spectrophotometer and Bioanalyzer 2100 System  were  employed to evaluate the quantity and quality of the total RNAs.
About 3 μg total RNA from each sample was used  to construct RNA library. Six sequencing libraries were generated using the NEBNext® Multiplex small RNA Library Prep Kit for Illumina®

value: Taiping chicken

value: ileum

value: two months

tag: gender

value: male


title: AS11-07881, Control, scATACseq

description:
AS11_07881
Staph_scATAC_integration.tar

value: PBMC


title: OU_077

description: Validation

value: less than or equal to 50

value: Non-pCR

value: LumA


title: Taiping_Ileum_FOS3


title: 12F_M_61

tag: brain region


title: 12F_M_60

tag: age


title: Taiping_Ileum_FOS1

tag: strain


title: AS11-07049, Control, scATACseq

description:
AS11_07049
Staph_scATAC_integration.tar


title: Taiping_Ileum_CT3


title: AS10-21035, Control, scATACseq

description:
AS10_21035
Staph_scATAC_integration.tar


title: 12F_M_59


title: 12F_M_58


title: Taiping_Ileum_CT2


title: OU_075

description: Training


title: OU_076

description: Validation


title: OU_073

description: Training

value: pCR (ypT0/N0)


title: OU_074

description: Training


title: AS09-13278, Control, scATACseq

description:
AS09_13278
Staph_scATAC_integration.tar


title: Taiping_Ileum_CT1


title: AS08-09890, Control, scATACseq

description:
AS08_09890
Staph_scATAC_integration.tar


title: 12F_M_56


title: 12F_M_57


title: 12F_M_55


title: Sample_D3_S69

city: Bristol

first: Ghadir

last: ElSamad

address: Whitson St.

country: United Kingdom

institute: University of Bristol

data_processing:
Original .fastq files were inspected using FastQC. As all samples passed initial QC no further trimming was applied
.fastq were aligned to the rat reference genome (Rn6) using RNA-STAR mapper
Reads were counted using featureCounts at a gene level
Differential expression analysis was performed using DEseq2
Assembly: Rn6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

growth_protocol: Male Wistar Han rats weighing 250–300 g (Envigo) were maintained under a 12:12 light-dark cycle at a constant temperature of 21-22°C and a relative humidity of 40%-50% with ad libitum access to food and water

extract_protocol: RNA extraction protocol not provided.

treatment_protocol: Rats were left to grow until age 18 months old and then dehydrated for 2 days

tag: cell type

value: Hypothalamic supraoptic nucleus

value: Wistar Han

tag: treatment

value: Dehydrated

value: 3 months


title: Sample_D4_S70


title: Sample_D5_S71


title: 12F_M_53


title: Sample_D2_S68


title: Sample_D1_S67


title: HC3

city: Darlinghurst

first: Cindy

middle: S.

state: New South Wales

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description: Healthy control

data_processing:
Raw fastq files were obatined using bcl2fastq2 Conversion Software v2.20 (Illumina).
Processed data were not produced for these samples.
Assembly: hg38

source_name: Cultured peripheral blood mononuclear cells

extract_protocol:
RNeasy kit (Qiagen)
TruSeq Stranded mRNA Library Preparation Kit (Illumina), 12 index Set A Ref:15032612

treatment_protocol: PBMC were stimulated in vitro with PMA/ionomycin for 16 h

tag: genotype

value: Healthy

value: Cultured PBMC


title: HC1

description: Healthy control

value: PBMC were stimulated in vitro with PMA/ionomycin for 16 h


title: DOCK8-I2

description: Heterozygous DOCK8 variant (I2 on pedigree diagram)

value: Heterozygous Carrier


title: 12F_M_52


title: OU_071

description: Validation

value: Positive

value: Negative

value: wP-FEC


title: Sample_C6_S66

value: Euhydrated

value: male


title: zfCM_21dpi_2

city: Utrecht

first: Phong

middle: Dang

last: Nguyen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: SORTseq

library_source: transcriptomic single cell

data_processing:
Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier (UMI) and followed by a 24 nt PolyA stretch and a number (<40) of transcript derived bases. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv", well numbers refer to the 384-well plate in the following ordre: A1 to A24 - B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2, containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded.
Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation
Supplementary files format and content: tab separated count matrices containg spliced, unspliced or total reads.

molecule: polyA RNA

organism: Danio rerio

source_name: Heart

extract_protocol:
Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates, each well containing 1 cell, containing Vapor-Lock oil with CEL-Seq2 barcoded primers, spike-in mRNA and dNTPs (Single Cell Discoveries). Plates were spun down and frozen at -80oC until ready for library prep.
Plates were processed by Single Cell Discoveries using the SORT-seq protocol. In this protocol, the CEL-seq2 protocol  is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the Illumina NextSeq platform.

treatment_protocol: Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.

tag: tissue

value: Heart

tag: cell line

value: cardiomyocyte


title: HC2

description: Healthy control


title: 12F_M_54


title: 12F_M_50


title: zfCM_7dpi_4

description: SORTseq


title: OU_068

description: Validation

value: greater than 50

tag: ct

value: Non-pCR

value: Basal


title: OU_069

description: Validation

value: less than or equal to 50

tag: cn

value: LumA


title: OU_066

description: Validation

tag: er

value: LumB


title: 12F_M_49


title: OU_070

description: Training

tag: hg

value: pCR (ypT0/N0)


title: OU_067

description: Training


title: zfCM_21dpi_1

description: SORTseq


title: Sample_C4_S64

value: Hypothalamic supraoptic nucleus

value: Wistar Han

value: 3 months

tag: Sex


title: 12F_M_48


title: OU_065

description: Training

value: Positive


title: 12F_M_47


title: Sample_C2_S63


title: 12F_M_51


title: OU_064

description: Validation

value: Negative


title: Sample_C1_S62


title: OU_063

description: Validation

value: wP-FEC


title: zfCM_7dpi_3

description: SORTseq


title: zfCM_7dpi_2

description: SORTseq


title: OU_072

description: Validation


title: zfCM_7dpi_1

description: SORTseq


title: Sample_C5_S65

value: Euhydrated


title: Sample_B6_S61

value: Dehydrated

value: 18 months

value: male


title: Sample_B5_S60


title: 12F_M_45


title: 12F_M_44


title: 12F_M_43


title: KFs, MDI medium plus lin1632, 8 Days

city: 海淀区

first: Jun

last: Li

state: 北京市

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

institute: Peking University

description: Targeted RNA

data_processing:
Data were analysed as previously described (Teder et al., 2018). First, sequencing reads were mapped to the reference sequences (left probes plus right probes) to produce total counts of each gene. The CPM (Counts of exon model per million mapped reads) matrix was then transferred from the count matrix and used in cluster analysis, Pearson correlation analysis, and PCA analysis. All scripts was descripted in (Teder et al., 2018).
Assembly: no
Supplementary files format and content: tab-delimited text files include CPM for each Sample

source_name: skin

extract_protocol:
For small molecule screening, 128 compounds were collected based on functions in the signaling pathway and cell fate transition. KFs were seeded at a density of 0.5 × 104 cells per well of a 96-well plate containing KF medium. The next day, the medium was changed to MDI medium (DMEM/high glucose, 1% ITS, 0.5mM isobutylmethylxanthine, 1 μM dexamethasone) plus 2 μM compounds. After 4 days, DMEM/high glucose with 1% ITS was added to the culture for another 4 days. The negative control was KF in KF medium for 8 days. The positive control was KF in AD medium for 4 days and then AM medium for another 4 days. Cells were harvested on day 8 for PHDs-seq library preparation.
Samples with compound treatments in a 96 well-plate were washed with pre-warmed PBS. 60 μl of lysis buffer containing 50mM Tris-HCl pH8.0, 75mM KCl, 6% Ficoll PM-400, 0.15% TritonX-100, and 0.5U/μl RNaseOUT (RNaseOut should be added before use) were added to each well. The 96-well plate was then incubated on a shaker at 900 rpm for 15 minutes. 4.286 μl of cell lysate were transferred to a new 96 well PCR plate. 0.714 μl reverse transcription mix containing 40mM MgCl2, 4μM strand switching primer (TSO), 0.1mM dNTP, 8U/μl Maxima reverse transcriptase, 1x ERCC, and RNaseOUT (RNaseOut should be added before use) were added to each well, mixed and slightly centrifuged for several seconds to collect all reactants on the bottom. The 96-well PCR plate was incubated at 42°C for 2 hours with a hot lid at 105°C. 6μl of hybridization-ligation mix (0.005 μM probe mix, 1U/μl Taq DNA ligase, 1x Taq DNA ligation buffer) was added to the RT products, mixed gently, and incubated at 60°C for 60 minutes with a hot lid of 105°C. After hybridization and ligation, the products were enriched with 15 ul of enrichment mixture (2 μl Dynabeads MyOne Carboxylic Acid beads plus 13 μl capture buffer containing 30% PEG-600, 2 M, NaCl, 5 mM Tris-HCl pH7.5, 10 mM EDTA, and 0.02% Tween-20). Next, 20 μl of PCR mixture (0.25 μM PHD-seq well barcode, 0.5 mM PHD-seq plate barcode, 1 x Vazyme LAmp Master Mix) were added to the enriched hybridization-ligation products, mixed, and incubated at 94°C for 5min, followed by two cycles of 95°C for 20 s, 57°C for 30 s and 72°C for 20 s. In addition, 10 cycles of 94°C for 20 s, 65°C for 30 s, and 72°C for 20 s with a final extension at 72°C for 60 s. The PCR products were pooled together into several 1.5 ml tubes which were placed on a magnet to remove the beads. The supernatant was purified with DNA Clean & Concentrator-100 column (Zymo Research, D4029) and eluted with 150 µl of ddH2O. The library was size-selected using AMPure XP beads. 150 µl of beads were added to 150 µl of the purified PCR product, incubated for 5 min, and captured by a magnet for 3 min after which the supernatant was discarded. The beads were eluted in 25 µl of ddH2O and incubated for 1 min at room temperature. After 1 min of incubation on the magnet, the supernatant was transferred to a clean 1.5 ml tube. The 208 bp library was visualized using agarose gel electrophoresis and quantified using a Qubit™ 4 NGS Starter Kit with WiFi (Q33240).

value: skin

value: fibroblast

value: WT

value: KFs with MDI medium plus lin1632 for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_061

description: Training

value: less than or equal to 50

value: Non-pCR

value: LumA


title: OU_060

description: Validation


title: KFs, MDI medium plus kv8kdin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus kv8kdin for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Y_27632, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Y_27632 for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_062

description: Training


title: KFs, MDI medium plus XMU_MP_1, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus XMU_MP_1 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_42


title: OU_059

description: Training

value: greater than 50

value: Positive


title: Sample_B2_S58

value: Hypothalamic supraoptic nucleus

value: Wistar Han


title: KFs, MDI medium plus Vemurafenib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Vemurafenib for 4 days and then medium was changed to AM medium for another 4 days.


title: Sample_B1_S57

value: Dehydrated

value: 18 months


title: Sample_A6_S56

value: Euhydrated

value: male


title: 12F_M_41


title: 12F_M_40


title: 12F_M_46


title: KFs, MDI medium plus UNC0638, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT

value: KFs with MDI medium plus UNC0638 for 4 days and then medium was changed to AM medium for another 4 days.


title: Sample_B3_S59


title: Sample_A5_S55


title: KFs, MDI medium plus Tripelennamine_HCl, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Tripelennamine_HCl for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_39


title: OU_057

description: Training

value: less than or equal to 50

value: Negative

value: wP-FEC

value: Non-pCR

value: LumA


title: KFs, MDI medium plus Trimethoxyphenol, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Trimethoxyphenol for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Tideglusib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Tideglusib for 4 days and then medium was changed to AM medium for another 4 days.


title: Sample_A2_S53

value: Hypothalamic supraoptic nucleus

value: Wistar Han


title: 12F_M_37


title: 12F_M_38


title: Sample_A1_S52

value: 18 months


title: KFs, MDI medium plus Telatinib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Telatinib for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_058

description: Validation

value: Positive

value: LumB


title: OU_056

description: Training

value: greater than 50

value: Basal


title: KFs, MDI medium plus TTNPB, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT

value: KFs with MDI medium plus TTNPB for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_053

description: Validation

value: less than or equal to 50

value: Negative

value: wP-FEC

value: pCR (ypT0/N0)


title: BulkVDJ_LC_2

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

data_processing:
Cell hashing data was aligned to HTO barcodes using CITE-seq-Count v1.4.2.
Raw read processing of scRNA-seq reads was performed as previously described35. Briefly, reads were aligned to the hg38 reference genome or Mmul_10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI). Whole transcriptome data was further analyzed in Seurat66. First, cells with less than 300 unique genes detected and genes detected in fewer than 5 cells were filtered out. Variable features were then determined using the FindVariableFeatures function, and the ScaleData function was then used to regress out the number of RNA features in each cell. The number of principal components used for visualization was determined by examination of the elbow plot, and two-dimensional embeddings were generated using uniform manifold approximation and projection (UMAP). Clusters were determined using Louvain clustering, as implemented in the FindClusters function in Seurat. For analysis of ST3-reactive B cell data, clusters of cells that exhibited high expression of mitochondrial genes or markers associated with other cell phenotypes (i.e. monocytes) were moved and the data was reprocessed. Differential gene expression analysis was performed for each cluster and between indicated cell populations using the FindMarkers function.
Processing of BCR sequence data was performed with pRESTO and Change-O from the Immcantation software suite69,70. First, potential errors in cell barcode and UMI sequence were corrected for errors up to one nucleotide mismatch with a directional UMI collapse, as implemented in UMI-Tools71. Data was filtered by Q-score using the FilterSeq.py function to remove any sequences with an average Q score below 25. Then, the MaskPrimers.py function was used to annotate sequences with the correct isotype (R1 index) and V-region (R2) primer, as well as to mask the corresponding primer regions. The PairSeq.py function was used to retain only read pairs that passed both the FilterSeq.py and MaskPrimers.py processing steps. The data was then segregated by cell barcode and UMI, and the BuildConsensus.py function was used to call consensus sequences for read 1 index and read 2 of each barcode and UMI separately. The AssemblePairs.py function was used to assemble these consensus sequences into a single overlapping sequence. The resulting sequences were then analyzed with IgBlast72 using reference sequences provided by IMGT.
Assembly: hg38
Assembly: mmul_10
Supplementary files format and content: tab separated values files and comma separated files

extract_protocol:
Whole human blood was obtained from Research Blood Components, LLC (Watertown, MA), and PBMC were isolated by means of density gradient centrifugation and cryopreserved. Upon use, PBMC were thawed into Aim-V medium (ThermoFisher). B cells were isolated using an EasySep Human Pan-B Cell Enrichment kit (Stemcell Technologies, Vancouver, Canada).
Biotinylated pneumococcal serotype 3 polysaccharide with a 5% biotin load (ST3, from Pfizer EPBD) was coupled with high concentration streptavidin-phycoerythrin (SA-PE) and streptavidin-allophycocyanin (SA-APC, both from BioLegend) in separate reactions. Biotinylated ST3 and the fluorophore-conjugated streptavidin reagents were prepared with PBS at 4X working solutions of 20 µg/mL and 200 µg/mL, respectively. Equal volumes of ST3 and SA-PE; and, separately, equal volumes of ST3 and SA-APC working solutions were combined, thoroughly mixed and incubated at 4 ºC protected from light for a minimum incubation period of 60 minutes with thorough mixing at 30 minutes and directly prior to use. Coupled ST3-PE and ST3-APC solutions were maintained at 4 ºC, protected from light until use.
Seq-Well

value: PBMC

value: B cell

value: Light chain


title: OU_054

description: Training


title: OU_052

description: Training

value: Non-pCR

value: LumA


title: BulkVDJ_LC_1


title: KFs, MDI medium plus TD114_2, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus TD114_2 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_33


title: BulkVDJ_HC_2

value: Heavy chain


title: OU_055

description: Training

value: greater than 50

value: Positive


title: KFs, MDI medium plus T0901317, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus T0901317 for 4 days and then medium was changed to AM medium for another 4 days.


title: Sample_A4_S54

value: Hypothalamic supraoptic nucleus

value: Wistar Han

value: Euhydrated

value: 18 months

value: male


title: 12F_M_32


title: OU_051

description: Training

value: Negative

value: wP-FEC


title: BulkVDJ_HC_1

value: PBMC

value: B cell


title: 12F_M_36


title: KFs, MDI medium plus Sunitinib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with MDI medium plus Sunitinib for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_34


title: KFs, MDI medium plus Sorafenib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Sorafenib for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_6_LC

value: Spike-in 1:1000


title: 12F_M_31


title: SpikeIn_6_HC


title: KFs, MDI medium plus Silmitasertib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Silmitasertib for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_6_DGE


title: KFs, MDI medium plus Sonidegib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus Sonidegib for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus SRT1720, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus SRT1720 for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_5_HC


title: KFs, MDI medium plus SP600125, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus SP600125 for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_5_LC


title: SpikeIn_5_DGE


title: KFs, MDI medium plus SGC_0946, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus SGC_0946 for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus SIS3, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus SIS3 for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_4_LC

value: Spike-in 1:100


title: 12F_M_29


title: 12F_M_30


title: 12F_M_25


title: 12F_M_27


title: 12F_M_28


title: 12F_M_24


title: OU_048

description: Training

value: less than or equal to 50

value: Positive

value: Negative

value: pCR (ypT0/N0)

value: Basal


title: KFs, MDI medium plus SF1670, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with MDI medium plus SF1670 for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_4_HC

value: PBMC

value: B cell


title: OU_049

description: Validation

value: greater than 50

value: wP-FEC


title: SpikeIn_4_DGE


title: 12F_M_26


title: OU_050

description: Validation

value: Non-pCR

value: LumB


title: OU_047

description: Validation

value: LumA


title: OU_046

description: Training


title: 12F_M_23


title: KFs, MDI medium plus SD_208, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus SD_208 for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_044

description: Training

value: less than or equal to 50


title: OU_042

description: Training

value: Positive


title: OU_039

description: Training

value: Negative


title: OU_040

description: Validation


title: OU_045

description: Validation


title: 12F_M_22


title: SpikeIn_3_LC

value: Spike-in 1:100


title: 12F_M_21


title: 12F_M_20


title: SpikeIn_3_HC


title: KFs, MDI medium plus SB431542, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus SB431542 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_19


title: SpikeIn_3_DGE


title: KFs, MDI medium plus Rosiglitazone_2, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus Rosiglitazone_2 for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_2_LC

value: Spike-in 1:20


title: KFs, MDI medium plus Rosiglitazone_1, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus Rosiglitazone_1 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_18


title: OU_038

description: Training


title: KFs, MDI medium plus RepSox, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus RepSox for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_2_DGE

value: PBMC

value: B cell


title: OU_043

description: Training

value: greater than 50

value: wP-FEC

value: pCR (ypT0/N0)


title: KFs, MDI medium plus Rapamycin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus Rapamycin for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_1_LC


title: KFs, MDI medium plus SAG, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus SAG for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_037

description: Validation

value: Positive

value: Negative

value: Non-pCR


title: 12F_M_16


title: OU_032

description: Training

value: less than or equal to 50

value: LumB


title: KFs, MDI medium plus RG108, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus RG108 for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_1_HC

value: Spike-in 1:20


title: 12F_M_15


title: OU_036

description: Validation


title: OU_033

description: Training

value: LumA


title: OU_041

description: Validation

value: Basal


title: 12F_M_14


title: KFs, MDI medium plus R616452, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus R616452 for 4 days and then medium was changed to AM medium for another 4 days.


title: SpikeIn_1_DGE

value: PBMC

value: B cell


title: SpikeIn_2_HC


title: OU_035

description: Training

value: wP-FEC


title: KFs, MDI medium plus R0492907, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus R0492907 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_17


title: 12F_M_13


title: PBMC_4_LC

value: No enrichment


title: KFs, MDI medium plus Ponesimod, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Ponesimod for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_034

description: Validation

value: greater than 50

value: Positive

value: Negative

value: Non-pCR


title: OU_030

description: Training

value: less than or equal to 50

value: pCR (ypT0/N0)

value: LumB


title: KFs, MDI medium plus Parnate, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus Parnate for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_029

description: Training


title: 12F_M_11


title: PBMC_4_HC


title: 12F_M_12


title: PBMC_4_DGE


title: OU_028

description: Training


title: KFs, MDI medium plus Panobinostat, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus Panobinostat for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_031

description: Validation

value: LumA


title: KFs, MDI medium plus PHA_793887, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus PHA_793887 for 4 days and then medium was changed to AM medium for another 4 days.


title: Bcell_enriched_4_LC

value: PBMC

value: B cell enrichment


title: 12F_M_10


title: Bcell_enriched_4_DGE


title: KFs, MDI medium plus PF_06651600, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus PF_06651600 for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus PFI_2HCl, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus PFI_2HCl for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_8


title: Bcell_enriched_4_HC


title: 12F_M_7


title: 12F_M_9


title: KFs, MDI medium plus PD173074, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus PD173074 for 4 days and then medium was changed to AM medium for another 4 days.


title: PBMC_3_LC

value: No enrichment


title: PBMC_3_HC


title: KFs, MDI medium plus PD0325901, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus PD0325901 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_6


title: 12F_M_5


title: PBMC_3_DGE


title: OU_025

description: Validation

value: less than or equal to 50

value: Positive

value: Negative

value: wP-FEC

value: Non-pCR

value: Basal


title: OU_026

description: Validation


title: 12F_M_4


title: OU_027

description: Training

value: LumB


title: OU_023

description: Training

value: LumA


title: Bcell_enriched_3_LC


title: OU_024

description: Training

value: greater than 50


title: OU_021

description: Validation


title: 12F_M_3


title: KFs, MDI medium plus Nifedipine, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with MDI medium plus Nifedipine for 4 days and then medium was changed to AM medium for another 4 days.


title: Bcell_enriched_3_HC

value: PBMC

value: B cell enrichment


title: KFs, MDI medium plus Nextmostat, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus Nextmostat for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_2


title: KFs, MDI medium plus NCGC00244536, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus NCGC00244536 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_1


title: PBMC_2_LC

value: No enrichment


title: KFs, MDI medium plus PBIT, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus PBIT for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Minocycline_Hydrochloride, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Minocycline_Hydrochloride for 4 days and then medium was changed to AM medium for another 4 days.


title: PBMC_2_HC


title: OU_022

description: Training

value: less than or equal to 50

value: Negative

value: Positive

value: wP-FEC


title: KFs, MDI medium plus Melatonin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Melatonin for 4 days and then medium was changed to AM medium for another 4 days.


title: Bcell_enriched_3_DGE


title: KFs, MDI medium plus ML277, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus ML277 for 4 days and then medium was changed to AM medium for another 4 days.


title: Islet, Tg

city: Nanjing

first: Yuqian

last: Yang

state: Jiangsu

address: 101 Longmian Avenue

department: Biochemistry and Molecular Biology

institute: Nanjing Medical University

description:
FPKM_2.txt
FPKM_Anno_2.txt
normalized_2.txt
rawcount_2.txt

data_processing:
Illumina Casava 1.8 was used to recognize and trasfer the image results to reads.
The error rate was recorded as "e". The quality of base was characterized as Qphred, and the Qphred = -10log10 (e) .
The reads were filtered obey the rules as follows: first, filter the reads with adapter, second, delete the reads with uncertain base, finally, filter the reads containing more than 50% bases that has a Qphred ≤ 20.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 according to the manufaturer's protocols.
Assembly: mm10

source_name: Islet

growth_protocol: WT and  TG mice were fasted for 12 hrs, then anesthetized and sacrificed by neck broken. Cut off the auricular appendage and exhaled blood, then fulfill the vessels and wash with pre-cooling PBS.

extract_protocol:
TRIZOL was used to extract total RNA.
3 µg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Islets were collected and quick-frozen by liquid nitrogen.

value: Islet

value: male

value: beta cell specific miR-203 transgene

value: fasted for 12 hrs


title: Bcell_enriched_2_LC

value: PBMC

value: B cell enrichment


title: Bcell_enriched_2_HC


title: KFs, MDI medium plus MK_0752, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT

value: KFs with MDI medium plus MK_0752 for 4 days and then medium was changed to AM medium for another 4 days.


title: PBMC_2_DGE

value: No enrichment


title: OU_020

description: Training

value: greater than 50

value: pCR (ypT0/N0)

value: Basal


title: Islet, Ctr

value: wild type


title: OU_016

description: Validation

value: less than or equal to 50

value: Positive

value: wP-FEC

value: Non-pCR


title: OU_019

description: Training

value: Negative


title: OU_017

description: Validation


title: KFs, MDI medium plus MI_3, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus MI_3 for 4 days and then medium was changed to AM medium for another 4 days.


title: 12F_M_0


title: OU_018

description: Validation

value: LumB


title: KFs, MDI medium plus MI_2, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus MI_2 for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_015

description: Validation


title: OU_014

description: Validation

value: LumA


title: PBMC_1_LC

value: PBMC


title: OU_012

description: Training


title: OU_013

description: Validation


title: Islet, tg214

description:
FPKM.txt
FPKM_Anno.txt
normalized.txt
rawcount.txt

value: Islet

value: male

value: beta cell specific miR-203 transgene

value: fasted for 12 hrs


title: PBMC_1_HC

value: No enrichment


title: KFs, MDI medium plus MI_463, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT

value: KFs with MDI medium plus MI_463 for 4 days and then medium was changed to AM medium for another 4 days.


title: PBMC_1_DGE


title: Bcell_enriched_2_DGE

value: B cell enrichment


title: OU_011

description: Training

value: less than or equal to 50

value: Positive

value: wP-FEC

value: pCR (ypT0/N0)


title: KFs, MDI medium plus Lithocholic_Acid, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Lithocholic_Acid for 4 days and then medium was changed to AM medium for another 4 days.


title: Islet, ctr1

value: wild type


title: KFs, MDI medium plus MHY1485, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus MHY1485 for 4 days and then medium was changed to AM medium for another 4 days.


title: Islet, tg290

value: Islet


title: Bcell_enriched_1_LC

value: PBMC


title: KFs, MDI medium plus Lapatinib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Lapatinib for 4 days and then medium was changed to AM medium for another 4 days.


title: CFAE+6-1_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

data_processing:
Bulk RNA-seq data were processed to obtain a gene count matrix of all samples using the featureCounts tool of the subread software. The count matrix was used for differential analysis with DESeq2 (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM and count values for each Sample

source_name: MEFs in CFAE+6  medium for Day4

extract_protocol:
Total RNA from cells was extracted using an EasyPure RNA Kit (Transgene, ER101-01) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext@ Ultra™  RNA Library Prep Kit for Illumina@ (#E7530) following manufacturer's protocols.

value: embryo

value: embryonic fibroblast

value: CFAE+6 medium for 4 days


title: KFs, MDI medium plus Lanifibranor, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus Lanifibranor for 4 days and then medium was changed to AM medium for another 4 days.


title: CFAE+6-2_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: WT


title: Bcell_enriched_1_HC

value: B cell enrichment


title: CFAE+8+MSC-2_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

source_name: MEFs in CFAE+8+MSC medium for Day4

value: CFAE+8+MSC medium for 4 days


title: Bcell_enriched_1_DGE


title: OU_010

description: Training

value: less than or equal to 50

value: Positive

value: wP-FEC

value: Non-pCR

value: LumA


title: CFAE+8+MSC-1_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207


title: KFs, MDI medium plus LY364947, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus LY364947 for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus LY294002, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus LY294002 for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_008

description: Validation

value: Negative


title: Islet, ctr2

value: Islet

value: male

value: wild type

value: fasted for 12 hrs


title: CFAE+8-2_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

source_name: MEFs in CFAE+8 medium for Day4

value: embryo

value: embryonic fibroblast

value: CFAE+8 medium for 4 days


title: Sepsis 19,Human, Blood

city: Seoul

first: kyeongman

last: Jeon

address: 81 Irwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

data_processing:
A quality control of raw sequencing data was performed using FastQC (Simon, 2010).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTX_Trimmer (Hannon Lab, 2014) and BBMap (Bushnell,2014).
Trimmed reads were mapped to the reference genome using TopHat (Cole Trapnell et al., 2009)
FPKM values were normalized based on Quantile normalization method using EdgeR within R (R development Core Team, 2016).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: blood

growth_protocol: Whole blood (2 mL) was also collected in in PAXgene tubes, using BD PAXgene blood RNA tubes (BD, cat. no. 762165).

extract_protocol:
Total RNA was isolated from whole blood using the TRIzol reagent (Invitrogen, USA). Messenger RNA (mRNA) was isolated using a Poly(A) RNA Selection Kit (Lexogen, Inc., Vienna, Austria).
Libraries were prepared from total RNA using a NEBNext Ultra II Directional RNA-Seq Kit (New England BioLabs, UK).

value: blood

tag: disease state

value: sepsis

tag: time

value: Day 0


title: Sepsis 20,Human, Blood


title: CFAE+8-1_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: WT


title: KFs, MDI medium plus LDH193189, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus LDH193189 for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus LDK378, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus LDK378 for 4 days and then medium was changed to AM medium for another 4 days.


title: Sepsis 17,Human, Blood


title: MEF-2_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

source_name: MEFs in MEF medium for Day4

value: MEF medium for 4 days


title: Sepsis 16,Human, Blood


title: KFs, MDI medium plus LCA, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus LCA for 4 days and then medium was changed to AM medium for another 4 days.


title: MEF-1_RNA

address: 北京市海淀区颐和园路5号北京大学王克桢楼207


title: Sepsis 15,Human, Blood


title: bC6FAE2_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

data_processing:
ATAC-seq reads were aligned to the mm10 reference genome by Bowtie2 (Langmead and Salzberg, 2012) with random chromosome cleaned. Samtool software (Li et al., 2009) was used to produce bam files. PCR duplicates in the bam files were removed by MarkDuplicates. Normalized read counts (RPKM) were visualized by bamCoverage (Ramírez et al., 2016) (bamCoverage --bam --outFileName --binSize 50 --numberOfProcessors max --normalizeUsing RPKM) and computeMatrix (computeMatrix scale-regions -R mm10bed.txt --beforeRegionStartLength 3000 --regionBodyLength 6000 --afterRegionStartLength 3000 --skipZeros --outFileName -p max). MACS2 (Gaspar, 2018; Zhang et al., 2008) was used for peak calling and annotation of ATAC-seq data.
Assembly: mm10
Supplementary files format and content: bigwig files for each Sample

extract_protocol: 1x104 cells were lysed in a buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.5% NP-40 to collect the nuclei with centrifugation at 500g at 4℃ for 5 min.

value: CFAE+6 medium for 4 days


title: Altre-WT Treg 2

city: Shanghai

first: Chenbo

last: Ding

state: None Selected

address: 280 Chongqing South Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-seq libraries were constructed using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech)
STAR was used to align the raw sequencing reads to mouse genome mm10 with default parameters after trimming adapter sequences with cutadapt
The libraries were sequenced on Illumina HiSeq X 4000 platform (paired-end 150-bp read length) by Geneseeq Technology Inc
Each sample obtained 50 million reads
Assembly: mm10
Supplementary files format and content: DESeq2 for identifying differentially expressed genes between the Altre-WT and Altre-KO samples

source_name: Liver

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Liver

value: Raw Tregs

value: Tregs

value: Altre-WT


title: Altre-KO Treg 1

value: Altre-KO


title: Altre-KO Treg 2


title: KFs, MDI medium plus KN_93, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus KN_93 for 4 days and then medium was changed to AM medium for another 4 days.


title: Altre-WT Treg 1


title: Sepsis 14,Human, Blood

value: blood


title: KFs, KF medium, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus KF for 4 days and then medium was changed to AM medium for another 4 days.


title: Sepsis 18,Human, Blood

value: sepsis

value: Day 0


title: OU_006

description: Validation

value: greater than 50

value: Positive

value: Negative

value: wP-FEC

value: Non-pCR

value: LumA


title: bC6FAE1_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: embryo

value: embryonic fibroblast

value: WT

value: CFAE+6 medium for 4 days


title: Sepsis 13,Human, Blood


title: WT Treg, 2

data_processing:
RNA-seq libraries were constructed using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech)
STAR was used to align the raw sequencing reads to mouse genome mm10 with default parameters after trimming adapter sequences with cutadapt
The libraries were sequenced on Illumina HiSeq X 4000 platform (paired-end 150-bp read length) by Geneseeq Technology Inc
Each sample obtained 50 million reads
Assembly: mm10
Supplementary files format and content: DESeq2 for identifying differentially expressed genes between the Altre-WT and Altre-KO samples
Supplementary files format and content: count, fpkm

source_name: Thymus

value: Thymus

value: Raw Tregs

value: Tregs

value: no


title: OU_007

description: Training

value: less than or equal to 50


title: WT Treg, 1


title: bC8FAEM2_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: CFAE+8+MSC medium for 4 days


title: OU_009

description: Training

value: pCR (ypT0/N0)


title: Sepsis 12,Human, Blood

value: blood

value: sepsis

value: Day 0


title: OU_004

description: Training

value: greater than 50

value: Positive

value: wP-FEC

value: LumB


title: KFs, MDI medium plus LAA_vitaminC, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus LAA_vitaminC for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Ivermectin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus Ivermectin for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_003

description: Training

value: Negative

value: Non-pCR

value: LumA


title: OU_002

description: Training

value: Basal


title: OU_001

description: Validation

value: less than or equal to 50


title: KFs, MDI medium plus Isx9, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Isx9 for 4 days and then medium was changed to AM medium for another 4 days.


title: OU_005

description: Training


title: WT Th17, 2

value: Thymus

value: Raw Th17

value: no


title: Sepsis 11,Human, Blood

value: blood

value: sepsis

value: Day 0


title: WT NaiveT, 2

value: Raw Naive T

value: Naive T


title: WT Th17, 1


title: Sepsis 10,Human, Blood


title: KFs, MDI medium plus Imatinib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus Imatinib for 4 days and then medium was changed to AM medium for another 4 days.


title: Sepsis 9,Human, Blood


title: bC8FAE1_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: embryo

value: embryonic fibroblast

value: WT

value: CFAE+8 medium for 4 days


title: KFs, MDI medium plus IWR1, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus IWR1 for 4 days and then medium was changed to AM medium for another 4 days.


title: Sepsis 8,Human, Blood


title: WT NaiveT, 1


title: bC8FAEM1_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: CFAE+8+MSC medium for 4 days


title: KFs, MDI medium plus IDE1, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus IDE1 for 4 days and then medium was changed to AM medium for another 4 days.


title: Treg, Altre-KO, 14 month 3

data_processing:
mRNA for RNA-seq analysis was purified using polyA+ selection and RNA-seq libraries were constructed by Yale Center for Genome Analysis (YCGA) using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech)
STAR was used to align the raw sequencing reads to mouse genome mm10 with default parameters after trimming adapter sequences with cutadapt
The libraries were sequenced on Illumina HiSeq X 4000 platform (paired-end 150-bp read length) by Geneseeq Technology Inc
Each sample obtained 50 million reads
Supplementary files format and content: mm10
Supplementary files format and content: DESeq2 for identifying differentially expressed genes between the Altre-WT and Altre-KO samples

value: Liver

value: Raw Tregs

value: Tregs

value: Altre knockout


title: 1478-MR-13 E12.5 orJ;mi replicate 4

city: Nashville

first: EDWARD

middle: M

last: LEVINE

state: TN

address: 1161 21st Ave S

department: Vanderbilt Eye Institute

institute: Vanderbilt University Medical Center

data_processing:
FASTQ files were generated from concatenated base call (.cbcl) files with Bcl2fastq2 conversion software (Illumina)
Paired end raw FASTQ files were assessed for quality by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) respectively
Reads were aligned to the reference mouse genome mm10 (GRCm38) using Spliced Transcripts Alignment to a Reference (STAR) version 2.6 (Dobin et al., 2013) using GENCODE comprehensive gene annotations (Release M14) as a reference.
HTSeq was used for counting reads mapped to genomic features (Anders et al., 2015)
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain genome mapped raw counts for each sample

source_name: retina

growth_protocol: Mice carrying the Vsx2<orJ> and Mitf<mi> mutant alleles underwent single night matings and embryos were collected at E12.5.

extract_protocol:
Qiagen Rneasy mini-Kit
NEBNext Poly(A) mRNA Magnetic Isolation Module followed by NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Retinal tissues were dissected from all other tissues, flash frozen in liquid nitrogen, and stored at -80 degrees C until use. Libraries were prepared and sequenced for all samples at the same time.

tag: strains

tag: condition

value: orJ; mi

value: Vsx2<orJ/orJ>; Mitf<mi/+>

value: retina


title: KFs, MDI medium plus IQ1, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus IQ1 for 4 days and then medium was changed to AM medium for another 4 days.


title: Sepsis 7,Human, Blood

value: blood

value: sepsis

value: Day 0


title: MEF1_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: embryo

value: embryonic fibroblast

value: WT

value: MEF medium for 4 days


title: MEF2_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207


title: Treg, Altre-KO, 14 month 1

value: no


title: Sepsis 5,Human, Blood


title: KFs, MDI medium plus IBET151, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus IBET151 for 4 days and then medium was changed to AM medium for another 4 days.


title: Sepsis 6,Human, Blood


title: 1478-MR-6 E12.5 orJ;mi replicate 2


title: KFs, MDI medium plus IBMX, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus IBMX for 4 days and then medium was changed to AM medium for another 4 days.


title: 1478-MR-12 E12.5 orJ;mi replicate 3


title: Treg, Altre-WT, 14 month 3

value: Liver

value: Raw Tregs

value: Tregs

value: Altre WT


title: bC8FAE2_ATAC

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

value: CFAE+8 medium for 4 days


title: Sepsis 4,Human, Blood


title: KFs, MDI medium plus Hesperetin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus Hesperetin for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Isoxazole_9, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Isoxazole_9 for 4 days and then medium was changed to AM medium for another 4 days.


title: 1478-MR-5 E12.5 orJ;mi replicate 1

value: orJ; mi

value: Vsx2<orJ/orJ>; Mitf<mi/+>

value: retina


title: Sepsis 3,Human, Blood

value: blood

value: sepsis

value: Day 0


title: Treg, Altre-WT, 14 month 1

value: no


title: KFs, MDI medium plus H89, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with MDI medium plus H89 for 4 days and then medium was changed to AM medium for another 4 days.


title: 1478-MR-11 E12.5 orJ replicate 4

value: orJ

value: Vsx2<orJ/orJ>; Mitf<+/+>


title: Sepsis2,Human, Blood


title: Treg, Altre-KO, 14 month 2

value: Liver

value: Raw Tregs

value: Tregs

value: Altre knockout


title: KFs, MDI medium plus GW4064, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus GW4064 for 4 days and then medium was changed to AM medium for another 4 days.


title: Sepsis 1,Human, Blood


title: SAM24374041

description: 10x Genomics 3' v3

data_processing:
Raw sequencing reads were processed and aligned to the mouse reference transcriptome (GRCm38) via the 10x software Cellranger (v3.1.0) using default parameters to generate the raw and filtered feature_bc matrices included as processed data files. CellBender (v0.2.0) was used to remove ambient RNA effects from raw_feature_bc_matrix matrices for each sample using the remove-background function with the following parameters: epochs=200, fpr=0.01, total-droplets-included=30000, and expected-cells=number of cells called by CellRanger to produce processed gene-by-cell count matrices corrected for ambient RNA.
Biological replicates were merged and analyzed using Seurat (v3.1.1) following the standard workflow. Briefly, cells with less than 500 UMIs or mitochondria RNA content greater than 25% were filtered.
Assembly: mm10
Supplementary files format and content: raw_feature_bc_matrices.h5 are provided as the unfiltered feature x cell-barcode matrices following 10x cellranger alignment containing all valid barcodes from GEMs (Gel Bead-In EMulsions) captured in the data . Provided as h5 files (Hierarchical Data Format, HDF).
Supplementary files format and content: filtered_feature_bc_matrices.h5 are provided as the filtered feature x cell-barcode matrices following 10x cellranger alignment containing all cell-associated barcodes. Provided as h5 files (Hierarchical Data Format, HDF).

extract_protocol:
Lumbar DRGs L4, L5, L6  (6 DRGs) from one mouse were used per biological replicate. We chopped the DRGs and enzymatically digested them using a combination of collagenase and trypsin with gentle shaking.  DRG cells were then dissociated by gentle trituration. The cell suspensions were purified by myelin elimination using magnetic anti-myelin beads and suspended in HibernateA containing 10% inactivated horse serum. Viable cells were counted using Calcein-AM labeling. Cells were washed 3x and suspended in HibernateA medium containing 10% inactivated horse serum, 0.2 U/uL RNase inhibitor for single cell capture and transcript library generation.
Libraries were generated using the 3’ gene expression library kit v3 (10X Genomics) following manufacturer's protocol.

value: Dorsal root ganglia

tag: animal id

value: 10 weeks old

value: Male

value: Scn9a loxP/loxP, Slc17a8.Cre Pos


title: KFs, MDI medium plus GW3965, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus GW3965 for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus GSK_J4, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus GSK_J4 for 4 days and then medium was changed to AM medium for another 4 days.


title: 1478-MR-4 E12.5 orJ replicate 2

tag: age

value: retina


title: 1478-MR-3 E12.5 orJ replicate 1


title: SAM24374040

description: 10x Genomics 3' v3

value: Scn9a loxP/loxP, Slc17a8.Cre Neg


title: Control 7,Human, Blood

value: blood

value: Day 0


title: SAM24374039

description: 10x Genomics 3' v3

value: 16-21 weeks old

value: Scn9a loxP/loxP, pCAAG.Cre.ER Pos


title: SAM24374038

description: 10x Genomics 3' v3

value: Female


title: 1478-MR-9 E12.5 control replicate 4

value: control


title: KFs, MDI medium plus GSK3ixv, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with MDI medium plus GSK3ixv for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus GSK429286A, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus GSK429286A for 4 days and then medium was changed to AM medium for another 4 days.


title: Control 6,Human, Blood


title: 1478-MR-8 E12.5 control replicate 3


title: Control 5,Human, Blood


title: SAM24374037

description: 10x Genomics 3' v3

value: Dorsal root ganglia

value: 10 weeks old

value: Scn9a loxP/wt, Slc17a8.Cre Neg


title: 1478-MR-2 E12.5 control replicate 2


title: SAM24374036

description: 10x Genomics 3' v3

value: Male


title: KFs, MDI medium plus GSK3326595, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus GSK3326595 for 4 days and then medium was changed to AM medium for another 4 days.


title: Treg, Altre-WT, 14 month 2

value: Liver

value: Raw Tregs

value: Tregs

value: Altre WT

value: no


title: KFs, MDI medium plus GO6983, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus GO6983 for 4 days and then medium was changed to AM medium for another 4 days.


title: Control 4,Human, Blood

value: blood

value: Day 0


title: 1478-MR-1 E12.5 control replicate 1

value: control

value: retina


title: SAM24353300

description: 10x Genomics 3' v3

value: 16-21 weeks old

value: Female

value: Scn9a loxP/loxP, pCAAG.Cre.ER Pos


title: KFs, MDI medium plus GNF5837, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT

value: KFs with MDI medium plus GNF5837 for 4 days and then medium was changed to AM medium for another 4 days.


title: Control 3,Human, Blood


title: Control 8,Human, Blood


title: 1478-MR-10 E12.5 orJ replicate 3

value: orJ

value: Vsx2<orJ/orJ>; Mitf<+/+>


title: 3725-AL-28 E12.5 orJ retina/vehicle control replicate 4

description:
E12.5 orJ retina/vehicle control replicate 4
polyA selection

growth_protocol: Whole retina tissue with the lens attached were collected from E12.5 orJ embryos, transferred into 24-well plates, and cultured in 500 µL of 1x DMEM/F12 (U.S. Biological, cat.# D9807-05), 1% FBS (ThermoFisher, cat.# 16140071), 1x N2-Plus supplement (R&D Systems, cat.# AR003), 33 mM glucose (Sigma, cat.# G7528), 1 mM Glutamax (ThermoFisher, cat.# 35050061), 1.3 mM NaHCO3 (ThermoFisher, cat.# 25080094), 5 mM HEPES (ThermoFisher, cat.# 15630080), 100 U/ml Pen/Strep solution (ThermoFisher, cat.# 15070063). EdU (final concentration: 10 µM) was added to the media for 30 min prior to the end of the culture period. Cultures were maintained for 24 hours at 37 degrees in a 5% CO2 atmosphere.

extract_protocol:
Trizol (Invitrogen)
NEBNext Poly(A) mRNA Magnetic Isolation Module followed by NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: 100 nM HX531 in 0.1% DMSO (test condition); 0.1% DMSO (ctrl/vehicle condition)

value: 0.1% DMSO


title: SAM24353299

description: 10x Genomics 3' v3

value: Dorsal root ganglia

value: Scn9a loxP/loxP, pCAAG.Cre.ER Neg


title: Control 2,Human, Blood


title: Control 1,Human, Blood


title: KFs, MDI medium plus GNE9605, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus GNE9605 for 4 days and then medium was changed to AM medium for another 4 days.


title: 3725-AL-27 E12.5 orJ retina/vehicle control replicate 3

description:
E12.5 orJ retina/vehicle control replicate 3
polyA selection


title: SAM24353297

description: 10x Genomics 3' v3


title: SAM24352445

description: 10x Genomics 3' v3

value: Male


title: 3725-AL-17 E12.5 orJ retina/vehicle control replicate 1

description:
E12.5 orJ retina/vehicle control replicate 1
polyA selection


title: 3725-AL-21 E12.5 orJ retina/100nM HX531 replicate 5

description:
E12.5 orJ retina/100nM HX531 replicate 5
polyA selection


title: Tonsil7_unexposed

first: Robert

last: Sebra

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

description: cultured human tonsil explant, untreated control

data_processing:
Sequencing data were de-multiplexed with bcl2fastq v2.20.0 (invoked by the mkfastq command in various Cell Ranger/Space Ranger versions).
Demultiplexed data were processed by Cell Ranger (v6.0.1 , v6.1.0, v7.0.1) and Space Ranger (v1.2.1).
HIV-1 transcripts were identified as reads were aligned to a joint reference that consists of 10X's GRCh38-2020-A Human reference and a custom HIV reference whose regions with known features are marked as exonic.
The pipeline grouped and de-duplicated reads confidently mapped to the transcriptome by 10X cellular barcodes and UMIs (Unique Molecular Identifiers), then summarized counts into feature-barcode matrices.
Assembly: GRCh38
Supplementary files format and content: info.tar: tar files containing Cell Ranger's or Space Ranger's log files
Supplementary files format and content: outs.tar: tar files containing Cell Ranger's or Space Ranger's output files, including count matrices and other analyses

source_name: tonsils

growth_protocol: Human tonsil explants were obtained from healthy tonsillectomy patients and dissected into tissue blocks cultivated on collagen rafts

extract_protocol:
Suspension cells in tonsil explant supernatants were harvested via centrifugation of supernatants at 2000 x g for 5 min
scRNA-Seq Libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to manufacturer's instructions.

treatment_protocol: Tonsil tissue was dissected into nine 1 mm explants which were subsequently cultured and exposed to HIV-1NL-CI, a CXCR4-tropic fluorescent reporter virus with mCherry in place of nef where nef is expressed on an IRES. Media was removed on days 2, 5, and 8 following HIV-1 NL-CI exposure, and cells were collected and washed

tag: hiv virus

value: unexposed

tag: batch

tag: data type

value: Single-Cell


title: Tonsil6_exposed

description: cultured human tonsil explant, exposed to HIV virus for 8 days

value: exposed


title: SAM24352444

description: 10x Genomics 3' v3

value: 16-21 weeks old

tag: genotype


title: Tonsil7_exposed


title: KFs, MDI medium plus GNE7915, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

tag: tissue

tag: cell type

tag: treatment

value: KFs with MDI medium plus GNE7915 for 4 days and then medium was changed to AM medium for another 4 days.


title: 3725-AL-20 E12.5 orJ retina/100nM HX531 replicate 4

description:
E12.5 orJ retina/100nM HX531 replicate 4
polyA selection

value: retina


title: KFs, MDI medium plus FPH1, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus FPH1 for 4 days and then medium was changed to AM medium for another 4 days.


title: Tonsil5_unexposed


title: KFs, MDI medium plus Fingolimod, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with MDI medium plus Fingolimod for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Forskolin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Forskolin for 4 days and then medium was changed to AM medium for another 4 days.


title: 3725-AL-6 E12.5 orJ retina/100nM HX531 replicate 3

description:
E12.5 orJ retina/100nM HX531 replicate 3
polyA selection


title: KFs, MDI medium plus FGF2, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus FGF2 for 4 days and then medium was changed to AM medium for another 4 days.


title: SAM24352443

description: 10x Genomics 3' v3

value: Dorsal root ganglia


title: SAM24352442

description: 10x Genomics 3' v3

value: Scn9a loxP/loxP, pCAAG.Cre.ER Pos


title: KFs, MDI medium plus EPZ004777, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus EPZ004777 for 4 days and then medium was changed to AM medium for another 4 days.


title: 3725-AL-5 E12.5 orJ retina/100nM HX531 replicate 2

description:
E12.5 orJ retina/100nM HX531 replicate 2
polyA selection


title: SAM24349929

description: 10x Genomics 3' v3

value: Male

value: Scn9a loxP/loxP, pCAAG.Cre.ER Neg


title: Tonsil5_exposed

value: Single-Cell


title: 3725-AL-18 E12.5 orJ retina/vehicle control replicate 2

description:
E12.5 orJ retina/vehicle control replicate 2
polyA selection

value: 0.1% DMSO


title: Tonsil4_unexposed

value: unexposed


title: 3725-AL-4 E12.5 orJ retina/100nM HX531 replicate 1

description:
E12.5 orJ retina/100nM HX531 replicate 1
polyA selection


title: SAM24349928

description: 10x Genomics 3' v3

value: 16-21 weeks old


title: Tonsil4_exposed

value: exposed


title: KFs, MDI medium plus Dorsomorphin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus Dorsomorphin for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus EPZ, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus EPZ for 4 days and then medium was changed to AM medium for another 4 days.


title: 3725-AL-12 E12.5 orJ retina/vehicle control replicate 3

treatment_protocol: 300 nM DBZ in 0.1% DMSO (test condition); 0.1% DMSO (ctrl/vehicle condition)

value: retina


title: Tonsil1_unexposed


title: KFs, MDI medium plus Disodium_clodronate_tetrahydrate, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus Disodium_clodronate_tetrahydrate for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Dexamethasone, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Dexamethasone for 4 days and then medium was changed to AM medium for another 4 days.


title: 3725-AL-10 E12.5 orJ retina/vehicle control replicate 1


title: 3725-AL-11 E12.5 orJ retina/vehicle control replicate 2


title: Tonsil1_exposed


title: Tonsil3_exposed_sorted-uninfected

description: cultured human tonsil explant, exposed to HIV virus for 8 days and FACS sorted for absence of production of HIV virus via mCherry reporter


title: Tonsil3_unexposed


title: 3725-AL-19 E12.5 orJ retina/300nM DBZ replicate 4

value: 300 nM DBZ in 0.1% DMSO


title: Tonsil2_unexposed

value: Spatial


title: KFs, MDI medium plus Decitabine, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Decitabine for 4 days and then medium was changed to AM medium for another 4 days.


title: Tonsil3_exposed


title: 3725-AL-2 E12.5 orJ retina/300nM DBZ replicate 2


title: 3725-AL-3 E12.5 orJ retina/300nM DBZ replicate 3


title: KFs, MDI medium plus Dasatinib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Dasatinib for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus DZNep, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus DZNep for 4 days and then medium was changed to AM medium for another 4 days.


title: 3725-AL-1 E12.5 orJ retina/300nM DBZ replicate 1


title: SAM24353298

description: 10x Genomics 3' v3

value: Dorsal root ganglia

value: Female

value: Scn9a loxP/loxP, pCAAG.Cre.ER Neg


title: 45 mM L-lactic acid, biol rep1

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq v2.20, and adapters were trimmed with Skewer v 0.2.2
Quality control of raw data was performed with FastQC v0.11.9 and summarized with MultiQC v1.13
The reads were aligned to the reference genome (R64-1-1 release of the S. cerevisiae genome) with hisat2 v2.2.1, sorted with samtools v1.9 and quantified with featureCounts from subread v2.0.4.
The resulting count table was further processed with the DESeq2 v1.34.0 for R v4.1.2 to compare expression levels.
All the code used is available at GitHub (https://github.com/drozdovapb/S_cerevisiae_lactate_transcriptome)
Assembly: R64-1-1 (GCA_000146045.2)
Supplementary files format and content: allSamples.featureCounts.txt is a plain text file containing raw counts obtained with the featureCounts function of the subread package.
Supplementary files format and content: normalized_counts_DESeq.csv is a plain text (comma-delimited) table with normalized counts obtained with DESeq2

organism: Saccharomyces cerevisiae

source_name: haploid vegetative cells

growth_protocol: The yeast strain used for this work was BY4742 (MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0; Brachmann et al., 1998). It was grown in synthetic medium containing 0.67% (w/v) yeast nitrogen base, 2% (w/v) glucose, 150 mM NaCl, 20 mg/L L-histidine HCl, 100 mg/L L-leucine, 30 mg/L L-lysine HCl, and 20 mg/L uracil at 28 °C with orbital shaking (120 rpm). The addition of NaCl had the purpose of mimicking the conditions in the blood serum for further use in sensor applications.

extract_protocol:
RNA isolation was performed with the RNeasy kit according to manual (RNeasy Mini Handbook) with slight modifications. Cells were homogenized by mechanical disruption. After the addition of RLT buffer and glass beads, the samples were vortexed 3 times for 3 minutes. After each vortexing step, the samples were cooled on ice. Then the lysate was centrifuged for 2 min at maximum speed, and the supernatant was transferred to new microcentrifuge tubes, combined with the same volume of 70% ethanol and mixed by pipetting.
Sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina) and sequenced at 2 x 100 bp with a NovaSeq 6000 (Illumina).

treatment_protocol: For the experimental exposure, the overnight suspension cultures in logarithmic phase (optical density at 600 nm (OD600) in the range of 0.9–1.0) were prepared. 1.5 ml of each culture was collected by centrifugation (1700 × g for 5 minutes at room temperature) and resuspended in 3 ml of the same media or media with 0.05, 0.5, 5, or 45 mM D-lactic acid, or 45 mM of L-lactic acid. The experimental cultures were exposed in the indicated media for 3 hours, collected by centrifugation and frozen at -80 °C until the analysis.

tag: agent

value: 45 mM L-lactic acid

value: haploid vegetative cells

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0

tag: strain

value: exposed to the same medium with 45 mM L-lactic acid added for 3 hours


title: 45 mM D-lactic acid, biol rep3

value: 45 mM D-lactic acid

value: exposed to the same medium with 45 mM D-lactic acid added for 3 hours


title: 45 mM D-lactic acid, biol rep2


title: 45 mM L-lactic acid, biol rep2


title: 45 mM L-lactic acid, biol rep3


title: KFs, MDI medium plus DMOG, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT

value: KFs with MDI medium plus DMOG for 4 days and then medium was changed to AM medium for another 4 days.


title: Tonsil3_exposed_sorted-infected

description: cultured human tonsil explant, exposed to HIV virus for 8 days and FACS sorted for production of HIV virus via mCherry reporter

value: exposed

value: Single-Cell


title: KFs, MDI medium plus Desloratadine, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Desloratadine for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus CucurbitacinB, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus CucurbitacinB for 4 days and then medium was changed to AM medium for another 4 days.


title: TTseq-HCT116-LEO1-608-P-A

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

institute: Wuhan University

description: TT-seq with HCT116 cells

data_processing:
ChIP-Rx reads were aligned to the Human reference genome GRCh38/hg38 and Mouse reference genome GRCm38/mm10 with Bowtie2 (Langmead and Salzberg, 2012), allowing only uniquely mapping reads with up to two mismatches. The aligned human reads were normalized using the aligned mouse reads. The human BAM files were normalized and converted to bigwig files using Samtools (Li et al., 2009; Orlando et al., 2014). ChIP Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008). Heatmaps and metaplots were made for the indicated windows using the average coverage (r.p.m.) using Deeptools 2.0 (Ramirez et al., 2016). Ngsplot was used to calculate the ratio of PAF1C occupancy to Pol II coverage.
PRO-seq reads were aligned to the human hg38 and Drosophila dm6 genome using Bowtie2. The resulting reads were normalized to spiked-in Drosophila reads and converted to bigwig files for visualization in the UCSC Genome Browser. Heatmaps and metaplots were made for the indicated windows using the average coverage using Deeptools 2.0 (Ramirez et al., 2016).
TT-seq reads were aligned to the Human reference genome GRCh38/hg38 or Drosophila reference genome BDGP Release 6/dm6 with Bowtie2 (Langmead and Salzberg, 2012). The aligned human reads were normalized using the aligned Drosophila reads. The human BAM files were normalized and converted to bigwig files using Deeptools 2.0 (Ramirez et al., 2016). Heatmaps, metaplots, and boxplots were made for the indicated windows using the average coverage.
Assembly: Homo sapiens .hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: TT-seq

source_name: Isolated from the colon

growth_protocol: HCT116 (ATCC CCL-247) cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Cat# S711-001, LONSERA). HCT116 analog-sensitive CDK12 (CDK12-AS, F813G), HCT116-3A, and LEO1-HaloTag knockin cell lines were generated by CRISPR-Cas9-mediated homology-directed repair (HDR). DLD1-INTS6-dTag cells (Zheng et al., 2020) were provided by Dr. Fei Xaiver Chen and were maintained in DMEM complete medium. Drosophila S2 cells were obtained from Invitrogen (Cat# R690-07) and maintained in Schneider's medium (Thermo Scientific, Cat# 21720024). Mouse embryonic fibroblast cells (3T3 MEFs WT) were grown in DMEM with 10% FBS. All cells were cultured at 37℃ with 5% CO2. Live cells were quantified using a TC20 automated cell counter (Bio-Rad).

extract_protocol:
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.
TT-seq was performed as previously described (Gregersen et al., 2020; Schwalb et al., 2016) with some modifications. Cells were labeled in media with 400 μM 4-thiouridine (4sU) (Sigma-Aldrich, Cat# T4509) for 10 min before harvest, and total RNA was extracted with TRIzol (Invitrogen, Cat# 15596-018), the labeled RNA (100 μg) was fragmented with NaOH and spike-in with 10% S2 RNA (10 μg). After biotinylated in a 300 μL reaction (100 μg RNA, 10mM HEPES-KOH, pH 7.5, 1mM EDTA, 0.167mg/ml MTSEA-biotin-XX (Sigma-Aldrich, Cat# M9938)), enriched the biotin-labeled RNA with Streptavidin M280 beads (Invitrogen, Cat# 11206D) and eluted by 100mM DTT. RNA was purified by 1.8 x RNAClean XP beads before library preparation.

value: Isolated from the colon

tag: cell line

value: Human colon


title: 5 mM D-lactic acid, biol rep3

value: 5 mM D-lactic acid

value: exposed to the same medium with 5 mM D-lactic acid added for 3 hours


title: TTseq-HCT116-LEO1-607-P-A

description: TT-seq with HCT116 cells


title: 5 mM D-lactic acid, biol rep2

value: haploid vegetative cells


title: TTseq-HCT116-WT

description: TT-seq with HCT116 cells


title: 45 mM D-lactic acid, biol rep1

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0


title: ChIPRx-HCT116-THZ531-60min-pol2

description: ChIP-seq with HCT116 cells

data_processing:
ChIP-Rx reads were aligned to the Human reference genome GRCh38/hg38 and Mouse reference genome GRCm38/mm10 with Bowtie2 (Langmead and Salzberg, 2012), allowing only uniquely mapping reads with up to two mismatches. The aligned human reads were normalized using the aligned mouse reads. The human BAM files were normalized and converted to bigwig files using Samtools (Li et al., 2009; Orlando et al., 2014). ChIP Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008). Heatmaps and metaplots were made for the indicated windows using the average coverage (r.p.m.) using Deeptools 2.0 (Ramirez et al., 2016). Ngsplot was used to calculate the ratio of PAF1C occupancy to Pol II coverage.
PRO-seq reads were aligned to the human hg38 and Drosophila dm6 genome using Bowtie2. The resulting reads were normalized to spiked-in Drosophila reads and converted to bigwig files for visualization in the UCSC Genome Browser. Heatmaps and metaplots were made for the indicated windows using the average coverage using Deeptools 2.0 (Ramirez et al., 2016).
TT-seq reads were aligned to the Human reference genome GRCh38/hg38 or Drosophila reference genome BDGP Release 6/dm6 with Bowtie2 (Langmead and Salzberg, 2012). The aligned human reads were normalized using the aligned Drosophila reads. The human BAM files were normalized and converted to bigwig files using Deeptools 2.0 (Ramirez et al., 2016). Heatmaps, metaplots, and boxplots were made for the indicated windows using the average coverage.
Assembly: Homo sapiens .hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: ChIP-Rx

extract_protocol:
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.
ChIP-Rx experiments were performed as previously described (Li et al., 2021; Wang et al., 2021). Briefly, 1×107 human cells were spiked-in with 1-2×106 MEF cells and were fixed with 1% paraformaldehyde in PBS for 10 minutes, and quenched with 0.125 M glycine for 5 minutes. Fixed cells were used for nuclei isolation and were sheared using the Diagenode Bruptor Plus with the high-power mode for 25 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). The chromatin was immunoprecipitated with 5 μg individual antibodies and 15 μL of pre-blocked Protein A/G beads (Santa Cruz, Cat# sc-2003). After wash for three times with wash buffer (50 mM HEPES-KOH at pH 7.5, 300 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate), the captured DNA was eluted and reverse-crosslinked with 200 μL of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS, 200 μg/mL proteinase K) by incubating at 55°C overnight. The DNA was purified by phenol-chloroform extraction and ethanol precipitation.

value: treated with THZ531 for 60 mins

tag: antibody

value: Pol II


title: 5 mM D-lactic acid, biol rep1


title: ChIPRx-HCT116-THZ531-45min-pol2

description: ChIP-seq with HCT116 cells

value: treated with THZ531 for 45 mins