title: Z00 occluded choroid chk206


title: Z00 open choroid chk205

status: Public on Jul 01 2024

type: SRA

city: Boston

first: Debora

last: Nickla

state: MA

address: 424 Beacon St

department: Dept. of Biosciences and Disease

country: USA

institute: New England College of Optometry

library_source: transcriptomic

data_processing:
raw data was processed by the standard Illumina pipeline to yeild trimmed fastq files
fastq data counted against transcripts (ensembl v105) with salmon
data summarized to gene-level with tximeta (bioconductor)
Assembly: GRCg6a (gene models – ensembl v105)
Supplementary files format and content: gzipped tab-delimited text – raw counts per ensembl gene ID per sample

molecule: total RNA

organism: Gallus gallus

source_name: choroid

extract_protocol:
RNA was extracted from choroid and retinal tissues using the QIAgen RNAeasy kit
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: chick eyes were occluded (goggled) or open

tag: tissue

value: choroid

tag: time point

tag: eye treatment

value: open

tag: Sex

value: M


title: SMXL7d53-GR hypocotyl, mock, rep1

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

data_processing:
Reads were mapped by STAR-2.7.8a with "--alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterMultimapNmax 1" option.
Reads per gene were counted by summarizeOverLaps function (GenomicAlignments v1.30.0 package in R) with "mode="union", ignore.strand = TRUE" option.
Raw counts were normalized by DESeq2 (v1.34.0 package)
Assembly: tair10 / araport11 annotation
Supplementary files format and content: rawCounts.csv is a csv format table provides raw counts for each sample and each gene.
Supplementary files format and content: normalized_counts.csv is a csv format table provides normalized counts for each sample and each gene.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Hypocotyl

growth_protocol: Plants were grown on soil at 21-22 degrees in short day conditions (10 h light and 14 h darkness) for three weeks and then transferred to long day conditions (16 h light and 8 h darkness) for one weak.

extract_protocol:
The hypocotyls were immediately harvested and pulverized with pestle and mortar. RNA was isolated with RNeasy Mini Kit (QIAGEN, Netherland) and genomic DNA contamination was removed by referring to the protocol of TURBO DNA-free™ Kit (Thermo Scientific; USA). Subsequent clean-up of RNA was performed by using RNeasy Mini Kit.
1.2 µg of total RNA/sample was used for the library preparation using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) with polyA mRNA workflow and Unique Dual Index primers (NEB). 12 cycles of amplification were performed.

treatment_protocol: 15 µM dex or equal volume of DMSO (mock) was treated by directly watering to 4-week-old plants. Plants were harvested 5 hours after the treatment.

value: Hypocotyl

tag: cell line

tag: genotype

value: WT

tag: treatment

value: mock


title: Z00 open retina chk205

source_name: retina

value: retina


title: Z00 occluded retina chk206

value: occluded


title: SMXL7d53-GR hypocotyl, mock, rep2


title: Z00 occluded choroid chk205


title: genomic DNA from myoblast sample 21

type: genomic

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

description: myoblast sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: myoblast sample 21

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from the muscle tissue using QIAamp DNA mini kit (Qiagen) and from the cultured myoblasts using the GenElute Mammalian Genomic DNA Miniprep Kit (Sigma), both according to standard instructions

tag: gender

value: Male

tag: sample type

value: Cultured Myoblasts

tag: age (yr)

tag: participant id


title: Z00 occluded retina chk205


title: 3D primary GBM cells, 176_CW2_2

type: RNA

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from 3D primary GBM cells exposed to CW2

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 ug were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized by TAC software using RMA and Repated Measure fuction for patients were applied

label: biotin

source_name: primary 3D GBM culture

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: Primary GBM cells were included in Matrigel and cultured for at least 20 days as 3D models in DMEM/F12 supplemented with 10% BIT9500, 20 ng/ml basic Fibroblast Growth Factor (bFGF) and 20 ng/ml Epidermal Growth Factor (EGF).

extract_protocol: RNA was extracted using QIAzol and miRNeasy Micro Kit from Qiagen.

treatment_protocol: After at least 20 days of growth GBM organoids were not exposed (sham) or exposed to two different milli-meter wave (30.5 GHz continuous wave [CW]) signals, including CW1 (incident power of 0.1 W [RMS] for 20 minutes) and CW2 (incident power of 0.2 W [RMS] for 10 minutes.

tag: cell type

value: HuTuP176 GBM primary culture


title: genomic DNA from myoblast sample 11

description: myoblast sample

source_name: myoblast sample 11


title: genomic DNA from muscle sample 5

description: muscle sample

source_name: muscle sample 5

value: Muscle tissue


title: genomic DNA from myoblast sample 19

description: myoblast sample

source_name: myoblast sample 19


title: Z00 open choroid chk204


title: genomic DNA from myoblast sample 20

description: myoblast sample

source_name: myoblast sample 20


title: 3D primary GBM cells, 176_CW1_1

description: Gene expression data from 3D primary GBM cells exposed to CW1


title: Z00 open retina chk204


title: genomic DNA from myoblast sample 17

description: myoblast sample

source_name: myoblast sample 17


title: genomic DNA from muscle sample 19

description: muscle sample

source_name: muscle sample 19


title: genomic DNA from muscle sample 18

description: muscle sample

source_name: muscle sample 18


title: genomic DNA from muscle sample 20

description: muscle sample

source_name: muscle sample 20


title: Z00 occluded retina chk204


title: Z00 occluded choroid chk204


title: WT_Veh_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Purified RNA was hybridized for 16 to 24 hours at 65°C in nCounter hybridization buffer with NanoString Reporter and Capture probes, using 8 μL Master Mix, 5 µL sample, and 2 µL Capture ProbeSet per sample.

scan_protocol: Once the hybridization reactions have been removed from the thermal cycler, proceed immediately to an nCounter Prep Station. This step can process up to 12 samples per run in approximately 2.5 to 3 hours. Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: The raw data as RCC files format were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform.

label: NanoString barcodes

organism: Mus musculus

source_name: hippocampus

label_protocol: Per manufacturer recommendations, https://nanostring.com/products/ncounter-assays-panels/oncology/metabolic-pathways/ . The purified RNA is diluted in nuclease-free water to 20 ng/uL. RNA (~100 ng) added for hybridization assay.

extract_protocol: The hippocampus tissue (5 mg) of 3xTg and 3xTg/Polβ+/- AD mice were prepared for the extraction of total RNA using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, #12183018A) according to the manufacturer’s protocol.

treatment_protocol: Mice were treated according to animal study protocol 361-OSD-2023. Mice were group housed and fed ad libitum. WT (C57BL6/J), 3xTgAD, 3xTgAD/PolB +/- transgenic mice were treated with Urolithin A (200 mg kg day−1) by oral gavage for 5 months.

value: hippocampus

tag: strain/background

value: Female

tag: age

value: Vehicle

value: 5 months


title: genomic DNA from myoblast sample 14

description: myoblast sample

source_name: myoblast sample 14


title: 3D primary GBM cells, 176_sham_2

description: Gene expression data from untreated 3D primary GBM cells

value: sham


title: genomic DNA from muscle sample 21

description: muscle sample

source_name: muscle sample 21


title: Z00 open choroid chk203

value: choroid

value: F


title: 3D primary GBM cells, 61_CW2_2

value: HuTuP61 GBM primary culture


title: 3D primary GBM cells, 176_CW1_2


title: 3D primary GBM cells, 176_sham_1


title: Z00 open retina chk203

value: open


title: genomic DNA from muscle sample 16

description: muscle sample

source_name: muscle sample 16


title: genomic DNA from myoblast sample 16

description: myoblast sample

source_name: myoblast sample 16


title: genomic DNA from muscle sample 17

description: muscle sample

source_name: muscle sample 17


title: genomic DNA from myoblast sample 15

description: myoblast sample

source_name: myoblast sample 15


title: genomic DNA from myoblast sample 18

description: myoblast sample

source_name: myoblast sample 18


title: genomic DNA from myoblast sample 10

description: myoblast sample

source_name: myoblast sample 10


title: Z00 occluded retina chk203

source_name: retina


title: 3D primary GBM cells, 61_CW2_1

source_name: primary 3D GBM culture


title: Z00 occluded choroid chk203

source_name: choroid


title: genomic DNA from muscle sample 14

description: muscle sample

source_name: muscle sample 14


title: genomic DNA from muscle sample 12

description: muscle sample

source_name: muscle sample 12


title: Z00 open retina chk202


title: Z00 open choroid chk202


title: genomic DNA from muscle sample 13

description: muscle sample

source_name: muscle sample 13


title: Z00 occluded choroid chk202


title: 3D primary GBM cells, 61_CW1_1


title: 3D primary GBM cells, 61_sham_1


title: genomic DNA from muscle sample 10

description: muscle sample

source_name: muscle sample 10


title: 3D primary GBM cells, 176_CW2_1


title: 3D primary GBM cells, 13_CW2_1

value: HuTuP13 GBM primary culture


title: 3D primary GBM cells, 61_CW1_2


title: Z00 occluded retina chk202


title: Z00 open choroid chk201


title: genomic DNA from muscle sample 11

description: muscle sample

source_name: muscle sample 11


title: Z00 open retina chk201


title: 3D primary GBM cells, 13_CW1_2


title: 3D primary GBM cells, 13_CW1_1


title: Z00 occluded retina chk201


title: HEK293T scRNA-seq

city: Guangzhou

first: Cheng

last: Chen

state: Guangdong

address: Kaiyuan Ave 190

country: China

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

description: DNBelab C4

library_source: transcriptomic single cell

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

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

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

value: human embryonic kidney


title: EM-seq C. teleta larva

status: Public on Jun 30 2024

city: London

first: Jose

middle: M

last: Martin-Duran

address: Mile End road

institute: Queen Mary University of London

library_source: genomic

data_processing:
RNA-seq of adult stages: raw reads were cleaned with fastp and mapped with kallisto
RNA-seq of control and treated samples: raw reads were cleaned with fastp, mapped with kallisto and processed with TElocal
WGBS and EM-seq: Adaptors were trimmed with fastp, aligned to their respective reference genomes, deduplicated and methylation called for all cytosine contexts (CpG, CHG, and CHH) using Bismark v0.22.3 with default options.
Nanopore: demultiplexed and base-called with Guppy, using the dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_sup_prom.cfg model for methylated CpGs.
Assembly: Owenia fusiformis: GCA_903813345.2; Capitella teleta: GCA_000328365.1; Dimorphilus gyrociliatus: GCA_904063045.1
Supplementary files format and content: tab delimited text files containing TPM (RNA-seq adult stages) and count values (RNA-seq drug treatments) and methylation levels per CG position (WGBS, EM-seq and Nanopore reads).

organism: Capitella teleta

source_name: Whole larva

extract_protocol:
Genomic DNA was extracted with the MagAttract kit (Qiagen) and total RNA was isolated with Monarch kit (New England Biolabs)
WGBS: Bisulphite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research); EM-seq was performed with New England Biolab NEBNext Enzymatic Methyl-seq kit; Nanopore libraries were built with the Rapid barcoding kit; RNA-seq: standard TruSeq Illumina strand-specific library

value: Whole larva

value: *library strategy:Enzymatic Methyl-seq


title: EM-seq C. teleta adult

source_name: Whole adult

value: Whole adult


title: 3D primary GBM cells, 13_sham_2


title: RNA-seq adult stage C. teleta


title: genomic DNA from muscle sample 9

description: muscle sample

source_name: muscle sample 9

value: Male


title: Nanopore methylation calls C. teleta senescent female adult replicate 2

source_name: Whole individual

value: Whole individual

value: *library strategy:Nanopore methylation


title: 3D primary GBM cells, 13_CW2_2


title: Nanopore methylation calls C. teleta senescent female adult replicate 1


title: genomic DNA from myoblast sample 12

description: myoblast sample

source_name: myoblast sample 12

value: Cultured Myoblasts


title: genomic DNA from myoblast sample 6

description: myoblast sample

source_name: myoblast sample 6


title: genomic DNA from myoblast sample 8

description: myoblast sample

source_name: myoblast sample 8


title: genomic DNA from myoblast sample 9

description: myoblast sample

source_name: myoblast sample 9


title: Nanopore methylation calls C. teleta competent larva replicate 2


title: Nanopore methylation calls C. teleta competent larva replicate 1


title: Nanopore methylation calls C. teleta 1 month juvenile replicate 2


title: EM-seq C. teleta gastrula

source_name: Whole gastrula

value: Whole gastrula


title: Nanopore methylation calls C. teleta 1 month juvenile replicate 1


title: Nanopore methylation calls C. teleta mature female adult replicate 2


title: genomic DNA from muscle sample 7

description: muscle sample

source_name: muscle sample 7

value: Muscle tissue


title: WGBS D. gyrociliatus adult

organism: Dimorphilus gyrociliatus


title: Z00 occluded choroid chk201

value: occluded


title: EM-seq O. fusiformis DMSO control larva reseq replicate 2

organism: Owenia fusiformis

value: 1% DMSO


title: EM-seq O. fusiformis oocyte

source_name: Oocyte

value: Oocyte


title: genomic DNA from myoblast sample 5

description: myoblast sample

source_name: myoblast sample 5


title: EM-seq O. fusiformis DMSO control larva reseq replicate 1


title: genomic DNA from muscle sample 4

description: muscle sample

source_name: muscle sample 4


title: EM-seq O. fusiformis zebularine treated larva reseq replicate 1

value: 50 uM Zebularine


title: EM-seq O. fusiformis DMSO control larva replicate 2


title: EM-seq O. fusiformis 5-azacytidine treated larva replicate 1

value: 10 µM 5-azacytidine


title: genomic DNA from myoblast sample 4

description: myoblast sample

source_name: myoblast sample 4


title: EM-seq O. fusiformis DMSO control larva replicate 1


title: EM-seq O. fusiformis zebularine treated larva replicate 2

value: 50 µM Zebularine


title: EM-seq O. fusiformis zebularine treated larva replicate 1


title: genomic DNA from muscle sample 3

description: muscle sample

source_name: muscle sample 3


title: 3D primary GBM cells, 61_sham_2

source_name: primary 3D GBM culture

value: sham

value: HuTuP61 GBM primary culture


title: RNA-seq Zebularine treated larva O. fusiformis, replicate 1

value: Whole larva


title: RNA-seq 5-azacytidine treated larva O. fusiformis, replicate 1


title: RNA-seq DMSO control larva O. fusiformis, replicate 2


title: EM-seq O. fusiformis zebularine treated larva reseq replicate 2


title: EM-seq O. fusiformis 5-azacytidine treated larva replicate 2

value: *library strategy:Enzymatic Methyl-seq


title: RNA-seq Zebularine treated larva O. fusiformis, replicate 2


title: genomic DNA from myoblast sample 2

description: myoblast sample

source_name: myoblast sample 2


title: RNA-seq DMSO control larva O. fusiformis, replicate 1

source_name: Whole larva


title: genomic DNA from muscle sample 1

description: muscle sample

source_name: muscle sample 2


title: RNA-seq 5-azacytidine treated larva O. fusiformis, replicate 2


title: RNA-seq adult stage O. fusiformis

source_name: Whole adult

value: Whole adult


title: EM-seq O. fusiformis sperm

source_name: Sperm

value: Sperm


title: genomic DNA from myoblast sample 3

description: myoblast sample

source_name: myoblast sample 3

value: Male


title: porcine blastoid 2, scRNAseq

city: Hangzhou

first: Chengchen

last: Zhao

state: Zhejiang

address: Dunyu Road No.600, Xihu District

institute: Westlake University

description: 10x Genomics

data_processing:
The scRNA-seq reads were mapped to the susScr11 reference genome using 10x Genomics Cell Ranger (v7.1.0) after quality control by Dr.seq2 (v2.2.1). Following that, Seurat (v4.3.0) was used to integrate samples using the transcription level of each gene in each sample as input. Dimensional reduction and clustering were performed using Seurat function RunUMAP() and FindCluster() after normalization. The specific expressed genes with an average log fold change > 0.8 and a differential expressed percentage > 30% for each cell type were found using the FindAllMarkers() function.
Assembly: susScr11
Supplementary files format and content: Table-separated values files and matrix files

organism: Sus scrofa

source_name: Blastoid

extract_protocol:
Porcine blastoids with ICM-like and TE-like compartments and cavities were picked up manually by mouth pipette and dissociated into single cells by 0.25% trypsin-EDTA at 37°C for 10-20 min. The dissociation was terminated by 15% FBS, and samples were centrifuged at 500 g for 5 min. Cell pellets were resuspended in DMEM/F12 and filtered through a 40-μm cell strainer. Single-cell suspensions were carried out with 10x Genomics Chromium Single Cell Kit for Single-cell RNA-seq.
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: Blastoid

value: porcine ESCs

value: porcine blastoids

value: day 6

value: iBlastoid medium


title: porcine blastoid 1, scRNAseq

description: 10x Genomics


title: genomic DNA from muscle sample 2

description: muscle sample

value: Muscle tissue


title: B16F10 DAC replicate 2 [ATAC-seq]

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
Real-Time Analysis (RTA) software
The raw fastq files were trimmed for the first and last 8 nucleotides, the multiqc was use to summarize the fastQC results, and the trimmed files were mapped to the M.Musculus (mm10) genome using bowtie2
The mitochondria genome was removed in the alignment process
The duplicated reads were removed by picard and sorted bam files were subject to peak calling with MACS2
Open chromatin regions and peak annotation were deducted with Diffbind and ChIPSeeker, respectively
Assembly: mm10
Supplementary files format and content: Peak files for open chromatin regions

growth_protocol: B16F10  cell line was a kind gift of Gordon Freeman (Dana-Farber Cancer Institute). 4T1 cells were provided by Fred Miller (Wayne State University). Cells were cultured with Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, VWR), 6 mM HEPES, 1.6 mM L-glutamine, 50 mM 2-mercaptoethanol, 100 U/ml penicillin G and 100 mg/ml streptomycin sulfate (Sigma-Aldrich). All cell lines were verified to be free of mycoplasma by PCR and were authenticated by morphology.

extract_protocol:
Fresh B16F10 and 4T1 cells were washed twice with cold PBS and lysed with 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin
Nuclei were transposed using the Nextera DNA Library Prep Kit.  Transposed libraries were amplified for 11 cycles and size selected for fragments ranging 200-1000 bp. ATAC-seq experiments were sequenced to a minimum depth of 30 million reads/sample.

treatment_protocol: B16F10 and 4T1 cells (2x10^4/well in 24 well plates) were treated with 0.1 uM or 1 uM of DAC for 48 hours, respectively. Dead cells were removed with dead cell removal microbeads and live cells were used for ATACseq

value: DAC for 48 h


title: 3D primary GBM cells, 13_sham_1

value: HuTuP13 GBM primary culture


title: genomic DNA from myoblast sample 1

description: myoblast sample

source_name: myoblast sample 1

value: Cultured Myoblasts


title: B16F10 DAC replicate 1 [ATAC-seq]


title: Sequencing data for 5mC from HEK293T by BS-seq

city: wuhan

first: neng

middle: bin

last: xie

address: 115 donghu road

institute: wuhan university

data_processing:
For initial quality control of the raw sequencing data in FASTQ format, we utilized FastQC software (version 0.11.8). To trim low-quality bases and remove adaptor sequences, we employed Cutadapt (version 3.5) in conjunction with Trimmomatic (version 0.39). Bismark (version 0.24.0) was then used to align the deaminase-treated or bisulfite-treated reads to the human reference genome (GRCh38.p13), with indexing facilitated by Bowtie2.41 Quantification of methylation at each cytosine site involved tallying the number of 'C' bases as 5mC sites (denoted as NC) and the number of 'T' bases as unmodified cytosine sites (denoted as NT). We defined sequencing depth as N = NC + NT and computed the coverage of samples using both Bismark and Samtools (version 1.9).
Methylated sites were statistically determined using a binomial test that factored in the counts of methylated cytosines (mC), the total count of cytosines (mC + umC), and the non-conversion rate of the bisulfite treatment. Sites were deemed methylated if they had an FDR-corrected p-value less than 0.05. For the calculation of methylation levels across the genome, we partitioned the sequence into bins of 10 kb. The methylation level (ML) for each bin or individual cytosine site was calculated as the proportion of methylated 'C' reads, defined by the formula: ML(C) = reads(mC) / (reads(mC) + reads(C)). Lastly, we identified differentially methylated regions (DMRs) using DSS software (version 2.12.0), which allowed for the analysis of methylation variation between different sample groups or conditions.
Assembly: GRCh38.p13
Supplementary files format and content: 5mC signals from TAD-seq(TXT)
Supplementary files format and content: 5mC signals from BS-seq(TXT)

source_name: cell line

extract_protocol:
Genomic DNA of HEk293T was extracted using Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA)
TAD-seq：The genomic DNA from HEK293T cells was isolated using the Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA) following the manufacturer's protocol. Unmodified genomic DNA from lambda bacteriophage (Sangon Biotech, Shanghai, China) was added to the genomic DNA as a spike-in control (0.1% of spike-in DNA was added). The mixture was then sheared to an average size of 200-400 bp using a JY92-II N Ultrasonic Homogenizer (Scientz Biotechnology Co., Ltd, China). The fragmented DNA mixture was end-repaired and adenylated using the Hieff NGS Ultima Endprep Mix kit (Yeasen Biotechnology Co., Ltd, Shanghai). Subsequently, DNAm-adaptors (Table S5) were ligated to both ends of the repaired DNA using the Hieff NGS Ultima DNA Ligation Module kit (Yeasen, Shanghai, China), and the resulting DNA was purified using 0.9× KAPA Pure beads (Roche). Additionally, L-5mC-dsDNA was added as a spike-in to evaluate the deamination rates of C and 5mC (0.1% of L-5mC-dsDNA was added). The DNA mixture was then oxidized by nTET and purified using 0.9× KAPA Pure beads. Subsequently, the resulting DNA was denatured and deaminated using A3Am protein. The deaminated DNA was amplified by PCR with 6 cycles using 1 U of EpiMark Hot Start Taq DNA polymerase (New England Biolabs), 0.2 mM of dNTP, 0.4 μM of pre-P5 primer, and 0.4 μM of pre-P7 primer. Following purification using 0.9× KAPA Pure beads, the DNA products were amplified by PCR with 8 cycles using 1 U of Q5 Hot Start High-Fidelity DNA polymerase (New England Biolabs), 0.2 mM of dNTP, 0.4 μM of P5-index primer, and 0.4 μM of P7-index primer. The PCR products were purified with 0.9× KAPA Pure beads and examined using 2% agarose gel electrophoresis. The library quality was assessed on the Agilent Bioanalyzer 2100 system and then sequenced on an Illumina NovaSeq 6000 platform (Novogene Co., Ltd, Nanjing, China).
BS-seq：The genomic DNA from HEK293T cells was isolated using the Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA) following the manufacturer's protocol. Unmodified genomic DNA from lambda bacteriophage (Sangon Biotech, Shanghai, China) was added to the genomic DNA as a spike-in control (0.1% of spike-in DNA was added). The mixture was then sheared to an average size of 200-400 bp using a JY92-II N Ultrasonic Homogenizer (Scientz Biotechnology Co., Ltd, China). Next, ssDNA fragements were Bisulfite treated. After BS treatment, unmethylated Cytosine will change into Uracil, while methylated Cytosine will stay unchanged. Then, methylation sequencing adapters ligation, size selection and PCR amplification steps were performed to the DNA fragments. The library kit (Accel-NGS Methyl-Seq DNA Library Kit(Swift, USA) adds a low complexity polynucleotide tail with an average length of 8 bases to the 3’ end of each fragment during the addition of the first NGS adapter molecule. If these tails are not trimmed bioinformatically from the sequencing data, it is normal and expected to observe them at the beginning of Read 2 (R2). When read length is close to fragment size, the tail may also be observed toward the end of Read 1 (R1) data. Therebefore, it’s highly recommended to trim 10 bases from the beginning of both R1 and R2 to eliminate any artifactual cytosine methylation introduced as a result of filling inoverhangs during end repair steps of conventional dsDNA library preparation and low quality bases due to bisulfite treatment. Subsequently, library qualitywas assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). Pair-end sequencing of sample was performed on an Illumina NovaSeq 6000 platform (Illumina, USA).
whole-genomic sequencing by TAD-seq and BS-seq

value: cell line

value: Human Embryonic Kidney


title: Sequencing data for 5mC from HEK293T by TAD-seq


title: LT2, Late tumor 4 - batch 2, scRNAseq

first: Judy

last: Lieberman

address: 200 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

data_processing:
Raw scRNA-seq reads were mapped to a customized mouse genome using the 10X Genomics cellranger v7.0.0 suite. The customized genome was an extended version of mouse genome (mm10: GENCODE vM23/Ensembl 98) with an added eGFP sequence to the reference. The customized eGFP sequence was retrieved from NCBI portal (https://www.ncbi.nlm.nih.gov/nuccore/JQ064510.1 “JQ064510.1 Synthetic construct clone eGFP-OsP5SM_E/R eGFP (eGFP) gene, complete cds”).
Assembly: mm10 (extended to include eGFP sequence using cellranger mkref function)
Supplementary files format and content: compressed folder contain tab-separated values files and matrix files

source_name: Breast cancer tumor

growth_protocol: Eight-week-old ErbB2ΔEx16+/-MTB+/- female mice were fed with 2 mg/ml doxycycline in the drinking water to induce multifocal breast tumor. Early tumors were isolated when tumors were grown for 5-10 days, while late tumors were grown for 30-35 days before collection. Samples were collected in two batches. First batch contains two early tumors and two late tumors, each from one tumor-bearing mouse. Second batch of samples contains two early and two late tumor samples, with each early sample contains early tumors pooled from three mice.

extract_protocol:
Tumors were digested with 100 μg/ml Liberase TL and 100 μg/ml DNase I (Merck Millipore) for 15 minutes at 37 °C, homogenized, and red blood cells were removed by 1x ACK Buffer (155mM NH4Cl, 10 mM KHCO3, and 0.1mM EDTA). Live cells were enriched twice with dead cell removal kit and filtered through 40 μm strainers. Single cell suspensions with more than 80% viability were resuspended in Ca2+ and Mg2+-free PBS with 0.5% BSA and kept on ice. Cell suspension was assessed for concentration and viability using the LunaFX7 automated cell counter. The concentration was adjusted to 1.4*106 cells/mL and 10 ml was loaded onto a full skirted 96-well Eppendorf plate.
The 10x Genomics Chromium Connect automated platform was used to perform automated single cell library construction using the Chromium Next GEM Single Cell 5' Kit v2, 16 rxns (10x Genomics, PN-1000263), using 14 cDNA and 16 SI-PCR cycles. Approximately 14,000 live cells per sample were loaded into the system, with an expectation to encapsulate at least 8,000 cells per sample. Indexing was performed on the same instrument using the Dual Index Kit TT Set A, 96 rxns (10x Genomics, PN-1000215). GEM generation was assessed at 45 min in the procedure and was found to be optimal for all samples. cDNA and gene expression libraries were quantified using Qubit 3.0 fluorometer, and quality was assessed using HS DNA chips with Agilent 2100 Bioanalyzer.

value: Breast cancer tumor


title: B16F10 control replicate 3 [ATAC-seq]


title: LT1, Late  tumor 3 - batch 2, scRNAseq


title: B16F10 control replicate 2 [ATAC-seq]


title: L1, Late tumor 1 - batch 1, scRNAseq


title: E2, Early tumor 2 - batch 1, scRNAseq


title: L2, Late tumor 2 - batch 1, scRNAseq


title: ET1, Early pooled tumor 1 - batch 2, scRNAseq


title: 4T1 DAC replicate 3 [RRBS]

data_processing:
The raw fastq files were trimmed for the adaptors and filling nucleotides using trim Galore
The Trimed reads were mapped to mouse genome (mm10) and methylation calls were performed using Bismark
Differentially methylated regions (DMR) between DAC-treated and control cell lines were determined using Metilene software package
Significant DMR in 4T1 cell line were determined using FDR<1E-16 cut-off. Significant DMR in B16 cell line were determined using FDR<1E-10 cut-off
Assembly: mm10
Supplementary files format and content: bigWig and bedGraph

extract_protocol:
genomic DNA was isolated with Quick-DNA Microprep Kit (ZYMO RESEARCH).
100 ng gDNA was used for library preparation following Zymo-Seq RRBS Library Kit

treatment_protocol: B16F10 and 4T1 cells (2x10^4/well in 24 well plates) were treated with 0.1 uM or 1 uM of DAC for 48 hours, respectively. Dead cells were removed with dead cell removal microbeads and live cells were used for RRBS


title: 4T1 DAC replicate 2 [RRBS]


title: B16F10 DAC replicate 3 [RRBS]


title: 4T1 control replicate 3 [RRBS]


title: 4T1 control replicate 1 [RRBS]


title: 4T1 control replicate 2 [RRBS]


title: E1, Early tumor 1 - batch 1, scRNAseq


title: B16F10 DAC replicate 3 [ATAC-seq]


title: B16F10 control replicate 1 [ATAC-seq]


title: B16F10 DAC replicate 2 [RRBS]


title: ET2, Early pooled tumor 2 - batch 2, scRNAseq


title: B16F10 control replicate 3 [RRBS]


title: 4T1 DAC replicate 1 [RRBS]


title: B16F10 control replicate 2 [RRBS]


title: B16F10 DAC replicate 1 [RRBS]


title: 4T1 DAC replicate 3 [ATAC-seq]


title: B16F10 control replicate 1 [RRBS]


title: 4T1 DAC replicate 2 [ATAC-seq]


title: 4T1 DAC replicate 1 [ATAC-seq]


title: 4T1 control replicate 3 [ATAC-seq]


title: Nanopore methylation calls C. teleta mature female adult replicate 1

source_name: Whole individual

value: Whole individual

value: *library strategy:Nanopore methylation


title: 4T1 control replicate 2 [ATAC-seq]


title: WGBS O. fusiformis adult

value: Whole adult


title: WGBS O. fusiformis larva

value: Whole larva


title: WGBS O. fusiformis gastrula

source_name: Whole gastrula

value: Whole gastrula


title: 4T1 control replicate 1 [ATAC-seq]


title: P4_sample1, replicate 1, ST

status: Public on Jun 26 2024

city: Nanchang

first: Tao

last: Hong

state: Jiangxi province

address: 17 Yong Wai Zheng Street

institute: the First Affiliated Hospital of Nanchang University

description: 10x Genomics

data_processing:
The snRNA-seq data from 10X Genomics were aligned and quantified using Cell Ranger Single-Cell Software (version 6.0.2). All downstream single-cell analyses were performed using Cell Ranger and Seurat (version 4.1.0) unless specifically stated otherwise. In brief, for each gene and each cell barcode (filtered by CellRanger), UMIs were counted to construct digital expression matrices.
Reads were demultiplexed and mapped to the reference genome GRCh38 using Space Ranger software v.1.0.0 (10x Genomics). Count matrices were loaded into Seurat (version 4.1.0) for all subsequent data filtering, normalization, dimensional reduction, and visualization. For each sample, spots were filtered for a minimum detected gene count of 200 genes. Data normalization was performed on independent tissue sections using the SCTransform function in Seurat. Dimensionality reduction and clustering were then performed via PCA at resolution 0.7 for the first 30 PCs. Signature scoring derived from snRNA-seq data, such as the abovementioned EC2 and EC3 scores, was performed using the AddModuleScore function with default parameters in Seurat. Additionally, to validate the results identified by the AddModuleScore function, cell type prediction probabilities were calculated for each spot using factor analysis with the FindTransferAnchors and TransferData functions in Seura.
Assembly: genome GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ACP close to the hypothalamus

extract_protocol:
frozen human ACP tissues were thawed on ice, minced into 1-mm3 pieces and homogenized in 1 ml cold Nuclei EZ Lysis Buffer (NEB) using a douncer (stroking ~10-20 times). Then, the homogenate was filtered through a 40-μm cell strainer and incubated in 2 ml of NEB for 5 minutes at 4 °C. Samples were spun for 5 minutes at 250-300 x g at 4 °C, and the pellet was resuspended in Nuclei Wash and Resuspension Buffer supplemented with DAPI. Nuclei suspensions were loaded into a MoFlo Astrios EQ Cell Sorter and collected in 1.5-ml tubes.
Visium spatial gene expression slides and reagent kits for formalin-fixed paraffin embedded (FFPE) tissue were used according to the manufacturer’s instructions (10x Genomics). Visium slides include 4 capture areas (6.5 x 6.5 mm), each with ~5,000 unique gene expression spots that are 55-m in diameter (with a 100 m center to center distance between spots). FFPE tissue blocks were prepared according to the manufacturer’s instructions (tissue preparation guide CG000408). H&E images were prepared according to the protocol (Deparaffinization, H&E Staining, Imaging and Decrosslinking, CG000409). A spatial gene expression assay was performed according to protocol CG00407.
SnRNA-seq libraries were acquired using the Chromium Single Cell V3.0 reagent kit following the manufacturer’s protocol (10X Genomics). Each nuclear suspension containing 235, 616, 1002, 1110 and 1305 nuclei/μl was loaded into an independent lane. Libraries were sequenced on a NovaSeq6000 platform (Illumina) according to the manufacturer’s instructions to generate 150-bp paired-end reads.
Libraries were prepared with TruSeq Illumina libraries and sequenced on an Illumina NovaSeq 6000 system at a minimum sequencing depth of 25,000 read pairs per tissue-covered spot on the capture area by IntegraGen (Evry). Sequencing was performed with the recommended protocol (read 1: 28 cycles; i7 index read: 10 cycles; i5 index read: 10 cycles; and read 2S: 50 cycles).
snRNA-seq

value: ACP close to the hypothalamus

value: 7years old


title: P3_sample2, replicate 2, snRNAseq

description: 10x Genomics

source_name: ACP distant from the hypothalamus

value: ACP distant from the hypothalamus

value: 11years old


title: P1_sample2, replicate 2, ST

description: 10x Genomics

value: 37years old


title: P5_sample1, replicate 1, ST

description: 10x Genomics

value: 55years old


title: P2_sample1, replicate 1, snRNAseq

description: 10x Genomics


title: P1_sample1, replicate 1, snRNAseq

description: 10x Genomics


title: P1_sample2, replicate 2, snRNAseq

description: 10x Genomics


title: P3_sample1, replicate 1, snRNAseq

description: 10x Genomics


title: P1_sample1, replicate 1, ST

description: 10x Genomics


title: Mouse_Rep2_scRNAseq

status: Public on Jun 25 2024

city: Leioa

first: Fernando

last: García-Moreno

state: Bizkaia

address: Barrio Sarriena s/n Edificio Sede

country: Spain

institute: Achucarro BCN

description: 10X Chronium v3.4

data_processing:
10X CellRangerv6.0.2 was employed for alignment and demultiplexing of FASTQ files to obtain feature-barcode matrices. The genome used as reference for mouse alignment were mm10-2020-A for mouse . The quality control statistics related to this alignment steps and others are summarized in Supplementary Table S4. Afterwards, data matrices were imported to R(v4.1.0), where Seurat (v4.1.0) (60)was employed to further analysis, as describe in their vignettes (https://satijalab.org/seurat/).
Assembly: mm10-2020-A for mouse
Supplementary files format and content: filtered_feature_bc_matrix 10x output
Supplementary files format and content: rds file: Processed Seurat object with only neurons

source_name: Brain

extract_protocol:
Isolation of birthdated cells for scRNAseq was performed as described in this article. Briefly, mouse embryos were birthdated at a neurogenic timepoint (E12) and sacrificed at P3 postnatal stage. Brains were extracted in ice-cold HBSS. Then, the pallial region was microdissected under a stereomicroscope, collected in ice-cold HBSS, pooled and cut into small pieces.Following enzymatic digestion, mouse P3 tissue was manually homogenized by carefully pipetting and tissue clogs were removed by filtering the cell suspension through a 40 μm nylon strainer to a 15 ml Falcon tube containing 4 mlof 25% fetal bovine serum (FBS) in HBSS. Dissociated cells were then centrifuged at 200g for 10 min at room temperature (RT) and EdU molecule was detected in the pelleted cells. Following reaction, cells were washed thrice by centrifugation at 200g for 10 min and suspended in 1 ml of HBSS then passed on a 50 μm cell strainer. PI-/EdU+ cells, gated to include only the top 10% brightest cells, were finally FAC-sorted: for the E6 chick E6 a Synergy 3200 2L sorter (Sony) was used; for the E15 chick sample a FACSAria (BD Biosciences) was used; and for both mice samples a FACS Jazz (BD Biosciences) was used.
Cells were processed for single cell GEM formation following the standard Chromium Single Cell 3’ v3.1. Briefly cells were placed at the Chromium chip with the beads and reagents for the RNA capture and cDNA amplification. After the emulsion were obtained, the cDNA was amplificated in a thermocycler. Post amplificated cDNA, now marked with individual cell barcode, were fragmented, ligated the sequencing adapters and amplified. After that, the PCR product were purified and quantified.
Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127, “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) User Guide” (Document number CG000315). Resulting libraries were sequenced on a Novaseq 6000 for an approximated 50.000 reads per cell.

value: Brain

value: Wild-type

tag: developmental stage


title: P2_sample2, replicate 2, snRNAseq

description: 10x Genomics


title: Mouse_Rep1_scRNAseq

description: 10X Chronium v3.3


title: NPC, WTsox1enhancerdCAS9control, H3K27ac, biol rep1

city: Philadelphia

first: Alessandro

last: Gardini

state: PA

address: 3601 Spruce St, Room 230

institute: The Wistar Institute

description: H3K27ac CUT&TAG in control WTsox1enhancerdCAS9 NPCs

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment: bowtie2
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)
Library strategy: CUT&TAG

source_name: NPC

growth_protocol: iPSCs were cultured on Geltrex-coated plates and maintained in StemMACS™ iPS-Brew XF (Miltenyi Biotec, cat#130-104-368). NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement.  SHSY5Y cells were maintained in the basal medium (45% of Minimum Essential Medium (MEM) (Corning, cat#10009CV), 45% of Nutrient Mixture F-12 Ham (Sigma-Aldrich, Cat#N4888) and 10% of fetal bovine serum (Corning, cat#35010CV)).

extract_protocol:
Profiling of histone markers in SH-SY5Y cells was performed with CUTANA™ CUT&Tag kit (Epicypher, cat#14-1101) following the manufacturer's protocol. Briefly, desired Concanavalin A (ConA) coated magnetic beads (Bangs Laboratories, cat#BP531) for all planned CUT&Tag reactions (11 μL per reaction) were processed together and activated in cold Bead Activation Buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 10 ul of activated ConA beads were aliquoted into each 8-strip PCR tubes for individual reactions and kept cold until needed. WT and INTS10 KO SH-SY5Y cells were harvest, counted and centrifuged for 3 min at 600⨉g at room temperature in two individual 1.5 mL tubes. Total desired amount of WT and INTS10 KO cells (200, 000 cells per experiment) were washed once with PBS at room temperature. To isolate nuclei, cell pellets were resuspended in cold Nulcear Extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 1 x Protease inhibitor), incubated for 10 min on ice and centrifuged for 3 minutes at 600⨉g at 4 °C to remove the supernatant. Fluffy nuclei pellets were resuspended in 100 μL/reaction cold NE buffer and aliquoted into 8-strip PCR tubes containing 10 μL of activated ConA beads. Nuclei-beads slurry were vortex gently to mix and incubated for 10 minutes at room temperature. 50 μL cold Antibody150 Buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 2 mM EDTA, 1X protease inhibitor ) containing 0.5 ug of H3K4me1 or H3K27ac antibody was added immediately to the beads after the removal of the supernant and vortex gently and thoroughly. The reactions were incubated on nutator overnight at 4 °C . On the next day, anti-rabbit secondary antibody master mix was prepared first by diluting secondary antibodies in cold Digitonin 150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 1X Protease inhibitor). After removing the supernatant from the beads slurry, 50 μL/reaction cold secondary antibody master mix was added to each reaction and mixed well by gentle vortexing. The reactions were incubated on nutator for 30 minutes at room temperature. After two washes with cold Digitonin 150 buffer (), 50 μL/reaction cold Digitonin 300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1 X protease inhibitor, 0.01% Digitonin ) containing 2.5 μL pAG-Tn5 was added to the beads slurry. Beads were thoroughly resuspened by gentle vortexing and incubated on nutator for 1 hour at room temperature. After two washes with 200 μL/reaction cold Digitonin 300 buffer, 50 μL/reaction cold Tagmentation buffer (Digitonin300 Buffer, 10 mM MgCl2 ) was added to each reaction and the tubes were incubated for 1 hour at 37 °C in a thermocycle. 50 μL/reaction RT TAPS buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA) was then used to wash the reactions and 5 μL/reaction RT SDS Release buffer (10 mM TAPS, pH 8.5, 0.1% SDS) was added to quench the tagmentation reaction. 15 μL/reaction RT SDS Quench buffer (0.67% Triton-X 100 in Molecular grade H2O) was then used to neutralize SDS, which inhibits PCR. Library amplification was performed directly on the entire reaction mixture by adding dual primers and CUTANATM High Fidelity 2x PCR Master Mix. After PCR, the library DNA was purified using AMPure XP beads (ThermoFisher, cat#A63881) and quantified by Qubit.
CUT&TAG (Kaya-Okur et al. 2020)

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs or SH-SY5Y were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Singel cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared. SH-SY5Y cells after selection with puromycin for 48 hours were trypsinized and plated into 10 cm tissue culture dishes. Single cells were maintained in the basal medium supplemented with 0.5 ug/ml of puromycin for the next 2-3 weeks until cell colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened by PCR initially ( Primers: INTS10-F, 5'- TATACCAGTGGCCTCTTGTC - 3', INTS10-R, 5' - CGTCTTCCTTTATCCATCTGCC - 3') and verified by Western Blot and Sanger sequencing.

value: NPC

value: neuronal progenitor cell differentated from pluripotent stem cells

value: No treatment

tag: cut&tag antibody

value: H3K27ac (abcam ab4729)


title: NPC, WTsox1enhancerdCAS9DOX1day, H3K27ac, biol rep1

description: H3K27ac CUT&TAG in WTsox1enhancerdCAS9 treated with Dox for 1 day NPCs

value: 1 day 1ug/mL doxycline


title: NPC, INTS10HET2tetinduciblesox2DOX1day, SOX2, biol rep1

description: SOX2 CUT&TAG in INTS10HET2tetinduciblesox2 treated with Dox for 1 day NPCs

value: SOX2 (cell signaling 23064S)


title: NPC, INTS10HET2tetinduciblesox2control, SOX2, biol rep1

description: SOX2 CUT&TAG in control INTS10HET2tetinduciblesox2 NPCs


title: NPC, WT, SOX2, CT biol rep1

description: H3K4me1 CUT&TAG in shSOX2 NPCs

value: wt


title: NPC, WT, H3K27me, biol rep1

description: H3K27me3 CUT&TAG in WT NPCs

value: H3K27me3 (cell signaling 9733)


title: NPC, INTS10het2, H3K27me, biol rep2

description: H3K27me3 CUT&TAG in INTS10HET2 NPCs


title: NPC, INTS10het2, H3K27me, biol rep1

description: H3K27me3 CUT&TAG in INTS10HET2 NPCs


title: V1 day 7 [CR3]

status: Public on Jun 28 2024

city: Duarte

first: Adolfo

middle: Garcia

last: Ocana

state: California

address: 1500 E Duarte Rd

department: Molecular and Cellular Endocrinology

institute: City of Hope Beckman Research Center

description: Sequenced with pair-end 150 bpss on an Illumina NovaSeq 6000 instrument.

data_processing:
Sequenced reads were trimmed for low-quality bases and adapter sequences using TrimGalore v0.6.0, a wrapper for cutadapt and fastQC. STAR v2.7.0e was used to align raw sequencing reads to the human GRCh37 reference genome. SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression.
Expression data were normalized per gene across samples by subtracting their mean and then dividing by their SD. This normalization was performed separately for the two donors to remove human variations.

source_name: Human islet graft

growth_protocol: Human islets were transplanted in Rag1-/- mice and treated with the drugs described below for 7 days.

extract_protocol:
total RNA was isolated using the RNAeasy mini kit (Qiagen) according to the manufacturer’s protocol,
TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II [Directional] RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Transplanted mice were treated with vehicle (water) or harmine (3mg/kg/d) plus exendin-4 (0.1mg/kg/d) with alzet minipumps.

value: Human islet graft

value: Human islet cells

value: V


title: RNA-seq MDA-MB-436_FOXC2-H122N_NHE1_KO_Rep2

status: Public on Jun 24 2024

city: San Francisco

first: Kyle

last: Kisor

address: 505 parnassus Ave

institute: UC San Francisco

description: Sample H_Rep2

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Perform alignments withHISAT2to the reference. HISAT2(Mortazavi et al., 2008)uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons.
Assembly: hg38
Supplementary files format and content: xls files for processed data with raw counts, fpkm, log fold change, and padj

source_name: breast

growth_protocol: MDA-MB-436 cells were maintained at 37°C and 5% CO2 in RPMI 1640 (Gibco:11875085) supplemented with Penicillin/Streptomycin (100U/mL each), and 10% FBS.

extract_protocol:
RNA was extracted with the RNeasy Mini kit (Qiagen, 74104) according to manufacturer instructions with sample concentrations assessed via NanoDrop
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library

treatment_protocol: NHE1-KO were generated via CRISPR/Cas9 resulting in decreased pHi. Cells were either untransfected or transfected with 1 µg of FOXC2-WT, -H122K, or -H122N with medium changed 8 h after transfection

value: breast

value: mammary gland

value: FOXC2-H122N overexpression


title: RNA-seq MDA-MB-436_FOXC2-H122N_NHE1_KO_Rep1

description: Sample H_Rep1


title: RNA-seq MDA-MB-436_FOXC2-H122K_NHE1_KO_Rep2

description: Sample G_Rep2

value: FOXC2-H122K overexpression


title: RNA-seq MDA-MB-436_FOXC2-H122K_NHE1_KO_Rep3

description: Sample G_Rep3


title: RNA-seq MDA-MB-436_FOXC2-H122K_NHE1_KO_Rep1

description: Sample G_Rep1


title: RNA-seq MDA-MB-436_FOXC2-WT_NHE1_KO_Rep2

description: Sample F_Rep2

value: FOXC2-WT overexpression


title: RNA-seq MDA-MB-436_FOXC2-H122N_NHE1_KO_Rep3

description: Sample H_Rep3


title: RNA-seq MDA-MB-436_FOXC2-WT_NHE1_KO_Rep3

description: Sample F_Rep3


title: RNA-seq MDA-MB-436_FOXC2-WT_NHE1_KO_Rep1

description: Sample F_Rep1


title: RNA-seq MDA-MB-436_untransfected_NHE1_KO_Rep1

description: Sample E_Rep1

value: untransfected


title: RNA-seq MDA-MB-436_untransfected_NHE1_KO_Rep2

description: Sample E_Rep2


title: NPC, WT, H3K27me, biol rep2

description: H3K27me3 CUT&TAG in WT NPCs

value: NPC


title: RNA-seq MDA-MB-436_FOXC2-H122N_control_Rep2

description: Sample D_Rep2

value: control


title: RNA-seq MDA-MB-436_FOXC2-H122N_control_Rep3

description: Sample D_Rep3


title: RNA-seq MDA-MB-436_FOXC2-H122N_control_Rep1

description: Sample D_Rep1


title: RNA-seq MDA-MB-436_FOXC2-H122K_control_Rep2

description: Sample C_Rep2


title: RNA-seq MDA-MB-436_FOXC2-H122K_control_Rep3

description: Sample C_Rep3


title: RNA-seq MDA-MB-436_FOXC2-WT_control_Rep3

description: Sample B_Rep3


title: RNA-seq MDA-MB-436_FOXC2-H122K_control_Rep1

description: Sample C_Rep1


title: RNA-seq MDA-MB-436_untransfected_control_Rep1

description: Sample A_Rep1


title: RNA-seq MDA-MB-436_FOXC2-WT_control_Rep1

description: Sample B_Rep1


title: RNA-seq MDA-MB-436_untransfected_control_Rep3

description: Sample A_Rep3


title: SELEX_FOXC2_Round2_pH7.8

library_source: other

data_processing:
Data processed by University of California, Davis Bioinformatics Core using the published ‘R’ “SELEX” package which is publicly available at: (bioconductor.org/packages/release/bioc/html/SELEX.html).
Assembly: synthetic
Supplementary files format and content: xls files for processed data with enrichment scores

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
After each round of selection and PCR amplification, product was purified using the MinElute PCR purification kit (Qiagen 28004)
The initial library was generated with 16bp randomized central region and flanking PCR sites. This was synthesized by Integrated DNA Technologies (IDT)

value: synthetic construct


title: SELEX_FOXC2_Round3_pH7.8


title: RNA-seq MDA-MB-436_FOXC2-WT_control_Rep2

description: Sample B_Rep2


title: SELEX_FOXC2_Round4_pH7.8


title: RNA-seq MDA-MB-436_untransfected_control_Rep2

description: Sample A_Rep2


title: SELEX_FOXC2_Round1_pH7.8


title: SELEX_FOXC2_Round4_pH7


title: SELEX_FOXC2_Round2_pH7


title: Unsporulated oocysts3.Input

status: Public on Jun 23 2024

city: Jinzhong

first: Qing

last: Liu

address: Taigu, Shanxi Province, PR China

institute: Shanxi Agricultural university

data_processing:
Cutadapt software (v1.9.3) was used to eliminate the reads containing adaptor contaminants and low quality bases.
HISAT2 software was applied to align clean reads of all libraries to the reference genome of E. tenella
MACS software was used to identify methylated sites on RNAs (peaks),and differentially methylated sites were identified by diffReps
The m7G-enriched motifs were identified with DREME.
Assembly: pEimTen1.1 GCA_905310635.1
Supplementary files format and content: The xlsx format sheet (named Gene Expression Profiling) showed gene_id,counts of all samples of the gene, normalized counts by edgeR, and annotation of the genes.
Supplementary files format and content: The xlsx format sheet (named Methylated_RNA_sites.mRNA) showed information about methylation sites,methylated RNA,enrichment information,and annotations.

organism: Eimeria tenella

source_name: Unsporulated oocysts

extract_protocol:
Input: Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA).IP:Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA), and then subjected to immunoprecipitation (IP) by using the GenSeq® m7G MeRIP Kit (GenSeq Inc.) following the manufacturer’s specifications.
RNA libraries for IP and input samples were constructed with the GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacture’s instructions.
MeRIP-seq and RNA-seq

tag: strain

value: SD-01 strain

value: Unsporulated oocysts


title: Unsporulated oocysts3.IP


title: RNA-seq MDA-MB-436_untransfected_NHE1_KO_Rep3

description: Sample E_Rep3

tag: tissue


title: SELEX_FOXC2_Round1_pH7


title: Unsporulated oocysts2.IP


title: Unsporulated oocysts1.IP


title: Sporulated oocysts1.IP

source_name: Sporulated oocysts

value: Sporulated oocysts


title: Sporulated oocysts3.IP


title: Sporulated oocysts3.Input


title: Sporulated oocysts2.IP


title: Unsporulated oocysts2.Input


title: MeDIP-MGH9243-adeno

status: Public on Jun 20 2024

first: Jacob

middle: Eli

last: Berchuck

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA mem.
For peak calling MACS2 was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using MACS2 using the CHIPS pipeline

source_name: PDX

extract_protocol:
QIAamp Circulating Nucleic Acid Kit (Qiagen)
KAPA HyperPrep Kit (KAPA Biosystems)

value: PDX

tag: disease state

value: LUAD

tag: assay

value: MeDIP-seq


title: MeDIP-MGH968-transformedSCLC

value: Transformed SCLC


title: MeDIP-MGH9183-adeno


title: MeDIP-MGH1528-denovoSCLC

value: De novo SCLC


title: Sporulated oocysts1.Input


title: MeDIP-MGH1525-denovoSCLC


title: MeDIP-MGH1518-denovoSCLC


title: MeDIP-MGH1512-denovoSCLC


title: MeDIP-MGH1522-denovoSCLC


title: MeDIP-MGH1506-denovoSCLC


title: SELEX_Starting_Library


title: SELEX_FOXC2_Round3_pH7


title: MeDIP-MGH1514-denovoSCLC


title: MeDIP-MGH1139-adeno


title: MeDIP-MGH1157-adeno


title: MeDIP-MGH1181-adeno


title: Unsporulated oocysts1.Input


title: MeDIP-MGH1505-denovoSCLC


title: MeDIP-MGH1112-adeno


title: Sporulated oocysts2.Input


title: MeDIP-MGH1062-adeno


title: MeDIP-MGH772-transformedSCLC


title: MeDIP-MGH1089-adeno


title: MeDIP-MGH1065-adeno


title: MeDIP-MGH10202-transformedSCLC


title: MeDIP-MGH10097-transformedSCLC


title: MeDIP-MGH1068-adeno


title: H3K4me3-MGH968-transformedSCLC

extract_protocol:
QIAquick DNA Purification Kit (Qiagen)
ThruPLEX DNA-seq Kit (TakaraBio)

value: H3K4me3 ChIP-seq


title: H3K4me3-MGH772-transformedSCLC


title: H3K4me3-MGH9243-adeno


title: H3K4me3-MGH9183-adeno


title: H3K4me3-MGH1525-denovoSCLC


title: H3K4me3-MGH1528-denovoSCLC


title: MeDIP-MGH1174-adeno


title: H3K4me3-MGH1518-denovoSCLC


title: H3K4me3-MGH1514-denovoSCLC


title: H3K4me3-MGH1512-denovoSCLC


title: H3K4me3-MGH1505-denovoSCLC


title: MeDIP-MGH1109-adeno


title: H3K4me3-MGH1504-denovoSCLC


title: H3K4me3-MGH1506-denovoSCLC


title: H3K4me3-MGH1174-adeno


title: H3K4me3-MGH1139-adeno-new


title: H3K4me3-MGH1112-adeno


title: H3K4me3-MGH1181-adeno


title: H3K4me3-MGH1109-adeno


title: H3K4me3-MGH10022-adeno


title: H3K4me3-MGH1068-adeno


title: H3K4me3-MGH1089-adeno


title: H3K27me3-MGHNA2-denovoSCLC

value: H3K27me3 ChIP-seq


title: H3K4me3-MGH1157-adeno


title: MeDIP-MGH10022-adeno


title: H3K4me3-MGH1065-adeno


title: H3K4me3-MGH10202-transformedSCLC


title: H3K4me3-MGH1062-adeno


title: H3K27me3-MGH772-transformedSCLC


title: H3K4me3-MGH10097-transformedSCLC


title: H3K27me3-MGH1522-denovoSCLC


title: H3K27me3-MGHNA1-denovoSCLC


title: H3K27me3-MGH968-transformedSCLC


title: H3K4me3-MGH1522-denovoSCLC


title: H3K27me3-MGH1525-denovoSCLC


title: H3K27me3-MGH1514-denovoSCLC


title: H3K27me3-MGH1506-denovoSCLC


title: H3K27me3-MGH1512-denovoSCLC


title: H3K27me3-MGH1528-denovoSCLC


title: H3K27me3-MGH1139-adeno


title: H3K27me3-MGH1181-adeno


title: H3K27me3-MGH1157-adeno


title: H3K27me3-MGH1505-denovoSCLC


title: H3K27me3-MGH1174-adeno


title: H3K27me3-MGH9243-adeno


title: H3K27me3-MGH9183-adeno


title: H3K27me3-MGH1109-adeno


title: H3K27me3-MGH1089-adeno


title: H3K27me3-MGH1065-adeno


title: H3K27me3-MGH1068-adeno


title: H3K27me3-MGH1062-adeno


title: H3K27me3-MGH10202-transformedSCLC


title: H3K27ac-MGH772-transformedSCLC

value: H3K27ac ChIP-seq


title: H3K27me3-MGH10097-transformedSCLC


title: H3K27ac-MGH1525-denovoSCLC


title: H3K27ac-MGH9183-adeno


title: H3K27ac-MGH1518-denovoSCLC


title: H3K27ac-MGH968-transformedSCLC


title: H3K27me3-MGH10022-adeno


title: H3K27ac-MGH1528-denovoSCLC


title: H3K27ac-MGH1514-denovoSCLC


title: H3K27ac-MGH1506-denovoSCLC


title: H3K27ac-MGH1504-denovoSCLC


title: H3K27ac-MGH1522-denovoSCLC


title: H3K27ac-MGH1512-denovoSCLC


title: H3K27ac-MGH1505-denovoSCLC


title: H3K27me3-MGH1112-adeno


title: H3K27ac-MGH1139-adeno-new


title: H3K27ac-MGH1157-adeno


title: H3K27ac-MGH1109-adeno


title: H3K27ac-MGH1089-adeno


title: H3K27ac-MGH1174-adeno


title: H3K27ac-MGH9243-adeno


title: H3K27ac-MGH1068-adeno


title: H3K27ac-MGH1065-adeno


title: H3K27ac-MGH1062-adeno


title: H3K27ac-MGH10022-adeno


title: H3K27ac-MGH10202-transformedSCLC


title: ATAC-MGH968-transformedSCLC

extract_protocol:
QIAquick DNA Purification Kit (Qiagen)
NEBNextUltra II DNA Library Prep Kit for Illumina (New England Biolabs)

value: ATAC-seq


title: ATAC-MGH9243-adeno


title: ATAC-MGH9183-adeno


title: ATAC-MGH772-transformedSCLC


title: ATAC-MGH1528-denovoSCLC


title: H3K27ac-MGH1181-adeno


title: ATAC-MGH1506-denovoSCLC


title: ATAC-MGH1181-adeno


title: ATAC-MGH1525-denovoSCLC


title: H3K27ac-MGH1112-adeno


title: ATAC-MGH1174-adeno


title: ATAC-MGH1109-adeno


title: ATAC-MGH1504-denovoSCLC


title: ATAC-MGH1139-adeno


title: ATAC-MGH1157-adeno


title: ATAC-MGH1065-adeno


title: ATAC-MGH1112-adeno


title: ATAC-MGH10202-transformedSCLC


title: ATAC-MGH10097-transformedSCLC


title: ATAC-MGH1522-denovoSCLC


title: ATAC-MGH1089-adeno


title: ATAC-MGH1518-denovoSCLC


title: ATAC-MGH1514-denovoSCLC


title: ATAC-MGH10022-adeno


title: ATAC-MGH1068-adeno


title: H3K27ac-MGH10097-transformedSCLC


title: T934

status: Public on Jun 13 2024

city: Memphis

first: Heather

last: Mefford

state: FL

address: 262 Danny Thomas Pl

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

description: DNA methylation array from individual with genetically unsolved DEE

hyb_protocol: Whole genome amplification (*Assay kit with arrays and reagents: Illumina Catalog #WG-317-1001) is performed on the bisulfite converted (and restored, if FFPE) DNA and the amplified material is then end point fragmented and precipitated. The pellets are resuspended and hybridized to the Methylation EPIC 850K array for approximately 20 hours.

scan_protocol: Red and green lasers are used for the excitation of the labeled nucleotides on the arrays and a CCD camera takes images of the sample sections. DMAP files, which must be downloaded for each lot of beadchips purchased from Illumina, are then used to pinpoint the location of each beadchip probe type on the array and extract and register the signal intensities. A variety of files are generated for each array (red and green.idats, .sdf, metrics, qc, and .jpegs). The .sdf, red and green.idats, a .csv (specifying sample and project information and hybridization locations), and the correct 850K EPIC manifest (.bpm) are used to create a project in GenomeStudio 2011.1 (free software).

data_processing:
All data were combined and loaded into the R package "minfi" for quality control and normalization (using the preprocessIllumina function). Individual CpG probes that failed (detection p>0.01) in >10% of samples; also, probes overlapping with common SNPs and those previously reported as cross-reactive were removed.
normalized beta value (0-1)

label: Cy3 and Cy5

source_name: peripheral blood

label_protocol: Cytosines are converted to Uracils (with the exception of methylated Cytosines) during a three-step sodium bisulfite treatment and column desulphonation (Zymo Research Catalog #D5004).

extract_protocol: DNA were extracted from peripheral-blood DNA samples using standard protocols, includuing the DNeasy Blood and Tissue Kit, the QIAamp DNA Blood Maxi Kit, and the Macherey-Nagel NucleoSpin Blood XL.

value: peripheral blood

tag: library name


title: ATAC-MGH1062-adeno


title: T918


title: T931


title: T863_rep1


title: T3240


title: T753


title: T3533


title: T2948

description: DNA methylation array from individual with DEE solved for CHD2


title: MeDIP-MGH1504-denovoSCLC


title: T863_rep2


title: T2868


title: T2837


title: T32826


title: T3337


title: T2985


title: T26554


title: T31942


title: T26781


title: T26568


title: T26409


title: T26967


title: T26729


title: T26862


title: T267


title: T2671


title: T26351


title: T26291


title: T2880


title: T26222


title: T26559


title: T26175


title: T26165


title: T26474


title: T26237


title: T26536


title: T26161


title: T2621


title: T26179


title: T25978


title: T25972


title: T25967_rep1


title: T25885


title: T2587


title: T2599


title: T25916


title: T25955


title: T25808_rep2


title: T25808_rep1


title: T25580


title: T25663


title: T25810


title: T25492


title: T2626


title: T2569


title: T25335


title: T25280


title: T25614


title: T25036


title: T2529


title: T24958


title: T25557


title: T24972


title: T25248


title: T25967_rep2


title: T25324


title: T25016


title: T25392


title: T24944_rep2


title: T25002


title: T25583


title: T24944_rep3


title: T24964


title: T25489


title: T24345


title: T24944_rep1


title: T24734


title: T24130


title: T23648


title: T24941


title: T23439


title: T23206


title: T23247


title: T23565


title: T22790


title: T23742


title: T22631


title: T22294


title: T21994


title: T24947


title: T21696


title: T21817


title: T21481


title: T21525


title: T21185


title: T21394


title: T21117_rep1


title: T20899


title: T20113


title: T20151


title: T20090


title: T1911


title: T18511


title: T1859


title: T18461


title: T17978


title: T17834


title: T17932


title: T17818


title: T1781


title: T17747_rep2


title: T1766


title: T17747_rep1


title: T17603


title: T17592


title: T21117_rep2


title: T17604


title: T17194


title: T17578


title: T1519


title: T20745


title: T17361


title: T16275


title: T1435


title: T18707


title: T17116


title: T1076


title: T1183


title: T112


title: T17577


title: T1083


title: e8478-1


title: e8335-1


title: e8323-1


title: e8334-1


title: e8243-1


title: e8276-1


title: e8275-1


title: e8274-1


title: e8128-1


title: e8091-1


title: e8086-1


title: e8133-1


title: e8273-1


title: e8190-1


title: e8047-1


title: e8025-1


title: e8087-1


title: e8077-1


title: e4913-1


title: e8043-1


title: e4872-1


title: e8026-1


title: e4870-1


title: e7878-1


title: e4849-1


title: e7877-1


title: e7465-1


title: e4847-1


title: e4776-4


title: e4874-1


title: e4871-1


title: e8051-1


title: e4911-1


title: e4707-1


title: e4708-1


title: e4866-1


title: e4703-1


title: e4741-1


title: e4700-1


title: e4701-1


title: e4853-1


title: e4779-1


title: e4691-1


title: e4776-1


title: e4744-1


title: e4743-1


title: e4740-1


title: e4679-1


title: e4676-1


title: e3927-1_rep2


title: e4549-1


title: e4706-1


title: e4873-1


title: e3777-1


title: e3638-1


title: e4696-1


title: e4698-1


title: e4694-1


title: e4689-1


title: e2797-1


title: e2793-1


title: e2800-1_rep1


title: e2797-4


title: e4686-1


title: e4561-1


title: e2788-1_rep2


title: e3927-1_rep1


title: e3926-1


title: e4095-1


title: T24944_fibroblast

value: fibroblast


title: e2800-1_rep2


title: e4688-1


title: 36252


title: e2788-4


title: e2788-1_rep1


title: 35721


title: 35874_rep1


title: 35643


title: e1700-1


title: 35638


title: 35874_rep2


title: e2788-6


title: 35457


title: 35288


title: 35209


title: 35426


title: 35197


title: 35061


title: 35072


title: 34893


title: e2237-1


title: 34635


title: 34952


title: e1692-1


title: 34607


title: 34501_rep2


title: 34501_rep1


title: 34461


title: 33919


title: 33711


title: 35636


title: 34466


title: 33482

value: saliva


title: 33607


title: 33402


title: 35451


title: 33697


title: 33386


title: 33241


title: 33244


title: 33364


title: 33151


title: 33055


title: 32969


title: 33001


title: 32924


title: 32801


title: 33143


title: 32794


title: 32453


title: 32692


title: 32251


title: 32191


title: 32678


title: 32275


title: 32474


title: 32328


title: 31818


title: 31942


title: 32826


title: 32203


title: 33473


title: 31761


title: 32120


title: 31322


title: 31297


title: 32028


title: 31253


title: 32443


title: 9831


title: 31729


title: 8245_rep2


title: 31518


title: 8245_rep1


title: 31292


title: 5915


title: 31224


title: RGC, experiment4, GEX, scRNA-seq

status: Public on Jun 12 2024

city: Houston

first: Justin

last: Ma

state: Texas

address: 1 Baylor Plaza, Baylor College of Medicine

department: ophthalmology

institute: Baylor College of Medicine

description:
10x Genomics
Ma_Atlas_filtered.csv

data_processing:
Demultiplexing was done using the Cell Ranger Multi Pipeline (in Cell Ranger v6.1.2) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/using/multi)
Assembly: GRCm38/mm10-2020A
Supplementary files format and content: We provide a universal comma-separated values file (.csv) for the filtered expression data. We also provide unprocessed barcode/feature/matrix data per experiment and the assignment confidence table based on a cell ranger's calculation using a confidence level of 0.9.

source_name: Retina

extract_protocol:
Fresh mouse retinas were dissected out from Vglut2-Tdtomato-Ai9 mice in oxygenated Ames media. Retinas are digested in papain and dissociated into single cells by manual trituration in low-ovomucoid solution. RGCs were enriched by negative-rod immunopanning using an anti-CD73 antibody. RGCs were labeled with a Thy1-APC antibody. RGCs were incubated with cholesteral-modified oligos using the 10x Genomics 3' CellPlex Kit (PN-1000261). RGCs from up to 6 retinas are pooled and resuspended in oxygenated Ames media, then enriched using FACS to isolate APC and Tdtomato positive cells. Unless specified, all steps were performed in oxygenated Ames, in the presence of Actinomycin D. All steps were also performed on individual retinas up until FACS.
Library construction was performed according to the manufacturer's instructions for the Chromium Next GEM 3' Kit v3.1

value: Retina

value: Retinal ganglion cells


title: RGC, experiment2, GEX, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: RGC, experiment5, GEX, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: 32974


title: 26351


title: 26720


title: 31770


title: 31069


title: 31067


title: 9741


title: 9714


title: 31768


title: 7135_rep2


title: 7135_rep1


title: 7068


title: 7067


title: MI_Heart_Treg_depleted_D4_rep3

status: Public on May 31 2024

city: Clayton

first: Mikaël

last: Martino

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

data_processing:
Fastq files were processed using the nfCore/RNAseq (v3.3) pipeline using the umi function (Patel, H., Ewels, P. & Peltzer, 2013, A. nf-core/rnaseq: nf-core/rnaseq v3.2 - Copper Flamingo, Zenodo)
Reads were aligned to the Mus musculus GRCm38 reference using STAR + Salmon aligner (Dobin, A., et al., 2013, Bioinformatics)
Reads were quantified using featureCounts (Liao, Y., et al., 2014, Bioinformatics) producing the raw genes count matrix and various quality control metrics.
Raw counts were then analysed with Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol)
Assembly: GRCm38
Supplementary files format and content: csv file where rows represent genes and each column represents different information, including gene name, gene ID and raw gene counts corresponding to the individual samples.

source_name: heart

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer’s instructions
RNA samples (20 ng) with RIN value ≥ 7 were used for library preparation. First strand synthesis was performed using a dT primer which also adds the Illumina P7 (5ʹ CAA GCA GAA GAC GGC ATA CGA GAT 3ʹ), 8 bp i7 index for each sample and a 10 bp unique molecular identifier (UMI). The modified reverse transcriptase reaction also adds a template switching sequence at the 5’ end of the RNA during the generation of indexed cDNA. These first stand indexed cDNA were pooled and amplified using primers to P7 and the template switch sequence. The Illumina P5 was added by tagmentation by Nextera transposase during amplification. The standard Illumina R1 primer was used (main cDNA read), followed by standard i7 primer for index/UMI. The R2 primer was present but not used as it will read into poly-A tail.

value: heart

tag: time

value: day 4 post-MI

value: monocytes/macrophages

value: Treg-depleted (FDG+DT)


title: MI_Heart_Treg_depleted_D4_rep1


title: 31243

tag: genotype


title: RGC, experiment3, GEX, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: MI_Heart_Control_D4_rep2

tag: treatment

value: Control (WT+DT)


title: RGC, experiment0, non-multiplex, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: MI_Heart_Treg_depleted_D7_rep3

value: day 7 post-MI


title: RGC, experiment1, GEX, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: MI_Heart_Control_D7_rep1


title: MI_Heart_Control_D4_rep3


title: MI_Heart_Treg_depleted_D4_rep2


title: MI_Heart_Control_D7_rep2


title: MI_Heart_Treg_depleted_D7_rep1


title: MI_Heart_Control_D7_rep3


title: MI_Heart_Control_D4_rep1


title: MI_Heart_Treg_depleted_D7_rep2


title: PHBI_168

status: Public on May 22 2024

city: Los Angeles

first: Jason

state: CA

address: 10833 Le Conte Ave, 43-229 CHS

institute: UCLA

data_processing:
Sequence reads were aligned to GENCODE human reference genome (v. 32) using HISAT2.
Transcripts were assembled and quantified using StringTie.
Transcript-level abundance estimates were imported and summarized into a counts matrix using tximport.
Assembly: GRCh38.p13
Supplementary files format and content: csv file containg counts estimated by tximport

source_name: lung

extract_protocol:
Total RNA was isolated by Zymo Direct-zol kit using on column DNAse treatment.
RNA libraries were preparing using TruSeq Stranded mRNA HT (RS-122-2103), dual index.

value: lung

tag: Sex

value: Female

tag: condition

value: PH

tag: ph subtype

value: APAH

tag: sequencingbatch


title: Exogenous Tregs before and after delivery

data_processing:
Mini-bulk reads were mapped to the Mus musculus GRCm38.p6 genome and ERCC spike-in sequences using the Subread aligner (v2.10.5) (Liao, Y., et al., 2013, Nucleic Acids Research) and assigned to genes using scPipe (v1.18.0) (Tian, L., et al., 2018, PLOS Computational Biology) with GENCODE M25 primary assembly annotation.
Gene-based annotations were obtained from the 'EnsDb.Mmusculus.v79' R/Bioconductor package (Rainer, J., 2017), which was used to map the GENCODE/Ensembl gene IDs to gene symbols and to other info (e.g., gene biotype, chromosome location).
Gene counts were exported as a matrix by scPipe with UMI-aware counting.
Technical replicates were aggregated by summing the UMI counts, resulting in 3 biological replicates for each of the 3 tissues.
The UMI-deduplicated count files were uploaded to the Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol).
Assembly: GRCm38.p6
Supplementary files format and content: CSV, Pseudobulked gene counts (UMI-deduplicated) for samples used for analysis. Rows represent genes and each column is one biological replicate sample which comes from pseudobulking and combining all technical replicates together. This is the file that was uploaded to Degust for differential gene expression analysis.
Supplementary files format and content: CSV, gene count matrix, rows represent genes and each column is a well, values corresponding to read counts (UMI-deduplicated)
Supplementary files format and content: CSV, sample sheet, rows represent a well and columns contain metadata on the sample in the well (for all samples prior to pseudobulking)

source_name: heart, mediastinal lymph nodes, spleen

extract_protocol:
For Day 0 Tregs, spleens of Foxp3(IRES-mRFP) mice were harvested and stained with CD4 antibody to sort CD4+ RFP+ Tregs. For tthe Day 3 recovered exogenous Tregs, C57BL6/J mice with tissue injuries (in bone, muscle, skin and heart tissues) that were treated with RFP+ Tregs from Foxp3(IRES-mRFP) mice were harvested, and subjected to enzymatic tissue digestion, followed by subsequent staining with surface antibodies for cell sorting. The recovered Tregs were purified by first excluding any dead cells, then excluding any potential contaminating CD11b, F4/80, Ly6G-positive myeloid cells, followed by selecting CD3, CD4 and RFP+ Tregs. All cells were directly sorted into the primer/lysis buffer mix in 384-well plates (50 cells/well) and then frozen for further processing. Cells from the same sample that were sorted in multiple wells (in increments of 50 cells per well) were later combined bioinformatically to create pseudobulked samples.
Minibulk transcriptome libraries were generated using a modified CEL-Seq2 protocol (Hashimshony et al., 2016, Genome Biol.) with the following adaptations: Samples were pooled after first strand cDNA synthesis, treated with Exonuclease 1 for 30 minutes, followed by a 1.2X bead clean-up. Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB #E6111S) in a final reaction volume of 20 ul and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) were used for all DNA purification and size selection steps.

value: Exogenous delivered Tregs (day 0) and recovered Tregs (day 3 post-Treg delivery)

value: heart, mediastinal lymph nodes, spleen

tag: cell type

value: Regulatory T cells

value: male

value: 10 weeks

value: Myocardial infarction + Treg-treated or Healthy spleen Tregs

tag: sample type

value: mixed sample (non-demultiplexed)


title: PHBI_166

tag: age


title: D4,7 Macrophages

data_processing:
Mini-bulk reads were mapped to the Mus musculus GRCm38.p6 genome and ERCC spike-in sequences using the Subread aligner (v2.10.5) (Liao, Y., et al., 2013, Nucleic Acids Research) and assigned to genes using scPipe (v1.18.0) (Tian, L., et al., 2018, PLOS Computational Biology) with GENCODE M25 primary assembly annotation.
Gene-based annotations were obtained from the 'EnsDb.Mmusculus.v79' R/Bioconductor package (Rainer, J., 2017), which was used to map the GENCODE/Ensembl gene IDs to gene symbols and to other info (e.g., gene biotype, chromosome location).
Gene counts were exported as a matrix by scPipe with UMI-aware counting.
The UMI-deduplicated count files were uploaded to the Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol).
Assembly: GRCm38.p6
Supplementary files format and content: CSV, gene count matrix, rows represent genes and each column is one sample, values corresponding to read counts (UMI-deduplicated). This is the file that was uploaded to Degust for differential gene expression analysis.
Supplementary files format and content: CSV, sample sheet, rows represent a well and columns contain metadata on all samples

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer’s instructions
1.1 μl of purified macrophage RNA (6 ng/ μl) from each sample was added to a well of a 384-well PCR plate (Greiner, 785290) containing 20 nM of an air dried indexed polydT primer (custom made, IDT). Minibulk transcriptome libraries were generated using a modified CEL-Seq2 protocol (Hashimshony et al., 2016, Genome Biol.) with the following adaptations: first strand cDNA synthesis was performed, then the samples were treated with Exonuclease 1 for 30 minutes, followed by a 1.2X bead clean-up. Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB #E6111S) in a final reaction volume of 20 ul and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) were used for all DNA purification and size selection steps.

value: Day 4 + 7 Treg-treated and untreated control

value: bone, skin, muscle, heart

value: Macrophages

value: Myocardial infarction + Tregs or PBS


title: PHBI_162

value: Unknown


title: PHBI_163


title: PHBI_165


title: PHBI_167


title: PHBI_160

value: Male


title: PHBI_159

value: lung


title: PHBI_158

value: Female


title: PHBI_156

value: PH

value: IPAH


title: PHBI_154

value: APAH


title: PHBI_152


title: PHBI_150


title: PHBI_169

value: HPAH


title: PHBI_148


title: PHBI_146


title: PHBI_144


title: PHBI_145


title: PHBI_147


title: PHBI_164


title: PHBI_143


title: PHBI_142


title: PHBI_149


title: PHBI_140

value: PVOD


title: PHBI_135

value: FD


title: PHBI_139


title: PHBI_137


title: PHBI_155


title: PHBI_136


title: PHBI_141


title: PHBI_134


title: PHBI_138


title: PHBI_128


title: PHBI_130


title: PHBI_132


title: PHBI_131


title: PHBI_129


title: PHBI_153


title: PHBI_151


title: PHBI_127


title: PHBI_124


title: PHBI_126


title: PHBI_123


title: PHBI_118


title: PHBI_120


title: PHBI_125


title: PHBI_115


title: PHBI_116


title: PHBI_114


title: PHBI_113


title: PHBI_121


title: PHBI_110


title: PHBI_109


title: PHBI_112


title: PHBI_107


title: PHBI_108


title: PHBI_105


title: PHBI_106


title: PHBI_103


title: PHBI_101


title: PHBI_100


title: PHBI_104


title: PHBI_097


title: PHBI_161


title: PHBI_096


title: PHBI_122


title: PHBI_093


title: PHBI_133


title: PHBI_094


title: PHBI_095


title: PHBI_091


title: PHBI_111


title: PHBI_088


title: PHBI_089


title: PHBI_084


title: PHBI_085


title: PHBI_090


title: PHBI_080


title: PHBI_083


title: PHBI_079


title: PHBI_087


title: PHBI_086


title: PHBI_092


title: PHBI_082


title: PHBI_098


title: PHBI_078


title: PHBI_073


title: PHBI_071


title: PHBI_076


title: PHBI_075


title: PHBI_069


title: PHBI_072


title: PHBI_070


title: PHBI_074


title: PHBI_068


title: PHBI_061


title: PHBI_065


title: PHBI_059


title: PHBI_057


title: PHBI_055


title: PHBI_056


title: PHBI_046


title: PHBI_045


title: PHBI_051


title: PHBI_049


title: PHBI_050


title: PHBI_077


title: PHBI_044


title: PHBI_043


title: PHBI_041


title: PHBI_040


title: PHBI_039


title: PHBI_042


title: PHBI_038


title: PHBI_032


title: PHBI_031


title: PHBI_030


title: PHBI_029


title: PHBI_054


title: PHBI_033


title: PHBI_053


title: PHBI_026


title: PHBI_028


title: PHBI_024


title: PHBI_052


title: PHBI_022


title: PHBI_027


title: PHBI_023


title: PHBI_025


title: PHBI_021


title: PHBI_018


title: PHBI_019


title: PHBI_020


title: PHBI_016


title: PHBI_015


title: PHBI_035


title: PHBI_017


title: PHBI_013


title: PHBI_011


title: PHBI_009


title: PHBI_037


title: PHBI_010


title: PHBI_005


title: PHBI_008


title: PHBI_014


title: PHBI_004


title: PHBI_002


title: sh-GFP, Female infected, 0 hour, replicate3

status: Public on May 15 2024

city: St Petersburg

first: Rui

last: Zhou

address: REB 4130, 501 6th Ave S

institute: Johns Hopkins University

data_processing:
Adaptor sequences and low-quality reads (those with an average quality score < 20) were removed from the paired-end raw data using Trim-galore (version 0.4.4).
The resulting cleaned reads were aligned to the Drosophila melanogaster (dm6) reference genome using the STAR splice-aware aligner (version 2.6.0c) with default parameters.
Ambiguous reads mapping to multiple regions in the genome and reads with a MAPQ score less than 10 were discarded.
Subread featureCounts (version 2.0.1) was then utilized for gene quantification, employing the FlyBase r6.40 gene annotation.
Genes without read counts in all samples were excluded from subsequent analysis.
Assembly: dm6
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text file include RPKM values for every gene and every sample

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Flies were maintained at room temperature with standard fly food (molasses formula).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Total RNA samples were subjected to cDNA library construction using illumina kit.

treatment_protocol: Newly hatched male and female flies of appropriate genotypes were collected and kept in fresh food vials for 4-7 days prior to RNA extraction.

value: whole fly

tag: cell line

value: w; Actin-Gal4/+; UAS-sh-GFP/+

value: newly emerged flies that have been kept in molasses formulation food at room temperature for 4-7 days


title: Hepatocyte organoids, RGF, Day 12, 1

city: Boston

first: Yuchen

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

data_processing:
Sequence alignment were performed using STAR aligner.
Paired reads were then counted using ‘featureCounts’ in The Subread software
Raw counts were normalized using the edgeR package
Assembly: mm10
Supplementary files format and content: tab delimited text file include normalized CPM values for each sample

source_name: liver

growth_protocol: The HOs were maintained in the original HO growth medium with growth factors (GFs) (+GF medium). The +GF medium for  HO culture contains Advanced DMEM/F12 with B27 minus vitamin A, 10mM HEPES, GlutaMAX™, and Penicillin-Streptomycin (Thermo Fisher Scientific), 15% RSPO1 conditioned medium (home-made), 3μm CHIR99021 (MCE), 50ng/ml EGF (Biolegend), 25ng/ml HGF (Biolegend), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Biolegend), 1μM A83-01 (Sigma), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 10 mM Nicotinamide (Sigma), and 1mM N-acetylcysteine (Sigma).

extract_protocol:
Organoids were retrieved from BME using Cultrex Organoid Harvesting Solution and pelleted by centrifuge at 50g for 3 minutes. RNA was isolated from the organoid pellet using PureLinkTM RNA mini kit (Thermo fisher scientific) according to the manufacturer's instruction.
DNA was removed from RNA using RapidOut DNA Removal Kit (Thermo Fisher Scientific) according to the manufacturer's instruction. After measuring RNA quantity and quality by Agilent 2200 TapeStation, 400ng-1000ng RNA per sample reaction were used for mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using xGen™ RNA Library Prep Kit (IDT) according to the manufacturer's instruction.

treatment_protocol: The HOs were switched to the maturation medium for HO maturation. The basal medium for human and mouse HO maturation is Growth factors removed (RGF) medium, which includes William's E Medium with B27 minus vitamin A, 10mM HEPES, GlutaMAXTM and Penicillin-Streptomycin (Thermo Fischer Scientific), 50μg/ml Primocin (InvivoGen), 15% RSPO1 conditioned medium (house-made), 3μM CHIR99021 (MCE), 1μM A83-01 (MCE), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 2.5 mM Nicotinamide (Sigma), and 1.25 mM N-acetylcysteine (Sigma). Additional components were added to RGF medium for hepatic maturation of HOs. For maturation of mouse HOs, these medium incude: RGF +T3: 10nM Triiodothyronine(T3) in RGF medium; RGF +DEX: 200nM dexamethasone (DEX) in RGF medium; RGF +T3 +DEX: 10nM T3 and 200nM DEX in RGF medium. For HO dedifferentiation, the HOs were cultured in the RGF +T3 condition for 6 days, and switched to +GF condition for another 6 days. To overexpress CTNNB1ΔN90 in the HOs, AAV-TBG-CTNNB1ΔN90 was mixed with fragmented HOs in BME at a concentration of 2x10^10 GC/ml during passage.

value: liver

value: Hepatocyte organoids

value: hepatocytes

value: wild type

value: RGF, Day12


title: Hepatocyte organoids, RGF, Day 12, 2


title: sh-GFP, Female infected, 0 hour, replicate2


title: Hepatocyte organoids, RGF, Day 12, 3


title: sh-GFP, Female infected, 0 hour, replicate1


title: sh-GFP, Male infected, 0 hour, replicate3

value: Male

value: w/Y; Actin-Gal4/+; UAS-sh-GFP/+


title: SL2+FHV

data_processing:
Illumina’s bcl2fastq.gz was used to convert bcl files to fastq.gz files and de-multiplex the samples.
The cleaned reads were aligned to the Drosophila melanogaster (dm3) reference genome using bowtie2 (version 2.2.5).
The find_circ v1.0 program, employing the parameters recommended by the developer, was then applied to detect circRNAs using the unmapped reads (Memczak et al., 2013).
Assembly: dm3
Supplementary files format and content: circRNAs bed file for each sample

growth_protocol: Drosophila SL2 cells are maintained in Schneider’s medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Total RNA samples were first subjected to ribosomal RNA depletion using Ribo-zero rRNA removal kit, and subsequently treated with RNase R for 30 minutes at 37oC. The resulting enriched circular RNA fraction was subjected to cDNA library construction using illumina kit.

treatment_protocol: Drosophila SL2 cells (~ 2X10^6 cells/mL) were 1) left untreated, 2) infected with Flock House virus (MOI 0.1) for 48 hours.

value: embryonic

value: infected with fly flock house virus


title: sh-R41, Male infected, 0 hour, replicate3

value: w/Y; Actin-Gal4/+; UAS-sh-circ_ATP8B/+


title: sh-R41, Female infected, 0 hour, replicate2

value: Female

value: w; Actin-Gal4/+; UAS-sh-circ_ATP8B/+


title: sh-R41, Female infected, 0 hour, replicate1


title: sh-GFP, Male infected, 0 hour, replicate1


title: sh-GFP, Male infected, 0 hour, replicate2


title: sh-R41, Female infected, 0 hour, replicate3


title: Chondrocyte_trunk_biolRep3

status: Public on May 14 2024

city: Muenster

first: Kleio

last: Petratou-Busswinkel

address: Röntgenstraße 16

institute: Institute for Cardiovascular Organogenesis and Regeneration

description: GFP negative, mCherry positive cells

data_processing:
Details on all steps listed below can be found on github: https://github.com/KleioP/ATAC_RNAseq_analysis
QC of sequences, adapter trimming using fastp
Sequence alignment to genome using bowtie2, and samtools to sort and index aligned reads
removal of mitochondrial reads using bedtools intersect, and removing duplicate reads using sambamba
shifting all reads +4/-5 bps to account for transposome cutting during chromatin tagmentation using the alignmentSieve (deeptools)
significant peaks were called with macs2 using the parameters -g 1.412e9 --keep-dup all --nomodel --shift -100 --extsize 200
Assembly: danRer11
Supplementary files format and content: BED files. Columns 1-5: 1. Chromosome 2. Peak Start coordinate 3. Peak End coordinate 4. Peak name 5. Score

organism: Danio rerio

source_name: trunk

extract_protocol:
ATAC-Seq was performed according to previously published protocols (Buenrostro et al., 2015), with the following modifications. Cells were incubated in lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, 0.1% NP40, 0.01% Digitonin) for 3min on ice. Lysis was stopped by resuspending in ice-cold wash buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween20) prior to centrifugation. The volume of enzyme added to the transposition reaction (1x Tagment DNA Buffer, 0.01% Digitonin, 0.1% Tween20, TDE1 enzyme) and the length of transposition were adjusted depending on the numbers of cells isolated in each sample. The Tagment DNA Buffer and TDE1 enzyme are both contained in the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, 20034197). Following amplified DNA purification (Buenrostro et al., 2015), AMPure XP SPRI beads (Beckman Coulter, A63881) were used (1.4x sample volume) to remove primer dimers from the chromatin sample according to manufacturer's instructions
According to Illumina NextSeq System instructions (Standard Normalization Method, including Phix Control)

value: trunk

value: trunk chondrocyte

tag: Stage

value: 15 days post fertilisation


title: Chondrocyte_trunk_biolRep2

description: GFP negative, mCherry positive cells


title: Chondrocyte_trunk_biolRep1

description: GFP negative, mCherry positive cells. Due to loss of files, provided here is the BAM output file from read-shifting step (see protocol and github page)


title: Chondrocyte_head_biolRep2

description: GFP negative, mCherry positive cells

source_name: head

value: head

value: head chondrocyte


title: Chondrocyte_head_biolRep1

description: GFP negative, mCherry positive cells


title: Chondrocyte_head_biolRep3

description: GFP negative, mCherry positive cells


title: PHBI_006

value: lung

value: PH

value: IPAH


title: sh-R41, Male infected, 0 hour, replicate2

value: whole fly

value: newly emerged flies that have been kept in molasses formulation food at room temperature for 4-7 days


title: Osteoblast_trunk_biolRep2

description: GFP positive, mCherry negative cells

value: osteoblast (non-classical)


title: SL2

value: wild type

value: naive


title: Osteoblast_head_biolRep2

description: GFP positive, mCherry negative cells

value: osteoblast (classical)


title: Osteoblast_head_biolRep3

description: GFP positive, mCherry negative cells


title: Osteoblast_head_biolRep1

description: GFP positive, mCherry negative cells. Due to loss of files, provided here is the BAM output file from read-shifting step (see protocol and github page)