title: 2-4h embryo Control Rep4

tag: treatment

value: Control


title: Arabidopsis ac4C IP replicate 2

status: Public on Jun 15 2023

type: SRA

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

country: China

institute: Hunan university

description: ac4C, rep2

library_source: transcriptomic

data_processing:
Adapters were removed from reads with the AdapterRemoval tool with adapter sequence 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'.
Reads were then mapped against the Arabidopsis (TAIR10) or rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
Assembly: TAIR10 and IRGSP-1.0
Supplementary files format and content: bigwig files were generated using bedGraphToBigWig; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 10-day-old seedlings

growth_protocol: Arabidopsis seedlings were grown on 1/2-strength Murashige and Skoog (MS) medium (1/2 MS) with 0.8% sucrose under long-day conditions (16 hr light/8 hr dark) at 21ºC ±2ºC. Oryza sativa L. ssp. japonica cultivar Nipponbare plants were grown on Yoshida solution in a growth chamber under short-day (SD) conditions (10 h light/14 h dark) with a light intensity of 800 mmol m-2 s -1.

extract_protocol:
Seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. ac4C IVT was spiked-in in a 1:5000 mass ratio. RNA was fragmented and isolated with IgG or ac4C antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. acRIP-seq libraries were prepared according to Arango, D. et al., Cell, 2018. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Hiseq 4000 platform as single-end 150 bp reads.
acRIP-seq

tag: rip antibody

value: ac4C (abcam, ab252215)

tag: variety

tag: age

tag: tissue

value: seedlings


title: 2-4h embryo shHDAC3 Rep1

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

data_processing:
usegalaxy.eu
RNA-seq reads were mapped to the Drosophila melanogaster (dm6) genome assembly using STAR with default parameters. RNA-seq count tables were generated with featureCounts and differential expression analysis (DE) of HDAC3 shRNA vs. Control, shRNA-resistant rescueWT,  shRNA-resistant rescueY303F,  shRNA-resistant rescueK26A or shRNA-resistant rescueHEBI was performed using DEseq2.
Assembly: dm6
Supplementary files format and content: xlsx file for RNA-seq count table

organism: Drosophila melanogaster

source_name: Whole embryo

growth_protocol: Embryos were grown at 25°C

extract_protocol:
Embryos were homogenized in 300 µL TRIzol LS Reagent followed by total RNA purification using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch).
RNA libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina).

value: Whole embryo

tag: genotype

value: tub-GAL4/shRNA HDAC3

tag: developmental stage

value: 2-4h after egg laying

value: HDAC3 shRNA


title: ACLY a

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.33, and then mapped to hg19 whole genome using hisat2-2.0.4
Raw counts were calculated using HtSeq-count
Differentially expressed genes were obtained using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample and edgeR output

molecule: polyA RNA

organism: Homo sapiens

source_name: Embryonic stem cell H9

extract_protocol: Poly-A mRNA was  enriched from between 1-10 µg of total RNA with oligo dT beads (Invitrogen). ~10-100 ng of poly-A mRNA recovered was used to construct multiplexed strand-specific RNA-seq libraries as per manufacturer’s instruction (NEXTflexTM Rapid Directional RNA-SEQ Kit, dUTP-Based, v2). Individual library quality was assessed with an Agilent 2100 Bioanalyzer and quantified with a QuBit 2.0 fluorometer before pooling for sequencing on a HiSeq 2000 (1x101 bp read). The pooled libraries were quantified using the KAPA quantification kit (KAPA Biosystems) prior to cluster formation.

treatment_protocol: Differentiation into definitive endoderm using RPMI/2%B27, Activin, CHIR99021, LY294002 +/- FGF2, SU5402 or TCS ERKi

tag: cell type

value: Definitive endoderm

value: Basal differentiation media

tag: cell line

value: Embryonic stem cell H9

tag: gender

value: Female


title: Arabidopsis ac4C IP replicate 1

description: ac4C, rep1


title: UD c

value: undifferentiated hESCs

value: Stem Cell media


title: Arabidopsis Input replicate 1

description: Input, rep1


title: Site A individual 13

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.6.6
Mapping on the reference Transcriptom of Hyla orientalis with Bowtie2 and RSEM
RSEM results imported with tximport in R and analysed with DESeq2
Polymorphism analysis with GATK haplotypeCaller v 4.2.0.0
Assembly: Unpublished de novo transcriptom assembly of Hyla orientalis
Supplementary files format and content: vcf with variant SNP

organism: Hyla orientalis

source_name: tibia muscle

extract_protocol:
Trizol extraction followed by column purification on Quick RNA Miniprep kit (Zymoreasearch)
Stranded mRNA kit (Illumina). Paired end with dual Index UD IDT (illumina)

treatment_protocol: Sampling of wild individuals in the chernobyl exclusion zone and in Slavutych area

value: tibia muscle

value: Wild type

tag: location

value: captured in chernobyl exclusion zone

tag: treatment group

value: exposed to radiocontamination


title: 2-4h embryo Control Rep3

value: Control


title: Site A individual 11


title: UD b


title: 2-4h embryo Control Rep2


title: Arabidopsis IgG control replicate 2

description: IgG, rep2

value: Rabbit IgG


title: Arabidopsis IgG control replicate 1

description: IgG, rep1

value: seedlings


title: UD a


title: 2-4h embryo Control Rep1

value: Whole embryo


title: blood that underwent CTC enichment [2019.05.01_HDM64_IFD_042619]

status: Public on Jun 14 2023

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

description:
High molecular weight DNA
barcode10

library_source: genomic

data_processing:
Nanopore sequencing reads (format: fast5) generated by Nanopore MinION device were first converted into fastq files using ONT Albacore software (v2.3.1) (https://nanoporetech.com/community). Demultiplexing was also performed during fast5 to fastq conversion.
DNA methylation information was extracted from both fast5 and fastq files using Nanopolish software (v0.10.2) (https://github.com/nanoporetech/nanopolish).
Nanopolish output files were used for downstream analysis.
Assembly: hg19 (human)
Supplementary files format and content: Nanopolish output files, which are TSV (Tab-Separated-Values) files with column headings.
Library strategy: DNA-Seq

molecule: genomic DNA

source_name: blood

extract_protocol:
Blood samples from either healthy donors or patients with localized or metastatic prostate cancer were subjected to CTC-ichip enrichment (10^4-fold leukocyte depletion). The enriched CTCs (ranging from 0.1% to 1% of residual leukocytes) were subjected to high molecule weight (HMW) DNA extraction using the HMW DNA extraction kit (QIAGEN).
High molecule weight (HMW) DNA was used to prepare sequencing library for Oxford Nanopore sequencing using the rapid barcoding kit (Nanopore#SQK-RBK004). For each sequencing run, 11 blood samples (either from healthy donors or cancer patients), together with 1 lambda DNA (unmethylated control), were uniquely barcoded and pooled together. Sequencing was performed using a Nanopore MinION device with R9.4 flowcell for 48 h, per manufacturer instructions.

tag: patient donor

tag: disease

value: Healthy Donor

value: blood

tag: flowcell

tag: kit


title: blood that underwent CTC enichment [2019.05.23_HDM66_IFD_052119]

description:
High molecular weight DNA
barcode03


title: blood that underwent CTC enichment [2019.05.23_HDM61_IFD_051619]

description:
High molecular weight DNA
barcode04


title: blood that underwent CTC enichment [2019.05.31_HDFM62_IFD_052419]

description:
High molecular weight DNA
barcode04


title: blood that underwent CTC enichment [2019.04.27_HDM69_IFD_032819]

description:
High molecular weight DNA
barcode06


title: blood that underwent CTC enichment [2019.04.27_HDF74_IFD_nodate]

description:
High molecular weight DNA
barcode02


title: blood that underwent CTC enichment [2019.03.29_HDM69_031119]

description:
High molecular weight DNA
barcode04


title: blood that underwent CTC enichment [2019.04.16_HDM80_IFD_032219]

description:
High molecular weight DNA
barcode01


title: blood that underwent CTC enichment [2019.05.23_HDM70_IFD_051619]

description:
High molecular weight DNA
barcode05


title: blood that underwent CTC enichment [2019.03.29_HDM67_031419]

description:
High molecular weight DNA
barcode02


title: blood that underwent CTC enichment [2019.05.23_HDF51_IFD_051419]

description:
High molecular weight DNA
barcode06


title: blood that underwent CTC enichment [2019.04.16_HDF41_IFD_031319]

description:
High molecular weight DNA
barcode07


title: blood that underwent CTC enichment [2019.03.15_HDM64_030819_IFD]

description:
High molecular weight DNA
barcode07


title: blood that underwent CTC enichment [2019.04.16_HDM64_IFD_040419]

description:
High molecular weight DNA
barcode03


title: blood that underwent CTC enichment [2019.04.16_HDM77_IFD_031219]

description:
High molecular weight DNA
barcode02


title: blood that underwent CTC enichment [2019.03.29_HDM69_031219]

description:
High molecular weight DNA
barcode01


title: blood that underwent CTC enichment [2019.02.28_HDM64_022219_IFD]

description:
High molecular weight DNA
barcode02


title: blood that underwent CTC enichment [2019.02.28_HDM62_022219_IFD]

description:
High molecular weight DNA
barcode03


title: blood that underwent CTC enichment [2019.03.11_RGU37_1_091718]

description:
High molecular weight DNA
barcode02

value: Localized cancer


title: blood that underwent CTC enichment [2019.05.31_HDF62_IFD_052319]

description:
High molecular weight DNA
barcode03


title: blood that underwent CTC enichment [2019.02.25_RGU43_010719]

description:
High molecular weight DNA
barcode03


title: blood that underwent CTC enichment [2019.02.28_HDM61_022219_IFD]

description:
High molecular weight DNA
barcode01


title: blood that underwent CTC enichment [2019.05.13_HDM60_IFD_051019]

description:
High molecular weight DNA
barcode08


title: Site A individual 10


title: blood that underwent CTC enichment [2019.02.25_RGU44_010719]

description:
High molecular weight DNA
barcode04


title: blood that underwent CTC enichment [2019.02.25_RGU99_102418]

description:
High molecular weight DNA
barcode07


title: blood that underwent CTC enichment [2019.02.25_RGU35_092618]

description:
High molecular weight DNA
barcode02


title: blood that underwent CTC enichment [2019.02.25_RGU103_100318]

description:
High molecular weight DNA
barcode08


title: blood that underwent CTC enichment [2019.04.27_HDF54_IFD_040219]

description:
High molecular weight DNA
barcode01


title: blood that underwent CTC enichment [2019.02.16_HDM70_101018]

description:
High molecular weight DNA
barcode09


title: blood that underwent CTC enichment [2019.02.12_RGU98_070518]

description:
High molecular weight DNA
barcode01


title: blood that underwent CTC enichment [2019.02.11_GU129_121118]

description:
High molecular weight DNA
barcode09

value: Metastatic cancer


title: blood that underwent CTC enichment [2019.02.25_RGU34_091918]

description:
High molecular weight DNA
barcode01


title: blood that underwent CTC enichment [2019.02.16_RGU108_080618]

description:
High molecular weight DNA
barcode06


title: blood that underwent CTC enichment [2019.02.12_RGU109_103118]

description:
High molecular weight DNA
barcode05


title: blood that underwent CTC enichment [2019.02.25_RGU45_020219]

description:
High molecular weight DNA
barcode05


title: blood that underwent CTC enichment [2018.11.04_GU216_18.07.05]

description:
High molecular weight DNA
barcode11


title: blood that underwent CTC enichment [2018.11.04_GU181_17.12.09]

description:
High molecular weight DNA
barcode08


title: vCAP cell line [2018.10.16_1ug_pure_vCap_gDNA]

description:
High molecular weight DNA
nobarcode

source_name: vCAP cancer cell line

value: vCAP cancer cell line


title: blood that underwent CTC enichment [2019.02.08_RGU-NS-13-116_070218]

description:
High molecular weight DNA
barcode04


title: blood that underwent CTC enichment [2019.02.08_RGU119_120618]

description:
High molecular weight DNA
barcode07


title: blood that underwent CTC enichment [2018.11.04_GU216_18.08.09]

description:
High molecular weight DNA
barcode12


title: blood that underwent CTC enichment [2019.02.08_RGU20_120718]

description:
High molecular weight DNA
barcode08


title: blood that underwent CTC enichment [2018.11.04_GU181_18.01.02]

description:
High molecular weight DNA
barcode09


title: blood that underwent CTC enichment [2019.02.08_RGU122_010419]

description:
High molecular weight DNA
barcode09


title: blood that underwent CTC enichment [2019.02.08_RGU124_010919]

description:
High molecular weight DNA
barcode11


title: blood that underwent CTC enichment [2018.11.04_GU181_17.11.07]

description:
High molecular weight DNA
barcode06


title: blood that underwent CTC enichment [2018.11.04_GU181_17.11.28]

description:
High molecular weight DNA
barcode07


title: Telencephalon, not building, biol rep 2, capture area D

city: Atlanta

first: Larry

last: Young

state: GA

address: 954 Gatewood Rd NE

department: Department of Psychiatry

institute: Emory University

description: Visium10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment, tissue/fiducial detection, barcode processing, and gene counting was conducted using Space Ranger software v1.3.1
Assembly: M_zebra_UMD2a
Supplementary files format and content: Gunzipped tab-separated values files, matrix files, and folder of spatial information

molecule: nuclear RNA

organism: Mchenga conophoros

source_name: Telencephalon

extract_protocol:
Telencephalon tissue samples were embedded in cryomolds (7mm x 7mm x 7mm) containing chilled OCT (Optimal Cutting Temperature embedding compound) and snap frozen. OCT-embedded tissue blocks were cryosectioned at 10 m thickness at -20C (CryoStar NX70). Tissue sections were mounted onto 6.5 mm2 capture areas on Visium Spatial Gene Expression Slides (10X Genomics). There are four capture areas per slide, each containing 5000 spatially-barcoded 55m-diameter spots. RNA quality of the tissue sections (RIN > 7) was confirmed using the Agilent RNA 6000 Nano Kit on the Bioanalyzer 2100 system (Agilent). Gene Expression slides containing tissue sections were processed according to manufacturer instructions (Methanol Fixation, H&E Staining, and Imaging – Visium Spatial Protocol (10X Genomics)). Slides were fixed in methanol for 30 minutes at -20C and stained with Hematoxylin and Eosin (H&E). Brightfield images of H&E-stained slides were taken at 1.33 m/pixel resolution (5X objective, Zeiss AxioObserver Z1 Fluorescent Microscope) and stitched using Zen 2 software (blue edition, Zeiss) prior to library construction.
Dual-index Illumina paired-end spatial gene expression libraries were prepared according to manufacturer instructions (Visium Spatial Gene Expression Reagent Kits User Guide (10X Genomics)). Fixed and stained tissue sections were permeabilized for 18 minutes and poly-adenylated mRNA released from cells was captured by primers on the underlying gene expression spots. Primers include a 10X spatial barcode, unique molecular identifier (UMI) and an Illumina read 1 sequencing primer. Incubation with reverse transcription (RT) reagents produced spatially barcoded, full-length cDNA. Barcoded cDNA was denatured, transferred into tubes, and amplified via PCR. Amplified cDNA was size-selected with SPRIselect. During final library construction, P5 and P7 paired-end construct sequences, i5 and i7 sample indices, and an Illumina read 2 primer sequence were added. Quality was assessed using high sensitivity DNA analysis on the Bioanalyzer 2100 system (Agilent).

value: Telencephalon

tag: strain

tag: behavioral state_before_euthanization

value: not building

value: adult (>180 days)


title: Telencephalon, not building, biol rep 2, capture area B

description: Visium10x Genomics


title: Telencephalon, not building, biol rep 2, capture area C

description: Visium10x Genomics


title: Telencephalon, not building, biol rep 2, capture area A

description: Visium10x Genomics


title: Telencephalon, not building, biol rep 1, capture area D

description: Visium10x Genomics


title: Telencephalon, building, biol rep 2, capture area D

description: Visium10x Genomics

value: building


title: Telencephalon, building, biol rep 2, capture area B

description: Visium10x Genomics


title: Telencephalon, building, biol rep 2, capture area A

description: Visium10x Genomics


title: Telencephalon, not building, biol rep 1, capture area C

description: Visium10x Genomics


title: Telencephalon, not building, biol rep 1, capture area B

description: Visium10x Genomics


title: Telencephalon, building, biol rep 2, capture area C

description: Visium10x Genomics


title: scATAC_RSeT_induced_GATA6_SOX17_hESC

city: Seattle

first: Nobuhiko

last: Hamazaki

state: Washington

address: Foege Building S-210 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
single cell 10x multiome (ATAC)
g6_s17_induced_cells_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Raw reads were analyzed using the CellRangerARC pipeline to generate ATAC and RNA fastq files for each sample, and then to align genomic and transcriptomic reads. Matrices were then read into Seurat and Signac using the Read10X_h5 command. For ATAC-seq data, peaks from standard chromosomes were used and peaks were additionally called using macs2 to add an additional Signac assay. Cells with >500 RNA UMI counts, <20% mitochondrial reads, >500 ATAC reads, TSS enrichment >1 and were called as singlets using scDblFinder were retained for downstream analysis. For UMAP projections, SCTransform was used for RNA counts with percent mitochondrial counts and cell cycle scores regressed. PCA and LSI graphs were used to generate a weighted nearest neighbor (wnn) embedding which accounts for both modalities. chromVAR was run to calculate motif accessibility score on the peaks assay.
Assembly: hg38
Supplementary files format and content: Subgroups of RNA/ATAC data were gathered and processed with cellrangerARC (Named "RNA" and "ATAC").
Supplementary files format and content: "peaks" matrix are the output of the macs2 peaks calling of the ATAC data

growth_protocol: All work presented here was approved by the Human Stem Cell Bank Steering Committee and adheres to the regulations of the UK Code of Practice for the Use of Human Stem Cell Lines.  Shef6 human ESCs were cultured on Matrigel-coated plates in mTESR medium (05825, STEMCELL Technologies) at 37°C, 20% O2, 5% CO2. Plates were coated with 1.6% growth-factor reduced Matrigel (356230, BD Biosciences) dissolved in DMEM/F12 (21331-020, Life Technologies) for 1 hour at at 37°C. hESCs were passaged with TrypLE (12604013, ThermoFisher Scientific). For the first 24 hours after passaging, 10 µM ROCK inhibitor Y-27632 (72304, STEMCELL Technologies) was added. Medium was changed every 24 hours. Cells were routinely tested for mycoplasma contamination by PCR (6601, Takara Bio). To convert primed hESCs to RSeT or PXGL culture conditions, cells were passaged to mitomycin-C inactivated CF-1 MEFs (3x103 cells/cm2; GSC-6101G, Amsbio) in media consisting of DMEM/F12 with 20% Knockout Serum Replacement (10828010, ThermoFisher Scientific), 100µM β-mercaptoethanol (31350-010, Thermo Fisher Scientific), 1x GlutaMAX (35050061, Thermo Fisher Scientific), 1x non-essential amino acids, 1x penicillin-streptomycin and 10ng/ml FGF2 (Department of Biochemistry, University of Cambridge) and 10µM ROCK inhibitor Y-27632 (72304, STEMCELL Technologies). For RSeT cells media was switched to RSeT media after 24 hours (05978, STEMCELL Technologies). Cells were maintained in RSeT and passaged as above every 4-5 days. For PXGL cells, conversion was performed as previously described (Bredenkamp, N. et al. 2019). Briefly, cells were cultured in 5% O2, 7% CO2 and media was switched to chemical resetting media 1 (cRM-1) consisting of N2B27 media supplemented with 1µM PD0325901 (University of Cambridge, Stem Cell Institute), 10ng/mL human recombinant LIF (300-05, PeproTech), and 1mM Valproic Acid. N2B27 contains 1:1 DMEM/F12 and Neurobasal A (10888-0222, Thermo Fisher Scientific) supplemented with 0.5x B27 (10889-038, Thermo Fisher Scientific), 0.5x N2 (made in house), 100µM β-mercaptoethanol, 1x GlutaMAX and 1x penicillin-streptomycin. cRM-1 media was changed every 48h for 4 days, after which media was changed to PXGL. PXGL media consists of N2B27 supplemented with 1µM PD0325901, 10ng/mL human recombinant LIF, 2µM Gö6983 (2285, Tocris) and 2µM XAV939 (X3004, Merck). PXGL cells were passaged every 4-6 days using TrypLE (12604013, Thermo Fisher Scientific) for 3 min. 10µM ROCK inhibitor Y-27632 and 1µL/cm2 Geltrex (A1413201, Thermo Fisher Scientific) were added at passage for 24 hours. For yolk sac-like cell or trophoblast differentiation, RSeT cells were passaged onto matrigel coated IBIDI chamber slides. 24 hours later, media was switched to ‘ACL’ (100ng/ml Activin-A, Qk001, QKINE, 3mM CHIR99021, 72052, STEMCELL Technologies, and 10ng/ml human LIF) for hypoblast induction or ‘PA’ (1mM PD0325901 and 1mM A83-01, 72022, STEMCELL Technologies) with or without 500nM lysophosphatidic acid – LPA (3854, Tocris).

extract_protocol:
To collect post-implantation embryo models for single cell sequencing, correctly organized embryoids at day 4, 6 and 8 were picked visually and washed through PBS twice in a 4-well dish before transfer to TrypLE. Samples were agitated by pipetting every 5 minutes for 10-20 minutes until dissociated. Enzymatic activity was inactivated through addition of 20% FBS in PBS at 2x volume. Cells were collected in a falcon tube, pelleted, and resuspended in freeze buffer consisting of 50 mM Tris at pH 8.0 (15-567-027, Fisher Scientific), 25% glycerol (G5516, Sigma-Aldrich), 5 mM Mg(OAc)2 (63052, Sigma-Aldrich), 0.1mM EDTA (15575020, ThermoFisher Scientific), 5mM DTT (R0861, ThermoFisher Scientific), 1x protease inhibitor cocktail (P8340, Sigma-Aldrich), 1:2500 dilution of superasin (AM2694, Invitrogen). For cell lines, 10,000 cells were counted, pelleted, resuspended in the freeze media above, snapped frozen in liquid nitrogen then stored at -80*C. For nuclei isolation and library construction, low input nuclei isolation protocol from 10x Genomics was performed. Briefly, frozen cell pellets were thawed in a 37°C water bath for 30 seconds, centrifuged (500g for 5 minutes at 4°C) to pellet the cells then the supernatant were aspirated. The cell pellets were washed with 200 ul 1x PBS with 0.04% BSA twice, centrifuged and aspirating the supernatant in between washes. Then, chilled lysis buffer (45 ul per sample) was added to the washed cell pellet and placed on ice for 3 minutes, then wash buffer (50 ul per sample) was added.
Washed isolated nuclei were resuspended in a diluted nuclei buffer. In this study, the isolated nuclei were resuspended in 5 ul of diluted nuclei buffer and were directly added to the transposition reaction. All the steps proceeding, 10x Genomics’ Single Cell Multiome ATAC and Gene expression protocol were followed to manufacturer’s specifications and guidelines.
The final libraries were loaded on the NextSeq 2000 using P2 100 cycle kit at 650 pM loading concentration with paired end sequencing following the recommended sequencing reads from 10x Genomics (28/10/10/90 cycles for gene expression libraries and 50/8/24/49 cycles for ATAC libraries).

treatment_protocol: To generate the three-dimensional stem cell-derived model of the post-implantation embryo, RSeT cells between 2 and 6 passages post-conversion to RSeT media were passaged as normal, and the following day (Day -3) the media for extraembryonic-like cells (induced GATA6, induced GATA6-SOX17 or induced GATA3-AP2g) was changed to N2B27 with 5% Knockout Serum Replacement and 1µg/mL DOX. This media was refreshed every 24 hours for 3 days. On day 0 (the day of aggregation), an Aggrewell dish (34415, STEMCELL Technologies) was prepared by pre-coating with anti-adherance solution (07010, STEMCELL Technologies) and centrifuging at 2000g for 5 minutes. Wells were washed twice with PBS prior to the addition of experiment media. This media consists of N2B27 with 5% knockout serum replacement, 1µg/mL doxycycline and 10µM Y-27632. Induced cells and wild type ESCs were enzymatically dissociated 1 hour after addition of 10µM Y-27632 to wells containing cells for post-implantation embryo model generation. Dissociated cells were pelleted and resuspended in experiment media and placed in gelatin-coated wells for MEF depletion. After 15-30 minutes cells were counted, mixed, and plated into an Aggrewell dish with a final calculation of 8 wildtype-ESC, 8 hypoblast-like and 16 trophoblast-like cells plated per microwell in the Aggrewell. On day 1, the media was subjected to two two-third changes of N2B27 with 5% knockout serum replacement and 1µg/mL doxycycline. On day 2, Aggrewells were subjected to a half change with hIVC1 media with 1.25 µg/mL hIGF1 (78022.1 STEMCELL Technologies) and 1µg/mL doxycycline. hIVC1 media consists of Advanced DMEM/F12 (12634-010 ThermoFisher Scientific) supplemented with 20% inactivated FBS (10270106, ThermoFisher Scientific), 1x Glutamax, 1X NEAA, 1x Essential AA, 1x ITS-X, 25U/mL Pen/Strep, 1.8mM Glucose (G8644, Sigma-Aldrich), 0.22% sodium lactate (L7900, Sigma-Aldrich), 8nM b-estradiol (50-28-2, Tocris) and 200ng/mL progesterone (P0130, Sigma-Aldrich). This media is used in half changes each day from day 3. On day 4, aggregates were manually picked using a mouth pipette under a dissecting microscope into individual wells of ultra-low attachment 96 well plates (CLS7007, Corning) in hIVC1 media with IGF1 and doxycycline as above for subsequent culture.

value: Human ESC


title: scATAC_RSeT_Shef6_hESC

description:
single cell 10x multiome (ATAC)
WT_RSeT_cells_atac_fragments.tsv.gz


title: scATAC_Day_6_human_stem_cell_model_exp48

description:
single cell 10x multiome (ATAC)
D6_model_atac_fragments.tsv.gz


title: Telencephalon, building, biol rep 1, capture area C

description: Visium10x Genomics


title: scATAC_Day_4_human_stem_cell_model_exp48

description:
single cell 10x multiome (ATAC)
D4_model_atac_fragments.tsv.gz


title: scRNA_RSeT_induced_GATA6_SOX17_hESC

description:
single cell 10x multiome (RNA)
cell_lines_RNA_matrix.rds


title: scRNA_RSeT_Shef6_hESC


title: scRNA_Day_8_human_stem_cell_model_exp48

description:
single cell 10x multiome (RNA)
human_model_RNA_matrix.rds


title: scRNA_Day_4_human_stem_cell_model_exp48


title: scRNA_RSeT_induced_GATA3_AP2y_hESC


title: DMH, mixed, rep 1 [DMH2]

city: Charlottesville

first: Lizzie

last: Godschall

state: Virginia

address: 1821 Jefferson park Ave, 12

institute: UVA

description: 10X Genomics v3.1

data_processing:
Sequencing reads were demultiplexed with bcl2fastq2 version 2.20.0 to produce fastq files and aligned using cellranger version 5.0.0 with "include introns" function on the mus musculus reference genome refdata-gex-mm10-2020
Cell Ranger h5 files were read into Seurat v4 (Hao et al., 2021 (PMID: 34062119)) in R (version 4.1.0) and RStudio (version 1.4.1717) and merged by brain region (DMH, SCN) for clustering analysis and integration.
Assembly: mm10  (refdata-gex-mm10-2020)
Supplementary files format and content: filtered_feature_bc_matrix.h5 containing feature and barcode matrices from 10X

organism: Mus musculus

source_name: hypothalamic tissue

extract_protocol:
Mice were sacrificed and brains were immediately extracted and dropped into ice cold Hanks’ Balanced Salt Solution (HBSS). After 2 minutes, brains were embedded in low melting point agarose (Precisionary Instruments, Natick, MA) and sectioned at 400 um on a Compresstome VF-200 Vibrating Microtome (Precisionary Instruments, Natick, MA, USA) into DNAse/RNAse free 1x PBS. Hypothalamic sections of interest were immediately collected into RNAprotect (Qiagen, Hilden, Germany) and kept in RNAprotect at 4oC overnight. The next day Lepr-Cre::TdTomato positive cells were visualized using a fluorescent stereoscope (Leica, Wetzlar, Germany). tdTomato fluorescence was used to approximate DMH and SCN boundaries during microdissection of these regions. DMH and SCN microdissected tissue samples were placed into Eppendorf tubes separated by brain region and feeding condition, and stored in -80C until nuclei isolation. DMH and SCN microdissected tissue samples were transferred from a -80oC freezer and into individual 2mL glass dounce homogenizer tubes (Kimble, Vineland, NJ, USA) to be homogenized according to a protocol modified from Habib et al., 2016 (PMID: 27471252). Tissue was homogenized in 1mL of buffer (16mM sucrose, 5mM CaCl, 3mM Mg(Ac)2, 10mM Tris pH 7.8, 0.1mM EDTA, 1% NP40, 1mM beta-mercaptoethanol in H2O) on ice, with 25 passes of pestle A and 25 passes of pestle B. An additional 4mL of buffer was added to the nuclei suspension and placed on ice for 5 minutes. Then 5 mL of 50% OptiPrep Density Gradient Medium [Sigma Aldrich, MO, USA] (30mM CaCl, 18mM Mg(Ac)2, 60mM Tris pH 7.8, 0.1 mM PMSF, 6mM beta-mercaptoethanol in H2O; in 60% (w/v) solution of iodixanol in sterile water) was added to nuclei on ice and inverted 10 times to mix. The nuclei suspension was layered onto 10 mL of 29% OptiPrep solution (Buffer + 50% OptiPrep) in a 38.5 mL Ultra-Clear tube (Beckman-Coulter, CA, USA) before being centrifuged at 7,333g for 30 minutes at 4oC. Supernatant was discarded and the nuclei pellet was resuspended in 1x PBS + 1% BSA (Sigma-Aldrich, MO, USA) + 2 mM Mg2+ + 0.1% RNase inhibitor (Sigma-Aldrich, MO, USA) for 15 minutes on ice. The nuclei suspension was pipetted through a 20 micron mesh filter along with 2 drops of propidium iodide (PI) Ready Flow reagent (Thermo Fisher, MA, USA) and immediately taken on ice to be FACS sorted using an SH800 (Sony, Tokyo, Japan) cell sorter. Sorting was gated to select for PI+ single nuclei. Nuclei were sorted through a 70 micron nozzle into a 2mL LoBind collection tube (VWR, PA, USA) containing 18.8uL of RT Reagent B from the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1. The remaining components of the 10X Step 1 mastermix were then gently mixed with the contents of the FACS collection tube and loaded into the 10X Genomics Chromium Controller Chip G.
The single-nuclei samples were processed into sequencing libraries using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 according to the manufacturer’s protocol (version 3.1, revision D). After generation of the GEMs (Gel Bead-In EMulsions) and reverse transcription of poly-adenylated mRNA, cDNA was amplified (10-14 cycles), enzymatically fragmented, and ligated to Illumina adapters. Sequencing libraries were indexed, size selected for 400-600bp using SPRIselect (Beckman Coulter, Indianapolis, IN, USA), and quantified by Qubit (v4.0, 1X high-sensitivity dsDNA kit, Thermo Scientific) and Bioanalyzer (Agilent, Santa Clara, CA, USA). Size-corrected library concentrations were used to pool libraries for equimolar representation. The pooled concentration was measured by KAPA Library Quant qPCR according to the manufacturer's instructions (KAPA Biosciences, Wilmington, MA) and by Qubit. Library pools were sequenced using a P100 cycle kit on the NextSeq 2000 (Illumina, CA, USA) in the University of Virginia School of Medicine Genome Analysis and Technology Core, RRID:SCR_018883. The sequencing structure was as follows: Read 1 was 28 bp (16 bp barcode, 12 bp UMI), Read 2 was 98 bp (cDNA) and Index 1 was 8 bp (single index). Overall, we had 7 DMH and 5 SCN sequencing library pools. 10X Batch 1 & 2 contained mixed pools of all feeding conditions, but 10X Batch 3 contained a unique feeding condition per library pool
snRNA-seq using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1

treatment_protocol: Indirect calorimetry in the CLAMS system (Columbus Instruments) was used to evaluate whole-body states and ambulatory locomotor activity during ad libitum, overnight fasted, or time and calorie restricted scheduled feeding (SF). All mice were on a 12:12 light-dark cycle with ad libitum access to food and water. Lepr-cre::tdTomato mice were singly housed and acclimated to the CLAMS for 3 days prior to experiment start. The night before scheduled feeding began, the SF cohort was fasted and cages were changed. Using both males and females, one cohort of mice was given 2-3 grams of SCD at zeitgeber time (ZT) 6 for 10 days. The overnight fasting cohort had ad libitum food access until the night before sacrifice, when food was removed and cages were changed. We repeated this experiment a total of 3 times with 2 mice per condition (n = 6 / condition total).

value: hypothalamic tissue

value: dorsomedial hypothalamus

tag: treatment

value: mixed groups

value: 13-21 weeks (at sacrifice)

tag: molecule type

value: nuclear poly-A RNA


title: DMH, mixed, rep 2 [DMH4]

description: 10X Genomics v3.1

tag: age


title: SCN, scheduled feeding, rep 3 [SCN5]

description: 10X Genomics v3.1

tag: tissue

value: suprachiasmatic nucleus

value: scheduled feeding


title: DMH, mixed, rep 1 [DMH1]

description: 10X Genomics v3.1

tag: genotype


title: SCN, ad libitum, rep 3 [SCN3]

description: 10X Genomics v3.1

value: ad libitum


title: SCN, fasted, rep 3 [SCN4]

description: 10X Genomics v3.1

value: fasted


title: DMH, mixed, rep 2 [DMH3]

description: 10X Genomics v3.1


title: SCN, mixed, rep 2 [SCN2]

description: 10X Genomics v3.1


title: scATAC_RSeT_induced_GATA3_AP2y_hESC

description:
single cell 10x multiome (ATAC)
g3_ap2y_induced_cells_atac_fragments.tsv.gz


title: Telencephalon, not building, biol rep 1, capture area A

description: Visium10x Genomics


title: scRNA_Day_6_human_stem_cell_model_exp48


title: DMH, ad libitum, rep 3 [DMH5]

description: 10X Genomics v3.1


title: DMH, scheduled feeding, rep 3 [DMH7]

description: 10X Genomics v3.1


title: DMH, fasted, rep 3 [DMH6]

description: 10X Genomics v3.1


title: SCN, mixed, rep 1 [SCN1]

description: 10X Genomics v3.1


title: Hepatocyte_irradiated_AL_40Weeks, #1

type: RNA

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression in 40Weeks irradiated AL hepatocyte

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20120224). Signal intensity data were normalized using Lowess normalization. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (MB-1; Funabashi Farm, Chiba, Japan) until 7-week-old, then changed to AL (95kcal/mouse/week) diet and CR (65kcal/mouse/week) diet (Funabashi Farm, Chiba, Japan), and sterilized water ad libitum.

extract_protocol: RNA was prepared using the AllPrep DNA/RNA Mini kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Mice were left untreated or were subjected to whole-body X-ray-irradiation (3.8 Gy, 0.6 Gy/min) at 1 week of age, then sampling at 7, 8, 10, and 40 weeks.

value: Hepatocyte

tag: time

value: 40 weeks


title: Hepatocyte_irradiated_AL_40Weeks, #3

tag: cell type


title: Hepatocyte_nonirradiated_AL_40Weeks, #3

description: Gene expression in 40Weeks nonirradiated AL hepatocyte


title: Hepatocyte_nonirradiated_AL_40Weeks, #2


title: Hepatocyte_irradiated_CR_40Weeks, #3

description: Gene expression in 40Weeks irradiated CR hepatocyte


title: Hepatocyte_nonirradiated_AL_40Weeks, #1


title: Hepatocyte_irradiated_AL_40Weeks, #2


title: Hepatocyte_irradiated_AL_10Weeks, #3

description: Gene expression in 10Weeks irradiated AL hepatocyte

value: 10 weeks


title: Hepatocyte_irradiated_CR_40Weeks, #2


title: Hepatocyte_nonirradiated_AL_10Weeks, #3

description: Gene expression in 10Weeks nonirradiated AL hepatocyte


title: Hepatocyte_nonirradiated_CR_40Weeks, #2

description: Gene expression in 40Weeks nonirradiated CR hepatocyte


title: Hepatocyte_irradiated_CR_40Weeks, #1


title: Hepatocyte_irradiated_AL_10Weeks, #1


title: Hepatocyte_nonirradiated_CR_10Weeks, #1

description: Gene expression in 10Weeks nonirradiated CR hepatocyte


title: Hepatocyte_irradiated_AL_8Weeks, #3

description: Gene expression in 8Weeks irradiated AL hepatocyte

value: 8 weeks


title: Hepatocyte_nonirradiated_AL_8Weeks, #3

description: Gene expression in 8Weeks nonirradiated AL hepatocyte


title: Hepatocyte_nonirradiated_AL_10Weeks, #1


title: Hepatocyte_nonirradiated_CR_10Weeks, #3


title: Hepatocyte_nonirradiated_CR_40Weeks, #3


title: Hepatocyte_irradiated_CR_10Weeks, #2

description: Gene expression in 10Weeks irradiated CR hepatocyte


title: Hepatocyte_irradiated_AL_10Weeks, #2


title: Hepatocyte_irradiated_CR_10Weeks, #3


title: Hepatocyte_irradiated_AL_8Weeks, #1


title: Hepatocyte_irradiated_AL_8Weeks, #2


title: Hepatocyte_nonirradiated_CR_40Weeks, #1


title: Hepatocyte_nonirradiated_AL_8Weeks, #1


title: Hepatocyte_nonirradiated_AL_10Weeks, #2


title: Hepatocyte_irradiated_CR_10Weeks, #1


title: Hepatocyte_nonirradiated_CR_10Weeks, #2


title: Hepatocyte_irradiated_CR_8Weeks, #1

description: Gene expression in 8Weeks irradiated CR hepatocyte


title: Hepatocyte_nonirradiated_CR_8Weeks, #3

description: Gene expression in 8Weeks nonirradiated CR hepatocyte


title: CALU6 DMSO 48h-1

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

department: MGH Cancer Center

institute: Harvard Medical School

data_processing:
FASTQ files were then processed using RNA Express module (Illumina) and raw counts were further processed in R (v.4.0.3) and edgeR to obtain relative gene expression.
Assembly: hg38
Supplementary files format and content: Excel file with normalized counts matrix of each sample

source_name: Lung

growth_protocol: CALU6 cells were grown in RPMI-1640 (Corning) media containing 10% FBS (Corning), Penicillin-Streptomycin (100 mg/ml, Millipore) and 1% GlutaMax (Gibco).

extract_protocol:
RNA was isolated by RNeasy Kit (Qiagen) following the manufacturer’s instructions and digested with DNase (Qiagen) from n=2 samples per condition.
mRNA-seq libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) kit according to manufacturer’s instructions. Libraries were then quantified by Kappa Library Quantification (Roche), pooled, and sequenced by single-end 75 base pairs using the Illumina NextSeq 500 platform.

treatment_protocol: CALU6 cells were cultured in 6-well plates (2.5 x 10e5 cells/well) and treated with KI696 (1 µM) or vehicle control for 24 or 48 hrs.

value: Lung

tag: cell line

value: NSCLC

value: WT

value: DMSO


title: CALU6 DMSO 24h-2


title: CALU6 DMSO 48h-2


title: CALU6 KI696 1 µM 48h-1


title: Hepatocyte_nonirradiated_AL_8Weeks, #2


title: Hepatocyte_irradiated_CR_8Weeks, #2


title: CALU6 KI696 1 µM 24h-1


title: CALU6 KI696 1 µM 48h-2


title: CALU6 DMSO 24h-1


title: Hepatocyte_nonirradiated_CR_8Weeks, #2


title: Hepatocyte_irradiated_7Weeks, #3

description: Gene expression in 7Weeks irradiated hepatocyte

value: irradiated

value: 7 weeks


title: Hepatocyte_nonirradiated_CR_8Weeks, #1


title: Hepatocyte_nonirradiated_7Weeks, #2

description: Gene expression in 7Weeks nonirradiated hepatocyte

value: nonirradiated


title: Hepatocyte_irradiated_7Weeks, #2


title: MDA-MB-231 shAMPKα2, Uninduced, Attached, 24 h

city: Bengaluru

first: Annapoorni

last: Rangarajan

state: Karnataka

address: DBG, Biological Sciences Division, IISc, CV Raman Road

department: Developmental Biology and Genetics

country: India

institute: Indian Institute of Science

data_processing:
Human genome (hg38) fastq file and genecode.v32 GTF were downloaded (from https://www.gencodegenes.org/human/release_32.html) and used as a reference genome.
STAR (v 2.7.1a) was used to generate indexed genome file with parameter options (--sjdbOverhang 74 bp and gencode.v32.gtf file).
All paired-end RNA-seq FastQ reads were aligned with STAR generated indexed genome with (-outSAMtype BAM SortedByCoordinate, --outSAMunmapped Within) optional parameters
Readcounts were generated using featureCounts (v1.5.0-p1) with aligned BAM files generated by STAR, with 'gene' as extraction feature type. Two read count files were generated for 'gene_name' and 'gene_id' group meta-features.
Feature counts were exported for quality control and normalization using edgeR (v) in R.
Fold change values were calculated by dividing normalized readcounts of sus_24 by att_24 conditions and LFC values were calculated by taking log2 of fold change values.
Z-score normalization was performed on the LFC values and Z-score > 2 was considered as upregulated and Z-score  < -2 was considered as downregulated genes.
Assembly: GRCh38.p13.primary_assembly, gencode.v32.primary_assembly.annotation.gtf
Supplementary files format and content: Processed files contain Featurecounts generated read counts in BED6 format (tab-delimited text file) for each sample.

source_name: Metastatic Breast Cancer

growth_protocol: MDA-MB-231 cells stably expressing shRNA against AMPKα2 in pTRIPZ backbone under Tet-On promoter were cultured in DMEM (Sigma-Aldrich) supplemented with 10% FBS with antibiotics and incubated in a 5% CO2 incubator at 37˚C. These cells were cultured without doxycycline induction for this study.

extract_protocol:
RNA was extracted from human cells using TRIzol and Qiagen RNeasy mini kit. 1 µg of Total RNA was used for library preparation.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® Ultra™ Directional RNA Library Prep Kit following Manufacturer’s protocol at Genotypic Technology Pvt. Ltd., Bangalore, India.

treatment_protocol: For suspension culture, attached cells were trypsinised, seeded onto 2% Noble Agar-coated plates and incubated for 24 h.

value: Metastatic Breast Cancer

value: TNBC

value: pTRIPZ-shAMPKalpha2 under Tet-On promoter


title: Hepatocyte_irradiated_7Weeks, #1


title: MDA-MB-231 shAMPKα2, Uninduced, Suspension, 24 h

value: Matrix-deprivation


title: Hepatocyte_nonirradiated_7Weeks, #3


title: TC16_S16

city: Los Angeles

first: Meng

last: Li

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

description:
TC16_S16
HBVHDVcoInfection_rawCounts.txt

data_processing:
RNA-Seq data were analyzed with Partek Flow version 10.0.21 (Partek Inc, Chesterfield, MO)
Raw sequencing reads were trimmed from both ends with the Quality Score method (bases with a quality score of <20 were trimmed from both ends and trimmed reads shorter than 25 nucleotides were excluded from downstream analyses)
Trimmed reads were mapped to human genome hg38 using Star version 2.7.3a with default parameter settings and using Gencode v36 annotation as guidance
Aligned reads were quantified to Gencode v36 annotation using the Partek E/M method
Genes with fewer than 10 raw reads in all samples were excluded from downstream analysis. Raw read counts were normalized using upper quartile normalization with an offset of 1.  Normalized counts were analyzed for differential expression using the Partek gene-specific analysis method.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: Human Hepatocytes

extract_protocol:
Total cellular RNA were extracted with Quick-RNA miniprep kit according to the manufacture's protocol followed by RNA quality assessment using Agilent 2100 bioanalyzer.
cDNA library were synthesized using NEB Next Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacture's protocol.

value: Human Hepatocytes

value: HBV GTA HDV GT1

value: HBV-HDV Co-Infection


title: CALU6 KI696 1 µM 24h-2


title: TC14_S14

description:
TC14_S14
HBVHDVcoInfection_rawCounts.txt

value: HBV GTA

value: HBV Mono-Infection


title: TC15_S15

description:
TC15_S15
HBVHDVcoInfection_rawCounts.txt


title: TC13_S13

description:
TC13_S13
HBVHDVcoInfection_rawCounts.txt


title: TC4_S4

description:
TC4_S4
HDVmonoInfection_rawCounts.txt

value: HDV GT1

value: HDV Mono-Infection


title: TC11_S11

description:
TC11_S11
HBVHDVcoInfection_rawCounts.txt

value: Mock Infection


title: TC12_S12

description:
TC12_S12
HBVHDVcoInfection_rawCounts.txt


title: TC3_S3

description:
TC3_S3
HDVmonoInfection_rawCounts.txt


title: TC2_S2

description:
TC2_S2
HDVmonoInfection_rawCounts.txt


title: TC1_S1

description:
TC1_S1
HDVmonoInfection_rawCounts.txt


title: Treg, input

city: La Jolla

first: Jesse

middle: R

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

data_processing:
Reads were aligned using BWA MEM to the mm9 genome. Peaks were called with MACS2.
Assembly: mm9
Supplementary files format and content: narrowPeak

source_name: Thymus

extract_protocol:
10 million Treg or Tcon cells were fixed in 1% formaldehyde for 10 min at room temperature, followed by the addition of glycine to quench the excess crosslinker. Cells were then washed in cold PBS, pelleted, flash-frozen in liquid nitrogen and  stored at −80 °C. Cell pellets were thawed on ice and incubated in cell lysis buffer (50 mM Hepes-KOH, pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) for 10 min. The isolated nuclei were washed with wash buffer (10 mM Tris-HCl, pH 8, 1 mM EDTA, 0.5 mM (ethylenebis(oxonitrilo)) tetra-acetate, 200 mM NaCl) and resuspended in shearing buffer (0.1% sodium dodecylsulfate (SDS), 1 mM EDTA, 10 mM Tris-HCl, pH 8). Nuclear chromatin was sheared in a Covaris E229 sonicator for 10 min to generate DNA fragments between ~200 bp and 1,000 bp. After clarification of insoluble material by centrifugation, the chromatin was incubated with CTCF antibody overnight at 4 °C. The next day, the antibody-bound DNA was incubated with Protein A + G Dynabeads (Invitrogen, catalog no. 10015D) in ChIP buffer (50 mM Hepes-KOH, pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), washed and treated with proteinase K and RNase A. Crosslinking was reversed by incubation at 55 °C for 2 h.
Purified ChIP DNA was used for library generation (NuGen Ovation Ultralow Library System v.2) according to the manufacturer’s instructions. ChIP–seq libraries were sequenced by an Illumina HiSeq2500 sequencer.

value: Thymus

tag: chip antibody


title: H3K4me3 4

city: Worcester

first: Sneha

last: Shah

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

institute: UMASS CHAN MEDICAL SCHOOL

data_processing:
For ChIP-seq data analysis, alignments were performed with Bowtie2 (2.1.0) using the GRCh38 (hg38) version 34 genome, duplicates were removed with Picard and TDF files for IGV viewing were generated using a ChIP-seq pipeline from DolphinNext (34). The broad peaks for H3K36me3 ChIP-Seq were called using the broad peak parameter MACS2. Narrow peaks for H3K4me3 ChIP were called using the narrow parameter in MACS2. deepTools (Ramírez et al., 2016) was used to plot heatmaps and profiles for genic distribution of H3K36me3 and H3K4me3 ChIP signals over input. IGV tools (2.6.2) were used for visualizing TDF files and all tracks shown were normalized for total read coverage.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings. broadPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak, broadPeak (except for Input sample)

source_name: Human Leukocytes

extract_protocol:
Eight mL fresh blood was collected from FXS male (N=10) and age-matched typically developing males (N=7) individuals (See Supplemental Table 1) in a BD vacutainer CPT (Cell Preparation Tube with sodium citrate- blue top tube, Becton Dickinson #REF362761). The tube was gently inverted 5 times and the sample was centrifuged for 25 minutes at 1500-1800 RCF at room temperature. The tubes were then inverted to collect the lymphocytes and other mononuclear cells resuspended in the upper liquid phase in a new 15mL tube. The samples were centrifuged again for 10 minutes at 300 RCF to obtain the PBMC (peripheral blood mononuclear cells) pellet. The PBMCs were rinsed with 1X Dublecco’s phosphate buffered saline w/o calcium or magnesium (D-PBS) (Invitrogen #14190-094). The PBMC pellet was resuspended in 250uL ice-cold D-PBS with protease inhibitors. Chromatin isolation and sequencing was performed as previously described (3). Briefly the cells were cross-linked with 1% formaldehyde and quenched with 150mM glycine. After centrifugation at 2000g for 10 min at 40C the cells were lysed. After homogenization the nuclei were harvested by centrifugation at 2000g for 5min at 40C. The nuclei were lysed by incubating for 20 mins on ice in nuclear lysis buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA). 0.5% SDS was added and the samples sonicated on a Bioruptor® sonicator at high power settings for 9 cycles (sonication: 30 sec on, 90 sec off) of 15min each at 4°C. The samples were centrifuged and diluted to adjust the SDS concentration to <0.1%. 10% of each sample was used as input. The remainder of the samples were divided into two and incubated with protein G dynabeads coupled overnight at 40C with antibodies against H3K36me3 (Abcam ab9050, 5μg per ChIP) or H3K4me3 (Active Motif- 39159, 5 μg per ChIP). After IP, the beads were washed and chromatin and de-crosslinked overnight at 65°C. After RNAse and proteinase K treatment the DNA was purified.
ChIP-Seq libraries were prepared by performing the following steps: ends repair using T4 DNA polymerase, A’ base addition by Klenow polymerase and Illumina adapter ligation using T4 Polynucleotide kinase from New England Biolabs (NEB). The library was PCR amplified using multiplexing barcoded primers. The libraries were pooled with equal molar ratios, denatured, diluted, and sequenced with NextSeq 500/550 High Output Kit v2.5 (Illumina, 75bp paired-end runs,) on a Nextseq500 sequencer (Illumina).

tag: gender

value: Male

value: TD

value: Human Leukocytes

value: H3K4me3 (Active Motif- 39159)


title: H3K4me3 3

value: FXS


title: Inp 3


title: Inp 4


title: Inp 5


title: H3K4me3 5


title: H3K4me3 6


title: Inp 6


title: Inp 2


title: CD4 T-cell,  CTCF ChIP-seq

value: CTCF


title: Treg, CTCF ChIP-seq

value: CD45+CD4+CD8-CD25+Foxp3-Thy1.1+ DSM mutant T-cells


title: Liver_cytoplasm_polyA

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
vast-tools was used to map the reads to a library of mRNAs using vast-tools align --expr, for either -sp hg38 or -sp mm10
Assembly: mm10 and hg38

molecule: cytoplasmic RNA

source_name: Liver

growth_protocol: Described in Gohr et al, 2022

extract_protocol:
Described in Gohr et al, 2022
Described in Gohr et al, 2022

treatment_protocol: Described in Gohr et al, 2022

value: Liver


title: H3K36me3 6

value: H3K36me3 (Abcam ab9050)


title: H3K4me3 2


title: CD4 T-cell,  input


title: H3K36me3 3


title: H3K36me3 4


title: H3K36me3 2


title: Cortex_cytoplasm_polyA

source_name: Cortex

value: Cortex


title: H3K36me3 5


title: WT-DP-2

city: Shenzhen

first: Wen

middle: Ting

address: No,1120,LianHua Road,FuTian District

institute: Shenzhen PKU-HKUST Medical Center

data_processing:
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases 2.5.1.
Alignment with Ribosome RNA (rRNA). Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation
Alignment with Reference Genome. An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1in a reference based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software
Assembly: Ensembl_release104
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each Sample

source_name: thymus

growth_protocol: DP  thymocytes from WT and Paxbp1 cKO mice were sorted by flow cytometry.

extract_protocol:
Total RNA was extracted from DP thymocytes using the RNeasy Kit (Qiagen, 74004) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: thymus

value: Primary cell

value: DP thymocytes

value: WT (Paxbp1fl/fl)

value: no treatment


title: WT-DP-1


title: WT-DP-3


title: Lck-KO-DP-2

value: Paxbp1 cKO (Paxbp1fl/fl Lckcre)


title: Lck-KO-DP-3


title: Lck-KO-DP-1


title: Hepatocyte_nonirradiated_7Weeks, #1

value: Hepatocyte

value: nonirradiated

value: 7 weeks


title: Cerebellum_cytoplasm_polyA

source_name: Cerebellum

value: Cerebellum


title: Liver_chromatin_ribominus

description: Chromatin associated RNA


title: Cortex_chromatin_ribominus

description: Chromatin associated RNA


title: nchip_Olfr1507mOSNs_H3K9me3_r1

city: New York

first: Elizaveta

last: Bashkirova

state: NY

address: 3227 Broadway

department: Biochemistry

institute: Columbia University

data_processing:
For RNA-seq, native ChIP-seq, omni ATAC-seq and CUT&RUN adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). The RNAseq libraries that were sequenced 75PE were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20, single cell RNA-seq were aligned with the Drop-seq pipeline (http://mccarrolllab.org/dropseq/). Native ChIP-seq, omni-ATAC-seq, and CUT&RUN  reads were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000).  HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Dip-c data was aligned according to the Dip-C pipeline (https://github.com/tanlongzhi/dip-c).
Filtering:  We filtered out unmapped reads and reads with a mapping quality below q30 with Samtools for RNA-seq, native ChIP-seq, omni-ATAC-seq, Cut&RUN and HiC and below q255 for single cell RNA-seq
For RNA-seq, native ChiP-seq, omni-ATAC-seq and Cut&RUN  BigWig files were generated using HOMER. For single cell RNA-seq digital expression matrices (DGE) were generated with drop-seq. For HiC ".cool" contact matixes were generated with cooler.
genome build: mm10
processed data files format and content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: GFP+ cells from the olfactory epithelium

growth_protocol: Used adult >8 weeks mice

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K9me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ cells were isolated with FAC-sorting

tag: genotype/variation

tag: tissue/cell type

value: Olfr1507 expressing mature olfactory sensory neurons (mOSN)


title: TDLN3

first: Pin-Ji

last: Lei

address: 100 Blossom Street

department: Department of Radiation Oncology

description: Single-cell RNA sequencing

data_processing:
Cellranger (Version 3.0.2, https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) was used to pre-process the fastq-format raw data. Cellranger aggr was used to combine data from different runs.
Seurat (Butler et al., 2018; Stuart et al., 2019) (Version 3.1.3, https://satijalab.org/seurat/) was used to perform the graph-based clustering and analysis of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: CellRranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: 4T1 breast cancer draining inguinal lymph node

growth_protocol: Six to ten week old, female Balb/c mice were housed in the E.L Steele Laboratories animal facility at Massachusetts General Hospital.

extract_protocol:
The primary tumors were cut into 1-2 mm pieces and dissociated into single cells. All analyzed lymph nodes were dissociated into single cells with digestion buffer (200 ug/ml collagenase I, 800 ug/mL Dispase, 100ug / ml DNase I). All samples used ACK buffer (Thermo Fisher) to lyse red blood cells and had the cell concentration and viability tested using a Nadia instrument (Dolomite Bio). The loading quantity of viable cells for 10x Genomics platform was estimated to capture around 5000 cells.
10x genomics Chromium Single Cell 3' Reagent (v2 Chemistry) was used for library preparation.
10x genomics single-cell mRNA sequencing.

treatment_protocol: 1x10e5 4T1 cells were injected into the fourth mammary fat pad (draining to the inguinal lymph node) in a volume of 25-50 ul per mouse.

value: Balb/c

tag: Sex

value: female

value: 6-10 week old

value: 4T1 murine breast cancer cell (TDLN)

tag: library sequencing

value: NextSeq High Output PE26/98


title: nchip_Olfr1507mOSNs_H3K79me3_r1

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)


title: nchip_Ngn1GFPbright_H3K9me3_r1

source_name: TdTomato - GFP +(bright) cells from the olfactory epithelium

growth_protocol: Newborn mice (P2-P4) were injected  IP with tamoxifen. 48 hours later mice were sacrificed and cells were collected

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting

value: immature olfactory sensory neurons (iOSN)


title: nchip_Ngn1GFPbright_H3K79me3_r1


title: nchip_Ngn1GFPdim_H3K9me3_r1

source_name: TdTomato - GFP +(dim) cells from the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting

value: mature olfactory sensory neurons (mOSN)


title: nchip_Mash1CreER_Ngn1GFPbright_H3K9me3_r1

source_name: TdTomato + GFP +(bright) cells from the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting

value: immediate neuronal progenitors (INP)


title: Cerebellum _chromatin_ribominus

description: Chromatin associated RNA


title: Primary tumor

description: Single-cell RNA sequencing

source_name: 4T1 primary tumor

value: 4T1 murine breast cancer cell (primary tumor)


title: nchip_MOE_H3K79me3_r1

source_name: Cells from the olfactory epithelium

extract_protocol:
Nuclei were extracted with dounce homogenization, then digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation and the olfactory epithelium was dissected.

value: WT

value: olfactory epithelium cells


title: nchip_Ngn1GFPdim_H3K79me3_r1


title: nchip_Mash1CreER_H3K9me3_r1

source_name: TdTomato + GFP- cells from the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP- tdTomato + cells were isolated with FAC-sorting

value: globose basal cells (GBC)


title: nchip_Mash1CreER_H3K79me3_r1


title: scRNAseq_Replicate2_Q3_Pool

data_processing:
Library strategy: scRNA-seq
For RNA-seq, native ChIP-seq, omni ATAC-seq and CUT&RUN adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). The RNAseq libraries that were sequenced 75PE were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20, single cell RNA-seq were aligned with the Drop-seq pipeline (http://mccarrolllab.org/dropseq/). Native ChIP-seq, omni-ATAC-seq, and CUT&RUN  reads were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000).  HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Dip-c data was aligned according to the Dip-C pipeline (https://github.com/tanlongzhi/dip-c).
Filtering:  We filtered out unmapped reads and reads with a mapping quality below q30 with Samtools for RNA-seq, native ChIP-seq, omni-ATAC-seq, Cut&RUN and HiC and below q255 for single cell RNA-seq
For RNA-seq, native ChiP-seq, omni-ATAC-seq and Cut&RUN  BigWig files were generated using HOMER. For single cell RNA-seq digital expression matrices (DGE) were generated with drop-seq. For HiC ".cool" contact matixes were generated with cooler.
genome build: mm10
processed data files format and content: DGE (digital expression matrix) with counts of UMIs (unique transcripts) for all detected genes for in each of the cells (identified by barcode). Also txt file containing the barcode and cell identity and other metadata for each cell.

source_name: 4 populations: TdTomato + GFP-, TdTomato + GFP +(bright), TdTomato - GFP +(bright), TdTomato - GFP +(dim)

extract_protocol:
Cells were FAC-sorted into 384 well plates and flash frozen
scRNA-seq libraries were prepared in 384 well plates by the New York Genome Center  using a TSO approach. Each well contained unique cell and molecular barcodes. After barcoding cDNA from wells were combined itnto 4 pools.

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The ventral segments (zone 3/4/5)  and dorsal segments (zone 1/2 ) of the olfactory epithelium were dissected separately.They were transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then 4 cell populations were isolated with FAC-sorting into a 384 well plate, retaining information about the zone and fluorescent identity of each cell.

value: 4 populations:globose basal cells (GBC), immediate neuronal progenitors (INP), immature olfactory sensory neurons (iOSN)


title: nchip_Mash1CreER_Ngn1GFPbright_H3K79me3_r1


title: scRNAseq_Replicate2_Q4_Pool


title: scRNAseq_Replicate1_Q4_Pool


title: scRNAseq_Replicate2_Q1_Pool


title: scRNAseq_Replicate1_Q3_Pool


title: scRNAseq_Replicate1_Q1_Pool


title: RNAseq_Zone5_Ngn1GFPdim_r1

source_name: TdTomato - GFP +(dim) cells from zone5 of the olfactory epithelium

extract_protocol:
Cells were lysed in Trizol (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
RNA: RNA-seq libraries were prepared using Ovation RNA-Seq System 1-16 for Model Organisms (Nugen 0348)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting


title: scRNAseq_Replicate1_Q2_Pool


title: RNAseq_Zone5_Ngn1GFPdim_r2


title: scRNAseq_Replicate2_Q2_Pool


title: RNAseq_Zone5_Ngn1GFPbright_r2

source_name: TdTomato - GFP +(bright) cells from zone5 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting


title: RNAseq_Zone5_Ngn1GFPbright_r1

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation.The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting


title: RNAseq_Zone5_Mash1CreER_Ngn1GFPbright_r1

source_name: TdTomato + GFP +(bright) cells from zone5 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting


title: RNAseq_Zone5_Mash1CreER_Ngn1GFPbright_r2


title: RNAseq_Zone1_Ngn1GFPdim_r2

source_name: TdTomato - GFP +(dim) cells from zone1 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting


title: RNAseq_Zone5_Mash1CreER_r2

source_name: TdTomato + GFP- cells from zone5 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP- tdTomato + cells were isolated with FAC-sorting


title: RNAseq_Zone5_Mash1CreER_r1


title: RNAseq_Zone1_Ngn1GFPbright_r2

source_name: TdTomato - GFP +(bright) cells from zone1 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting


title: RNAseq_Zone1_Ngn1GFPdim_r1


title: RNAseq_Zone1_Mash1CreER_Ngn1GFPbright_r2

source_name: TdTomato + GFP +(bright) cells from zone1 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting


title: RNAseq_Zone1_Mash1CreER_r2

source_name: TdTomato + GFP- cells from zone1 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP- tdTomato + cells were isolated with FAC-sorting


title: RNAseq_Zone1_Mash1CreER_Ngn1GFPbright_r1


title: RNAseq_Zone1_Mash1CreER_r1

source_name: TdTomato + GFP- cells from zone1of the olfactory epithelium


title: Epithelium_TCF_1

city: Mainz

first: Natalia

last: Soshnikova

address: Langenbeckstr. 1

department: Institute for Molecular Medicine

country: Germany

institute: University Medical Centre of the Johannes Gutenberg University

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bclfastq (v.2.19.1).
Fastq files were mapped with STAR_v2.5.2b onto the iGenomes mm9 reference.
Bigwig tracks were generated using Deeptools
Reads per gene were counted using featureCounts v. 1.5.1. Read counts are based on uniquely mapping reads. For mapping as well as read counting the reference gene model downloaded from UCSC on March 6th 2013 was used (as provided with iGenomes).
The differential expression analysis was performed using Bioconductor release 3.6/DESeq2 v1.18.1 using standard parameters for testing and modeling as well as independent filtering. RPKM values were calculated per gene based on on FPM (robust counts per million mapped fragments) values provided by DESeq2 and divided by the gene length and multiplied with 1000.
Genes were deemed sign. diff. regulated with an FDR below 0,01.
Assembly: mm9
Supplementary files format and content: tab separated file containing counts per gene
Supplementary files format and content: sequencing depth normalised bigwig files

source_name: small intestine

extract_protocol:
500 embryonic intestinal epithelial cells were isolated by FACS directly in 7ml of lysis buffer (Clontech) supplemented with 5% RNase inhibitor and stored at -80°C. PolyA+ mRNA was used for cDNA synthesis using SMARTer v4.0 kit (Clontech) according to the manufacturer’s instructions. Amplification was performed for 15 cycles.
After cDNA fragmentation (Covaris), libraries were prepared using Ovation Ultralow Library System (NuGEN) according to the manufacturer’s instructions.

value: small intestine

tag: developmental stage

value: 13.5 day embryo

value: Epithelium

value: Shh-cre-egfp:Tcf7l1 lox/lox


title: Epithelium_TCF_2


title: Epithelium_WT_1

value: wild type


title: Epithelium_WT_2


title: peripheral blood young Stroke Day 14 replicate1 (male)

first: Josef

last: Anrather

address: 407 East 61st Street

department: BMRI

institute: Weill Cornell Medical College

description: Drop-seq

data_processing:
Demultiplexed fastq files were cleaned of reads not passing the Illumina Passing Filter with fastq_illumina_filter (version 0.1) and processed with the Drop-seq Tools (version 2.3.0) pipeline
Count matrices were processed with the R package Seurat (version 4,1), data were integrated across samples with the R package Harmony (version 0.1.1).
Assembly: mm10
Supplementary files format and content: comma-separated matrix and metadata files

source_name: peripheral blood

extract_protocol:
Brain single cell suspensions were obtained by enzymatic digestion with papain (Neural Tissue Dissociation Kit (P), #130-092-628, Miltenyi Biotec) following the manufacturer's instructions. Four to five hemispheres were pooled for each experiment. In order to increase cell viability and to preserve the transcriptional state during the generation of single-cell suspensions, Brilliant Blue G (BBG, P2X7 receptor antagonist, 1M, Sigma), actinomycin D (RNA polymerase inhibitor, 5g/ml, Sigma) and AP-5 (25 nM, NMDA receptor blocker, Tocris) were added to the dissociation solution. Next, cell suspension was filtered through a 70 m filter, resuspended in 30% Percoll (GE Healthcare)-HBSS containing 1M BBG, and spun for 10 minutes at 700 g. After gradient centrifugation, the myelin layer was removed, and the cell pellet was resuspended in 2%FBS-PBS buffer and filtered through a 40 m filter. Isolated cells were washed and resuspended in 100 l of blocking buffer per hemisphere to proceed for FACS staining and cell sorting.
For isolation of peripheral leukocytes, mice were anesthetized with pentobarbital (100 mg/Kg, i.p.) and 0.5 ml of blood was drawn from the heart and transfer into tubes containing sodium heparin (20 Units). BBG (1M) and actinomycin D (5g/ml) inhibitors were added during the isolation procedure. For each experiment the blood from two mice (1 ml total blood) was pooled and erythrocytes were lysed. After erythrolysis, blood cells were resuspended in MACS buffer (PBS supplemented with 2% FBS, 2 mM EDTA; 300 μl/107 cells), incubated with a biotinylated Ter-119 antibody (Biolegend) and purified with anti-biotin microbeads according to the manufacturer's instructions (Miltenyi Biotec). Afterward, cells were washed and resuspended in 0.01% BSA-PBS at a concentration of 105 leukocytes /ml.

tag: strain

value: 8-10 week old

value: male

value: peripheral blood

value: Peripheral blood leukocytes

value: Stroke

tag: time point

value: Day 14


title: peripheral blood young Stroke Day 2 replicate4 (male)

description: Drop-seq

tag: treatment

value: Day 2


title: peripheral blood young Stroke Day 14 replicate2 (male)

description: Drop-seq


title: Epithelium_TCF_3


title: peripheral blood young Stroke Day 2 replicate2 (male)

description: Drop-seq


title: peripheral blood young Stroke Day 2 replicate3 (male)

description: Drop-seq


title: peripheral blood young Stroke Day 2 replicate1 (male)

description: Drop-seq


title: Epithelium_WT_3


title: peripheral blood young Sham Day 2 replicate4 (male)

description: Drop-seq

value: Sham


title: peripheral blood young Stroke Day 14 replicate3 (male)

description: Drop-seq


title: peripheral blood young Sham Day 2 replicate3 (male)

description: Drop-seq


title: Hepatocyte_irradiated_CR_8Weeks, #3

treatment_protocol: Mice were left untreated or were subjected to whole-body X-ray-irradiation (3.8 Gy, 0.6 Gy/min) at 1 week of age, then sampling at 7, 8, 10, and 40 weeks.

value: Hepatocyte

value: 8 weeks


title: RNAseq_Zone1_Ngn1GFPbright_r1

value: immature olfactory sensory neurons (iOSN)


title: peripheral blood young Sham Day 2 replicate1 (male)

description: Drop-seq


title: brain aged Stroke Day 2 replicate2 (female)

description: Drop-seq

source_name: brain

value: 17-20 month old

value: female

value: brain

value: Sorted CD45high, microglia, endothelial cells


title: brain aged Stroke Day 2 replicate1 (female)

description: Drop-seq


title: brain aged Stroke Day 2 replicate1 (male)

description: Drop-seq


title: brain aged Sham Day 2 replicate1 (female)

description: Drop-seq


title: brain young Stroke Day 14 replicate4 (male)

description: Drop-seq


title: brain aged Sham Day 2 replicate1 (male)

description: Drop-seq


title: brain young Stroke Day 14 replicate3 (male)

description: Drop-seq


title: brain young Stroke Day 14 replicate2 (male)

description: Drop-seq


title: brain young Stroke Day 14 replicate1 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate4 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate1 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate2 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate3 (male)

description: Drop-seq


title: brain young Sham Day 2 replicate3 (male)

description: Drop-seq


title: brain young Sham Day 2 replicate4 (male)

description: Drop-seq


title: brain young Sham Day 2 replicate2 (male)

description: Drop-seq


title: peripheral blood young Sham Day 2 replicate2 (male)

description: Drop-seq


title: brain young Sham Day 2 replicate1 (male)

description: Drop-seq


title: Immediate-day14-SC-r8

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards).
Processed reads were mapped to the reference genome/transcriptome with tophat v2.1.1 (--no-novel-juncs --library-type fr-firststrand).
Cuffnorm from the cufflinks package (v2.2.1) was used to quantify transcripts (--library-type fr-firststrand).
Assembly: Mouse mm10 (UCSC)
Supplementary files format and content: tab-delimited text files include raw counts per annotated gene for each sample

source_name: regenerative bridge from common peroneal to tibial nerve graft

growth_protocol: standard mouse housing in research facility

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. For RNA extracted from distal stump samples, RNA concentration was determined with a Nanodrop and integrity assessed on a Fragment Analyzer.
For RNA extracted from distal stump samples, rRNA was depleted from 100ng total RNA input using the RiboZero Magnetic Gold H/M/R Kit (Illumina). Directional RNA-seq libraries were prepared from rRNA-depleted RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). For RNA extracted from 1000 FACS-sorted macrophage and Schwann cells, cDNA was generated and amplified with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara);  RNA-seq libraries were prepared with the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs) using 4ng amplified cDNA from macrophage samples and 1.5ng from Schwann cell samples.

treatment_protocol: common peroneal nerve graft performed to tibial nerve, either immediately or after an 8 week delay period; a single cell suspension was isolated from the regenerative bridge and sorted using FACS to isolate macrophages and Schwann cells.

value: F

tag: mouseid

tag: repair timing

value: immediate

tag: collection day

value: Schwann cells


title: Immediate-day14-SC-r7

tag: tissue

value: regenerative bridge from common peroneal to tibial nerve graft


title: Immediate-day14-SC-r4

value: M


title: Immediate-day14-SC-r2


title: Immediate-day14-SC-r5


title: Immediate-day14-SC-r3


title: Delay-day14-SC-r8

value: delay


title: brain aged Stroke Day 14 replicate1 (female)

description: Drop-seq

tag: age

value: Stroke


title: Delay-day14-SC-r6

tag: cell type


title: Delay-day14-SC-r4


title: Immediate-day5-SC-r8


title: Immediate-day5-SC-r7


title: Delay-day14-SC-r1


title: Delay-day14-SC-r2


title: Delay-day14-SC-r3


title: Immediate-day5-SC-r3


title: Immediate-day5-SC-r4


title: Immediate-day5-SC-r5


title: Delay-day5-SC-r9


title: Delay-day5-SC-r8


title: Immediate-day14-SC-r6


title: Immediate-day5-SC-r2


title: Delay-day5-SC-r7


title: Immediate-day14-SC-r1


title: Delay-day5-SC-r6


title: Delay-day5-SC-r3


title: Delay-day5-SC-r5


title: Delay-day5-SC-r2


title: Delay-day5-SC-r4


title: Immediate-day14-MAC-r6

value: macrophage


title: Immediate-day14-MAC-r7


title: Immediate-day14-MAC-r8


title: Immediate-day14-MAC-r4


title: Delay-day5-SC-r1


title: Delay-day14-SC-r7


title: Immediate-day14-MAC-r5


title: Immediate-day14-MAC-r3


title: Immediate-day14-MAC-r2


title: Immediate-day5-SC-r1


title: Immediate-day14-MAC-r1


title: Delay-day14-MAC-r6


title: Delay-day14-MAC-r4


title: Delay-day14-MAC-r8


title: Delay-day14-MAC-r7


title: Delay-day14-MAC-r1


title: Delay-day14-MAC-r3


title: Delay-day14-MAC-r2


title: Immediate-day5-MAC-r8


title: Immediate-day5-MAC-r6


title: Immediate-day5-MAC-r5


title: Immediate-day5-MAC-r4


title: Immediate-day5-MAC-r7


title: Immediate-day5-MAC-r3


title: Immediate-day5-MAC-r2


title: Immediate-day5-MAC-r1


title: Delay-day5-MAC-r9


title: Delay-day5-MAC-r8


title: Delay-day5-MAC-r6


title: Delay-day5-MAC-r7


title: Delay-day5-MAC-r5


title: Delay-day5-MAC-r2


title: Delay-day5-MAC-r3


title: Delay-day5-MAC-r4


title: Delay-day5-MAC-r1


title: Immediate-day5-DS-r8

value: distal stump


title: Immediate-day5-DS-r7


title: Immediate-day5-DS-r6


title: Immediate-day5-DS-r4


title: Immediate-day5-DS-r2


title: Delay-day5-DS-r8


title: Delay-day5-DS-r9


title: Immediate-day5-DS-r3


title: Delay-day5-DS-r7


title: Delay-day5-DS-r3


title: Delay-day5-DS-r6


title: Delay-day5-DS-r4


title: Delay-day5-DS-r5


title: Heart, KO5

city: Pittsburgh

first: Adam

middle: C

last: Straub

state: Pennsylvania

address: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
FASTQ files were aligned to mouse genome (GRCm39) using STAR using the default settings.
Reads aligned to exons were summarized using featureCounts in Rsubread.
Assembly: GRCm39
Supplementary files format and content: readcount.csv

source_name: Heart

extract_protocol:
Frozen heart tissue (30-50 mg) was pulverized over liquid nitrogen using a mortar and pestle. RNA was isolated from powdered tissue using Qiagen RNeasy mini kit (Qiagen 74106) and purified with RNeasy MinElute Cleanup Kit (Qiagen 74204). Each sample was assessed for quantity and quality using a Qubit 2.0 fluorometer and Agilent Bioanalyzer Tape Station 2200.
Library preparation was done using Illumina TruSeq Stranded Total RNA sample prep kit. The cDNA libraries were quantitated and validated for quality similar to the purified RNA prior to being pooled (1.8 pM final concentration).

value: Heart

tag: genotype

value: CYB5R3fl/fl, Myh6-CreERT2

value: Tamoxifen


title: Heart, KO4


title: Heart, KO2


title: Heart, KO1


title: Delay-day5-DS-r2


title: Heart, KO6


title: Heart, WT5

value: CYB5R3wt/wt, Myh6-CreERT2


title: Heart, WT6


title: Heart, WT2


title: Heart, WT1


title: Heart, WT3


title: Alb/MDA-9 replicate 4

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

data_processing:
The demultiplexing, barcoded processing, gene counting were using the Cell Ranger software v6.0.1
Single cell RNA-seq data analysis using Seurat version v4.0.4; 1. Quality control on the gene count matrices of samples 2. Samples integration and feature selection 3. Dimension reduction and clustering 4. Cell type identification 5. Differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files generated from the Cell Ranger

source_name: Liver

extract_protocol:
Non-hepatocyte cells from the liver were isolated by differential centrifugation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, non-hepatocyte cells from liver were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Liver

value: Non-hepatocyte cells

value: No treatment


title: Alb/MDA-9 replicate 2


title: Alb/MDA-9 replicate 3


title: Alb/MDA-9 replicate 1


title: Immediate-day5-DS-r1


title: WT replicate 1

value: WT


title: WT replicate 3


title: Delay-day5-DS-r1


title: WT replicate 2


title: Balb_22

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
RNA-SEQ reads (30-6M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm10
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: allografted CT26.WT tumors

extract_protocol:
Allografted CT26.WT tumors isolated from mice and total RNA isolated using Qiagen RNeasy mini kit.
The integrity of the total RNA was determined using a bioanalyzer (Agilent) and concentration were assessed by Qubit (ThermoFisher Scientific).  A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NextSeq 500 in a 75-base single-end mode according to the manufacturer’s protocol.

treatment_protocol: Allografted CT26.WT tumors isolated from mice fed with either a high methionine diet containing 0.86% methionine (0.86%) or a methionine restricted diet containing 0.172% methionine (0.172%).

tag: background

value: Balb/c mice

value: Male

value: mouse colon carcinoma cells

tag: timepoint

value: treated with diets for 3-4 weeks

value: 0.86% high methionine  diet

value: wild-type


title: Balb_23

tag: gender


title: Balb_24


title: WT replicate 4


title: TDLN2

city: Boston

institute: Massachusetts General Hospital

description: Single-cell RNA sequencing

source_name: 4T1 breast cancer draining inguinal lymph node

treatment_protocol: 1x10e5 4T1 cells were injected into the fourth mammary fat pad (draining to the inguinal lymph node) in a volume of 25-50 ul per mouse.

value: Balb/c

value: female

value: 6-10 week old

value: 4T1 murine breast cancer cell (TDLN)

value: NextSeq High Output SE75


title: Naïve LN1

description: Single-cell RNA sequencing

source_name: inguinal lymph node

value: inguinal lymph node cell (naive)


title: Heart, WT4

value: Heart

value: CYB5R3wt/wt, Myh6-CreERT2

value: Tamoxifen


title: Naïve LN2

description: Single-cell RNA sequencing


title: Balb_16

value: 0.172% methionine deficient diet


title: Balb_21


title: Balb_19


title: Balb_20


title: Balb_18


title: Heart, KO3

value: CYB5R3fl/fl, Myh6-CreERT2


title: Balb_15

value: Balb/c mice


title: Balb_17

value: Male


title: Balb_ 14

value: mouse colon carcinoma cells


title: NSG_10

value: NSG mice

value: treated with diets for 3-4 weeks


title: NSG_9

value: 0.86% high methionine  diet

value: wild-type


title: NSG_12


title: Balb_13


title: NSG_11


title: NSG_7


title: TDLN1

description: Single-cell RNA sequencing

value: Balb/c

value: female


title: NSG_6


title: NSG_4


title: NSG_3


title: Liver, 5-months post engraftment, LK03V/REDHC, replicate 2, snRNA-seq

city: Westmead

first: Suzanne

last: Scott

state: NSW

address: 214 Hawkesbury Rd

country: Australia

institute: Children's Medical Research Institute

description:
Rod_ASV_3_4
LK03V/REDHC2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: Combined GRCh38, mm10, AAV reference
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

extract_protocol:
To identify and characterize cell states associated with AAV transduction in human heptocytes, we employed a droplet-based (10x chromium) single nucleus transcriptomics approach. Hepatic nuclei were isolated and profiled from (a) human hepatocytes before engraftment, (b) liver samples from FRG mice engrafted with human hepatocytes, and (c) liver samples from FRG mice engrafted with human hepatocytes, treated with two AAV vectors (LLK03, REDH).
Libraries were prepared from single nucei.  Breifly, nuclei were isoalted from flash-frozen chunks of tissue, which were homogenized using a Kimble Dounce tissue grinder, followed by straining with a 40 μm cell strainers, two rounds of centrifugation at 500g.  Nuclei were stained with DAPI and proridium iodide, followed by FACS sorting to isolate PI-positive nuclei. Libraries were then prepared using a 10x Genomics Chromium Single Cell 3’v3 Reagent Kits were used according to manufacturer’s instructions.
snRNA-seq

value: Liver

value: Hepatocytes

value: 5-months post-engraftment, LK03V/REDHC

tag: time

value: 5-months post engraftment


title: NSG_2


title: Liver, 5-months post engraftment, LK03V/REDHC, replicate 1, snRNA-seq

description:
Rod_ASV_3_3
LK03V/REDHC1


title: Liver, 5-months post engraftment, replicate2, snRNA-seq

description:
ROD_C5
high2

value: 5-months post-engraftment


title: Liver, 5-months post engraftment, replicate1, snRNA-seq

description:
ROD_C4
high1


title: Input_H3K9me3_T1678_GS8

first: Ben

last: Wittner

address: 149 13th Street

data_processing:
ULI NChIP-seq and Cut and Run reads were first trimmed by trimgalore (v0.4.3) (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were mapped to the human genome using BWA men (Li and Durbin, 2009). Duplicated reads were marked by sambamba (Tarasov et al., 2015) and further removed using samtools (Li et al., 2009).
MACS2 (v2.0.10) (Zhang et al., 2008) was used to call the peaks and deepTools (Ramirez et al., 2016) were used to compute the ChIP-seq or Cut and Run signal.
Assembly: hg19 (human)
Supplementary files format and content: bigWig file giving the read coverage at each genomic location

source_name: prostate epithelial cell

extract_protocol:
For ULI NChIP-seq, nuclei from different cell lines were isolated in Nuclear Isolation Buffer (Sigma) supplemented with 1% Triton-X 100, 1% Deoxycholate and 1X complete protease inhibitor. Chromatin was digested by MNase enzyme (NEB, 1:10 diluted) at 21°C for 7.5 min.
DNA from ULI NChIP or Cut and Run assay was used to prepare sequencing library using NEBNext Ultra II DNA Library Prep Kit (NEB, Cat#E7645L).

tag: antibody

tag: disease

value: cancer

tag: genome build

tag: patient donor

value: prostate epithelial cell