title: Budding yeast, Untagged control, 10s, rep1

city: Eugene

first: Laura

middle: Emily

last: McKnight

state: Oregon

address: 1318 Franklin Blvd Room 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Demultiplexed reads were received as FASTQ files.
Reads were aligned to the Ensembl R64-1-1 genome with Bowtie2 in 'end-to-end' mode. Reads for different fragment sizes (small fragment (SF): 0-120bp, large fragment (LF) 140-180bp, full fragment (FF) 0-200bp) were aligned separately using Bowtie2 flags '-I' and '-X'. The following flags were also used: '--no-unal', '--no-mixed', and '--no-discordant'.
Samtools was used to sort, filter (MAPQ > 30), and index aligned DNA fragments.
Coverage calculation was performed using Deeptools2 'bamCoverage' and the following flags: '-bs 1', '-of bigwig', '--normalizeUsing RPGC', '--effectiveGenomeSize 12100000', '--centerReads', and '-e'.
The pipeline used to process SpLiT-ChEC data is available at https://github.com/Bankso/SCAR.
Assembly: GCA_000146045.2
Supplementary files format and content: bigWig (.bw) files contain RPGC-normalized coverage for fragments of noted length. Fragments were separately aligned to the S. cerevisiae reference genome before coverage was calculated.
Library strategy: SpLiT-ChEC

organism: Saccharomyces cerevisiae

source_name: log phase yeast

growth_protocol: Yeast cultures were grown at 30℃ in yeast peptone media supplemented with 2% raffinose, to mid-log phase.

extract_protocol:
DNA was extracted with Phenol-Chloroform-Isoamyl alcohol and concentrated using ethanol precipiation. DNA fragments >500bp were removed using 3x vol Agencourt AmPureXP SPRI beads.
Libraries were prepared with the NuGen Ovation Ultralow V2 kit using 10 ng DNA as input and 13 cycles of PCR amplification. For post-adapter ligation and post-amplification purifications, 1.8x vol of Agencourt AmPureXP SPRI beads were used.

treatment_protocol: MNase-SpyCatcher expression was induced for 2 hours by adding galactose (2% final concentration) to yeast cultures. After harvesting, cells were permeabilized and treated with 2mM Ca2+ to initiate DNA digestion by MNase. Samples were collected at several digestion timepoints (10s, 20s, and 60s) and MNase activity was immediately quenched after collection.

value: W303; pGAL-MNase-SpyCatcher002

value: Untagged

value: log phase yeast

value: 2 mM Ca2+ 10s


title: hNSC treated with TCQA_rep2

status: Public on Jul 03 2023

type: RNA

city: Tsukuba

first: Yu Jia

last: Chen

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from human neural stem cells treated with 10uM TCQA for 24 hours

hyb_protocol: Purified and fragmented aRNA was hybridized using the GeneChip MG-430 PM microarray (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: Scanning was performed with the GeneAtlas Imaging Station (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
Data analysis was performed using the Partek Express software (Partek Inc., St. Louis, MO, USA) provided by Affymetrix as part of their GeneAtlas system. Compared with the non-treated cells, fold change in expression in the TCQA-treated group was calculated and converted to log 2 data.
RMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human neural stem cells treated with 10uM TCQA for 24 hours

label_protocol: Biotin-labeled amplified RNA (aRNA) was synthesized by in vitro transcription using the GeneChip 3’ IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA).

growth_protocol: The hNSCs derived from H9 hNSCs were purchased from Gibco, Japan. The hNSCs were cultured in 60 mm Petri dishes (BD Falcon) with a growth medium Knock OutTM:1:1 (v/v) mixture of Dulbecco’s minimum essential medium (Sigma, U.S.A.) and Ham’s F-12 nutrient mixture (Sigma, U.S.A.) supplemented with 2% StemPro neural supplement, 20 ng/mL of fibroblast growth factor (FGF) basic recombinant human, 20 ng/mL epidermal growth factor (EGF) recombinant human and 2 mM GlutaMAX-I supplement. For adhesion, 60-mm Petri dish  coated with CELLStart were used. The hNSCs were cultured at 37ºC in a 95% air / 5% CO2 humidified incubator. The medium was changed every two days to keep cells undifferentiated.

extract_protocol: The total RNA was extracted from the cells using ISOGEN kit (Nippon Gene Co. Ltd., Toyama, Japan) following manufacturer’s instructions.

treatment_protocol: The hNSCs were seeded in 60-mm Petri dishes at the density of 2.5×104 cells/cm2 and were incubated at 37ºC for 48 h. After that, cells were treated with differentiation medium with or without 10 μM of TCQA and were incubated at 37ºC for 24 h.

tag: cell

value: Human Neural Stem Cell


title: hNSC treated with TCQA_rep1


title: Budding yeast, Untagged control, 20s, rep1

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: strain

tag: genotype

tag: cell type

tag: treatment

value: 2 mM Ca2+ 20s


title: Ube3a_HOM_12mo_Rep1

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
Reads were quality-ﬁltered by requiring at least 90% of bases to have a quality score greater than 20 using fastq_quality_ﬁlter in FASTX-toolkit.
Adapter sequences were removed using cutadapt
Reads were then aligned to the mm9 reference genome using STAR 2.5.2b
Transcript abundance was measured using salmon, and differential expression tests were performed using DESeq2 corrected for library batch
Assembly: mm9
Supplementary files format and content: VST normalized expression values from DESeq2, corrected by library batch

molecule: polyA RNA

organism: Mus musculus

source_name: Cerebral cortex

growth_protocol: Male and female adult C57BL/6J mice (Stock #: 000664) were obtained from Jackson Laboratories (Bar Harbor, ME) and housed in standard polycarbonate cages with cob bedding, shelter, and nesting material. Males were housed singly and females were housed in groups of up to five mice per cage. Mice had ad libitum access to food (Prolab Isopro RMH 3000, LabDiet, St. Louis, MO) and water and were maintained on a 12:12 hr light/dark cycle. Mice were mated in 2 hr sessions and copulation was confirmed by presence of a vaginal plug. The beginning of the mating session when the plug was found was defined as E0.0. All experimental procedures were approved by the Animal Care and Use Committee at UNC-Chapel Hill in accordance with NIH Guidelines

extract_protocol:
Either 2 or 4 hr after the injection, dams were sacrificed via CO2 followed by cervical dislocation. Embryos were dissected from the placenta and stage-matched based on somite number (2 hr: 19-20 somites; 4 hr: 20-21 somites). A maximum of two embryos per litter were used to minimize litter effects. RNA from the rostroventral neural tube (RVNT) from each embryo was isolated using the RNeasy Plus Micro kit (Qiagen, Germantown, Maryland) as previously described (Boschen et al., 2020). RNA from a total of 6 embryos per condition and time point (24 total embryos) were submitted for RNA-seq.
Libraries for RNA sequencing (RNA-seq) were prepared using the SMARTr Ultra Low Input RNA (Clontech, Mountainview, CA) and Nextera XT DNA (Illumina, San Diego, CA) kits by the UNC High Throughput Sequencing Facility. Samples were pooled prior to sequencing, after RNA extraction and library preparation was complete. Six total pools (1 sample/group/pool) and 1 pool per lane were used. Paired-end (50bp) sequencing was performed on an Illumina HiSeq 4000.

treatment_protocol: Pregnant dams were administered a single dose of 2.9 g/kg ethanol (25% vol/vol; Pharmaco-Aaper, Brookfield, CT) in Lactated Ringer’s solution via i.p. injection on E9.0 to target neurulation. Blood alcohol concentrations ± standard error, collected from a separate cohort of dams (n = 6), were 366.8 ± 30.3 mg/dl 30 min after injection and 337.9 ± 18.8 mg/dl 2 hr after injection. Control mice were administered an equal volume of Lactated Ringer’s solution (1.5 ml/100 g body weight).

tag: age

tag: librarybatch


title: Budding yeast, Untagged control, 60s, rep1

value: 2 mM Ca2+ 60s


title: prt6-1, 7-d-old continuous light grown seedlings, Biological replicate 4

city: Nottingham

first: Michael

last: Holdsworth

address: University of Nottingham, University Park

country: United Kingdom

institute: University of Nottingham

data_processing:
Sequence reads were trimmed for adaptor sequences and low quality sequences using default parameters of skewer v0.2.2
Trimmed sequenes were mapped to Arabidopsis thaliana genome (TAIR10) using  default parameters of hisat2 v2.1.0
Only uniquely mapped were used for further downstream analysis.
Read counts for each gene are calculated using featureCounts v1.6.0.
Supplementary files format and content: rawcounts.txt

organism: Arabidopsis thaliana

source_name: 7-d-old total seedlings

growth_protocol: Seeds were sterilised and grown on 1/2 MS agar plates without sucrose for 7 days in continuous light conditions

extract_protocol: Total RNA was extracted using RNAeasy minikit and sent for RNA sequencing

treatment_protocol: 7 days old seedlings of WT and mutant lines were harvested untreated

tag: tissue

value: 7-d-old total seedlings


title: Budding yeast, Abf1, 60s, rep2


title: Ube3a_WT_12mo_Rep1


title: prt6-1, 7-d-old continuous light grown seedlings, Biological replicate 3


title: Budding yeast, Abf1, 20s, rep2


title: 9hrPBS rep1

city: Davis

first: Qizhi

last: Gong

state: CA

address: One Shields Avenue

department: Cell Biology and Human Anatomy

institute: University of California Davis, School of Medicine

data_processing:
Raw reads were processed with HTStream v.1.0 (https://s4hts.github.io/HTStream/) to perform raw sequence data QA/QC, remove adapter contamination and low-quality bases/sequences.
Trimmed reads were aligned to the Mus musculus genome, using the aligner STAR v. 2.6.0c (Dobin, et al. 2013) to generate raw counts per gene.
RNA data analyzed with limma-voom Bioconductor pipeline
Genome_build: GRCm38 primary assembly genome with GENCODE v.M15 annotation
Supplementary_files_format_and_content: tab-delimited text files with raw counts of reads aligned to each gene.

source_name: olfactory mucosa

extract_protocol:
Trizol extraction with Zymo RNA clean and concentrator
3'Tag RNA-seq library constructed according to Illumina protocol

value: olfactory mucosa

value: PBS

tag: time point


title: 9hrPBS rep2


title: Ube3a_PATHET_6mo_Rep1


title: Retina, WT, 10X V2 Chemistry

city: Houston

first: John

last: O'Brien

state: Texas

address: 4401 Martin Luther King Blvd

department: Vision Science

institute: University of Houston College of Optometry

description: Pool of 3 adult zebrafish retinas between 4 and 8 months old

library_source: transcriptomic single cell

data_processing:
Sequences were run through the 10x Genomics CellRanger V3.1.2.0 pipeline. First, sequences were demultiplexed into FASTQ files through CellRanger mkfastq. FASTQ files were then aligned to the Zf reference genome (GCA_000002035.4_GRCz11) through CellRanger count. Output files were run through Babraham Bioinformatics’ FASTQC V0.11.9 to check on the quality of the sequences used for analysis. Sequences had a normal distribution of GC content as well as base call accuracy above 99%. Over 93% of reads mapped successfully to the genome. All computational analysis was performed through Texas Advanced Computing Center (TACC) Lonestar5 computing service. Scripts were written in Notepad++ v7.6.2 and uploaded to TACC through PuTTY V0.72.
After alignment, quality control was assessed through FASTQC. Aligned data were run through the Seurat V3.1.1 package [27] in R V3.6.1.
In the Seurat processing, any cell that was determined to be an outlier or contained greater than 10% mitochondrial genes was removed. Low-abundant genes (expressed in fewer than 10 cells) and cells of potentially low quality (percentage of mitochondrial genes >10%) were removed from downstream analysis.  P23H and WT datasets contained between 200 and 4,700 genes and 200 and 6,000 genes per cell, respectively (Table S4). PCElbowPlots were performed and 20 principal components were used for downstream analysis of each dataset. PC1 to PC20 were used to construct nearest neighbor graphs in the PCA space followed by Louvain clustering and non-linear dimensional reduction by tSNE to visualize and explore the clusters. Each cluster was assigned a cell type based on their expression of cell type-specific marker genes (Table S1). Dot plots, Heatmaps, Violin Plots and tSNE cluster maps were all generated through Seurat’s vignettes V3.2. Expression levels are expressed in a base 2 log scale.
Assembly: GCA_000002035.4_GRCz11
Supplementary files format and content: Tab Separated Values files
Supplementary files format and content: Matrix files

organism: Danio rerio

source_name: Whole retina

growth_protocol: Zebrafish fish were grown in 14hr light:10hr dark cycle conditions and collected between 4 and 8 months of age

extract_protocol:
3 fish of the same strain were collected in the morning between nine and eleven a.m., 2 to 4 hours after light onset in the fish room, in Falcon tubes containing 0.15% Tricaine/MS222 and incubated on ice for 10 minutes. Zebrafish were decapitated and eyeballs were detached and placed in dissecting medium containing Leibovitz's L-15 medium (Gibco 21083027). Each retina was then extracted and placed in a 1.5 mL microcentrifuge tube with 300 µL of dissociation solution containing L15 and Earle's Balanced Salt Solution (EBSS; Gibco 14155063) in a 3:1 ratio. After all retinas were collected, the dissociation solution was replaced with 200 µL of Papain solution (50 U/mL in EBSS; Worthington Biochemical LK003178) and retinas were incubated at 28˚C. After 20 minutes of incubation, retinas were gently triturated 20-30 times with fire-polished glass pipettes. Supernatants were collected and incubated with Papain for another 40 minutes with trituration performed every 10 minutes. Papain reaction was terminated by adding 2x volume of 0.1% BSA in L15: EBSS medium. Tubes were centrifuged at 400g for 5 minutes to pellet the cells. The supernatant was removed and washed again with 0.05% BSA. The supernatant was removed and cells were finally suspended in 100 µl of 0.05% BSA.
The cell samples were submitted for 3’ sc-RNA library preparation and sequencing through the Baylor College of Medicine Single Cell Genomics Core facility. Single-cell Gene Expression Libraries were prepared usingChromium Next GEM Single Cell 3’ Reagent Kits v2 and v3.1(10x Genomics, Pleasanton, CA). In brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS are broken and cDNA from every single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing and adaptor ligation. The final library was generated by amplification. cDNA libraries were sequenced on an Illumina HiSeq2500.
3' SC RNA Seq

value: Whole retina

tag: FISH line

value: WT AB; ZIRC_ZL1

value: 4 to 8 months old

value: WT

tag: disease state

value: control

tag: 10x chemistry

value: 10X V2 Chemistry


title: hNSC mantained in differentiation medium_rep1

description: Gene expression data from human neural stem cells maintained in differentiation medium for 24 hours

source_name: Human neural stem cells maintained in differentiation medium for 24 hours


title: prt6-1, 7-d-old continuous light grown seedlings, Biological replicate 2


title: Budding yeast, Abf1, 10s, rep2


title: Ube3a_WT_E14.5_Rep2


title: Ube3a_MATHET_6mo_Rep1


title: 6hrVSV rep3

value: VSV


title: prt6-1, 7-d-old continuous light grown seedlings, Biological replicate 1


title: 6hrVSV rep2


title: Col-0, 7-d-old continuous light grown seedlings, Biological replicate 4


title: 9hrPBS rep3


title: 6hrVSV rep1


title: Budding yeast, Abf1, 20s, rep1

value: W303; pGAL-MNase-SpyCatcher002


title: Budding yeast, Abf1, 60s, rep1


title: 6hrPBS rep3


title: Ube3a_WT_6mo_Rep1


title: Col-0, 7-d-old continuous light grown seedlings, Biological replicate 2


title: 6hrPBS rep2


title: Ube3a_PATHET_1mo_Rep1


title: Budding yeast, Abf1, 10s, rep1


title: Col-0, 7-d-old continuous light grown seedlings, Biological replicate 3


title: Ube3a_MATHET_1mo_Rep1


title: 6hrPBS rep1


title: Early embryos wild-type input for H3K4me3 rep 2

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: A fraction of the input total chromatin that was used for H3K4me3 ChIP on wild-type

data_processing:
Reads were aligned to ce11 with bowtie2.
Low-quality (q<30), duplicate reads and modENCODE-blacklisted reads were discarded.
Reads were normalized to inputs (as log) using Deeptools
Assembly: ce11
Supplementary files format and content: bigWig (except for Input sample)

organism: Caenorhabditis elegans

source_name: early embryo

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation. Starved L1s were plated on peptone-enriched NGM plates seeded with OP50. L1s were grown until young adult at 20˚C. Worms were harvested, washed with M9 and floated on sucrose to remove remaining bacteria.

extract_protocol:
For each histone modification ChIP-seq, samples were sonicated using a microtip to achieve mostly 200–800 bp DNA fragments, and immunoprecipated overnight using 5 µg of anti-H3K4me3 antibody. The wash steps were performed as in previously described (Kudron et al 2018; Han et al. 2019).
DNA was purified on Zymo ChIP DNA Clean & Concentrator kit (Zymo Research #D5205) and used for ChIP library preparation. Samples were sequenced on an Illumina NovaSeq using 100bp paired-end sequencing.

treatment_protocol: Worm samples were cross-linked with 2% formaldehyde for 30 min at room temperature and then quenched with 1 M Tris pH 7.5. The pelleted worms were subsequently flash frozen in liquid nitrogen and stored at −80°.

value: early embryo

tag: developmental stage

value: Young adult

tag: antibody

value: wild-type


title: Early embryos wild-type input for H3K4me3 rep 1


title: Col-0, 7-d-old continuous light grown seedlings, Biological replicate 1


title: 3hrVSV rep2


title: Ube3a_WT_1mo_Rep1


title: Ube3a_HOM_1mo_Rep1


title: Early embryos wild-type H3K4me3 rep 2

description: ChIP was performed with anti-H3K4me3 on wild-type early embryos


title: Early embryos wild-type H3K4me3 rep 1


title: 3hrVSV rep1


title: Ube3a_PATHET_E14.5_Rep1


title: Ube3a_MATHET_E14.5_Rep1


title: LSK_NMRE-KO (Hi-C)

city: New York

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health

data_processing:
Read alignment: The Hi-C reads were aligned by the BWA aligner (v0.7.17). Params: "-A1 -B4 -E50 -L0".
Filtering: Mapped reads were filtered by the GenomicTools tools-hic filter command integrated in HiC-bench for known artifacts of the Hi-C protocol. HiC-Bench: https://github.com/NYU-BFX/hic-bench
Valid pairs: We used the accepted intra-chromosomal read-pairs (‘ds.accepted intra’) and filtered out multi-mapped reads (‘multihit’), read-pairs with only one mappable read (‘single sided’), duplicated read-pairs (‘ds.duplicate’), low mapping quality reads (MAPQ < 20), read-pairs resulting from self-ligated fragments.
Normalization: Contact matrices were generated using the HiC-Bench pipeline and ICE correction was performed using the algorithm detailed in Imakaev et al. (2012) publication. For this, we used the matrix-ic functionality built into HiC-bench which uses the ‘mirnylib.numutils’ python library.
Loop calling: We used the HiC valid pairs with the FitHiC tool (v2.0.7) to identify significant interactions. Parameters: resolution=10kb ; q-value <= 0.01; Min. distance=30kb; Max. distance=1Mb.
Virtual4C: HiC-Bench ‘virtual4C’ pipeline was used to compute the interactions of each selected viewpoint in a roll-window fashion. We summed the valid read pairs in a 5 kb area centered at 200 bp bins that covered the area of +-2.5 Mb from the viewpoint (25k bins per viewpoint). The interactions were normalized by the total number of valid pairs of the sample.
Assembly: mm10
Supplementary files format and content: *.reg.txt files contain the HiC valid read pairs (both intra and inter-chromosomal).

source_name: Bone marrow-derived LSK cells

extract_protocol:
Chromatin was extracted and processed by Arima HiC+ kit following manufacturer's instructions.
HiChIP libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit.

value: Bone marrow-derived LSK cells

value: NMRE-KO

tag: Sex

value: Female


title: 3hrPBS rep3


title: LSK_NMRE-WT (Hi-C)

value: Wild-type


title: Ube3a_HOM_6mo_Rep1


title: Ube3a_HOM_E14.5_Rep1


title: 3hrPBS rep2

value: olfactory mucosa


title: CD4TCells_aGCA_rep19

city: Paris

first: Paul

last: Régnier

address: 83 boulevard de l'hôpital

country: France

institute: AP-HP

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Then, raw IDAT files were processed using illuminaio Bioconductor R package and concatenated into a single text file. Data were further background-corrected using limma Bioconductor R package and inter-chip batch effects were removed using ComBat method from sva Bioconductor R package. In the end, the following samples numbers remained and were analyzed: 15 CD4+ T cells from HD and 19 CD4+ T cells from aGCA.

source_name: CD4+ T cells, GCA

label_protocol: not provided

extract_protocol: CD3+ CD4+ T cells were sequentially isolated from PBMCs of aGCA or HD using Dynabeads Untouched Human T Cells kit and Dynabeads CD4+ isolation kit (Thermofisher Scientific). Sample purities were assessed afterwards and were all > 95%. Total RNA from CD4+ T cells was then extracted using the NucleoSpin RNA kit (Macherey-Nagel) and quantified by a NanoDrop 1000 spectrophotometer. 5 samples with RNA concentration < 20ng/µL were excluded. For quality control, RNA dilution was performed using Agilent RNA 6000 Nano Kit and 1µL of the sample was run on the Nano chip using an Agilent 2100 electrophoresis bioanalyzer. The quality of total RNA was assessed using the profile of the electropherogram and the RNA integrity number (RIN) was calculated. The whole samples showed RINs between 7.1 and 9.5. For Illumina Beadarrays, cRNA samples were prepared using Illumina TotalPre-96 RNA Amp kit (LifeTechnologies) and hybridized to Illumina Human HT-12 v4 beadarrays.

value: CD4+ T cells

tag: group

value: aGCA


title: Ube3a_WT_E14.5_Rep1


title: s2_KO [scRNA-seq]

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

data_processing:
The raw count data generated from Cell Ranger pipeline was processed using Seurat v 4.3.0 by following the standard pipeline.
Assembly: mm10
Supplementary files format and content: Raw Counts
Supplementary files format and content: Zipped folder containing barcode, matrix and features tsv files.

source_name: Adipose

extract_protocol:
CD45-CD31- SVF cells were isolated by negative selection with MicroBeads (Miltenyi Biotec) from SAT of Azin2-/- and wt mice (2 mice pooled per genotype) fed for 8 weeks a HFD. 10,275 wt and 11,004 Azin2-/- cells were FACS sorted and subjected to droplet-based single cell RNA-sequencing.
The samples were processed using the 10x Genomics protocol for single cell 3’ RNA-seq v3. Libraries were sequenced on an Illumina NextSeq500 in 75 base pair paired-end mode. The raw sequencing data were processed with the Cell Ranger software (v2.1.0) provided by 10X Genomics.

value: Adipose

value: Stromal Vascular Fraction


title: CD4TCells_aGCA_rep17


title: 3hrVSV rep3


title: 3hrPBS rep1

value: PBS


title: s1_WT [scRNA-seq]

value: WT


title: CD4TCells_aGCA_rep18


title: CD4TCells_aGCA_rep16


title: tNCCs, treated 100uM cyclopamine, Sample3

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

data_processing:
Read aligment with STAR, counts generated by featurecounts (subread). Expression from DESeq2 using normTransform function
Supplementary files format and content: tab delim text file
Supplementary files format and content: tab delim text file

source_name: neural crest cells

growth_protocol: Embryos reared at 28C until 24hpf.

extract_protocol: standard Illumina Kit for stranded RNAseq

treatment_protocol: For cyclopamine treated samples, embryos were treated with 100uM cyclopamine from 50% epiboloy to 24hpf

value: neural crest cells

value: wildtype

value: 100uM Cyclopamine, 50%epiboly to 24hpf


title: ALD5

city: Jinan

first: Yuan

last: Detian

email: yuandt@sdu.edu.cn, lishiyang@sdu.edu.cn

address: Wenhuaxi Road 44

country: China

institute: Shandong University

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline (version 2.2.0) provided by 10 × Genomics was used to demultiplex cellular barcodes, align reads and generate the featurebarcode unique molecular identifier (UMI) matrices based on the human reference genome GRCh38.
We processed the unique molecular identifier (UMI) count matrix using the Seurat R package (v2.4.3)
Intercellular communication were analyzed in an unbiased manner using the CellChat package (v1.5.0) [10.1038/s41467-021-21246-9] to identify significant ligand-receptor pairs within healthy, ALD and NAFLF samples.
Assembly: GRCh38
Supplementary files format and content: Expression matrices provided as CSV files

source_name: Liver

extract_protocol:
Each tissue sample was placed in a sterile Petri dish on ice. The tissue was subsequently minced to smaller pieces of less than 3 mm. Sample pieces were transferred to a gentle MACS C Tube (Miltenyi #130-093-237) containing 5 ml digestion enzyme mix. The C tube was then placed on a gentleMACS Octo Dissociator for mechanical dissociation. Upon run completion, the sample was incubated for 30 min at 37  C under continuous low shaking. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300 x 3 g and 4 C for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco). Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Single-cell RNA-seq libraries were prepared with Chromium Single cell 30 Reagent v2 Kits according to the manufacturer’s protocol. The Chromium Single Cell 30 Library and Gel Bead Kit v2 (PN-120237), Chromium Single Cell 30 Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used. Briefly, single-cell suspensions were loaded on the Chromium Single Cell Controller Instrument (10 × Genomics) to generate single cell gel beads in emulsions (GEMs). After generation of GEMs, reverse transcription reactions were engaged barcoded fulllength cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform (HiSeq X Ten), and 150 bp paired-end reads were generated.
10x Genomics Single Cell Transcriptome Sequencing

value: Liver

tag: cell line

value: alcoholic liver disease


title: Slow-twitch NCC, tg(sox10:mRFP), Sample2


title: CD4TCells_aGCA_rep14


title: ALD3

description: 10x Genomics


title: Input_Azin2_WT_REP1

data_processing:
Nextflow (v 22.02.1) [3] was used to run the nf-core/chipseq: 2.0.0 [4] workflow pipeline with the following parameters : --genome GRCm38 --macs_pvalue 0.1 --max_cpus 4 --macs_gsize 1.87e9.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig and narrowPeak

extract_protocol:
Immunoprecipitation was performed by incubating the sheared chromatin with the magna ChIP protein A/G magnetic beads and an antibody  against H3K27Ac (Millipore 17- 683).
Libraries were generated using the NEBNext Ultra II DNA library Prep kit kit (Illumina Inc)

value: Adipocyte Progenitor


title: ALD4

description: 10x Genomics


title: CD4TCells_aGCA_rep13


title: ALD2

description: 10x Genomics


title: Input_Azin2_KO_REP8


title: Slow-twitch Muscle, tgPAC(Prdm1a:eGFP), Sample2

source_name: slow-twitch muscle

value: slow-twitch muscle


title: Slow-twitch NCC, tg(sox10:mRFP), Sample1


title: LegNeu

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
Sequencing reads were aligned to the Drosophila melanogaster genome (FlyBase r6.31) using Cell Ranger Count (version  4.0.0).
Ambient RNAs were removed using the DecontX from Celda package (version 1.10.1).
Potential multiplets detected by DoubletFinder (version 2.0.3) were filtered.
For further analysis of the snRNA-seq data, we utilized Scanpy (version 1.9.1).
To ensure high quality data, we removed nuclei with extreme UMIs (UMI < 1000 or UMI > 3000) or high levels of mitochondrial transcripts (more than 5% of total UMIs).
UMI reads were log normalized and highly variable genes were  selected. Variations in mitochondrial percentage and total UMIs were regressed out, and expressions of highly variable  genes were scaled to unit variance.
Data were dimensionally reduced using the first 20 principal components and computed for the neighborhood graph with 10 nearest neighbors.
To visualize the non-linear dimensionality reduction, we used Uniform Manifold Approximation and Projection (UMAP). Nuclei were clustered using the Leiden graph-clustering method.
Assembly: Flybase version r6.31
Supplementary files format and content: Tab-separated value files
Supplementary files format and content: h5ad files contatining cell barcodes, age, cell-type information

organism: Drosophila melanogaster

source_name: Proximal femur

extract_protocol:
Proximal femurs from 666 flies (iav-Gal4>unc84-2xGFP; 2-3 days old) were dissected and put into 1.5ml RNAase free Eppendorf tubes, flash-frozen using liquid nitrogen, and stored at –80°C. Single-nucleus suspensions were prepared following the protocol we described previously (McLaughlin et al., 2022). Nuclei were stained by Hoechst-33342 (1:1000; >5min). Next, we collected nuclei using Fluorescence activated cell sorting (FACS). We used the BD Aria III sorter for collecting nuclei. Since the iav+ nuclei are labeled with nuclear GFP, we gated the population first by Hoechst signal and then by GFP. Nuclei were collected into a 1.5ml tube with 200ul 1x PBS with 0.5% BSA as the receiving buffer (RNase inhibitor added). In total 5,596 GFP+ nuclei were collected. Nuclei were spun down for 10 min at 1000g at 4 ̊C, and then re-suspended using 43.2ul 1x PBS with 0.5% BSA (RNase inhibitor added).
We performed snRNA-seq using the 10x Genomics system with 3’ v3.1 kit with following settings. All PCR reactions were performed using the Biorad C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. 13 cycles were used for cDNA amplification and 16 cycles were used for sample index PCR. As per 10x protocol, 1:10 dilutions of amplified cDNA and final libraries were evaluated on Agilent TapeStation. The final library was sent to Novogene Corporation Inc. for Illumina NovaSeq PE150 S4 partial lane sequencing with the single index configuration Read 1 28 cycles, Index 1 (i7) 8 cycles, and Read 2 91 cycles.

value: Proximal femur


title: tNCCs, treated 100uM cyclopamine, Sample4


title: Input_Azin2_KO_REP1


title: Input_Azin2_WT_REP2


title: Slow-twitch Muscle, tgPAC(Prdm1a:eGFP), Sample1


title: RNA from 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 6

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University, College of Veterinary Medicine Room #T7006, Vet Research Tower 618 Tower Rd.

department: Cell and Molecular Biology

institute: Cornell University

description: JT24_CKDL210013616-1a-GC10-GD05_HF532DSX2_L2

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq) or aligned and quantified using STAR/Salmon (RNA-seq)
smRNA- and RNA-seq data was normalized using DESeq2. smRNA-seq data was rlog transformed followed by limma batch correction.
Assembly: mm9 (small RNAseq) or vM10 (RNAseq).
Supplementary files format and content: Normalized counts

source_name: Humanized Male Adipose

extract_protocol: Libraries were prepared according to the protocol outlined in Chu, T. et al. Nature Genetics (2018)

treatment_protocol: 129S6/SvEvTac (WT and humanized for both sexes) mice expressing exposed to 400ppb of iAs for 4 weeks

value: male

tag: genetic modification

value: expressing the human ortholog of AS3MT

value: exposed to 400ppb of iAs


title: ALD1

description: 10x Genomics


title: Input_Azin2_KO_REP2


title: WT, Doxycycline 24h, rep 3

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

data_processing:
Read adapters were trimmed with the bbduk tool from bbtools (https://sourceforge.net/projects/bbmap/)
Paired-end reads were aligned to the human transcriptome reference sequence (Release 40; Obtained from www.gencodegenes.org) using kallisto
Expression values were summarized at the gene level using the lengthScaledTPM method from tximport
Inter experiment gene level expression data was scaled to library size with edgeR using the TMM method
Non-expressed genes were filtered out with filterByExpr function from edgeR; Unwanted and hidden sources of variation were removed from the data using sva; Differential gene expression analysis was performed using limma.
Assembly: hg38
Supplementary files format and content: tsv; gene-level lenght-scaled TPM values

source_name: adrenal cortex

growth_protocol: human adrenocortical carcinoma cell line HAC15 containing a CYP11B2 promoter-driven secreted Gaussia luciferase reporter (HAC15-B2Luc) were grown in DMEM-F12 containing 10% cosmic calf serum (CCS), 1% insulin-transferrin-selenium, and antibiotics (penicillin, streptomycin and gentamicin) and maintained in a 37°C humidified atmosphere (5% CO2).

extract_protocol:
Total RNA was extracted from cells using RNeasy plus mini kit (Qiagen, Valencia, CA). The purity and integrity of the RNA were checked spectroscopically using a Nano Drop spectrometer (Nano Drop Technologies).
10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method

treatment_protocol: Cells were transduced with the SLC30A1WT and SLC30A151_57del lentiviruses to generate the cell lines HAC15B2Luc-Doxy-SLC30A1WT and HAC15B2Luc-Doxy-SLC30A151_57del respectively, followed by antibiotic selection with geneticin (Gaussia luciferase selection marker, 1 mg/mL) and blasticidin (SLC30A1 selection marker, 2 µg/mL).  Cells were plated at a density of 75,000 cells/well in a 48-well dish for 48 hours. After incubation in a low serum medium (DMEM/F-12 containing 0.1% CCS and antibiotics) for 24 hours, expression of SLC30A1WT and SLC30A151_57del in the cells was initiated by addition of 1 μg/mL Doxy (Sigma Aldrich, St. Louis, MO) for the indicated times.

value: adrenal cortex

value: adrenocortical carcinoma cell line

value: SLC30A1 WT

value: Doxycycline 24h


title: CD4TCells_aGCA_rep11

value: CD4+ T cells

value: aGCA


title: CD4TCells_aGCA_rep12


title: CD4TCells_aGCA_rep15


title: Input_Azin2_WT_REP2b

value: Adipose

value: WT


title: CD4TCells_aGCA_rep10


title: H3K27ac_Azin2_WT_REP2


title: RNA from 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 5

description: JT23_CKDL210013616-1a-GB07-AK1880_HF532DSX2_L2

tag: strain


title: CD4TCells_aGCA_rep8


title: WT, Doxycycline 24h, rep 2

tag: genotype


title: H3K27ac_Azin2_WT_REP2b

tag: cell type


title: WT, Doxycycline 24h, rep 1

tag: treatment


title: RNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 4

description: JT22_CKDL210013616-1a-AK892-AK1874_HF532DSX2_L2

source_name: WT Male Adipose

value: expressing the mouse ortholog of AS3MT


title: RNA from 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 4

description: JT21_CKDL210013616-1a-7UDI315-AK895_HF532DSX2_L2


title: H3K27ac_Azin2_KO_REP8


title: RNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 6

description: JT19_CKDL210013616-1a-7UDI254-AK2329_HF532DSX2_L2

source_name: WT Female Adipose

value: female


title: RNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 6

description: JT18_CKDL210013616-1a-7UDI237-AK1867_HF532DSX2_L2

source_name: Humanized Female Adipose


title: H3K27ac_Azin2_KO_REP2


title: WT, Doxycycline 0h, rep 2

value: Doxycycline 0h


title: H3K27ac_Azin2_KO_REP1

value: Adipocyte Progenitor


title: WT, Doxycycline 0h, rep 1


title: RNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 5

description: JT17_CKDL210013616-1a-AK863-AK984_HF532DSX2_L2


title: RNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 5

description: JT16_CKDL210013616-1a-7UDI258-7UDI248_HF532DSX2_L2


title: Mutant, Doxycycline 24h, rep 3

value: SLC30A1 mutant


title: Mutant, Doxycycline 24h, rep 2


title: CD4TCells_aGCA_rep9


title: SAT_no_WT [RNA-seq]

data_processing:
RNA-Seq
Low quality nucleotides were removed Illumina fastq filterer/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner  using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENC
HTSeq-0.6.1p1  was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
Assembly: mm10
Supplementary files format and content: Tab-Delimited Gene-Wise Raw read counts text file

extract_protocol:
1 μg RNA was isolated from SAT/GAT with the Nucleospin RNA kit (Macherey-Nagel) and used for construction of sequencing libraries.
Strand-specific paired-end sequencing libraries from total RNA were constructed using TruSeq stranded Total RNA kit (Illumina Inc).

tag: strain background

value: subcutaneous adipose tissue

value: high-fat diet (60% kcal fat)


title: WT, Doxycycline 0h, rep 3


title: SAT_no_KO [RNA-seq]


title: Mutant, Doxycycline 24h, rep 1


title: RNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 5

description: JT15_CKDL210013616-1a-AK1875-AK1879_HF532DSX2_L2

value: expressing the human ortholog of AS3MT


title: H3K27ac_Azin2_WT_REP1


title: SAT_LWT [RNA-seq]


title: RNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 4

description: JT14_CKDL210013616-1a-AK899-AK1873_HF532DSX2_L2

value: exposed to 400ppb of iAs


title: Mutant, Doxycycline 0h, rep 3

value: adrenal cortex


title: SAT_LR_WT [RNA-seq]


title: CD4TCells_aGCA_rep3


title: CD4TCells_aGCA_rep7


title: CD4TCells_aGCA_rep1


title: CD4TCells_aGCA_rep4


title: Mutant, Doxycycline 0h, rep 2

value: adrenocortical carcinoma cell line


title: CD4TCells_aGCA_rep6


title: Mutant, Doxycycline 0h, rep 1


title: CD4TCells_aGCA_rep2


title: SAT_9921 [RNA-seq]


title: RNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 4

description: JT13_CKDL210013616-1a-AK1334-7UDI292_HF532DSX2_L2


title: RNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 3

description: JT8_CKDL210013616-1a-GH12-GF11_HF532DSX2_L2

source_name: WT Male Liver

extract_protocol: Libraries were prepared according to the NEBNext Ultra II Directional RNA kit protocol following PolyA enrichment

value: male

value: Liver


title: RNA from 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 3

description: JT9_CKDL210013616-1a-AK1863-GA03_HF532DSX2_L2

source_name: Humanized Male Liver


title: rhFGF19_100ng

first: Tianli

state: Shandong

address: 107 West Wenhua Road

department: Department of General Surgery

institute: Qilu Hospital of Shandong University

description: 50ng/ml rhFGF19 stimulation for 73 hours

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: hg19
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: human hepatic stellate cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (allwegene, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LX-2 cells

tag: agent


title: CD4TCells_HD_rep15

source_name: CD4+ T cells, HD

value: CD4+ T cells

value: HD


title: RNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 3

description: JT7_CKDL210013616-1a-AK844-AK1878_HF532DSX2_L2

source_name: WT Female Liver

tag: tissue


title: rhFGF19_50ng

description: 100ng/ml rhFGF19 stimulation for 72 hours


title: CD4TCells_aGCA_rep5

value: aGCA


title: CD4TCells_HD_rep14


title: RNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 2

description: JT6_CKDL210013616-1a-AK898-AK1872_HF532DSX2_L2

source_name: Humanized Female Liver


title: SAT_9918 [RNA-seq]

value: Adipose

value: WT


title: SAT_2R_KO [RNA-seq]


title: ND6 [RNA-seq]

value: low-fat diet (10% kcal fat)


title: CD4TCells_HD_rep13


title: vehicle

description: control group without hFGF19 stimulation

value: vehicle


title: SAT_LR_KO [RNA-seq]


title: RNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 2

description: JT4_CKDL210013616-1a-AK2044-AK1952_HF532DSX2_L2

value: female

value: expressing the mouse ortholog of AS3MT


title: RNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 2

description: JT5_CKDL210013616-1a-AK843-7UDI298_HF532DSX2_L2


title: RNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 3

description: JT3_CKDL210013616-1a-AK1853-7UDI283_HF532DSX2_L2

extract_protocol: Libraries were prepared according to the NEBNext Ultra II Directional RNA kit protocol following Ribosomales Depletion


title: gRNA readout in PC3, day21, replicate2

city: TAMPA

first: Liang

last: Wang

state: FL

address: 14059 Riveredge Drove

institute: Moffitt Cancer Center

description: Amplicon of gRNA integration

data_processing:
count_spacers.py (https://github.com/fengzhanglab/Screening_Protocols_manuscript/blob/master/count_spacers.py) was used to quantify gRNA count from Read1 file
Supplementary files format and content: Raw count matrix of gRNA, rows as gRNA design name, column as each sample
Library strategy: Amplicon-seq

source_name: prostate carcinoma bone metastasis

growth_protocol: All cells were screened in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA was extracted with a midi-prep kit with Rnase treatment.
gRNA integration was amplified from the gDNA of each sample. The gDNA amount was equivalent to at least 5 million cells.

treatment_protocol: Cells were passaged with a minimal number of 5 million (equivalent to 500-fold library size) after confirming single guide RNA integration (MOI ~ 0.3)

value: prostate carcinoma bone metastasis

tag: time point

value: Screening endpoint2


title: gRNA readout in PC3, day1, baseline

description: Amplicon of gRNA integration

value: Screening baseline


title: CD4TCells_HD_rep10


title: CD4TCells_HD_rep12


title: gRNA readout in PC3, day21, replicate1

description: Amplicon of gRNA integration

value: Screening endpoint1


title: ND1 [RNA-seq]

source_name: Adipose

value: subcutaneous adipose tissue


title: ND3 [RNA-seq]


title: CD4TCells_HD_rep7


title: CD4TCells_HD_rep9


title: RNA from 129S6/SvEvTac female mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 1

description: JT2_CKDL210013616-1a-7UDI228-7UDI200_HF532DSX2_L2

value: exposed to 400ppb of iAs


title: CD4TCells_HD_rep8


title: RNA from 129S6/SvEvTac female mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 1

description: JT1_CKDL210013616-1a-AK690-7UDI304_HF532DSX2_L2

value: expressing the human ortholog of AS3MT

value: Liver


title: gRNA readout in DU145, day21, replicate2

description: Amplicon of gRNA integration

source_name: prostate carcinoma brain metastasis

value: prostate carcinoma brain metastasis


title: GAT_R_WT [RNA-seq]

value: epigonadal adipose tissue

value: high-fat diet (60% kcal fat)


title: gRNA readout in DU145, day21, replicate1

description: Amplicon of gRNA integration


title: gRNA readout in DU145, day1, baseline

description: Amplicon of gRNA integration


title: GAT_no_WT [RNA-seq]

value: Adipose


title: GAT_R_KO [RNA-seq]


title: ND5 [RNA-seq]

value: WT


title: CD4TCells_HD_rep6

value: CD4+ T cells

value: HD


title: GAT_no_KO [RNA-seq]


title: RNA from 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 1

description: JT11_CKDL210013616-1a-AK850-AK2430_HF532DSX2_L2

value: male


title: RNA from 129S6/SvEvTac male mice expressing the human ortholog of AS3MT exposed to 400ppb of iAs 2

description: JT12_CKDL210013616-1a-AK2045-AK2431_HF532DSX2_L2


title: gRNA readout in BPH1, day21, replicate2

description: Amplicon of gRNA integration

source_name: immortalized benign prostatic hyperplasia


title: CD4TCells_HD_rep3


title: RNA from 129S6/SvEvTac male mice expressing the mouse ortholog of AS3MT exposed to 400ppb of iAs 1

description: JT10_CKDL210013616-1a-AK889-7UDI229_HF532DSX2_L2

value: expressing the mouse ortholog of AS3MT


title: CD4TCells_HD_rep4


title: RNA-seq in PC3, shRUVBL1, replicate2

description: RNA-seq of stable knockdown experiments

data_processing:
bowtie2 based rsem was used to quantify gene expression from RNA-seq data with ensembl GRCh38 fasta and gtf references
Supplementary files format and content: rsem expected count and FPKM matrix in each cell line, with rows as gene stable id, and column as each sample name. A result file for each sample also attached for other possible analysis

extract_protocol:
Total RNA was extracted with mini-prep kit with Dnase digestion
RNA libraries for RNA-seq were prepared using standard RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were infected with lentivirus enveloped with either shRNA control or shRNA targeting RUVBL1 at low MOI, 0.5~0.7

value: prostate carcinoma bone metastasis


title: gRNA readout in BPH1, day21, replicate1

description: Amplicon of gRNA integration

value: immortalized benign prostatic hyperplasia


title: GAT_LR_WT [RNA-seq]


title: GAT_L_KO [RNA-seq]


title: gRNA readout in BPH1, day1, baseline

description: Amplicon of gRNA integration

value: Screening baseline


title: GAT_LR_KO [RNA-seq]


title: Mammary tumor DTX, Replicate 2, scRNAseq

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: 615 Michael Street, Whitehead Biomedical Research Building

department: Department of Pediatrics

institute: Emory University

description: 10x Genomics

data_processing:
scRNA-Seq data after standard quality control was aligned to the reference genome (genome="mm10", version="2020-A") using the 10x Cell Ranger pipeline. Preprocessed and filtered normalized data were subjected to unsupervised analysis using principal component analysis (PCA) (Seurat v2.0 Bioconductor package) to identify principal components with significant variation that was used as input for UMAP analysis to determine overall relationship among cells.
Assembly: mm10
Supplementary files format and content: Barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: Mammary fat pad

extract_protocol:
For in vitro experiments multi-cellular tumor stromal spheroids treated with VEH or DTX were digested with TrypLE and Accumax and passed through 40 µm strainers to obtain single cell suspension, which was processed using 10x Genomics kits. For in vivo experiments, 4th mammary fat pads (mfp) were collected from mice at necropsy. To prepare for flow cytometric analysis, mfp was digested in DMEM/F-12 (1:1) media containing collagenase, hyaluronidase, DNase I, and passed through a 70 µm strainer to obtain a single cell suspension. Red blood cells were lysed using the ACK lysis buffer. After which cells were processed using 10x Genomics kits.
ScRNA-seq libraries were prepared using the Next GEM Chromium single cell 3′ reagent kits V3.1 with feature barcode technology for cell surface protein (10x Genomics) and sequenced using NextSeq 500 high output kits and Novaseq S4 PE100 kits (Illumina).

value: D2.0R injected in the mfp

value: Tumor

value: Mammary fat pad

value: Balb/c

tag: age

value: 6-8 weeks


title: Mammary tumor VEH, Replicate 2, scRNAseq

description: 10x Genomics


title: CD4TCells_HD_rep5


title: CAR + GMCSF-CCR (20211027_30102615270522-01_Sample10_10)

city: London

first: Matteo

last: Righi

state: --None--

address: The MediaWorks, 191 Wood Lane

institute: Autolus Therapeutics

description: total mRNA from  activated CAR T cells expressing GMCSF CCR

hyb_protocol: CodeSet Hybridization Setup MAN-10056 (https://www.nanostring.com/download_file/view/863/3778) + nCounter SPRINT® Profiler User Manual MAN-10017 (https://www.nanostring.com/download_file/view/254/3778)

scan_protocol: nCounter® Sprint Profiler

data_processing: nCounter® Sprint Profiler

source_name: Transduced T cells

extract_protocol: Total mRNA was collected using the PureLink RNA Mini Kit (ThermoFisher) following manufacturer protocol.

treatment_protocol: CAR T cells grown for 24h with or without CAR activation via anti GD2 scFv idiotype

tag: individual

value: CAR T cell

tag: activation status

value: activated CAR T cells

tag: expressing

value: GMCSF CCR


title: RNA-seq in PC3, shRUVBL1, replicate1

description: RNA-seq of stable knockdown experiments


title: CAR + IL18-CCR (20211027_30102615270522-01_Sample12_12)

description: total mRNA from  activated CAR T cells expressing IL18 CCR

value: IL18 CCR


title: Mammary tumor DTX, Replicate 1, scRNAseq

description: 10x Genomics


title: CD4TCells_HD_rep2


title: CD4TCells_HD_rep1


title: GAT_9921 [RNA-seq]

value: Adipose

value: epigonadal adipose tissue

value: WT

value: high-fat diet (60% kcal fat)


title: CAR (20211027_30102615270522-01_Sample07_07)

description: total mRNA from  activated CAR T cells

value: control


title: RNA-seq in PC3, shRNA control, replicate2

description: RNA-seq of stable knockdown experiments

value: prostate carcinoma bone metastasis

value: shRNA control


title: CAR + IL7-CCR (20211027_30102615270522-01_Sample09_09)

description: total mRNA from  activated CAR T cells expressing IL7 CCR

value: IL7 CCR


title: CAR + IL2-CCR (20211027_30102615270522-01_Sample08_08)

description: total mRNA from  activated CAR T cells expressing IL2 CCR

value: IL2 CCR


title: HFD6 [RNA-seq]

value: subcutaneous adipose tissue


title: RNA-seq in PC3, shRNA control, replicate1

description: RNA-seq of stable knockdown experiments


title: HFD5 [RNA-seq]


title: CAR + IL18-CCR (20211027_30102615270522-01_Sample06_06)

description: total mRNA from non activated CAR T cells expressing IL18 CCR

value: non activated CAR T cells


title: RNA-seq in BPH1, shRUVBL1, replicate2

description: RNA-seq of stable knockdown experiments

value: immortalized benign prostatic hyperplasia


title: HFD4 [RNA-seq]


title: Trip co-culture 3D, scRNAseq

description: 10x Genomics

source_name: 3D culture in RGF BME

value: Cancer cells, Endothelial cells and Fibroblasts

value: 3D culture in RGF BME


title: Mammary tumor VEH, Replicate 1, scRNAseq

description: 10x Genomics

value: D2.0R injected in the mfp

value: Tumor

value: Mammary fat pad

value: Balb/c

value: 6-8 weeks


title: RNA-seq in BPH1, shRNA control, replicate2

description: RNA-seq of stable knockdown experiments


title: HFD3 [RNA-seq]

value: Adipose

value: WT


title: RNA-seq in BPH1, shRUVBL1, replicate1

description: RNA-seq of stable knockdown experiments


title: CAR + GMCSF-CCR (20211027_30102615270522-01_Sample04_04)

description: total mRNA from non activated CAR T cells expressing GMCSF CCR

value: CAR T cell

value: GMCSF CCR


title: CONTROL_rep2

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were first trimmed by adapter sequence (CTGTCTCTTATACACATCT) in the forward and reverse directions using Cutadapt with default parameters.
Subsequent analysis of the data was conducted according to a published protocol with no modification (protocols.io DOI: 10.17504/protocols.io.bjk2kkye). Reads were aligned to the mm10 mouse genome, and samples were spike-in normalized according to the protocol by calculating a scale factor from reads aligning to the E. coli genome. Peak calling for both WT and ARM-mutant samples was conducted using the Seacr algorithm using the “non” (non-normalized) and “stringent” parameters.
Assembly: mm10
Supplementary files format and content: bed

source_name: V6.5 mESC

growth_protocol: Murine embryonic stem cells were cultured in 2i/LIF media on tissue culture plates coated with 0.2% gelatin (Sigma, G1890). The 2i/LIF media contained: 960 mL DMEM/F12 (Life Technologies, 11320082), 5 mL N2 supplement (Life Technologies, 17502048; stock 100X), 10 mL B27 supplement (Life Technologies, 17504044; stock 50X), 5 mL additional L-glutamine (GIBCO 25030-081; stock 200 mM), 10 mL MEM nonessential amino acids (GIBCO 11140076; stock 100X), 10 mL penicillin-streptomycin (Life Technologies, 15140163; stock 10^4 U/mL), 333 mL BSA fraction V (GIBCO 15260037; stock 7.50%), 7 mL b-mercaptoethanol (Sigma M6250; stock 14.3 M), 100 mL LIF (Chemico, ESG1107; stock 10^7 U/mL), 100 mL PD0325901 (Stemgent, 04-0006-10; stock 10 mM), and 300 mL CHIR99021 (Stemgent, 04-0004-10; stock 10 mM).

extract_protocol:
CUT&Tag was performed according to manufacturer instructions for the CUT&Tag-IT Assay Kit (Active Motif 53160)
Libraries were constructed according to manufacturer instructions for the CUT&Tag-IT Assay Kit (Active Motif 53160)
CUT&Tag

treatment_protocol: Cells were treated with 1 µg/mL doxycyline for 6 hours.

value: V6.5 mESC

value: Murine embryonic stem cell

value: EMPTY-transgene

tag: antibody

value: HA ab (Abcam ab9110)


title: RNA-seq in BPH1, shRNA control, replicate1

description: RNA-seq of stable knockdown experiments

value: shRNA control


title: 3D D2.0R, scRNAseq

description: 10x Genomics

value: Cancer cells


title: TSO DTX, scRNAseq

description: 10x Genomics

value: Cancer cells, Endothelial cells and Fibroblasts


title: CAR + IL7-CCR (20211027_30102615270522-01_Sample03_03)

description: total mRNA from non activated CAR T cells expressing IL7 CCR

value: non activated CAR T cells

value: IL7 CCR


title: CONTROL_rep1


title: Lateral choroid plexus, Postnatal day 63, Mbnl2 KO, sample 2

city: Gainesville

first: Curtis

last: Nutter

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description:
rRNA depleted
Adult_2KO_2

data_processing:
aligned using STAR
alignment analyzed using rMATS
alignment analyzed using DESEQ2
alignment analyzed using HOMER
Assembly: GRCm38/mm10
Supplementary files format and content: DataFileS1_Nutter_Final is an excel file which contains tabs with paired group comparisons of alternative splicing changes from rMATS or differential expression from DESeq2. There are also tabs with gene counts for all expressed genes for all sample groups.

source_name: choroid plexus, lateral

extract_protocol:
All animal procedures were conducted in accordance with NIH Guidelines and approved by the UF IACUC. Mbnl2-/- knockout (Mbnl2 KO) mice were generated previously and bred to obtain congenic (N10) animals on the FVB/NJ background. Timed mating’s were performed to obtain littermate wild-type FVB/NJ and Mbnl2-/- (KO) prenatal timepoint embryos, and embryonic timepoints (E13.5) were collected followed by choroid plexus (ChP) isolation. Postnatal timepoint (P1, P14, and P63) mice were euthanized and the ChP isolated. For ChP isolation, mice were euthanized, and the brain carefully transferred to cold PBS. To isolate the LVChP, the brain was cut coronally approximately 1/3 from the top to open the lateral ventricles. The lateral ventricles were identified and carefully opened to allow visualization and removal of the LVChP by gentle separation along the base. Individual ChP samples were genotyped, sex identified, and RNA isolated. Before library preparation, RNA samples were evaluated and pooled (2-4) for sufficient RNA. All experiments prior to P21 were comprised of equal numbers of males/females, in contrast to P21+ which were all males. Females were needed to generate additional embryonic timepoints.
For RNA isolation, tissue samples were homogenized in 300 μL TRI Reagent (Zymo R2050-1-200) and incubated at 25ºC for 10 min. Total RNA was isolated using the Direct-zol RNA miniprep kit (Zymo), following the manufacturer’s instructions, including an on-column DNase I digestion step. RNA concentration was determined using the Qubit 4 Fluorometer with a broad range RNA quantification broad range kit (Invitrogen). RNA quality was checked using a Fragment Analyzer (Agilent) and depleted of rRNA (rRNA Depletion Kit v2 Human/Mouse/Rat, NEB).
cDNA libraries prepared using the Ultra II Directional RNA Library, NEB. Mouse developmental ChP libraries were generated using 168 ng of total RNA input and sequenced on Illumina NextSeq500 platform.

value: choroid plexus, lateral

value: FVB/NJ

tag: Sex

value: male

tag: developmental stage

value: Postnatal day 63


title: CAR + IL2-CCR (20211027_30102615270522-01_Sample02_02)

description: total mRNA from non activated CAR T cells expressing IL2 CCR

value: IL2 CCR


title: CAR + IL18-CCR (20211026_30102615290522-01_Sample11_11)

value: activated CAR T cells

value: IL18 CCR


title: CAR (20211027_30102615270522-01_Sample01_01)

description: total mRNA from non activated CAR T cells

value: CAR T cell

value: control


title: SOX2-MU_rep2

tag: cell line

value: V6.5 mESC

value: Murine embryonic stem cell


title: Lateral choroid plexus, Postnatal day 63, Mbnl2 KO, sample 1

description:
rRNA depleted
Adult_2KO_1


title: SOX2-MU_rep1

value: HA ab (Abcam ab9110)


title: Lateral choroid plexus, Postnatal day 14, Mbnl2 KO, pool 3

description:
rRNA depleted
P14_2KO_3

value: pooled male and female

value: Postnatal day 14


title: TSO VEH, scRNAseq

description: 10x Genomics

value: Cancer cells, Endothelial cells and Fibroblasts

value: 3D culture in RGF BME


title: CAR + GMCSF-CCR (20211026_30102615290522-01_Sample10_10)

value: GMCSF CCR


title: CAR + IL7-CCR (20211026_30102615290522-01_Sample09_09)

value: IL7 CCR


title: Lateral choroid plexus, Postnatal day 14, Mbnl2 KO, pool 2

description:
rRNA depleted
P14_2KO_2

value: choroid plexus, lateral

value: FVB/NJ


title: SOX2-WT_rep2


title: Lateral choroid plexus, Postnatal day 63, Mbnl2 KO, sample 3

description:
rRNA depleted
Adult_2KO_3

value: male

value: Postnatal day 63


title: KLF4-MU_rep2


title: SOX2-WT_rep1


title: CAR + IL2-CCR (20211026_30102615290522-01_Sample08_08)

value: activated CAR T cells

value: IL2 CCR


title: KLF4-MU_rep1


title: CD4TCells_HD_rep11

extract_protocol: CD3+ CD4+ T cells were sequentially isolated from PBMCs of aGCA or HD using Dynabeads Untouched Human T Cells kit and Dynabeads CD4+ isolation kit (Thermofisher Scientific). Sample purities were assessed afterwards and were all > 95%. Total RNA from CD4+ T cells was then extracted using the NucleoSpin RNA kit (Macherey-Nagel) and quantified by a NanoDrop 1000 spectrophotometer. 5 samples with RNA concentration < 20ng/µL were excluded. For quality control, RNA dilution was performed using Agilent RNA 6000 Nano Kit and 1µL of the sample was run on the Nano chip using an Agilent 2100 electrophoresis bioanalyzer. The quality of total RNA was assessed using the profile of the electropherogram and the RNA integrity number (RIN) was calculated. The whole samples showed RINs between 7.1 and 9.5. For Illumina Beadarrays, cRNA samples were prepared using Illumina TotalPre-96 RNA Amp kit (LifeTechnologies) and hybridized to Illumina Human HT-12 v4 beadarrays.

value: CD4+ T cells

tag: group

value: HD


title: Lateral choroid plexus, Postnatal day 1, Mbnl2 KO, pool 3

description:
rRNA depleted
P1_2KO_3

tag: strain

value: Postnatal day 1


title: WT_cort4

city: San Diego

first: Tiziano

last: Pramparo

address: 3611 Valley Centre Drive

department: R&D

institute: Travere

description:
SAMPLE 24
WT vehicle sample 4

data_processing:
Raw counts were normalized using the average value across biological replicates of five reference genes (ACTB, B2M, GAPFH, HPRT1, RPLP0).
Fold changes (FC) were calculated as the ratio of the normalized gene expression in the test sample to the normalized gene expression in the control sample (2-ΔCt). P values were calculated based on a Student’s t test of the replicate 2-ΔCt values for each gene in the control group and test groups, and unadjusted P values <0.05 were considered for downstream analyses.

label: SYBR

source_name: cortex

growth_protocol: Animals were housed in rooms with 70°F temperature, 55% relative humidity and a 14/10-h light/dark cycle. Animals had free access to rodent chow and water.

extract_protocol: Kidney cortical glomeruli were isolated following transcardiac perfusion with 4-μM Dynabeads

treatment_protocol: Mice were given vehicle (0.5% methylcellulose 4000 cps, 0.25% Tween-80 in distilled water) or sparsentan by oral gavage once daily.

tag: condition

value: WT

value: cortex

value: vehicle

value: week 7


title: Lateral choroid plexus, Postnatal day 1, Mbnl2 KO, pool 2

description:
rRNA depleted
P1_2KO_2

value: pooled male and female

tag: genotype


title: WT_cort3

description:
SAMPLE 23
WT vehicle sample 3

tag: treatment


title: 11w_tyk2_ko_beta-cells

city: Saga City

first: Keiichiro

last: Mine

state: Saga

address: 5-1-1 Nabeshima

institute: Saga university

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

source_name: purified pancreatic beta-cells from Tyk2 gene knockout NOD mice

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: NOD

value: pancreatic beta-cells

tag: gender

value: female

value: Tyk2 gene knockout


title: 11w_tyk2_wt_beta-cells

source_name: purified pancreatic beta-cells from wild type NOD mice

value: wild type


title: CAR + GMCSF-CCR (20211026_30102615290522-01_Sample04_04)

tag: cell type

value: CAR T cell

value: non activated CAR T cells

value: GMCSF CCR


title: CAR + IL18-CCR (20211026_30102615290522-01_Sample05_05)

value: IL18 CCR


title: WT_cort2

description:
SAMPLE 22
WT vehicle sample 2

tag: tissue


title: 6w_tyk2_ko_beta-cells


title: KLF4-WT_rep2

value: V6.5 mESC

value: Murine embryonic stem cell

value: HA ab (Abcam ab9110)


title: 6w_tyk2_wt_beta-cells


title: Lateral choroid plexus, Postnatal day 1, Mbnl2 KO, pool 1

description:
rRNA depleted
P1_2KO_1

value: choroid plexus, lateral

value: FVB/NJ

value: Postnatal day 1


title: KLF4-WT_rep1


title: Lateral choroid plexus, Embryonic day 13.5, Mbnl2 KO, pool 2

description:
rRNA depleted
E13_2KO_2

value: Embryonic day 13.5


title: WT_cort1

description:
SAMPLE 21
WT vehicle sample 1

value: WT

value: cortex

value: vehicle

value: week 7


title: Lateral choroid plexus, Postnatal day 14, Mbnl2 KO, pool 1

description:
rRNA depleted
P14_2KO_1

value: pooled male and female

value: Postnatal day 14


title: CAR + IL7-CCR (20211026_30102615290522-01_Sample03_03)

value: CAR T cell

value: IL7 CCR


title: AS_SP_cort4

description:
SAMPLE 20
Alport treated sparsentan sample 4

value: Alport

value: sparsentan


title: AS_SP_cort3

description:
SAMPLE 19
Alport treated sparsentan sample 3


title: CAR + IL2-CCR (20211026_30102615290522-01_Sample02_02)

value: non activated CAR T cells

value: IL2 CCR


title: CAR (20211026_30102615290522-01_Sample07_07)

description: total mRNA from  activated CAR T cells

value: activated CAR T cells

value: control


title: Puberty LC ER+ 2

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations Grcm38.87 and normalized to 20 millions of aligned reads.
Assembly: Grcm38 / mm10
Supplementary files format and content: .csv / Normalized gene expression

source_name: mammary gland

extract_protocol:
RNA extraction from FACS isolated cells was performed using Rneasy micro kit (QIAGEN) according to the manufacturer's recommendations.
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: mammary gland

value: ER+ luminal cells

value: ERrtTA/TetOCre/rosaYFP


title: Lateral choroid plexus, Embryonic day 13.5, Mbnl2 KO, pool 1

description:
rRNA depleted
E13_2KO_1

value: choroid plexus, lateral

value: FVB/NJ

value: Embryonic day 13.5


title: Puberty LC ER+ 1


title: CAR + IL18-CCR (20210819_30102615310522-01_Sample12_12)

value: IL18 CCR


title: Lateral choroid plexus, Postnatal day 63, wild type, sample 3

description:
rRNA depleted
Adult_wt_3

value: male

value: wild type

value: Postnatal day 63


title: CAR (20211026_30102615290522-01_Sample01_01)

value: CAR T cell


title: Puberty LC ER- 2

value: ER- luminal cells


title: Lateral choroid plexus, Postnatal day 63, wild type, sample 2

description:
rRNA depleted
Adult_wt_2


title: Lateral choroid plexus, Postnatal day 63, wild type, sample 1

description:
rRNA depleted
Adult_wt_1


title: AS_SP_cort2

description:
SAMPLE 18
Alport treated sparsentan sample 2

value: Alport

value: cortex

value: sparsentan

value: week 7


title: Lateral choroid plexus, Postnatal day 14, wild type, pool 3

description:
rRNA depleted
P14_wt_3

value: pooled male and female

value: Postnatal day 14


title: Puberty LC ER- 1

value: mammary gland


title: AS_cort3

description:
SAMPLE 15
Alport vehicle sample 3

value: vehicle


title: AS_SP_cort1

description:
SAMPLE 17
Alport treated sparsentan sample 1


title: Puberty BC 1

value: BC luminal cells

value: ERrtTA/TetOCre/rosaYFP


title: Puberty BC 2


title: Lateral choroid plexus, Postnatal day 14, wild type, pool 2

description:
rRNA depleted
P14_wt_2

value: choroid plexus, lateral

value: FVB/NJ


title: Pregnancy LC ER+ 2

value: ER+ luminal cells


title: AS_cort4

description:
SAMPLE 16
Alport vehicle sample 4


title: AS_cort2

description:
SAMPLE 14
Alport vehicle sample 2


title: CAR (20210819_30102615310522-01_Sample07_07)

description: total mRNA from  activated CAR T cells

value: activated CAR T cells

value: control


title: CAR + IL2-CCR (20210819_30102615310522-01_Sample08_08)

value: CAR T cell

value: IL2 CCR


title: Pregnancy LC ER+ 1


title: Lateral choroid plexus, Postnatal day 1, wild type, pool 3

description:
rRNA depleted
P1_wt_3

value: wild type

value: Postnatal day 1


title: Lateral choroid plexus, Postnatal day 14, wild type, pool 1

description:
rRNA depleted
P14_wt_1


title: CAR + GMCSF-CCR (20210819_30102615310522-01_Sample10_10)

value: GMCSF CCR


title: CAR + IL18-CCR (20210819_30102615310522-01_Sample06_06)

value: non activated CAR T cells

value: IL18 CCR


title: WT_glom4

description:
SAMPLE 12
WT vehicle sample 4

source_name: glomerulus

value: WT

value: glomerulus

value: week 7


title: AS_cort1

description:
SAMPLE 13
Alport vehicle sample 1

value: Alport

value: cortex

value: vehicle


title: CAR + GMCSF-CCR (20210819_30102615310522-01_Sample04_04)


title: Pregnancy LC ER- 1

value: mammary gland

value: ER- luminal cells

value: ERrtTA/TetOCre/rosaYFP


title: Lateral choroid plexus, Postnatal day 1, wild type, pool 2

description:
rRNA depleted
P1_wt_2

value: choroid plexus, lateral

value: FVB/NJ

value: pooled male and female


title: CAR + IL7-CCR (20210819_30102615310522-01_Sample03_03)

value: CAR T cell

value: IL7 CCR


title: CAR + IL7-CCR (20210819_30102615310522-01_Sample09_09)

value: activated CAR T cells


title: Pregnancy BC 2

value: BC luminal cells


title: Lateral choroid plexus, Embryonic day 13.5, wild type, pool 3

description:
rRNA depleted
E13_wt_3

value: wild type

value: Embryonic day 13.5


title: WT_glom2

description:
SAMPLE 10
WT vehicle sample 2

value: WT

value: glomerulus


title: CAR + IL2-CCR (20210819_30102615310522-01_Sample02_02)

value: non activated CAR T cells

value: IL2 CCR


title: Lateral choroid plexus, Embryonic day 13.5, wild type, pool 2

description:
rRNA depleted
E13_wt_2


title: Pregnancy LC ER- 2


title: Adult LC ER+ 2

value: ER+ luminal cells


title: Lateral choroid plexus, Embryonic day 13.5, wild type, pool 1

description:
rRNA depleted
E13_wt_1


title: WT_glom1

description:
SAMPLE 9
WT vehicle sample 1

value: vehicle

value: week 7


title: Adult LC ER+ 1

value: mammary gland

value: ERrtTA/TetOCre/rosaYFP


title: WT1

city: Bethesda

first: Kai

last: Yu

state: Maryland

address: 50 South Drive, Bldg 50, Room 5151

institute: NHGRI

description: 10x Genomics

data_processing:
Sequences from the Chromium platform were de-multiplexed and aligned using CellRanger ver. 3.1.0 from 10x Genomics
Assembly: mm10
Supplementary files format and content: The file "filtered_feature_bc_matrix.h5" is the aggregated data, read-depth normalized. This file was used for all downstream analyses.

source_name: bone marrow

extract_protocol:
Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium.
Single-cell RNA-seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis, cDNA preparation and library construction was prepared following the manufacturers protocol.

value: bone marrow

value: sorted c-Kit+ cells


title: CAR (20210819_30102615310522-01_Sample01_01)

value: CAR T cell

value: control


title: CAR + IL18-CCR (20210818_30102615420522-01_Sample12_12)

value: activated CAR T cells

value: IL18 CCR


title: Adult LC ER- 2

value: ER- luminal cells


title: AS_SP_glom3

description:
SAMPLE 7
Alport treated sparsentan sample 3

value: Alport

value: sparsentan


title: WT_glom3

description:
SAMPLE 11
WT vehicle sample 3

value: WT

value: glomerulus


title: Lateral choroid plexus, Postnatal day 1, wild type, pool 1

description:
rRNA depleted
P1_wt_1

value: choroid plexus, lateral

value: FVB/NJ

value: pooled male and female

value: wild type

value: Postnatal day 1


title: CAR + IL7-CCR (20210818_30102615420522-01_Sample09_09)

value: IL7 CCR


title: CAR + GMCSF-CCR (20210818_30102615420522-01_Sample10_10)

value: GMCSF CCR


title: PRE1

description: 10x Genomics

value: bone marrow

value: sorted c-Kit+ cells


title: Adult LC ER- 1

value: mammary gland

value: ERrtTA/TetOCre/rosaYFP


title: AS_SP_glom2

description:
SAMPLE 6
Alport treated sparsentan sample 2

value: week 7


title: AS_SP_glom1

description:
SAMPLE 5
Alport treated sparsentan sample 1


title: CAR + IL2-CCR (20210818_30102615420522-01_Sample08_08)

value: CAR T cell

value: activated CAR T cells

value: IL2 CCR


title: Adult BC 2

value: basal cells


title: Pregnancy BC 1

value: BC luminal cells


title: CAR (20210818_30102615420522-01_Sample07_07)

description: total mRNA from  activated CAR T cells

value: control


title: AS_glom4

description:
SAMPLE 4
Alport vehicle sample 4

value: Alport

value: glomerulus

value: vehicle


title: Neg_Control, replicate 4, scRNAseq

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Seurat Object rds file

source_name: lymph node

extract_protocol:
Metastases from tumor-bearing mice were microsurgically dissected using sterile micro-surgical tools. SS, IF and F regions were dissected in negative controls. Later, samples were disrupted into single cell suspension as described for flow cytometry, using sterile nuclease-free tools. Single cells were barcoded using the 10x Chromium Single Cell platform, and cDNA libraries were prepared according to the manufacturer’s protocol (Single Cell 3′ v3, 10x Genomics, USA). In brief, cell suspensions, reverse transcription master mix and partitioning oil were loaded on a single cell chip, then run on the Chromium Controller. Reverse Transcription was performed within the droplets at 53 °C for 45 minutes. cDNA was amplified for a 12 cycles total on a Biometra thermocycler. cDNA size selection was performed using SpriSelect beads (Beckman Coulter, USA) and a ratio of SpriSelect reagent volume to sample volume of 0.6. cDNA was analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 minutes at 32 °C, followed by end repair and A-tailing at 65 °C for 30 minutes. cDNA was double-sided size selected using SpriSelect beads. Sequencing adaptors were ligated to the cDNA at 20 °C for 15 minutes. cDNA was amplified using a sample-specific index oligo as a primer, followed by another round of double-sided size selection using SpriSelect beads. Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for quality control. cDNA libraries were sequenced on a  281 NextSeq500 Illumina platform aiming for 50,000 reads per cell. Base calls were converted to reads with the software Cell Ranger (10x Genomics; version 3.1)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: lymph node

tag: treatment group


title: AS_SP_glom4

description:
SAMPLE 8
Alport treated sparsentan sample 4

value: sparsentan

tag: age


title: CAR + IL18-CCR (20210818_30102615420522-01_Sample06_06)

tag: individual

value: non activated CAR T cells

value: IL18 CCR


title: Neg_Control, replicate 3, scRNAseq

description: 10x Genomics


title: Puberty LC ER-

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “HEADCROP:10 CROP:70 ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60”
ATAC-seq paired-end reads were then aligned to mouse genome Grcm38 using Bowtie2 (version 2.2.6) using options “-X 2000 --fr --very-sensitive --no-discordant --no-unal --no-mixed –non-deterministic”.
Mitochondrial reads, reads from unmapped or random contigs and reads with a mapping quality less than 20 were removed using samtools.
Duplicate reads were removed by Picard tools.
Peak calling was performed on each individual sample by macs2 (version 2.1.0.20151222) using options “-f BAMPE -g mm -q 0.05 --nomodel --call-summits -B –SPMR”
Assembly: Grcm38/mm10
Supplementary files format and content: .txt / quantified peak intensity,
Supplementary files format and content: .bigwig / display of continuous-valued data in track format

extract_protocol:
100000 sorted cells were collected in 1mL of PBS supplemented with 3% FBS at 4oC. Cells were centrifuged and cell pallets were resuspended in 100ul of lysis buffer (TrisHCl 10mM, NaCl 10mM, MgCl2 3mM, Igepal 0.1%) and centrifuged at 500g for 25 minutes at 4oC. Supernatant was carefully discarded and nuclei were resuspended in 50ul of reaction buffer (Tn5 transposase 2.5ul, TD buffer 22.5ul, from Nextera DNA sample preparation kit, Illumina, and 25ul H20). The reaction was performed at 37oC for 30min and was stopped by addition of 5ul of clean up buffer (NaCl 900mM, EDTA 300mM). DNA was purified using the MiniElute purification kit (QIAGEN) following manufacturer protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations.
DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations

value: ER- luminal cells


title: Neg_Control, replicate 2, scRNAseq

description: 10x Genomics


title: AS_glom2

description:
SAMPLE 2
Alport vehicle sample 2


title: CAR + GMCSF-CCR (20210818_30102615420522-01_Sample04_04)

tag: activation status

value: GMCSF CCR


title: Puberty LC ER+

value: mammary gland

value: ER+ luminal cells

value: ERrtTA/TetOCre/rosaYFP


title: AS_glom1

description:
SAMPLE 1
Alport vehicle sample 1

value: week 7


title: Puberty BC


title: Neg_Control, replicate 1, scRNAseq

description: 10x Genomics


title: CAR + IL7-CCR (20210818_30102615420522-01_Sample03_03)

value: CAR T cell

tag: expressing

value: IL7 CCR


title: Sample 11_MB4_GlcNAc-2

city: Eugene

first: Timothy

middle: Jarrod

last: Smith

state: Oregon

address: 1229 University of Oregon

institute: University of Oregon

data_processing:
Quality control and adapter trimming was performed with bcl2fastq
Read mapping was performed with HISAT2
Read quantification was performed using Subread’s featureCounts
Read counts were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm
Subsequent values were then converted to counts per million (cpm).
Assembly: GCF_000801015.1
Supplementary files format and content: Tab-delimited text file with  with cpm values for each sample

organism: Aeromonas sp. ZOR0001

source_name: Aer01 isolate

extract_protocol:
RNA was harvested using Rneasy mini plus kit (QIAGEN)
RNA libraries for RNA-seq were prepared by SeqCenter as detailed at https://www.seqcenter.com/illumina-dna-sequencing/

value: Aer01 isolate

value: 0.4% GlcNAc


title: Control, replicate 6, scRNAseq

description: 10x Genomics

value: control


title: Sample 9_MB1_GlcNAc-3


title: LEU1

description: 10x Genomics

value: bone marrow

value: sorted c-Kit+ cells


title: Sample 10_MB4_GlcNAc-1


title: Adult BC 1

value: basal cells


title: CAR + IL2-CCR (20210818_30102615420522-01_Sample02_02)

value: IL2 CCR


title: Pregnancy LC ER-


title: Control, replicate 5, scRNAseq

description: 10x Genomics

value: lymph node


title: Pregnancy BC


title: Sample 8_MB1_GlcNAc-2


title: CAR (20210818_30102615420522-01_Sample01_01)

value: non activated CAR T cells


title: Sample 7_MB1_GlcNAc-1


title: Adult LC ER-

value: ER- luminal cells


title: CAR + IL18-CCR (20210817_30102615320522-01_Sample12_12)

value: activated CAR T cells

value: IL18 CCR


title: Pregnancy LC ER+

value: mammary gland

value: ER+ luminal cells


title: Treated, replicate 2, scRNAseq

description: 10x Genomics

value: treated


title: Treated, replicate 4, scRNAseq

description: 10x Genomics


title: Treated, replicate 1, scRNAseq

description: 10x Genomics


title: Adult LC ER+

value: ERrtTA/TetOCre/rosaYFP


title: Sample 6_WT_GlcNAc-3

value: WT


title: Adult BC


title: CAR + IL7-CCR (20210817_30102615320522-01_Sample09_09)

value: CAR T cell

value: IL7 CCR


title: Sample 5_WT_GlcNAc-2

value: Aer01 isolate

value: 0.4% GlcNAc


title: Treated, replicate 3, scRNAseq

description: 10x Genomics


title: Control, replicate 4, scRNAseq

description: 10x Genomics

value: control


title: CAR + GMCSF-CCR (20210817_30102615320522-01_Sample10_10)

description: total mRNA from  activated CAR T cells expressing GMCSF CCR

value: GMCSF CCR


title: Sample 4_WT_GlcNAc-1


title: AS_glom3

state: CA

description:
SAMPLE 3
Alport vehicle sample 3

value: Alport

value: glomerulus

value: vehicle

value: week 7


title: Control, replicate 3, scRNAseq

description: 10x Genomics

value: lymph node


title: CAR + IL18-CCR (20210817_30102615320522-01_Sample06_06)

value: non activated CAR T cells

value: IL18 CCR


title: A3-3

city: San Antonio

first: Brian

middle: P.

last: Hermann

address: 1 UTSA Circle

institute: University of Texas at San Antonio

data_processing:
RNA-seq reads were trimmed adapter with cutadapt (v1.9), then discard reads with length less than 15 and quality less than 20. Filtered reads were aligned to mm9 reference with STAR (v2.5.2b) with parameters of --outFilterMismatchNoverLmax 0.04.
Assembly: mm9
Supplementary files format and content: TXT: fpkm table generated with featureCounts at gene level

source_name: Type A3 differentiating spermatogonia

growth_protocol: All procedures using mice adhered to guidelines outlined in the National Research Council Guide for the Care and Use of Laboratory Animals and were approved by the Animal Care and Use Committee at East Carolina University (approval A3469-01). Uchl1-eGfp mice were obtained from The Jackson Laboratory (stock #22476). Originally on a C57BL/6 genetic background, these mice were outcrossed with CD-1 mice (Charles River Laboratories, stock #022) to increase litter sizes and reduce dam cannibalism. Outbred CD-1 mice were purchased as dam with pups (Charles River Laboratories, stock #022). Both mouse lines were used for these studies, and the day of birth was designated as postnatal day (P)0. Mice were humanely euthanized by decapitation prior to P7, and by asphyxiation in CO2 followed by cervical dislocation after P7.

extract_protocol:
Single Cell Suspension  Testes were removed and placed in Krebs-Ringer Bicarbonate Buffer (EKRB). For each experiment, testes from at least 3 adult males or 5 pups from a given litter were detunicated and transferred to a solution containing 4.5 ml of 0.25% trypsin (Gibco) and 0.5 ml DNase1 (7 mg/ml, Sigma-Aldrich) and incubated in a 37°C water bath for 3 min. Then, additional 1 ml of DNase1 was added and incubated in a 37°C water bath for another 3 min. An additional 1 ml DNase1 was added and the mixture was pipetted up and down to further break up the testes, followed by a 1 min incubation in a 37°C water bath. One ml of fetal bovine serum (FBS, ATCC) was added to deactivate the trypsin, and the mixture was triturated to break apart any remaining clumps of intact testis. The cell mixture was filtered through a 40 μm sieve and centrifuged at 600 x g for 7 min. The resulting cell pellet was suspended in either sorting media containing 3% FBS + 10mM EDTA + 10mM HEPES in PBS and used for FACS or fixed in ethanol for ploidy analysis.     Fluorescence-activated cell sorting (FACS)  EGFP+ germ cells from Uchl1-eGfp mice were sorted on a Becton Dickinson AriaFusion cell sorter. A 100 mW 488 nm laser was used for excitation of the EGFP signal, and a 530/30 bandpass filter was used for detection of the emitted fluorescence. Dead cells were removed using forward and side scatter gating as well as fluorescence gating on cells excluding DAPI (Thermo Fisher #D1306). Single DNA-containing cells were identified using DRAQ5 fluorescent probe (Thermo Fisher #62254). Doublets were removed using FSC-height vs FSC-area plots. An 85 m nozzle was used for sorting, and the flow rate was controlled to 5,000-9,000 events/sec. Cells were recovered in sorting buffer (15% FBS + 10 mM EDTA + 10 mM HEPES in 1X PBS) in 5 ml polypropylene tubes (Corning LS, 352063) pre-coated with 10% BSA. Cell purity was assessed by reanalyzing a small aliquot of the sorted cells by immunostaining.     RNA Preparation:  Males with synchronized spermatogenesis were euthanized from mice at P17 for isolation of type B spermatogonia and at P19 for isolation of preleptotene spermatocytes. The latter were obtained from mice with an RA-sufficient and -deficient environment. FACS was used to isolate 2-3 x 106 type B spermatogonia and 2-3 x 106 preleptotene spermatocytes (3-4 males, each litter). Total RNA was isolated from cells using the GeneJet RNA purification kit (Thermo Scientific).
Libraries were produced with the Illumina TruSeq Stranded mRNA kit according to manufacturer recommendations.

treatment_protocol: To synchronize spermatogenesis, potent and selective inhibitor of RA-synthesis bis-(dichloroacetyl)-diamine/WIN18,446 (Cayman Chemical, #14018) was resuspended in vehicle (DMSO, final concentration 100 µg/g of body weight) and was given orally for ten consecutive days (P1-P11) to block spermatogonial differentiation. Next, on P11, mice received one subcutaneous injection of 10 µl exogenous RA (10 µg/µl) in DMSO to initiate spermatogonial differentiation. Following RA injection, WIN,446 was discontinued, enabling resumption of endogenous RA synthesis.


title: CAR (20210817_30102615320522-01_Sample07_07)

description: total mRNA from  activated CAR T cells

value: activated CAR T cells


title: Sample 3_WT_Glu-3

value: 0.4% Glucose


title: Control, replicate 2, scRNAseq

description: 10x Genomics


title: Sample 2_WT_Glu-2


title: Control, replicate 1, scRNAseq

description: 10x Genomics


title: A3-1


title: CAR + GMCSF-CCR (20210817_30102615320522-01_Sample04_04)


title: CAR + IL7-CCR (20210817_30102615320522-01_Sample03_03)


title: Sample 1_WT_Glu-1


title: CAR + IL2-CCR (20210817_30102615320522-01_Sample08_08)

value: IL2 CCR


title: PreLep RA-deficient-3

data_processing:
RNA-seq reads were trimmed adapter with cutadapt (v1.9), then discard reads with length less than 15 and quality less than 20. Filtered reads were aligned to mm9 reference with STAR (v2.5.2b) with parameters of --outFilterMismatchNoverLmax 0.04.
Genome_build: mm9
Supplementary_files_format_and_content: TXT: count table generated with featureCounts at gene level

source_name: preleptotene spermatocytes

treatment_protocol: To synchronize spermatogenesis, potent and selective inhibitor of RA-synthesis bis-(dichloroacetyl)-diamine/WIN18,446 (Cayman Chemical, #14018) was resuspended in vehicle (DMSO, final concentration 100 µg/g of body weight) and was given orally for ten consecutive days (P1-P11) to block spermatogonial differentiation. Next, on P11, mice received one subcutaneous injection of 10 µl exogenous RA (10 µg/µl) in DMSO to initiate spermatogonial differentiation. Following RA injection, mice were treated in one of two regimens: 1) discontinuation of WIN18,446 treatment, enabling resumption of endogenous RA synthesis (referred to as RA-sufficient synchronization), 2) continuation of WIN18,446 treatment to block endogenous RA synthesis (referred to as RA-deficient synchronization). Mice were humanely euthanized on specific subsequent days corresponding to different stages of germ cell differentiation. Specifically, type B spermatogonia were isolated from P17 synchronized testes, while preleptotene spermatocytes were isolated from P19 synchronized testes (both RA-sufficient and RA-deficient)

value: preleptotene spermatocytes


title: PreLep RA-deficient-2


title: PreLep RA-deficient-1


title: A1-3

source_name: Type A1 differentiating spermatogonia


title: A1-2


title: A1-1