title: 195_GUA Human melanoma cell line 195, cultured in-vitro + treated w/ guadecitabine

city: Milan

first: Andrea

last: Anichini

address: Via Venezian 1

department: Research

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: Human melanoma cell line 195, cultured in-vitro and treated with guadecitabine

hyb_protocol: Hybridization of each fragmented and labeled target was performed using the GeneChip® Hybridization, Wash and Stain Kit. A single GeneChip® Human Clariom S was then hybridized with each biotin-labeled sense target.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files.

data_processing: Data normalization, analysis and statistical evaluations were performed with Transcriptome Analysis Console (TAC) Software (Affymetrix). Affymetrix algorithm name = sst-rma-gene-full

label_protocol: The total RNA (20 ng to 50 ng) was reverse transcribed using GeneChip® WT Pico Reagent Kit.  The resulting cDNA was used as a template for in vitro transcription using the same kit. The obtained antisense cRNA was purified using Nucleic Acid Binding Beads and used as a template for reverse transcription to produce single-stranded DNA in the sense orientation. During this step, dUTP was incorporated. The DNA was then fragmented using uracyl DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) and labeled with DNA reagent covalently linked to biotin using terminal deoxynucleotidyl transferase.

growth_protocol: Melanoma cell lines were grown in RPMI1640 medium supplemented with FCS 5%.

extract_protocol: RNA was extracted from melanoma cell lines by TRIzol (Invitrogen). Melanin removal was carried out by the CTAB-UREA method. Samples were treated with DNase1 (Qiagen) and purified by RNeasy MinElute Cleanup Kit (Qiagen). The quality of total RNA was first assessed using the RNA 6000 Pico Assay RNA chips run on an Agilent Bioanalyzer 2100 (Agilent Technologies). RNA from tumor nodules was extracted as described in Covre A et al. Oncoimmunology 2015;4:8, e1019978.

treatment_protocol: Gene expression was assessed in cell lines 313 and 195 treated in vitro with guadecitabine at t=24h and t=96h. RNA was extracted at T=144h. RNA was also isolated from tumor nodules surgically excised from immunodeficient mice treated or not with guadecitabine as described in: Covre A et al. Seminars in Oncology 2015;42:506-513.

value: metastatic melanoma

tag: type of lesion

value: lymph node metastasis

tag: gender

value: male

tag: ajcc stage

value: III


title: microglia, ATV:RSV-1-Day (NH3G)

status: Public on Nov 23 2022

type: SRA

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

library_source: transcriptomic

data_processing:
BCL files output by the sequencer were demultiplexed with 10X Genomics' cellranger mkfastq command (version 3.1.0)
Raw reads (FASTQ files) were processed with 10X Genomics' cellranger count command (version 4.0.0) with the following arguments: --transcriptome=refdata-gex-mm10-2020-A --expect-cells=10000
Assembly: mm10
Supplementary files format and content: HDF5 files with raw counts per gene per droplet, produced by cellranger (version 4.0.0) as raw_feature_bc_matrix.h5
Supplementary files format and content: filtered counts for all droplets that passed QC in Matrix Market (mtx) format, gzip-compressed
Supplementary files format and content: 3 CSV files with metadata accompanying the mtx file: cell_barcodes.csv, gene_symbols.csv, filtered_counts_metadata.csv

molecule: polyA RNA

organism: Mus musculus

source_name: Cortex and hipocampus

growth_protocol: hTfR KI mice were used for this study and this mouse model was originally generated at Denali. Animals were bred at JAX Laboratories and transferred to Denali at least two weeks before the initiation of the study for acclimation. Animals were housed in standard conditions in Denali’s vivarium with ad libitum access to food and water.

extract_protocol:
Sixteen mice were divided into three batches for processing, each batch contains all five conditions, and a 16th animal was added to the third batch as a control sample.  Mice were perfused with PBS and each hemibrain was dissociated using the Adult Brain Dissociation kit Mouse and Rat (Miltenyi, 130-107-677).  Single cell suspensions were labeled with CD45 MicroBeads Mouse (Miltenyi, 130-052-301) for MACS sorting of microglia.  The enriched microglia cells stored in PBS with 1% BSA were filtered through a 30 μm strainer and counted via hemocytometer for single cell capture using the Chromium Controller (10X Genomics).  Each sample was loaded with a target recovery of 10,000 cells.
Single cell libraries were constructed using the Chromium Single Cell 3ʹ Reagent Kits v3 (10X Genomics, PN-1000075).  Each library was barcoded with single indexing using the Chromium i7 Multiplex Kit (10X Genomics, PN-120262), and combined equimolar into a pool for sequencing on a MiSeq sequencer (Illumina) to determine actual single cell capture rate.  A final sequencing pool was combined using the MiSeq cell count values to target a minimum of 20,000 read pairs per cell.  The final sequencing pool was shipped to SeqMatic (Fremont) for sequencing on a NovaSeq 6000 with an S2 flowcell (28X91X8).

treatment_protocol: Mice were dosed with ATV:4D9 (10mg/kg) or ATV:RSV (10 mg/kg) antibodies a single time.

tag: Sex

value: Male

tag: tissue

value: brain

tag: tissue region

value: Cortex and hipocampus

tag: cell type

value: microglia

tag: strain

tag: age

tag: age unit

value: months

tag: batch

tag: genotype

value: hTfR KI

tag: treatment

tag: treatment dose

tag: treatment dose unit

value: mg/kg

tag: treatment duration

tag: treatment duration unit

value: days


title: acute myeloid leukemia (AML)_DR73

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from Ensembl genome browser website. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups  (three biological replicates per condition) was performed using DESeq2 R package.
The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially  expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts, FPKMs

molecule: total RNA

organism: Homo sapiens

source_name: leukemia blast cells

extract_protocol:
Total RNA was extracted with miRNeasy Kits (NEB).
A total amount of 1µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for lliumina® (NEB, USA) following manufacturer 's recommendations.
Transcriptomic RNA-sequencing of poylA enrichmed molecules

value: leukemia blast cells

tag: disease state

value: AML

tag: aml status

value: de novo

tag: fab type

value: m


title: acute myeloid leukemia (AML)_DR72

tag: Sex


title: S67_single cell rna seq by Smart Seq2

city: Cambridge

first: Liming

last: Tao

address: 415 Main Street

institute: Broad Institute of Harvard and MIT

description:
single cell SS2 for AAVS1 KO
ss2_processed.tar
ss2_processed.tar/AAVS912_1.dge.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
Cumulus pipeline for SmartSeq2
Cumulus pipeline for bulkRNA
CRISPResso2
Genome_build:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary_files_format_and_content: matrix

source_name: HSC

growth_protocol: cells were cultured at 37oC and 5%O2 in serum-free HSC media comprised of StemSpan  II medium (Stem Cell Technologies) supplemented with CC100 cytokine cocktail (Stem Cell Technologies), 100ng/ml TPO (Peprotech) and 35nM UM171 (Stem Cell Technologies). Confluency was maintained between 2e5-1e6 cells/ml.

extract_protocol:
mRNA isolated by  polyT beads
Smart Seq2

treatment_protocol: AAVS1  or MECOM KO

value: HSC

value: AAVS1 KO


title: microglia, ATV:4D9-1-Day (NH2G)

tag: tissue


title: S62_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR71

value: f


title: 195_NT Human melanoma cell line 195, cultured in-vitro and not treated

type: RNA

label: biotin

value: metastatic melanoma

tag: type of lesion

value: lymph node metastasis

tag: gender

value: male

tag: ajcc stage


title: S61_single cell rna seq by Smart Seq2

tag: cell type


title: microglia, ATV:4D9-28-Day (NH1G)

value: Male

value: brain

tag: tissue region

tag: strain

tag: age

tag: age unit


title: T36_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line + treated w/ guadecitabine

description: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 195 human melanoma cell line and treated with guadecitabine

value: tumor nodule removed from immunodeficient mouse

value: s.c. human melanoma xenograft


title: acute myeloid leukemia (AML)_DR70


title: S60_single cell rna seq by Smart Seq2

tag: genotype


title: Mouse-hepatocyte-RNA-seq-hemin-80uM-rep2

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

country: China

institute: Wuhan University

description: RNA-seq

data_processing:
Biotin CUT&Tag Reads were aligned to the human genome (UCSC hg38) and Escherichia coli genome with Bowtie2 version 2.2.6, using parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The aligned reads were normalized with total reads aligned (reads per million, r.p.m.) and spiked-in E.coli reads
ChIP-Rx reads were aligned to the human genome (UCSC hg38) and mouse genome (mm10) with Bowtie2 version2 2.2.6 , using parameters: --local --very-sensitive. The resulting reads were normalized with the aligned mouse reads.
qPRO-seq reads were aligned to the human hg38 genome. The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m.) and converted to bigwig files for visualization in the UCSC genome browser. Heatmap and metagene plots were made for the indicated windows using the average coverage (r.p.m.).
G4-CUT&Tag and R-loop CUT&Tag reads were aligned to the human genome (UCSC hg38) and Escherichia coli genome with Bowtie2 version 2.2.6 [61], using parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The aligned reads were normalized with total reads aligned (reads per million, r.p.m.) and spiked-in E.coli reads.
RNA-seq reads were aligned to the human genome (UCSC hg38) or mouse genome (mm10) (the RNA-seq were normalized with the spiked-in Drosophila reads), respectively. Alignments were processed with HISAT2, allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads. The read counts across each gene were counted with featureCounts version 2.0.0.
Assembly: Homo sapiens .hg38
Assembly: Mus musculus.mm10
Assembly: Escherichia coli K-12 substr. MG1655
Assembly: Drosophila melanogaster.dm6
Supplementary files format and content: Library normalized bigWig files were provided for all samples

source_name: Mouse hepatocyte RNA-seq with Hemin replicate2

growth_protocol: HEK293T and HeLa were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, LONSERA). Drosophila S2 cells were obtained from Invitrogen and maintained in Schneider's medium. Mouse embryonic fibroblasts (MEF) cells were grown in DMEM with 10% FBS. All cells were cultured at 37°C with 5% CO 2 . Cells were confirmed to be mycoplasma negative using MycoBlue Mycoplasma Detector (Vazyme, D101-01). Live cells were quantified using a TC20 automated cell counter (Bio-Rad).

extract_protocol:
Following Hemin treatment for 6 hours, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer’s instructions.
Biotin-PEG4-Hemin was combined with the Tn5-based CUT&Tag strategy to identify Hemin binding sites in the genome. Briefly, one million HEK293T or HeLa cells were resuspended in NE1 buffer (20 mM HEPES at pH 7.9, 10 mM KCl, 0.5 mM spermidine,0.1% Triton X-100, 20% Glycerol, 1× protease inhibitors) and incubated on ice for 10 minutes. After centrifugation at 1, 300 g for 10 minutes, nuclei were isolated and collected. These nuclei were washed once with PBS and resuspended with 100 μL of wash buffer (20 mM HEPES at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors). 10 μL pre-activated concanavalin A coated magnetic beads (Smart-Lifesciences) were added to these nuclei and incubated on a rotator for 10 minutes at room temperature. The supernatant was removed and bead-bound nuclei were resuspended in 100 μL of dig-wash buffer (0.05% digitonin, 20 mM HEPES at pH 7.5,150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) containing 2 mM EDTA.Biotin-PEG4-Hemin was added to the sample and rotated overnight at 4°C in the dark.For the control sample, biotin-PEG4-hydrazide was used to replace biotin-PEG4-Hemin. These nuclei were washed three times in 200 μL of dig-wash buffer to remove unbound biotin-PEG4-Hemin or biotin-PEG4-hydrazide. Then anti-biotin rabbit mAb was diluted 100-fold in 100 μL of dig-wash buffer with 2 mM EDTA and was added to the nuclei with one-hour rotation at room temperature in the dark. After washing once with dig-wash buffer, these nuclei were resuspended with 100 μL of dig-wash buffer with 2 mM EDTA and 1 μL of mouse anti-rabbit IgG, incubated for another one hour at room temperature in the dark, and washed three times with dig-wash buffer. A 1:250 dilution of pA-Tn5 adapter complex (~0.2 μM) was prepared in 100 μL of dig-300 buffer (0.05% digitonin, 20 mM HEPES at pH 7.5, 300 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) and added to the nuclei followed by one-hour rotation at room temperature in the dark. After five washes with dig-300 buffer, the bead-bound nuclei were resuspended with 40 μL of tagmentation buffer (10 mM TAPS-NaOH at pH 8.5, 10 mM MgCl 2 , 7.5% DMF) and incubated at 37°C for one hour. To terminate the tagmentation reaction, 1.5 μL of 0.5 M EDTA, 0.5 μL of 10% SDS and 1 μL of 20 mg/mL proteinase K were added and incubated at 55°C for 1 hour and then for 15 minutes at 75°C. The DNA was extracted with Sera-Mag carboxylate-modified magnetic beads (GE Healthcare) for library preparation. 21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high- fidelity 2× master mix. The libraries were purified with 0.56-0.85× volume of Sera- Mag carboxylate-modified magnetic beads and subjected to the Bioanalyzer DNA analysis and Illumina sequencing.
ChIP-Rx was performed with 1×10 7 human cells and 1×10 6 MEF cells for spike-in normalization as described in a previous study [21]. For immunoprecipitation, sonicated chromatin was incubated with 10 μg specific antibodies and 15 μL of pre- blocked Protein A/G beads (Smart-Lifesciences). After extensive washes, the captured DNA was eluted for library preparation using the NEBNext Ultra II DNA library prep kit for Illumina before sequencing on a NovaSeq 6000.
qPRO-seq was performed as previously reported (Judd et al. 2020; Li et al. 2021).
G4-CUT&Tag and R-loop CUT&Tag were performed as previously described( Wang et al. 2021; Li et al. 2021)
RNA Sequencing (RNA-seq) Following Hemin treatment for 6 hours, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer’s instructions. 1 μg total RNA was spike-in with 100 ng Drosophila S2 RNA and was further used for mRNA isolation with VAHTS mRNA Capture Beads (Vazyme, N401) following the manufacturer's instructions. Then library preparation was done using the NEBNext Ultra II Directional RNA Library Prep Kit, followed by sequencing on a NovaSeq 6000.

treatment_protocol: Following Hemin treatment for 2 hours or 6 hours, cells were collected.

tag: cell line

value: Mouse hepatocyte

tag: tag

value: Derived from mouse liver

tag: treatment

value: treated with Hemin for 6 hours

tag: antibody


title: acute myeloid leukemia (AML)_DR07

value: leukemia blast cells

tag: disease state

tag: aml status


title: S59_single cell rna seq by Smart Seq2


title: microglia, ATV:4D9-14-Day (NH5G)

tag: Sex

value: Cortex and hipocampus

value: microglia

value: months

tag: batch

value: hTfR KI

tag: treatment dose

tag: treatment dose unit

value: mg/kg

tag: treatment duration

tag: treatment duration unit

value: days


title: T34_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line + treated w/ guadecitabine

source_name: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 195 human melanoma cell line and treated with guadecitabine

tag: tissue

tag: type of lesion


title: Mouse-hepatocyte-RNA-seq-hemin-80uM-rep1

description: RNA-seq

source_name: Mouse hepatocyte RNA-seq with Hemin replicate1


title: acute myeloid leukemia (AML)_DR68

tag: cell type

value: AML

value: de novo

tag: fab type

tag: age

value: m


title: Mouse-hepatocyte-RNA-seq-ctrl-rep2

description: RNA-seq

source_name: Mouse hepatocyte RNA-seq replicate2

tag: cell line

value: untreated


title: S58_single cell rna seq by Smart Seq2

value: HSC

tag: genotype

value: AAVS1 KO


title: Mouse-hepatocyte-RNA-seq-ctrl-rep1

description: RNA-seq

source_name: Mouse hepatocyte RNA-seq replicate1

tag: tag

tag: treatment


title: S56_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR64

tag: disease state


title: acute myeloid leukemia (AML)_DR62

tag: aml status


title: T35_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line + treated w/ guadecitabine

value: tumor nodule removed from immunodeficient mouse

value: s.c. human melanoma xenograft


title: T30_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line

description: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 195 human melanoma cell line


title: acute myeloid leukemia (AML)_DR65

tag: Sex

value: f


title: T29_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line

source_name: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 195 human melanoma cell line


title: Ro5-3335_3

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

data_processing:
Illumina CASAVA 1.8 software was used for basecalling.
Following adapter trimming, reads containing adapters, low quality ((Qscore<= 5)), or with N>10% were removed.
Clean reads were mapped to the GRCm38 genome assembly using STAR v2.7.
Differential expression analysis was performed using the DESeq2 R package 1.30.1.
Genes with a fold change ≥1.5 and an adjusted p value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix tables for differential expressed genes in C57BL/6 astrocytes treated with SB431542, Ro5-3335 and HLM006474, including baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, and Gene name.

source_name: Primary cultured astrocytes

growth_protocol: Astrocytes were isolated from either C57BL/6 neonatal mice. Cultured astroytes were growing in DMEM/F12 media with 10% FBS.

extract_protocol:
Total RNA was extracted from cultured C57BL/6 astrocytes treated with vehicle, SB431542, Ro5-3335 and HLM006474 using the RNeasy Plus Micro Kit (Qiagen; 74034).  Library preparation was performed by Novogene (Sacramento, US), using at least 1 ug of total RNA per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultured astrocytes were treated with vehicle, SB431542, Ro5-3335 and HLM006474 inhibitors for 24 hours.

tag: strain

value: Retinas and optic nerves

value: post natal day 1-3

value: wild type


title: T33_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line + treated w/ guadecitabine


title: T32_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line + treated w/ guadecitabine


title: S52_single cell rna seq by Smart Seq2


title: T26_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line


title: T28_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line


title: acute myeloid leukemia (AML)_DR61

value: leukemia blast cells


title: S54_single cell rna seq by Smart Seq2


title: S57_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR59

value: AL


title: S53_single cell rna seq by Smart Seq2


title: S51_single cell rna seq by Smart Seq2


title: Ro5-3335_2


title: acute myeloid leukemia (AML)_DR60


title: acute myeloid leukemia (AML)_DR67


title: SB431542_3


title: S50_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR57

value: sAML


title: T25_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 195 human melanoma cell line


title: 313_GUA Human melanoma cell line 313, cultured in-vitro + treated w/ guadecitabine

description: Human melanoma cell line 313, cultured in-vitro and treated with guadecitabine

value: metastatic melanoma

value: lymph node metastasis

tag: gender

value: male

tag: ajcc stage

value: III


title: T86_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line + treated w/ guadecitabine

description: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 313 human melanoma cell line and treated with guadecitabine


title: acute myeloid leukemia (AML)_DR58

value: AML

value: de novo


title: SB431542_2


title: 313_NT Human melanoma cell line 313, cultured in-vitro and not treated


title: HLM006474_3


title: T84_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line + treated w/ guadecitabine

source_name: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 313 human melanoma cell line and treated with guadecitabine


title: T83_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line + treated w/ guadecitabine


title: acute myeloid leukemia (AML)_DR56

value: m


title: Ro5-3335_1


title: S49_single cell rna seq by Smart Seq2

value: HSC

value: AAVS1 KO


title: SB431542_1


title: S46_single cell rna seq by Smart Seq2


title: T81_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line + treated w/ guadecitabine

value: tumor nodule removed from immunodeficient mouse

value: s.c. human melanoma xenograft


title: S48_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR55

value: f


title: acute myeloid leukemia (AML)_DR54


title: S47_single cell rna seq by Smart Seq2


title: HLM006474_2

value: Retinas and optic nerves

value: post natal day 1-3


title: acute myeloid leukemia (AML)_DR53

value: leukemia blast cells


title: HLM006474_1

value: wild type


title: T82_GUA Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line + treated w/ guadecitabine


title: T66_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line

description: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 313 human melanoma cell line


title: S45_single cell rna seq by Smart Seq2


title: Vehicle_3

value: Vehicle


title: acute myeloid leukemia (AML)_DR52


title: T67_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line

source_name: Tumor nodule isolated from an immunodeficient mouse injected s.c. with 313 human melanoma cell line


title: Vehicle_4


title: S44_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR51


title: S43_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR50


title: Vehicle_2


title: Vehicle_1


title: S42_single cell rna seq by Smart Seq2


title: T65_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line


title: acute myeloid leukemia (AML)_DR05


title: SPP1 KO_4

data_processing:
Illumina CASAVA 1.8 software was used for basecalling.
Following adapter trimming, reads containing adapters, low quality ((Qscore<= 5)), or with N>10% were removed.
Clean reads were mapped to the GRCm38 genome assembly using STAR v2.7.
Differential expression analysis was performed using the DESeq2 R package 1.30.1.
Genes with a fold change ≥1.5 and an adjusted p value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table for differential expressed genes in Spp1 KO astrocytes, including baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, and Gene name.

growth_protocol: Astrocytes were isolated from either C57BL/6 wild-type or Spp1 KO neonatal mice. Cultured astrocytes were growing in DMEM/F12 media with 10% FBS.

extract_protocol:
Total RNA was extracted from cultured astrocytes isolated from either C57BL/6 wild-type or Spp1 KO neonatal mice using the RNeasy Plus Micro Kit (Qiagen; 74034).  Library preparation was performed by Novogene (Sacramento, US), using at least 1 ug of total RNA per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: S41_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR49


title: T63_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line


title: CS_ABEMA_2 CST30, human melanoma cell line, treated with abemaciclib

data_processing: Data analysis and statistical evaluations were performed with Transcriptome Analysis Console (TAC) Software (Affymetrix). Affymetrix algorithm name = sst-rma-gene-full

source_name: Human melanoma cell line

extract_protocol: RNA was extracted from melanoma cell lines by TRIzol (Invitrogen). Melanin removal was carried out by the CTAB-UREA method. Samples were treated with DNase 1 (Qiagen) and purified by RNeasy MinElute Cleanup Kit (Qiagen). The quality of total RNA was first assessed using the RNA 6000 Pico Assay RNA chips run on an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Gene expression was assessed in cells treated twice with drugs at T1=24h and T2=96 h. Gene expression was assessed at T=144h.

value: Male

value: nodal metastasis

tag: mutational subset

value: BRAF-MUTANT


title: SPP1 KO_2


title: SPP1 KO_3


title: acute myeloid leukemia (AML)_DR47

value: BAL


title: S38_single cell rna seq by Smart Seq2


title: SPP1 KO_1


title: acute myeloid leukemia (AML)_DR48

value: AML


title: acute myeloid leukemia (AML)_DR46

value: de novo


title: wt_4


title: S37_single cell rna seq by Smart Seq2


title: CS_GSK_2 CST30, human melanoma cell line, treated with GSK126


title: CS_ABEMA_1 CST30, human melanoma cell line, treated with abemaciclib


title: acute myeloid leukemia (AML)_DR45

value: m


title: wt_3


title: T64_NT Tumor nodule from immunodeficient mouse injected s.c. w/ 313 human melanoma cell line


title: acute myeloid leukemia (AML)_DR44


title: S40_single cell rna seq by Smart Seq2

value: HSC


title: S35_single cell rna seq by Smart Seq2

value: AAVS1 KO


title: CS_JQ1_2 CST30, human melanoma cell line, treated with JQ1


title: S39_single cell rna seq by Smart Seq2


title: S34_single cell rna seq by Smart Seq2


title: wt_1


title: wt_2


title: S33_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR42


title: CS_GSK_1 CST30, human melanoma cell line, treated with GSK126


title: S32_single cell rna seq by Smart Seq2


title: CS_ITF_1 CST30, human melanoma cell line, treated with givinostat


title: elav>mcherry_RNAi_rep3

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Targeted DamID data were analysed using pipeline described in Marshall and Brand, 2015
Assembly: dm6
Supplementary files format and content: Processed TaDa data in .gff files with score representing log2 Dam-fusion/Dam-only

organism: Drosophila melanogaster

source_name: L3 CNS

growth_protocol: Drosophila were cultured under standard conditions at 25 degrees

extract_protocol: Adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of adaptors. Libraries were generated using the illumina TruSeq library kit

treatment_protocol: Flies were moved from 18 to 29 degrees C for 24 hours preceeding dissection to induce expression of Dam-fusion proteins.

value: neurons

value: mcherry RNAi


title: acute myeloid leukemia (AML)_DR40


title: CS_JQ1_1 CST30, human melanoma cell line, treated with JQ1


title: S36_single cell rna seq by Smart Seq2


title: CS_GUADE_1 CST30, human melanoma cell line, treated with guadecitabine


title: acute myeloid leukemia (AML)_DR04


title: CS_GUADE_2 CST30, human melanoma cell line, treated with guadecitabine


title: elav>mcherry_RNAi_rep2


title: S31_single cell rna seq by Smart Seq2


title: elav>Mi2_RNAi_rep3

value: Mi2 RNAi


title: S29_single cell rna seq by Smart Seq2


title: S30_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR39


title: acute myeloid leukemia (AML)_DR38


title: CS_NT_1 CST30, human melanoma cell line, not treated


title: acute myeloid leukemia (AML)_DR41


title: acute myeloid leukemia (AML)_DR43


title: CS_ITF_2 CST30, human melanoma cell line, treated with givinostat


title: S28_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR37

value: tAML

value: f


title: VR_ABEMA_2 VRG100, human melanoma cell line, treated with abemaciclib

value: Female

value: primary tumor

value: NRAS-MUTANT


title: elav>Mi2_RNAi_rep2


title: CS_NT_2 CST30, human melanoma cell line, not treated

value: Male


title: VR_ABEMA_1 VRG100, human melanoma cell line, treated with abemaciclib


title: acute myeloid leukemia (AML)_DR36

value: leukemia blast cells


title: elav>mcherry_RNAi_rep1


title: S26_single cell rna seq by Smart Seq2


title: S27_single cell rna seq by Smart Seq2


title: elav>mep_Dam2

description: DNA amplicons from methylated gDNA

library_source: genomic

data_processing:
Library strategy: DamID
Targeted DamID data were analysed using pipeline described in Marshall and Brand, 2015
Assembly: dm6
Supplementary files format and content: Processed TaDa data in .gff files with score representing log2 Dam-fusion/Dam-only

molecule: genomic DNA


title: acute myeloid leukemia (AML)_DR35

value: sAML


title: VR_GSK_2 VRG100, human melanoma cell line, treated with GSK126


title: elav>mep_Dam1

description: DNA amplicons from methylated gDNA


title: acute myeloid leukemia (AML)_DR34


title: nsyb>dam2

description: DNA amplicons from methylated gDNA

value: mature neurons


title: VR_GSK_1 VRG100, human melanoma cell line, treated with GSK126


title: elav>Mi2_RNAi_rep1


title: S24_single cell rna seq by Smart Seq2


title: nsyb>dam1

description: DNA amplicons from methylated gDNA


title: acute myeloid leukemia (AML)_DR33

value: AML


title: VR_JQ1_2 VRG100, human melanoma cell line, treated with JQ1


title: VR_JQ1_1 VRG100, human melanoma cell line, treated with JQ1


title: acute myeloid leukemia (AML)_DR32

value: de novo


title: Wor>dam2

description: DNA amplicons from methylated gDNA

value: NSCs


title: S23_single cell rna seq by Smart Seq2

value: HSC


title: VR_ITF_2 VRG100, human melanoma cell line, treated with givinostat


title: S22_single cell rna seq by Smart Seq2

value: AAVS1 KO


title: Wor>dam1

description: DNA amplicons from methylated gDNA


title: S25_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR03

value: m


title: acute myeloid leukemia (AML)_DR31


title: elav>Dam_2

description: DNA amplicons from methylated gDNA

value: neurons


title: VR_ITF_1 VRG100, human melanoma cell line, treated with givinostat


title: S20_single cell rna seq by Smart Seq2


title: elav>Dam_1

description: DNA amplicons from methylated gDNA


title: acute myeloid leukemia (AML)_DR29


title: nsyb>Dam-Mi2_rep2

description: DNA amplicons from methylated gDNA


title: S19_single cell rna seq by Smart Seq2


title: nsyb>Dam-Mi2_rep1

description: DNA amplicons from methylated gDNA


title: acute myeloid leukemia (AML)_DR28


title: acute myeloid leukemia (AML)_DR27


title: S18_single cell rna seq by Smart Seq2


title: S17_single cell rna seq by Smart Seq2


title: wor>Dam-HDAC1_rep2

description: DNA amplicons from methylated gDNA


title: VR_NT_2 VRG100, human melanoma cell line, not treated


title: acute myeloid leukemia (AML)_DR24


title: S16_single cell rna seq by Smart Seq2


title: VR_NT_1 VRG100, human melanoma cell line, not treated


title: S55_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR23


title: VSS98, human melanoma cell line

treatment_protocol: Gene expression was assessed in cells in exponential growth phase, no treatment was used.

value: nodal metastasis

value: BRAF-MUTANT


title: wor>Dam-MTA1-like_rep1

description: DNA amplicons from methylated gDNA


title: wor>Dam-MTA1-like_rep2

description: DNA amplicons from methylated gDNA


title: S14_single cell rna seq by Smart Seq2


title: SLN91, human melanoma cell line


title: VR_GUADE_2 VRG100, human melanoma cell line, treated with guadecitabine


title: acute myeloid leukemia (AML)_DR22

value: f


title: wor>Dam-Mep1_rep2

description: DNA amplicons from methylated gDNA


title: acute myeloid leukemia (AML)_DR26


title: SGN89, human melanoma cell line

value: Female


title: RZZ79, human melanoma cell line


title: acute myeloid leukemia (AML)_DR21


title: acute myeloid leukemia (AML)_DR20


title: wor>Dam-Mep1_rep1

description: DNA amplicons from methylated gDNA


title: VRG100, human melanoma cell line

value: primary tumor


title: S11_single cell rna seq by Smart Seq2


title: PLN74, human melanoma cell line

value: lung metastasis

value: BRAF/NRAS WILD TYPE


title: PCN71, human melanoma cell line

value: Male


title: acute myeloid leukemia (AML)_DR02

value: leukemia blast cells

value: sAML


title: wor>Dam-HDAC1_rep1

description: DNA amplicons from methylated gDNA


title: S10_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR19

value: AML


title: MNT59, human melanoma cell line

value: NRAS-MUTANT


title: elav>Dam-HDAC1_rep2

description: DNA amplicons from methylated gDNA


title: S9_single cell rna seq by Smart Seq2


title: S13_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR18


title: S15_single cell rna seq by Smart Seq2


title: elav>Dam-HDAC1_rep1

description: DNA amplicons from methylated gDNA


title: S12_single cell rna seq by Smart Seq2


title: S8_single cell rna seq by Smart Seq2


title: S21_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR17

value: de novo


title: elav>Dam-MTA1-like_rep2

description: DNA amplicons from methylated gDNA


title: GBB45, human melanoma cell line

value: cutaneous metastasis


title: elav>Dam-MTA1-like_rep1

description: DNA amplicons from methylated gDNA


title: wor>Dam-Mi2_rep2

description: DNA amplicons from methylated gDNA

value: NSCs


title: S6_single cell rna seq by Smart Seq2

value: HSC

value: AAVS1 KO


title: wor>Dam-Mi2_rep1

description: DNA amplicons from methylated gDNA


title: acute myeloid leukemia (AML)_DR15

value: m


title: FCC38, human melanoma cell line

value: nodal metastasis

value: BRAF-MUTANT


title: FRN39, human melanoma cell line


title: S5_single cell rna seq by Smart Seq2


title: S7_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR14


title: S4_single cell rna seq by Smart Seq2


title: elav>Dam-Mep1_rep1

description: DNA amplicons from methylated gDNA

value: neurons


title: S3_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR12


title: acute myeloid leukemia (AML)_DR13

value: f


title: S2_single cell rna seq by Smart Seq2


title: elav>Dam-Mi2_rep1

description: DNA amplicons from methylated gDNA


title: elav>Dam-Mi2_rep2

description: DNA amplicons from methylated gDNA


title: acute myeloid leukemia (AML)_DR11


title: acute myeloid leukemia (AML)_DR16


title: S1_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR10


title: Six2+ NP from newborn Six2CreTet2/3f/f  mouse, replicate 1, WGBS

city: Philadelphia

first: Xiujie

last: Liang

state: Pennsylvania

address: 12-188 Smilow Translational Research Center, 3400 Civic Center Blvd

department: Department of Medicine

institute: University of Pennsylvania

data_processing:
For scRNA-seq, the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). For WGBS, adapter and low-quality reads were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Bismark version 0.19.1 was used for read alignment to the mouse genome (mm10), deduplication, and quantification of CpG methylation level. De novo genome segmentation based on DNA methylation was performed using SMART version 2.2.8 with default thresholds.
Assembly: mm10
Supplementary files format and content: For scRNA-seq, Tab-separated values files and matrix files
Supplementary files format and content: For WGBS, CpG methylation value files in bigwig format

source_name: Nephron progenitor

extract_protocol:
For scRNA-seq, kidneys were digested using Multi Tissue dissociation kit 1. Debris were removed using Miltenyi Debris Removal Solution and dead cells were removed using the Miltenyi Dead Cell Removal kit. Cell number and viability were assessed using Countess AutoCounter. For WGBS, Six2-positive cells were isolated by FACS and genomic DNA was isolated from Six2-positive cells using the DNeasy Blood & Tissue Kit.
For scRNA-seq, we generated single cell suspension from whole kidney samples and loaded 10,000 cells onto the Chromium Controller (10X Genomics, PN-120223) on a Chromium Single Cell B Chip (10X Genomics, PN-120262) and processed to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, CG000183). Libraries were generated using Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, PN-1000092) and Chromium i7 Multiplex Kit (10X Genomics, PN-120262) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Quantification analysis was performed by Illumina Library Quantification Kit (KAPA Biosystems, KK4824). The library was sequenced on Illumina HiSeq 4000 system with 2x150 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, 8 bp I7 index for sample index and 91 bp Read2 for transcript. For WGBS, DNA concentration was measured using Picogreen. DNA quality was checked by Agilent genomic DNA screentape. The library kit is Accel-NGS® Methyl-Seq DNA Library. The library was sequenced on HiSeqX (150bp PE).

value: Newborn

value: Nephron progenitor


title: elav>Dam-Mep1_rep2

description: DNA amplicons from methylated gDNA


title: Six2+ NP from newborn SixCre mouse, replicate 1, WGBS


title: acute myeloid leukemia (AML)_DR01


title: aml_mecom2_bulkRNA-seq

description:
bulkrna_seq
S14

data_processing:
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
Cumulus pipeline for bulkRNA
Genome_build:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary_files_format_and_content: expected_count, TPM, FPKM

source_name: MUTZ-3 cells

growth_protocol: cells were cultured at 37oC and 5%O2 in serum-free HSC media comprised of StemSpan  II medium (Stem Cell Technologies) supplemented with CC100 cytokine cocktail (Stem Cell Technologies), 100ng/ml TPO (Peprotech) and 35nM UM171 (Stem Cell Technologies). Confluency was maintained between 2e5-1e6 cells/ml.     MUTZ-3 cells (DSMZ) were cultured at 37oC in alpha-MEM (Life Technologies) supplemented with 20% FBS, 20% conditioned media from 5637 cells (ATCC) (Kappas and Bautch, 2007) and 1% penicillin/streptomycin. Confluency was maintained between 7e5-1.5e6/ml.

treatment_protocol: AAVS1  or MECOM KO or MECOM rescue

value: Mecom KO


title: NT tissue

city: Jining

first: Rou

last: Zhao

address: 89 Guhuai Road

institute: Affiliated Hospital of Jining Medical College

description: one sample from NT tissue

data_processing:
The sequencing and data analysis of the database was completed by Shanghai Ouyi Biomedical Technology Co., Ltd. The raw reads generated in high-throughput sequencing are in fastq format. In order to ensure the quality of sequencing, the FastQC software is used for quality control evaluation of the raw off-machine data. The 10x genomics official software CellRanger is used to perform data quality statistics on the original data and compare to the reference genome. The software uses the Barcode sequence markers in the identification sequence to distinguish cells and the UMI markers of different mRNA molecules in each cell for high-throughput single-cell transcription The group performs quantification and obtains quality control statistical information such as high-quality cell number, gene median value, and sequencing saturation.
Use the Seurat software package to perform further quality control and processing on the data based on the preliminary quality control results of Cellranger. Theoretically, the number of genes expressed by most cells, the number of UMIs, and the amount of mitochondrial gene expression will be concentrated in a certain area. According to this feature, we first filter out delocalized cells by fitting a generalized linear model, and then according to nUMI, nGene and percent .mito The distribution of three indicators, filtering out low-quality cells such as double cells, multiple cells or dead cells.
Use gene expression to perform PCA (principal component) linear dimensionality reduction analysis, and visualize PCA results in a two-dimensional space through tSNE (non-linear dimensionality reduction) or UMAP. If there are batches between samples, the mutual nearest neighbors method (mutual nearest neighbors) is used to correct the batch effect of single-cell expression profile data.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz (barcode-1 represents GC cells, barcode-2 represents NT cells), features.tsv.gz, matrix.mtx.gz

source_name: GC-patient

extract_protocol:
Tumors were obtained after resection in the operating room and were used to prepare single-cell suspensions. Tissue samples were cut into small pieces and transferred to tubes containing 4.7 mL of Dulbecco’s modified essential medium, 200 L H, 100 L R, and 25 L AMACS C. MACS™ was separated 3 times, and the sample was incubated at 37 °C for 30 min at each dissociation step interval.
After disassembly, the sample was passed through a filter with a diameter of 40 μm, and the suspension was centrifuged at 300 × g for 7 min to completely remove the supernatant. Next, erythrocytes were removed using erythrocyte lysate (10×) (Sigma–Aldrich, St. Louis, Mo, USA). Finally, a dead cell removal kit (Miltenyi Biotec) was used to ensure cell viability >90%.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adjacent normal tissue

tag: tumor state

value: Poorly differentiated


title: H446 NTgRNA, BRD4, Bethyl

city: Bethesda

first: Haobin

last: Chen

state: MD

address: 10 Center Drive, Room 3-5888

department: Thoracic Surgery Branch

institute: National Institutes of Health

data_processing:
Fastq files were processed using PartekFlow.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, discarding reads left with < 25 bp.
ChIP-seq reads were aligned to the UCSC hg19 genome using BWA-backtrack version 0.7.12 with the parameters '-n 0.04 -o 1 -e -1 -d 10 -i 5 -k 2 -E 4 -R 30 -t 32'.
Duplicated reads were discarded. Peaks were called using MACS v2.1.1 with the significance cut-off q-value <=0.05.
Assembly: hg19
Supplementary files format and content: narrowPeak (NEUROD1) and BroadPeak (H3K27Ac, RPII, BRD2, BRD3, BRD4) files.

growth_protocol: RPMI, 10% heat-inactivated FBS, 1x penicillin/streptomycin. Cells were cultured at 37 ⁰C at 5% CO2 in a humidified atmosphere.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Sonic Dismembrator (Fisher brand Model 705).
Libraries were constructed using entire ChIPed DNA or 300 ng of the input DNA using a NEBNext Ultra II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter). Estimation of library quality and quantity was performed using a Bioanalyzer and Qubit assays.

value: small cell lung cancer SCLC-N subtype

value: WT

tag: chip antibody


title: aml_mecom1_bulkRNA-seq

description:
bulkrna_seq
S13

value: AML


title: H446 ND1-KO, BRD3, Bethyl

value: NEUROD1 knockout


title: aml_aavs3_bulkRNA-seq

description:
bulkrna_seq
S12


title: H446 NTgRNA, BRD3, Bethyl


title: aml_mecom3_bulkRNA-seq

description:
bulkrna_seq
S15


title: myeloid cells, Suc3

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 370 W. 9th Avenue

department: Physiology and Cell Biology

institute: The Ohio State Universtiy

data_processing:
Sequencing alignment, hisat2 v2.2.1
read count matrix formation, htseq 0.11.3
differential anaysis, DEseq2 v1.32.0
Genome_build: mm39
Supplementary_files_format_and_content: count matrix (.txt)
Supplementary_files_format_and_content: DESeq2 analysis (.csv). DESeq2 analaysis was carried out comparing all 3 groups. Nomenclature example: 'Prd_vs_Veh.csv' compares Prednisolone vs Vehicle conditions. 'Suc' stands for 'Sucrose' which is the Vehicle

source_name: Quadriceps

extract_protocol:
RNA was extracted using a NucleoSpin RNA XS kit (Takara, 740902)
DNBseq preparation method (BGI)

treatment_protocol: Mice were treated with spironolactone, prednisolone, or vehicle for 7 days prior to extraction.

value: mdx

tag: tissue

value: Quadriceps

value: myeloid cells

value: 4.5 weeks

value: vehicle


title: aml_aavs2_bulkRNA-seq

description:
bulkrna_seq
S11

tag: cell type

value: AAVS1 KO


title: H446 ND1-KO, BRD4, Bethyl


title: myeloid cells, Suc2


title: H446 NTgRNA, BRD2, CST


title: H446 ND1-KO, BRD2, CST


title: aml_aavs1_bulkRNA-seq

description:
bulkrna_seq
S10


title: GC tissue

description: one sample from GC tissue

value: Gastric cancer tissue


title: myeloid cells, Suc1


title: lthscr_mecom3_bulkRNA-seq

description:
bulkrna_seq
S9

source_name: hsc cell lines

value: HSC

value: primary cells for HSC

value: MECOM over express rescue


title: H446 ND1-KO, Pol II, EMD/Millipore

description: H446_ND1-KO_Pol II

value: RPII (EMD/Millipore, #05-623)


title: Bisulfite converted DNA from NPC43_2

city: Hong Kong

first: Ka Yue Larry

last: Chow

address: 21 Sassoon Road

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Trimmomatic was used for removing adapter sequences and poor quality bases.
BSMAP was used for aligning the reads onto hg19
BSMAP was used to quantify the methylation ratio of each CpG sites
Genome_build: hg19
Supplementary_files_format_and_content: The Bigwig files represent the methylation ratio of CpG sites with more than 10 coverage. Converted from bedgraph using UCSC utility

source_name: NPC Cell Line

growth_protocol: NP361 and NP550 were cultured with keratincyte-serum free medium and EpiLife (1:1) with supplements and 10% FBS (GIBCO, Invitrogen).  NP69 was cultured in Keratinocyte-SFM medium (Gibo; Thermo Fisher  Scienific, Inc.), supplemented with Bovine Pituitary Extract (BPE) and 1 ng/ml epidermal growth factor (EGF). C17, C666 , and NPC43 were cultured in RPMI-1640 medium supplented with 10% fetal bovine serum.

extract_protocol:
DNA was extracted by AllPrep DNA/RNA Mini Kit (Qiagen). SeqCapEpi Enrichment System was used for library preparation.
SeqCapEpi Enrichment System

treatment_protocol: EpiTect Bisulfite Kit was used for bisulfite conversion of DNA. Experimental procedure follows the protocol.


title: Methylation Control (100%)

source_name: Methylation Control

tag: control

value: Methylation Control (100percent)


title: Methylation Control (50%)

value: Methylation Control (50percent)


title: Methylation Control (0%)

value: Methylation Control (0percent)


title: lthscr_mecom2_bulkRNA-seq

description:
bulkrna_seq
S8


title: Bisulfite converted DNA from C666_2


title: H446 NTgRNA, Pol II, EMD/Millipore

description: H446_NTgRNA_Pol II

value: small cell lung cancer SCLC-N subtype

value: WT


title: lthscr_mecom1_bulkRNA-seq

description:
bulkrna_seq
S7


title: myeloid cells, Spr3

tag: age

value: spironolactone


title: Bisulfite converted DNA from NPC43

tag: cell line


title: myeloid cells, Spr2

value: mdx


title: lthsc_mecom3_bulkRNA-seq

description:
bulkrna_seq
S6

tag: genotype

value: Mecom KO


title: H446 ND1-KO, NEUROD1, CST

value: NEUROD1 knockout

value: NEUROD1 (CST, #4373)


title: Bisulfite converted DNA from C666


title: H446 NTgRNA, NEUROD1, CST


title: lthsc_mecom2_bulkRNA-seq

description:
bulkrna_seq
S5


title: lthsc_mecom1_bulkRNA-seq

description:
bulkrna_seq
S4


title: Bisulfite converted DNA from NP550EBV

source_name: Nasopharyngeal Tissue Cell Line


title: Bisulfite converted DNA from C17


title: H446 ND1-KO, H3K27Ac, Abcam

value: H3K27Ac (Abcam, #ab4729)


title: myeloid cells, Prd3

value: Quadriceps

value: myeloid cells

value: 4.5 weeks

value: prednisolone


title: myeloid cells, Prd2


title: H446 NTgRNA, H3K27Ac, Abcam


title: Bisulfite converted DNA from NP550


title: lthsc_aavs3_bulkRNA-seq

description:
bulkrna_seq
S3

value: HSC

value: primary cells for HSC

value: AAVS1 KO


title: lthsc_aavs2_bulkRNA-seq

description:
bulkrna_seq
S2


title: myeloid cells, Prd1


title: H446 ND1-KO, Input


title: myeloid cells, Spr1


title: T1

city: Suita

first: Yuki

last: Makino

state: Osaka

address: 2-2, Yamadaoka

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Osaka University Graduate School of Medicine

data_processing:
The libraries were sequenced by a DNBSEQ-G400RS (MGI Tech, China) platform in 2 x 100 bp paired-end mode.
BD Rhapsody™ WTA Analysis Pipeline on Seven Bridges Genomics (https://www.sevenbridges.com/) was used for alignment, filtering, and unique molecular identifier counting to determine the number of mRNA molecules per cell.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw counts for every molecule per cell

source_name: liver tumor

extract_protocol:
Liver tumors were enucleated from the liver and enzymatically dissociated into a single-cell suspension using a tumor dissociation kit (Miltenyi Biotec, Bergisch Gladbach, Germany). The single-cell suspension was then loaded into a BD Rhapsody cartridge (BD Biosciences, San Jose, CA) to isolate the single-cell transcriptome.
Libraries were generated using a BD Rhapsody WTA amplification kit (BD Biosciences).

value: 12 months

value: male


title: Bisulfite converted DNA from NP361EBV


title: T2


title: lysR_A

status: Public on Nov 22 2022

city: Hangzhou

first: Lijuan

last: Wu

state: Zhejiang

address: 28 Shui Dao Suo Road, Fuyang District

institute: China national rice research institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Clean reads were mapped to the Burkholderia sp. JP2-270 reference genome (CP029824-CP029828) using Bowtie 2-2.2.3.
Then Htseq v0.6.1 was used to count the reads numbers mapped to each gene. FPKM (Fragment Per Kilobase of transcript sequence per Millions base pairs sequenced) was used to estimate gene expression levels.
Genome_build: NCBI accession number: CP029824-CP029828
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Burkholderia sp. JP2-270

source_name: cell

extract_protocol:
Briefly, a total of 3 µg RNA per sample was obtained and rRNA were depleted using Ribo-Zero rRNA removal kit (G- bacteria). The mRNA were fragmented using diavalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5 X). Then, the cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacture’s instructions. The cDNA fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA), and then 3µl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion HighFidelity DNA polymerase, Universal PCR primers and Index Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The resultant samples were sequenced on an Illumina Hiseq 2000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bysR deletion

tag: growth

value: 24 hour after inoculation


title: H446 NTgRNA, Input

value: small cell lung cancer SCLC-N subtype

value: WT


title: lysR_C


title: lthsc_aavs1_bulkRNA-seq

description:
bulkrna_seq
S1


title: lysR_B


title: Bisulfite converted DNA from NP361


title: WT_B

value: Wild type


title: WT_C


title: WT_A


title: 24hr Gastrula Cells, replicate 4, scRNAseq

city: Bethlehem

first: Michael

middle: John

last: Layden

state: PA

address: 111 Research Dr

department: Biological Sciences

institute: Lehigh University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
QC, clustering,  and expression analysis  were done using Seurat v4 (
Supplementary files format and content: Nematostella vectensis SIMRbase genome (https://simrbase.stowers.org/starletseaanemone)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Nematostella vectensis

source_name: Whole embryo

extract_protocol:
Gastrula stage embryos were dissociated in calcium- and magnesium-free 1/3X seawater (CMF/NM) with ethylenediaminetetraacetic acid (EDTA) and 0.25% trypsin (henceforth called dissociation solution, pH 7.4-7.6) at 37°C as previously described (Torrez-Mendez 2019), with modifications. Briefly, cells were acclimated into the dissociation solution through a stepwise incubation first in CMF/NM (5 minutes RT, pH 8.0), then with CMF/NM + EDTA (10 minutes RT, pH 8.0), and finally incubated in pre-warmed dissociation solution for ~20 minutes at 37°C, with gentle pipetting every 5 minutes, until a single cell suspension was obtained. Once cells were fully dissociated, an equal volume of cold CMF/NM + 0.05% BSA (pH 7.8) was added. The single-cell suspension was then filtered through a 30µm filter and spun 300 rpm for 15 minutes at 4°C to pellet the cells. Cells were washed and resuspended 3x in cold CMF/NM + 0.05% BSA (spun at 300 rpm for 7 minutes at 4°C). Cell viability was determined by staining the cells with Hoechst 33342 (10mg/µl) and Sytox green for 20 minutes, and quantifications were performed using a hemocytometer.
Library construction was performed using the Chromium Next GEM single Cell 3’ v3.1 protocol (10x Genomics) following manufacturer’s instructions. The concentration of the cell suspension + master mix added to the chip for GEM generation was calculated to target 10,000 cell recovery. Four separate replicates were run on a single chip, and 4 separate cDNA libraries were generated. Quality of the final libraries was assessed using a Bioanalyzer (Agilent).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Whole embryo

value: Gastrula Cells

tag: developmental stage

value: 24 hours post fertilization


title: 24hr Gastrula Cells, replicate 3, scRNAseq

description: 10x Genomics


title: 24hr Gastrula Cells, replicate 2, scRNAseq

description: 10x Genomics


title: BRM17, human melanoma cell line

value: Male

tag: type of lesion

value: nodal metastasis

value: BRAF-MUTANT


title: CL19, human melanoma cell line

value: Female

value: visceral metastasis


title: CLM27, human melanoma cell line


title: 24hr Gastrula Cells, replicate 1, scRNAseq

description: 10x Genomics


title: GML41, human melanoma cell line


title: BLS6, human melanoma cell line

value: cutaneous metastasis


title: 7-days post amputation, epicardial cells, scRNA-seq

city: New York

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation done with Cell Ranger software v3.0.2
Sample integration (batch correction), expression value normalization, clustering, cell type annotation and so on were done with SCTransform, scater, and scran. For more details and the cell type annotation information, see https://github.com/abcwcm/Cao_Epicardium
Assembly: GRCz10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Danio rerio

source_name: heart (ventricle)

growth_protocol: Standard zebrafish breeding conditions

extract_protocol:
Hearts were dissociated into single cells and the epicardial cells were isolated by FACS as described previously (PMID 26657776).
Library prep was performed according to the manufacturer’s instructions (single cell 3' v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with, amplified by PCR and the appropriate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
Single Cell 3' GEM (Gel Bead Kit v3, Chromium Single Cell B Chip Kit)

treatment_protocol: Heart amputation injury

value: epicardial cells

value: heart (ventricle)

value: EK (tcf21:nucEGFP)

value: 6 months

tag: treatment

value: partial ventricular amputation


title: 3-days post amputation, epicardial cells, scRNA-seq

description: 10x Genomics


title: Test2_22_P_Normalfolate

city: Taiyuan

first: Haixia

last: Luo

address: 382 Wuyi Road

institute: The Second Hospital of Shanxi Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human  Clariom® D Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: normal cervical epithelium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The tissue that was harvested indivdually from the cervix were stored at iquid itrogen temperatures at once with protected by Rnasin inhibitor.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: After grinded under the ice, cervix tissue were collected for further total RNA extraction.

value: normal cervical epithelium


title: CST30, human melanoma cell line

city: Milan

first: Andrea

last: Anichini

address: Via Venezian 1

institute: Fondazione IRCCS Istituto Nazionale dei Tumori


title: VR_GUADE_1 VRG100, human melanoma cell line, treated with guadecitabine

value: primary tumor

value: NRAS-MUTANT


title: Test2_3_B_Normalfolate

source_name: HPV16 positive cervical squamous cell carcinoma

value: cervical squamous cell carcinoma


title: Test2_14_B_Normalfolate


title: GRD43, human melanoma cell line


title: CPN20, human melanoma cell line


title: Test2_23_B_Normalfolate


title: Test2_1_B_Normalfolate


title: Test2_12_B_Normalfolate


title: Test2_11_P_Normalfolate


title: Test2_24_P_Normalfolate


title: DSM35, human melanoma cell line


title: BNV13, human melanoma cell line


title: ARS2, human melanoma cell line


title: Test2_15_P_Normalfolate


title: HD8_UNTR_stimulated

first: Eduardo

last: Gomez Castaneda

address: 30 Guilford Street

department: Institute of Child Health

institute: UCL

data_processing:
Basecalling was performed with Illumina RTA software (which is done on-board the instrument) and demultiplexing was performed using bcl2fastq 2.20.
Adapter sequences were removed using cutadapt 2.10 removing the last base of each read (-u -1 -U -1). A minimun length of 20bp was required to keep a read after trimming adapter sequences.
Read quality was checked for every file (2 files per sample) using FastQC 0.11.9.
mCherry, scFv_CAT_HL and ScFV_FMC63_HL  genes were included into the genome build and annotations as described in the supplementary material of the publication (https://github.com/EduardoGCCM/CATvsFMC63_Michelozzi). Sequences were mapped to the human genome using STAR 2.7.3a.
Exonic sequences were summarised with the featureCounts function from the subread 2.0.0 software package. Only uniquely mapped sequences were considered.
Genome_build: GRCh38.p12 (https://www.gencodegenes.org/human/release_31.html)
Supplementary_files_format_and_content: counts.txt is a matrix of raw counts for every gene and sample.

source_name: Peripheral blood

growth_protocol: Freshly isolated peripheral blood mononuclear cells (PBMCs) from HD1-HD8 were cultured in TexMACSTM medium (Miltenyi Biotec, Bergisch Gladbach, Germany), an optimised T cell medium. To induce T cell expansion, CD3/CD28 Dynabeads (CTSTM DynabeadsTM CD3/CD28, Thermo Fisher Scientific) were added to cells in MACS GMP Cell Differentiation Bags (Miltenyi Biotec) at a 1:3 lymphocyte:bead ratio. CD3/CD28 Dynabeads were magnetically removed from the culture on Day 5 and CAR T cells rested for 48h before proceeding to antigen stimulation.

extract_protocol:
1,000 T cells/CAR T cells were FACS sorted in single PCR tubes containing 4µL of QIAGEN lysis buffer from QIAseq FX Single Cell RNA Library Kit (QIAGEN, Hilden, Germany) and stored at -80°C.
We used the QIAseq FX Single Cell RNA Library Kit (QIAGEN, Hilden, Germany) that includes reverse transcription, cDNA amplification and PCR-free NGS library preparation. Libraries were purified using AMPure XP magnetic beads (Beckman Coulter Inc.,) according to the manufacturer instructions. After beads purification the libraries were resuspended in 50μL of buffer EB (Qiagen) and stored at -20 °C. Size and concentration of the libraries generated was assessed using High Sensitivity Bioanalyzer (Agilent, Santa Clara, CA, USA) and Qubit High-Sensitivity DNA kit (InvitrogenTM, Thermo Fisher Scientific), respectively. Libraries were equimolarly pooled to a final concentration of 10nM.

treatment_protocol: (Lentiviral transduction of T cells) Following overnight activation with CD3/CD28 Dynabeads, 0.5 x 106 beads-activated T cells from HD1-HD8 were suspended in 0.5mL of TexMACS, transduced to express CD19 CAR construct (FMC63 or CAT) with 1mL of LV supernatant in RetroNectinÒ (Takara Bio, Kusatsu, Shiga, Japan)-coated 24-well plates and spinoculated at 1,000g for 40min at room temperature. Generally, 6-8 x 106 beads-activated T cells per donor per construct were seeded for transduction. Transduction efficiency was assessed by FACS evaluating mCherry (LV fluorescent marker) expression, at Day 8 (7 days after transduction). Untransduced beads-activated T cells per each donor were used as a control throughout the experiment and were subjected to the same experimental conditions of LV-transduced ones. (NALM6 and CAR T cells co-cultures) To assess the anti-tumour activity of anti-CD19 CAR T cells, we set-up co-cultures with CD19 expressing NALM6 for 3, 24 or 96h (stimulated conditions) on Day 7 (6 days after transduction and 2 days post-CD3/CD28 Dynabeads removal). Briefly, beads-activated T cells from HD1-HD8 were incubated for 24h in optimised T cell medium before stimulation. 0.1 x 106 UNTR or FMC63 or CAT beads-activated T cells were seeded in 96-well plates in complete TexMACS medium in a 1:1 ratio with irradiated (40Gy) NALM6. Generally, 0.1-1.5 x 106 beads-activated T cells per donor per condition (UNTR, FMC63 and CAT) were stimulated. Unstimulated, beads-activated T cells per each donor, condition and time point were kept in culture under the same experimental conditions of antigen-stimulated T cells.

tag: donor

tag: car construct

value: UNTR

tag: date of sorting

tag: stimulation

value: stimulated

value: T-cell


title: HD8_CAT_stimulated

value: CAT


title: Exosomes of HUMSCs 2

city: Tianjin

first: Sheng

last: Li

state: Xiqing District

institute: The First Teaching Hospital of Tianjin University of Traditional Chinese Medicine

description: miRNA expression in exosomes

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

scan_protocol: After purification the labeled RNAs were hybridized onto the microarray. After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05. Target genes of differentially expressed miRNAs were the intersection predicted with  2 databases (miRDB, miRWalk). GO analysis and KEGG analysis were applied to determine the roles of these target genes. Hierarchical Clustering was performed to show the distinguishable miRNAs expression pattern among samples.

source_name: Differential centrifugation to extract exosomes in the supernatant of HUMSCs

label_protocol: Briefly, total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

growth_protocol: HUMSCs were cultured in mesenchymal stem cell medium (MSCM) (Gibco, MA, USA) supplemented with 10% exosome-free fetal bovine serum (FBS) (Gibco) in 5% CO2 at 37℃. HUMSCs from passages 3–5 was pretreated with 10 μmol/L TSA  in MSCM supplemented with 10% exosome-free FBS for 24 h until collection of the medium.

extract_protocol: Total RNA in exosomes was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity(RIN) was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The conditioned supernatants of MSCs pretreated with or without TSA were collected and centrifuged at 300 ×g for 10 min. The supernatant was centrifuged at 10000 ×g for 30 min and filtered through a sterile 0.22-μm pore filter. The filtered solution was ultracentrifuged at 120,000 ×g for 2 h. Lastly, the supernatant was discarded to obtain the exosome precipitate

value: Human umbilical vein mesenchymal stem cell-derived exosomes

value: control


title: Exosomes of HUMSCs 3

description: miRNA expression in exosomes


title: Exosomes of HUMSCs 1

description: miRNA expression in exosomes


title: Exosomes of HUMSCs treated with TSA for 24h 1

description: miRNA expression in exosomes

source_name: Differential centrifugation to extract exosomes in the supernatant of HUMSCs pretreated with TSA for 24 h

value: pretreated with TSA for 24 h


title: Exosomes of HUMSCs treated with TSA for 24h 2

description: miRNA expression in exosomes


title: epicardial cells, scRNA-seq

description: 10x Genomics

tag: strain

value: no treatment


title: HD8_FMC_stimulated

value: FMC


title: Exosomes of HUMSCs treated with TSA for 24h 3

description: miRNA expression in exosomes


title: Test2_13_P_Normalfolate


title: HD7_UNTR_stimulated


title: Test2_21_B_Normalfolate


title: HD7_FMC_stimulated


title: BRB8, human melanoma cell line

source_name: Human melanoma cell line

tag: gender

value: Female

value: cutaneous metastasis

tag: mutational subset

value: BRAF-MUTANT


title: HD7_CAT_stimulated


title: HD5_FMC_stimulated


title: HD5_UNTR_stimulated


title: Test2_2_P_Normalfolate


title: Test2_5_B_Normalfolate


title: Test2_4_P_Normalfolate


title: HD6_FMC_stimulated


title: HD6_UNTR_stimulated


title: HD6_CAT_stimulated


title: HD4_FMC_stimulated


title: HD5_CAT_stimulated


title: HD4_UNTR_stimulated


title: HD8_FMC_non_stimulated


title: HD8_UNTR_non_stimulated


title: HD8_CAT_non_stimulated


title: HD4_CAT_stimulated


title: HD6_UNTR_non_stimulated


title: HD7_FMC_non_stimulated


title: HD7_CAT_non_stimulated


title: HD4_FMC_non_stimulated


title: HD7_UNTR_non_stimulated


title: HD6_CAT_non_stimulated


title: HD6_FMC_non_stimulated


title: HD5_UNTR_non_stimulated


title: HD1_UNTR_stimulated


title: HD5_CAT_non_stimulated


title: HD5_FMC_non_stimulated


title: HD1_CAT_stimulated


title: HD2_UNTR_stimulated


title: HD2_CAT_stimulated


title: HD4_CAT_non_stimulated


title: HD2_UNTR_non_stimulated


title: HD1_FMC_stimulated


title: HD3_FMC_stimulated


title: HD3_CAT_stimulated


title: HD2_FMC_stimulated


title: HD4_UNTR_non_stimulated


title: HD2_CAT_non_stimulated


title: HD1_UNTR_non_stimulated


title: HD1_CAT_non_stimulated


title: HD1_FMC_non_stimulated


title: P0 GFP positive cells

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw fastq files were processed with Cell Ranger 3.1.0 with default mapping arguments.
Reads were mapped to the mouse mm10 genome and counted with GRCm38.84 annotation.
Next, the cellranger aggr command was executed to adjust the sequencing depth of different samples to the same level.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix table, metadata, and UMAP were exported from the Seurat object containing 23534 filtered cells.

source_name: female gonad

extract_protocol:
Single cells were added to the 10x Chip channels. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs.
RNA libraries were prepared for sequencing using 10x Single Cell 3' Library & Gel Bead Kit v2  protocol

treatment_protocol: Tamoxifen injection to the  pregnant mice at E13.5 to label the Foxl2 positive cells of mT/mG; Foxl2-CreERT2 mice.Dosage:9mg/40g

tag: Stage

value: post natal day 0

tag: background strain

value: mT/mG; Foxl2-CreERT2

tag: tissue

value: gonad

tag: Sex

value: female


title: HD3_UNTR_non_stimulated

tag: cell type


title: HD3_FMC_non_stimulated


title: HD3_CAT_non_stimulated


title: HD3_UNTR_stimulated


title: muscle, mdx, 9m age, antibiotics, rep3

city: Cincinnati

first: Mattia

last: Quattrocelli

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads were trimmed using Trimmomatic
Alignment to mm10 and isoform TPM counts were obtained through Kallisto

source_name: tibialis anterior muscle

extract_protocol:
Total RNA was isolated through Trizol and purified through Qiagen Rneasy columns
True-Seq stranded mRNA library (Illumina)

value: tibialis anterior muscle

tag: genotype

value: antibiotics


title: HD2_FMC_non_stimulated


title: muscle, mdx, 9m age, control, rep3


title: muscle, mdx, 9m age, germ-free, rep1

value: germ-free


title: muscle, mdx, 9m age, antibiotics, rep1


title: muscle, mdx, 9m age, germ-free, rep2


title: muscle, WT, 3m age, control, rep2


title: muscle, WT, 3m age, control, rep3


title: P14 GFP positive cells

value: post natal day 14


title: muscle, mdx, 3m age, control, rep2


title: muscle, mdx, 3m age, control, rep1


title: muscle, mdx, 3m age, control, rep3


title: 4C, testis part of ovotestis

city: Berlin

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

institute: Max Planck Institute for Molecular Genetics

data_processing:
Raw reads were pre-processed and mapped to the reference genome (talOcc4) using BWA. Finally, reads were summarized and normalized by coverage (RPM) for each fragment generated by neighboring restriction enzyme sites. The viewpoint and its flanking fragments (1.5 kb upstream and downstream) were removed for data visualization and a window of 10 fragments was used to smoothen the data.
Assembly: talOcc4
Supplementary files format and content: bedgraph
Library strategy: 4C

organism: Talpa occidentalis

source_name: Adult testis part

extract_protocol:
Embryonic tissues were dissociated with trypsin, filtered through a cell strainer to obtain a single cell suspension and subsequently fixed in 2% formaldehyde.
4C-seq libraries were prepared according to standard protocols. For the first digestion NlaIII was used, and for the second digestion DpnII was used. A total of 1.6 mg of each library was amplified by PCR for the viewpoint in the promoter of Sall1
The libraries were sequenced using Illumina HiSeq technology according to standard procedures

value: Adult testis part

value: wildtype


title: E14.5 GFP positive cells

value: embryonic day 14.5


title: muscle, mdx, 3m age, antibiotics, rep3


title: muscle, mdx, 3m age, antibiotics, rep2


title: muscle, mdx, 3m age, germ-free, rep1


title: muscle, mdx, 3m age, germ-free, rep2


title: muscle, mdx, 3m age, germ-free, rep3


title: muscle, mdx, 9m age, antibiotics, rep2


title: muscle, mdx, 9m age, control, rep1

value: control


title: EBF1-dTAG_N_6h_input

city: Freiburg

first: Nikolay

last: Zolotarev

address: Stübeweg, 51

department: Cellular and Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Quality control and read mapping was done using snakePipes (v2.5.1), an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2 (v2.3.5.1).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with normalization on sequencing depth (CPM). Additionaly bigwig files for a-Brg1 ChIP samples were normalised for ChIP efficiency from EBF1-independent peaks (number of reads in EBF1-independent peaks/total number of reads, Wang et al., 2020).
Peak calling was performed using MACS2 (v2.2.7.1) with default settings.
Assembly: mm10
Supplementary files format and content: One .narrowPeak file containing the MACS2 output for each ChIP sample.
Supplementary files format and content: One bigwig file (.bw) for each sample.

source_name: A-MuLV transformed pro-B cells

growth_protocol: Production of A-MuLV transformed cells with the replacement of endogenous EBF1 by exogenous modified genes was described in Boller et al. 2016. A-MuLV transformed cells were cultured in the RPMI 1640 medium with 10% FCS; 1x Penicillin-Streptomycin-Glutamine; 0.06 mM β-mercaptoethanol.

extract_protocol:
Brg1 ChIP was performed according to the protocol of Bossen et al., 2015 with the following changes.  Cells were harvested and washed with PBS. The cell pellet was resuspended in 10-20 ml PBS. 150 mM EGS (Sigma-Aldrich) stock solution in DMSO was added 1:100 to the cell suspension. Tubes were incubated on a rotator for 15 min at RT. 37% formaldehyde stock solution was added to the final concentration of 1%. Tubes were incubated on a rotator for 15 min at RT. Quenching was performed by adding 2M Glycine to the final concentration 0.2 M.  The cell pellet was resuspended in 4 ml buffer Lysis buffer 1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; PIM) and incubated on ice for 10 minutes. The cell pellet was resuspended Lysis buffer 3 (10mM Tris-HCl, pH 8.0; 200 mM NaCl; 1 mM EDTA, pH 8.0; 0.5 mM EGTA, pH 8.0; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine; PIM) about 1.5-3 x 106 cells per 100 μl buffer.  Chromatin was sheared with a Bioruptor (20-25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C). A small aliquot of chromatin was decrosslinked to check the fragment size on the agarose gel. 30 μl of Dynabeads Protein G (Thermo Fisher) suspension per sample was coupled with 0.5 μg of Brg1 (Abcam, ab110641), or with 2 μg FLAG (M2, Sigma-Aldrich, F1804) antibody, or IgG in 200 μl of PBS with 0.5% BSA. 10-20 μg DNA was used for 1 ChIP reaction. Chromatin was added to beads and incubated on rotator ON at 4°C. Beads were washed with Wash buffer I (50 mM Tris-HCl, pH 8.0; 150 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1 % Triton X-100; 1 mM EDTA pH 8.0); Wash buffer II (50 mM Tris-HCl, pH 8.0; 500 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1% Triton X-100; 1 mM EDTA pH 8.0); Wash buffer III (10 mM Tris-HCl, pH 8.0; 250 mM LiCl; 0.5 % NP-40; 0.5 % NaDOC; 1 mM EDTA pH 8.0) and TE buffer. Every wash was on the rotator for 5 minutes at 4°C. Chromatin was eluted with 100 μl Elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65°C for 30 min. Samples were reverse-crosslinked, treated with 100 μg/ml RNase A and 100 μg/ml Proteinase K, and purified with QIAquick PCR Purification Kit.
NEBNext Ultra II DNA Library Prep Kit for Illumina was used for library preparation according to the manufacturer's protocol.

treatment_protocol: Cells were treated with dTAG-13 (final concentration 0.5 uM) or DMSO for 6 hours.

tag: cell line

value: A-MuLV transformed pro-B cells

value: dTAG-13 6h

tag: chip antibody


title: EBF1-dTAG_N_6h_a-Brg1_ChIP


title: muscle, WT, 3m age, control, rep1


title: P1 1

first: Robert

last: Morell

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description: Sample 13 P1_1

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v3.0.1 using default settings.
Downstream data analysis was performed on the CellRanger cell-gene filtered matrix, using the Seurat R package V3.2
Cell Ranger outputs were imported into Seurat (v3.2) using the ‘Read10x’ and ‘CreateSeuratObject’ functions with the parameters min.cells = 3, min.features = 200. Cells with > 15,000 total RNA molecules and >5% hemoglobin or mitochondrial transcripts were also removed. Data were normalized, scaled and underwent dimensional reduction using the standard Seurat workflow. Predicted doublets were removed with DoubletFinder and a predicted doublet rate of 5%. Each dataset was then re-normalized, scaled and dimensionally reduced using standard Seurat workflow. The top 20 principal components from Seurat’s “RunPCA” function were used to define the dimensions of the UMAP non-linear dimensional reduction analysis which was then viewed on a 2D UMAP plot. An unsupervised clustering analysis was also carried out using the same number of principal components. Neuronal clusters were identified using known neuronal marker genes (Tubb3, Snhg11, Nefl, Nefm, Nefh) and genes known to be expressed early in the SGNs (Pou4f1, Gata3, Neurod1). Neuronal clusters were subset from each individual dataset for further analysis.
At each individual timepoint isolated neuron clusters were merged using Seurat’s standard integration workflow to account for batch effects. For the integration of all timepoints together, neuron datasets for each timepoint were merged before carrying out standard Seurat work flow for PCA analysis. Harmony (v1.0) integration was then applied to this dimensionally reduced object to account for batch effects between the individual datasets. For all merged objects clustering analysis was re-done. Clusters were checked for quality and were removed if their identity could not be determined (< 3 significant genes defining their expression, low or no expression of neuronal marker genes, and/or top 10 marker genes matching > 1 cell type (eg: a mixture of glial and neuronal genes).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrices of raw and normalized counts, generated from Seurat. The barcode names in SGN_Combined_counts.csv and SGN_Combined_counts_norm.csv are formatted such that the number after the "1_" corresponds to the "Sample *", so that e.g., GTAATGCGTTGCCAAT-1_6,GTACAACGTGGCCCAT-1_6, correspond to "Sample 6 E16_2A".

source_name: Spiral ganglion

extract_protocol:
spiral ganglia (SG) were roughly dissected out of the cochlea with some sensory epithelia and mesenchyme still attached. At E16 SG were separated into basal and apical portions by cutting through the middle turn. At E14, E16 and E18, three biological replicates were collected containing pooled tissue from sperate litters. At P1, two biological replicates were collected.
Dissociation at E14 and E16: Pooled SG were dissociated for 14 minutes in 0.05% Trypsin-EDTA at 37˚C, with two vigorous triturations. Trypsin was neutralized with the addition of an equal volume of FBS.
Dissociation at E18 and P1: Pooled SG were dissociated for 25 minutes in Papain (20U/mL) at 37˚C, with triturations every 5 mins. Papain was neutralized with the addition of Ovomucoid inhibitor.
Dissociated cells were passed through a 20μm strainer, spun down at 300 x g and then resuspended in PBS with 0.4mg/mL BSA and 0.2U/mL RNase inhibitor at a density of 1,100 cells/ml
The single-cell suspension was loaded onto the droplet-based single-cell barcoding system (10x Chromium Controller, 10x Genomics) and a Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics) was used to prepare single-cell, barcoded 3’ cDNA libraries according to the manufacturer’s instructions. The libraries were sequenced on a NextSeq2000 instrument (Illumina).
scRNA-Seq

value: cochlea

value: Spiral Ganglion Neurons

tag: location

value: whole ganglion

tag: age


title: EBF1-dTAG_N_0h_a-Brg1_ChIP

tag: treatment

value: DMSO 6h


title: muscle, mdx, 9m age, control, rep2


title: E18 1

description: Sample 10 E18_1


title: E18 2

description: Sample 11 E18_2


title: E16 3 base

description: Sample 9 E16_3B

value: Basal portion of ganglion


title: EBF1-dTAG_N_0h_input


title: E16 2 base

description: Sample 7 E16_2B


title: E16 2 apex

description: Sample 6 E16_2A

value: Apical portion of ganglion


title: E16 1 base

description: Sample 5 E16_1B


title: E16 1 apex

description: Sample 4 E16_1A


title: E18 3

description: Sample 12 E18_3


title: Ascl1+shH2AZ#5_day2_b2_rep2

city: Stanford

first: Justyna

middle: A.

last: Janas

state: CA

address: 265 Campus Drive

institute: Stanford University

data_processing:
Primary data processing, including adapter trimming, genomic alignment to mm10 using Bowtie2 (v 2.3.4.3), mitochondrial and duplicate read removal, peak calling and reproducibility analysis using MACS2 and IDR, respectively, were performed using ENCODE ATAC-seq pipeline v1.2.0 (Consortium, 2012) (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Reproducible peaks selected with IDR (idr threshold ≤ 0.05) were aggregated. Read counts for each region were obtained using featureCounts package, followed by normalization and differential accessibility analysis using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file containing normalized read counts determined for the aggregated day2 samples peak set

source_name: E13.5 fibroblast

growth_protocol: Homozygous TauEGFP knock-in mice (Tucker et al., 2001) were bred with C57B/6 mice (Jackson Laboratory). Mouse embryonic fibroblasts (MEFs) were isolated from embryonic day (E)13.5 heterozygous embryos and maintained in DMEM (Invitrogen) supplemented with 10% cosmic calf serum.

extract_protocol: ATAC-seq was performed based on previously described protocol (Corces et al., 2017).

treatment_protocol: MEFs were transduced with indicated lentiviruses. The cells were treated with doxycycline (dox) two days post-infection to induce transgene expression.

tag: transduction

value: Ascl1-transduced shH2AZ

value: E13.5 fibroblast

tag: time post-induction

value: 2 days


title: Ascl1+shH2AZ#5_day2_b2_rep1


title: Ascl1+shH2AZ#4_day2_b2_rep2


title: Ascl1+shH2AZ#3_day2_b2_rep2


title: Ascl1+shH2AZ#3_day2_b2_rep1


title: E14 3

description: Sample 3 E14_3


title: E14 1

description: Sample 1 E14_1


title: E14 2

description: Sample 2 E14_2


title: Ascl1+shH2AZ#4_day2_b2_rep1


title: Ascl1+shNTC_day2_b2_rep1

value: Ascl1-transduced control shRNA


title: Ascl1+shNTC_day2_b2_rep2


title: rtTA+shNTC_day2_b2_rep1

value: rtTA control


title: BYSR-2

data_processing:
Basecalls performed using CASAVA version 1.4
The clean reads were obtained by filtering the raw data using FASTP with the default parameters. The clean reads were mapped to the Burkholderia sp. JP2-270 reference genome (CP029824-CP029828) using BWA-MEM.
Peaks were generated with MACS2 with the following setting: p-value (0.05), Enrichment Fold (1).IDR (Li et al., 2011) software was used to merge peaks of two technical repeated samples, and the reliability of repeated peak was scored.
Genome_build: NCBI accession number: CP029824-CP029828
Supplementary_files_format_and_content: peak text files

source_name: cells

extract_protocol:
DAP-seq was carried out in duplicate on Burkholderia sp. JP2-270 genomic DNA. Specifically, the Halo-BysR protein was expressed using the TNT SP6 Wheat Germ Protein Expression System (Promega, Fitchburg, WI, USA). The Halo Tag-BysR protein was purified using magnetic HaloTag beads (Promega) and verified by Western blotting with the anti-HaloTag antibody (Promega).
Genomic DNA was extracted from JP2-270 using DNAiso (Takara, Japan). Genomic DNA library was generated using NEXTflex Rapid DNA Seq kit (Bioo Scientific, USA) following the manufacturer’s instructions. The purified protein was incubated with DNA library at 30 ° C for 2 h, and then the unbound DNA fragments was washed away. Then, the BysR-bound DNA fragments were recovered and PCR-amplified. The resultant products were sequenced using the Illumina NovaSeq platform with the sequencing strategy of PE150.
DAP-seq


title: BYSR-1


title: BYSR-input


title: CMO_pool3

city: South San Francisco

first: David

last: Tatarakis

email: tatarakis@dnli.com, genomics@dnli.com

address: 161 Oyster Point Blvd

department: Discovery Genomics

institute: Denali Therapeutics

description: 10X Genomics

data_processing:
Mapping, demultiplexing, hash demultiplexing, and gene counting were performed using Cell Ranger v6.1.1. The 'cellranger multi' pipeline was used.
Assembly: mm10
Supplementary files format and content: Matrix Market format counts matrix
Supplementary files format and content: Comma seperated values format files for genes, cell barcodes, and cell-level meta data

source_name: Brain

extract_protocol:
Mice were perfused with cold PBS and cortical and hippocampal tissues were dissected and dissociated into a single cell suspension using the Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677), according to the manufacturer’s protocol.  Tissues were diced into 0.5 cm pieces and placed in the CTube contianing enzyme mix 1 followed by addition of enzyme mix 2.   Dissociation was performed by the gentleMACS Octo Dissociator using the 37C_ABDK_01 program.  Samples were filtered through a 70 µm strainer and sedimented at 300Xg for 10 minutes in 4C followed by centrifugation in debris removal solution at 3000Xg for 10 minutes in 4C.  After debris removal, cells were washed with cold D-PBS and centrifuged at 1000Xg for 10 mintues in 4C and resuspended in FACS buffer.  Four batches of single cell suspensions, with one replicate of each condition, were labeled with CD11b antibody and cell multiplex oligos per user guide (10X Genomics, CG000391 Rev A).  Equal proportions of cells from each sample were combined into one pool per batch and 100,000 live, CD11b+ cells were FACS sorted on FACS Aria III (BD Biosciences with a 100 μm nozzle) into 1% BSA in PBS.
Single cell capture and library preparation was performed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 per user guide (10X genomics, CG000388 Rev A).  Briefly, gel bead-in-emulsion (GEM) were generated by loading single cells in RT master mix onto the Chip G microfluidic along with partitioning oil and gel beads that contain an Illumina R1 primer sequence, Unique Moldecular Identifier, 10X barcode, and capture sequences for either mRNA transcripts or cell multiplex oligos.  After cDNA amplification of RT materials from the GEMs, transcriptional cDNA was separated from cell multiplex oligo cDNA via NucleoMag bead purification (Takara, 7444970.50), proceeded by library preparation of both sets of cDNA.  Transcriptional libraries were pooled equimolar for a sequencing run on an Illumina MiSeq instrument to estimate the number of cells captured in each library.  This MiSeq capture information was used to pool libraries in equal proportions for sequencing coverage of 50,000 reads per cell across libraries and 5000 reads per Cell multiplex oligo.  Sequencing on the Illumina NovaSeq 6000 instrument generating paired-end reads (28x10x10x90 bases) was performed by SeqMatic (Fremont, CA).

value: Brain

value: myeloid

value: mixed sample (non-demultiplexed)


title: P7 GFP positive cells

value: post natal day 7

value: mT/mG; Foxl2-CreERT2

value: gonad

value: female


title: E16 3 apex

description: Sample 8 E16_3A

value: cochlea

value: Spiral Ganglion Neurons


title: PAO1161 empty vector control (EV), biological rep3

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description:
PAO1161 EV_3(GSM4975404)
RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx

data_processing:
base calling: bcl2fastq v2.20 (Illumina)
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.1 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.28.0.
Assembly: CP032126
Supplementary files format and content: Raw counts of sequencing (FeatureCounts output summarized for all samples) (PA3973_raw_counts.csv).
Supplementary files format and content: A table with DE data for all genes and normalized abundance measurements (EdgeR output) (RNA-seq_deltaPA3973_vs_WT.xlsx).
Supplementary files format and content: A table with DE data for all genes and normalized abundance measurements (EdgeR output) (RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx ).

organism: Pseudomonas aeruginosa

source_name: logarithmic phase of liquid culture

growth_protocol: Cells of P. aeruginosa PAO1161 derivative strains were taken from a deep-frozen stock, spread on L-agar plates and grown overnight at 37oC. Bacteria from single colonies were then used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth and grown with shaking at 37oC.  For analysis of overexpression of strains P. aeruginosa PAO1161 cells were transformed (method of Irani and Rowe, 1997) with pKKB3.11 carrying lacIQ-tacp-PA3973 or empty vector pAMB9.37 (lacIQ-tacp) to obtain PAO1161/pKKB3.11 (lacIQ-tacp-PA3973) and PAO1161/pAMB9.37 (lacIQ-tacp), respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml-1 chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 µg/ml-1 chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 µg/ml-1) and IPTG (0.05 mM) and grown with shaking at 37oC. Aliquots of 2 ml from logarithmic phase cultures (OD600 0.5) were subjected to RNA extraction.

extract_protocol:
2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero™ rRNA Removal Kit (Bacteria) (MRZMB126, Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, E7420). Libraries were sequenced using standard Illumina protocols.

value: PAO1161 leu-

value: pAMB9.37 (lacIQ-tacp)

value: logarithmic phase of liquid culture


title: PAO1161 empty vector control (EV), biological rep2

description:
PAO1161 EV_2(GSM4975403)
RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx


title: rtTA+shNTC_day2_b2_rep2


title: CMO_pool1

description: 10X Genomics


title: CMO_pool2

description: 10X Genomics


title: PAO1161 empty vector control (EV), biological rep1

description:
PAO1161 EV_1(GSM4975402)
RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx


title: PAO1161 PA3973 overproducer, biological rep2

description:
PAO1161_PA3973oe_2
RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx

value: pKKB3.11 (lacIQ-tacp-PA3973)


title: PAO1161 PA3973 overproducer, biological rep1

description:
PAO1161_PA3973oe_1
RNA-seq_PA3973overproduction_vs_cells_with_empty_vector.xlsx


title: AKI, GFP+, 6 months, rep4, ATAC library

city: Los Angeles

first: Kari

middle: Ann

last: Koppitch

address: 1425 San Pablo Street, BCC 312

department: Stem Cell

institute: USC

description: 10X Chromium multiome ATAC + gene expression kit

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) including the INTACTGFP sequence with the Cell Ranger ARC software (version 2.0.1) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger-arc aggr. The aggregated data files are provided (Aggregated_filtered_feature_bc_matrix.h5, Aggregated_atac_fragments.tsv.gz, Aggregated_atac_fragments.tsv.gz.tbi).
Assembly: mm10 including INTACTGFP sequence
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression and peak by cell matrices
Supplementary files format and content: Tab-separated file containing fragment information
Supplementary files format and content: Index of the tab-separated file

source_name: Kidney tissue

extract_protocol:
Nuclei were isolated from flash-frozen kidney tissue and processed for single cell multiome ATAC + gene expression sequencing according to the 10X Genomics protocol. All reagents were prepared according to the online protocol. In brief, the tissue of a half kidney was thawed and minced on ice, transferred into NP40 lysis buffer (including Nonidet P40 Substitute, Sigma-Aldrich, 74385), homogenized using a pellet pestle and incubated for 5 minutes on ice. Subsequently, the nuclear suspension was filtered through a 70µm strainer, the flow through was centrifuged, the supernatant removed and the pellet incubated with 1% BSA-PBS + 1U/ul Rnase Inhibitor (Sigma-Aldrich, 3335402001) for 5 minutes on ice. After centrifugation, the pellet was resuspended in 500ul 1% BSA-PBS + 1U/ul Rnase Inhibitor supplemented with 5 ul 7AAD ready made solution (Sigma-Aldrich, SML1633). Nuclei were sorted according to the gating strategy provided in supplemental Figure 3 on a cooled BD Aria I with a 100um nozzle into BSA-PBS + Rnase Inhibitor to achieve a final concentration of 1% BSA-PBS + 1U/ul Rnase Inhibitor.
10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E)

value: Kidney tissue

tag: group

value: AKI, GFP+, 6 months

value: Kidney cells

value: Tamoxifen (0.0375mg/g)


title: AKI, GFP-, 6 months, ATAC library

value: AKI, GFP-, 6 months