title: MDA-MB-231_Parental_mCherryHNNRPK-ΔNLS

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
bcl2fastq/2.20.0 was used to convert bcl to fastq
For RNA-Seq fastq files were aligned using star/2.7.2b or TopHat(2)
differential expression was done using cuffdiff (cufflinks/2.2.1)
PARCLIP was analysed using Parpipes (https://github.com/ohlerlab/PARpipe)
Assembly: hg38

source_name: Triple-negative breast cancer

growth_protocol: MDA-MB-231 cells were authenticated by short-tandem repeat profiling, performed by ATCC. MDA-MB-231 KRT19 KO cells generated using the CRISPR/Cas9 system and cells stably expressing GFP or GFP-KRT19 generated using the lentiviral system, Cells were grown in Dulbecco’s modified essential medium (DMEM; Gibco, Grand Island, NY) supplemented with 10% Fetal Bovine Serum (GE Healthcare, Logan, UT) and 1% penicillin/streptomycin (Gibco) in a humidified incubator at 5% CO2 and 37°C.

extract_protocol:
For RNA-seq analysis, total RNAs from three biological replicates each of untransfected parental and KRT19 KO cells, transfected with siHNRNPK, control siRNA, HNRNPK ∆NLS or vector.
Ribosomal RNA was depleted of using the NEBNext® rRNA Depletion Kit and cDNA libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).
RNA was barcoded using the NEBNext Multiplex Oligos for Illumina (NEB).

treatment_protocol: For siRNA, RNAimax lipofectamine (Invitrogen, Waltham, MA) was used to transfect HNRNPK smartpool siRNA (Dharmacon) or non-targeting siRNA (Qiagen) according to the manufacturer’s protocol. For overexpression plasmids, jetOptimus DNA transfection reagent (Polyplus, Illkirch, France) was used according to the manufacturer’s protocol.

value: parental

value: mCherryHNNRPK-deltaNLS


title: MDA-MB-231_K19_KnockOut_mCherryHNNRPK-ΔNLS

status: Public on Jul 06 2023

type: SRA

city: Bethesda

state: MD

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: genotype

value: K19 KO

tag: treatment


title: MDA-MB-231_Parental_mCherryHNNRPK-WT

value: mCherryHNNRPK-WT


title: 7F_M_375

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: GP

tag: age

tag: strain


title: MDA-MB-231_K19_KnockOut_mCherry

value: mCherry


title: MDA-MB-231_K19_KnockOut_mCherryHNNRPK-WT


title: SKIN_AGE35_F_GR2_Gt141

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Circular RNAs were identified using CIRCexplorer v1.1.10.
Assembly: hg19
Supplementary files format and content: *geneCOUNT.txt: Tab-delimited text files containing counts.
Supplementary files format and content: *circRNA.txt: Tab-delimited text files containing circRNA annotation.

source_name: primary skin fibroblasts

growth_protocol: Punch skin biopsies were obtained from the inner axilla of 82 healthy GESTALT participants. Skin biopsies were minced into smaller pieces and distributed into 3 wells of 6-well collagen-coated plates to establish the human dermal fibroblast cultures.

extract_protocol:
After expansion, total RNA was isolated using the Direct-zolTM RNA MiniPrep kit (Zymo Research) following the manufacturer’s instruction.
Ribo-RNA depletion with Low Input RiboMinus Eukaryote System v2 (Thermo Fisher Scientific). Ribo-RNA-depleted samples were then used for cDNA synthesis with Ovation® RNA-Seq System V2 (Nugen) following the manufacturer’s protocol. Following cDNA fragmentation and size selection, libraries were prepared using Illumina TruSeq ChIP Library Preparation Kit (Illumina) according to manufacturer’s protocol.

tag: cell type

value: primary skin fibroblasts

tag: Sex

value: Female

tag: age (years)


title: SKIN_AGE32_M_GR1_Gt042

value: Male


title: species mixture experiment with mouse and human to determine doublet rate

city: London

first: Rory

middle: James

last: Maizels

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

library_source: transcriptomic single cell

data_processing:
data processed with dynast, outputted into separate adatas for each cell
data then collated into one adata object with replicate, timepoint, and other informations stored in metadata
cells with fewer than 1000 reads removed to exclude ambient RNA
Assembly: mm10
Supplementary files format and content: h5ad, anndata

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: human H9 and mouse HM1

growth_protocol: human grown in StemFlex, mouse in KnockOut, with additives

extract_protocol:
fixed in methanol + DEPC, stored -80°C
custom sci-RNA-seq protocol
combinatorial indexing with 2 x 384 barcode rounds

value: human H9 and mouse HM1

value: mESC + hESC


title: 7F_M_372


title: MDA-MB-231_Parental_mCherry


title: SKIN_AGE32_F_GR1_Gt144


title: Liver, 5-months post engraftment (low engraftment), replicate1, snRNA-seq (dataset II)

city: Westmead

first: Suzanne

last: Scott

state: NSW

address: 214 Hawkesbury Rd

country: Australia

institute: Children's Medical Research Institute

description:
Nuclear RNA
low1

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

source_name: Liver

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

tag: tissue

value: Liver

value: Hepatocytes

value: 5-months post-engraftment

tag: sample type

value: 5-months post engraftment


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

description:
Nuclear RNA
LK03V/REDHC2

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


title: 7F_M_373


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

description:
Nuclear RNA
LK03V/REDHC1


title: 7F_M_374


title: 7F_M_371


title: Liver, 5-months post engraftment (low engraftment), replicate2, snRNA-seq (dataset II)

description:
Nuclear RNA
low2


title: SKIN_AGE31_M_GR1_Gt119


title: Liver, 5-months post engraftment, replicate2, snRNA-seq (dataset II)

description:
Nuclear RNA
high2


title: Liver, 5-months post engraftment, LK03C/REDHV, replicate 1, snRNA-seq (dataset II)

description:
Nuclear RNA
LK03C/REDHV1

value: 5-months post-engraftment, LK03C/REDHV


title: Liver, 5-months post engraftment, replicate1, snRNA-seq (dataset II)

description:
Nuclear RNA
high1


title: 7F_M_370


title: SKIN_AGE31_M_GR1_Gt025


title: 7F_M_369


title: SKIN_AGE31_M_GR1_Gt005


title: DIV5, Ezh1 cKO, rep2

city: New York

first: Kärt

last: Mätlik

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Reads were mapped to mm10 using Rsubread (version 1.30.6) (Liao et al., 2019)
Transcript abundance was calculated using Salmon (version 0.8.2) (Patro et al., 2017)
Counts were retrieved using Tximport (version 1.8.0) (Love et al., 2016)
Normalized, fragment extended signal bigWigs were created using rtracklayer (version 1.40.6) (Lawrence et al., 2009)
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes transcript counts for each sample
Supplementary files format and content: bigWig

source_name: cerebellum

growth_protocol: Primary GCPs were isolated from the cerebella of P7 Ezh1(wt/wt);Atoh1-Cre and Ezh1(fl/fl);Atoh1-Cre mice as described in (Hatten, 1985), plated and cultured for 5 DIV.

extract_protocol:
RNA from cultured GCs was isolated using RNeasy Micro Kit (Qiagen) with on-column DNA digestion. RNA integrity was determined using Bioanalyzer RNA 6000 Pico kit (Agilent) prior to library preparation.
RNAseq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina in conjunction with the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina. Libraries were sequenced at the Rockefeller University Genomics Resource Center using a NextSeq 500 sequencer to obtain 75-bp single-end reads.

value: cerebellum

value: cultured primary granule cells

tag: time


title: DIV5, Ezh1 cKO, rep3


title: DIV5, Ezh1 cKO, rep4


title: DIV5, Ezh1 cKO, rep1


title: SKIN_AGE31_F_GR1_Gt090


title: SKIN_AGE31_M_GR1_Gt130


title: DIV5, Ezh1 wt, rep4


title: Liver, 5-months post engraftment, LK03C/REDHV, replicate 2, snRNA-seq (dataset II)

description:
Nuclear RNA
LK03C/REDHV2


title: DIV5, Ezh1 wt, rep5


title: 7F_M_367


title: DIV5, Ezh1 wt, rep3


title: 7F_M_365


title: SKIN_AGE28_M_GR1_Gt123


title: 7F_M_366


title: DIV5, Ezh1 wt, rep1


title: piloting original scifate protocol with our cell system

data_processing:
data processed with dynast, outputted into separate adatas for each cell
data then collated into one adata object with replicate, timepoint, and other informations stored in metadata
cells with fewer than 500 reads removed to exclude ambient RNA
Assembly: mm10
Supplementary files format and content: h5ad, anndata

source_name: mESC HM1

growth_protocol: mESC neural tube differentiation protocol. Grown in N2B27 with supplements. D0: FGF, D2: FGF+CHIR, D3-8: RA+SAG, cells collected from day 4

extract_protocol:
fixed in 4% PFA
sci-RNA-seq protocol
combinatorial indexing, two rounds of 384 barcodes

value: mESC HM1

value: differentiating HM1s


title: 7F_M_364

value: GP


title: SKIN_AGE29_M_GR1_Gt135


title: postnatal day 30, scRNA-seq

city: Charlottesville

first: Jason

middle: Paul

last: Smith

state: VA

address: 409 Lane Rd

department: Pediatrics

institute: University of Virginia

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
Pregnant mice were injected with tribromoethanol at enough dose to keep alive but anesthetized. Then, the small fetuses were removed one by one. A small squash from the lung was used to identify the GFP+ pups at E12, using an EvosFLC cell imaging system (LifeTechnologiesTM, California, USA). Once they were identified, the metanephros area was removed under microscopy and harvested in ice cold dPBS. The tissue was then minced carefully with a razor blade and transferred to 1.7mL Eppendorf tube. 300 μL of TryPLETM Express (Gibco, New York, USA) was added and incubated at 37∘C for 5 minutes. Then, 600 μL of DMEM + 5% FBS was added to the Eppendorf tube. The mixture was homogenized by pipetting up and down. The solution was then filtered with a 40 μm nylon cell strainer. Tissue chunks were removed from the mesh surface, placed again in an Eppendorf tube and the process repeated a second time. Meanwhile, the flow-through filtrate was placed in a new Eppendorf tube and centrifuged at 4∘C, 150g for 5 minutes. The supernatant was removed and the pellet resuspended with resuspension buffer. All the tubes were combined in the end and the cells were ready for single-cell capture. For later timpoints, animals were anesthetized with tribromoethanol (300 mg/kg). P5 and P30 mice kidneys were excised and decapsulated. Then, the kidney cortices were dissected, minced with a razor blade, and transferred into a 15 mL tube with 5 mL of enzymatic solution (0.3% collagenase A [Millipore-Sigma], 0.25% trypsin [Millipore-Sigma], and 0.0021% DNase I [Millipore-Sigma]). The tubes were placed inside a shaking incubator (80 RPM) for 15 minutes at 37∘C. The solution was pipetted up/down 10 times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected in a fresh tube on ice. The enzymatic solution was added to the 15 mL tube containing the remaining undigested cortices, and the digestion procedure was repeated a total of 3 times. The supernatants were pooled and centrifuged at 800 g for 4 minutes at 4∘C using a Sorvall RT7 refrigerated centrifuge (Sorvall, Newtown, CT). The cell pellet was resuspended in fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 μm nylon cell strainer (Corning Inc., Corning, NY) and washed with buffer 1. The flow-through was poured through a sterile 40 μm nylon cell strainer (Corning Inc.) and washed with buffer 1. The flow-through was centrifuged at 1,100 g for 4 min at 4∘C. The cell pellet was resuspended in 1.5 mL of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Millipore-Sigma)]. DAPI (Millipore-Sigma) was added to the cells to identify the living cells. The GFP positive cells were collected by Fluorescent-Activated Cell Sorting (FACS) and resuspended in DMEM (Dulbecco’s Modified Eagle Medium, Gibco, Netherlands) with 10% FBS (Fetal Bovine Serum) for immediate use. The sorters were either an Influx Cell Sorter (Becton Dickinson, Franklin Lakes, NJ) or a FACS Aria Fusion Cell Sorter (Becton Dickinson), both located at the Flow Cytometry Core Facility at the University of Virginia.
Sorted GFP-positive cells were spun down at 500g for 10 minutes in a Sorvall RT7 refrigerated 4∘C centrifuge (Sorvall, Newtown, CT). Then, the supernatant was carefully removed, and the cell pellet was resuspended in dPBS (Dulbecco’s Phosphate Buffered Saline, Gibco, UK) with 0.04% BSA (UltraPureTM Bovine Serum Albumin, Invitrogen, Lithuania) 10 times with wide-bore tips. The process was repeated once, and the cells were counted with the CellometerMini (Nexcelon Bioscience, Massachussets, USA). Experiments with more than 500 cells/μL, viability higher than 85%, and absence of clumps were chosen to proceed. Single cells were loaded and captured with the Chromium System (10X Genomics, Pleasanton, CA) following the manufacturer’s recommendation using the Chromium Next GEM Chip G with reagents of Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10X Genomics). The GEMs were generated and incubated to generate the barcoded cDNA. cDNA was cleaned with Dynabeads and amplified by PCR. cDNA was then enzymatically fragmented, end-repaired, poly-A tailed, adaptor-ligated, and amplificated by PCR. The constructed libraries were sequenced on an Illumina HiSeq 2500/4000 platform (150-bp paired-end reads).

value: FoxD1+ cells

value: kidney

value: 30 day old pups


title: 7F_M_363


title: SKIN_AGE28_M_GR1_Gt001

value: primary skin fibroblasts

value: Male


title: SKIN_AGE28_F_GR1_Gt137

value: Female


title: kidney-4 [D299kid]

city: Shanghai

first: Xiaoyue

last: Jiang

state: Shanghai

address: 145 Middle Shandong road

department: Rheumatology

country: China

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Data preprocessing and genomic alignment
Transcript splicing、lncRNA prediction、and Gene quantification
Differential screening analysis and Functional Analysis
CircRNA prediction, Expression analysis and Interaction research
Gene structure optimization and New transcript prediction
Assembly: GRCm38
Supplementary files format and content: table-delimited text files induces raw counts for each sample
Supplementary files format and content: table-delimited text files induces FPKM values for each sample

growth_protocol: Female NZB/BINJ mice and male NZW/LacJ mice were purchased from The Jackson Laboratory. NZB/NZW F1 mice were produced by hybridizing crosses between female NZB/BINJ mice and male NZW/LacJ mice. All animals were maintained in a specific pathogen-free facility at Shanghai Rat&Mouse Biotech Company in a 12-h light/12-h dark cycle and free acquirement to sterile water and a standard mouse diet. 383 Animal studies were approved by the Institutional Animal Care and Use Committee at

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.

treatment_protocol: These mice were intraperitoneally administrated with diosmetin (50mg/kg, Selleck Chemicals) or vehicles every other day for 394 continuous treatment cycles of 6 weeks.

value: kidney cells

value: NZB/NZW F1 mice

value: diosmetin


title: 7F_M_368


title: kidney-3 [D297kid]

value: vehicle


title: kidney-2 [D295kid]


title: kidney-5 [D300kid]


title: kidney-1 [D292kid]


title: SKIN_AGE27_M_GR1_Gt142


title: 7F_M_362


title: DIV5, Ezh1 wt, rep2


title: SKIN_AGE30_M_GR1_Gt122


title: DNA from blood from OldHetRec6

city: Boston

first: Jesse

last: Poganik

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Adapter removal and quality trimming for the analysis of DNA methylation reads were performed using TrimGalore v0.4.1 following previously established protocols (Krueger and Andrews, 2011; Meer et al., 2018; Petkovich et al., 2017)
Trimmed reads were mapped to the mouse genome (GRCm38.p2/mm10) using Bismark v0.15.0. (Krueger and Andrews, 2011)
Coverage files outputted by Bismark were then used for further analyses.
Assembly: mm10
Supplementary files format and content: Bismark .cov files with methylation calls and coverage for each locus

source_name: Old heterochronic recovery

growth_protocol: This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol:
DNA from samples was isolated by using the DNeasy Blood & Tissue Kit (Qiagen 69506), and then eluted from columns in 100 μl of 10 mM TrisHCl buffer, pH 8.0. 2 μl of RNase A (Life Technologies) was added to each sample. Samples were incubated at room temperature for 2 min, and isolated genomic DNA was purified by using the Genomic DNA Clean & Concentrator™-10 kit (Zymo D4011). DNA was eluted in 25 μl of 10 mM Tris-HCl buffer, pH 8.0 and quantified using a Qubit 2.0 (Life Technologies AM2271).
RRBS libraries were prepared following the protocol previously established (Petkovich et al., 2017), using 100 ng of DNA for each sample. Each library included 10 samples. To avoid an overlap of batch effect and age-related changes, we randomized samples across libraries. The libraries were sequenced using an Illumina HiSeq2500, with 150bp paired-end reads. 20% of mouse genomic DNA library was spiked in to compensate for low complexity of the libraries.

treatment_protocol: Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old or 20-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis.

tag: mouse strain

value: C57BL/6 WT

value: blood

tag: mouseid


title: 7F_M_361


title: SKIN_AGE27_F_GR1_Gt055


title: SKIN_AGE26_F_GR1_Gt045


title: DNA from blood from OldHetRec4


title: DNA from blood from OldHetRec5


title: 7F_M_360


title: 7F_M_359


title: DNA from blood from OldHetRec1


title: 7F_M_358


title: DNA from blood from OldHet3

source_name: Old heterochronic parabiosis


title: 7F_M_357


title: SKIN_AGE25_M_GR1_Gt046


title: DNA from blood from OldHet4


title: SKIN_AGE25_F_GR1_Gt085


title: DNA from blood from OldHet2


title: DNA from blood from OldHet1


title: SKIN_AGE23_M_GR1_Gt022


title: DNA from blood from OldHet6


title: SKIN_AGE22_M_GR1_Gt073


title: 7F_M_355


title: RNA-seq_OV organoid, Day 5, GFP positive, replicate 2

city: Edinburgh

first: Liusaidh

middle: Jane

last: Owen

address: Crewe Road South

department: MRC HGU

institute: University of Edinburgh

data_processing:
Kallisto v 0.43.1 was used to align and quantify reads. Coding regions of DNA and non-coding RNA from the mouse genome mm10 were used to create the transcriptome index.
Kallisto quant was used to quantify reads for each library (bootstraps: 100)
The kallisto abundance estimates were used as inputs to DESeq2, using a design matrix of timepoints. The estimateSizeFactors function was used to compute sizefactors for normalization, and the lfcShrink function, with type=‘ashr’ for log-fold- change shrinkage (Stephens, 2016), was used to contrast timepoints. To select differentially expressed genes we used an FDR threshold of 0.001 and a log2-fold-change threshold of 1.5. We also use DEseq2 to select a set of “house-keeping" or stably expressed genes, by requiring these genes to display absolute log2 fold-changes < 0.1 for every successive day comparison, and have a mean (across days) normalized expression > 30.
Assembly: mm10
Supplementary files format and content: Tab separated file of the DEseq2 normalised count data representing expression values of genes for each sample. There are additional metadata columns showing gene names and genomic locations, whether each gene is differentially expressed between the noted time points and if the gene was included in our eye field or housekeeping gene set.

source_name: Rx-GFP K/I EB5

growth_protocol: Rx-GFP mESCs from the Riken BRC Cell Bank (cell number AES0145) were maintained under feeder free conditions. Cells were cultured on 0.1% gelatin coated tissue culture flasks  in GMEM media supplemented with 1X non- essential amino acids, 1 mM Sodium pyruvate, 10 μM 2-Mercaptoethanol, 10% knock out serum replacement (KOSR), 1% FCS and LIF. Care was taken to avoid over-confluency or undesirable differentiation of cells.

extract_protocol:
RNA was isolated using the Zymo Direct-zol RNA MicroPrep kit following manufacturer’s instructions. Quality and integrity of the RNA samples were analysed by bioanalyser.
Libraries were prepared using the TruSeq library prep kit (Illumina) according to manufacturer’s protocols.

treatment_protocol: SFEBq differentiation of OV organoids was performed as described previously (Wataya et al., 2008; Eiraku et al., 2011). Briefly, mESCs were dissociated and 4500 cells were plated in differentiation media (supplemented GMEM with 1.5% KOSR) in a Nunclon low cell adhesion 96 well plate. This is defined as day 0. On day 1, growth factor reduced Matrigel was added to a final concentration of 2%. Differentiation status was assessed using fluorescent imaging with the presence of GFP used as a measure of Rax expression. On days 0–5 of optic vesicle differentiation, triplicate samples of cells were collected from 24 pooled organoids which were dissociated and sorted using FACS to select for live single cells. Samples at days 4 and 5 were also sorted on the basis of GFP expression giving a GFP positive and negative sample for each of these time points.

value: Rx-GFP K/I EB5

value: ESC

value: optic vesicle organoid differentiation

value: Day 5


title: RNA-seq_OV organoid, Day 5, GFP positive, replicate 3


title: RNA-seq_OV organoid, Day 5, GFP positive, replicate 1


title: DNA from blood from OldHetRec2


title: DNA from blood from OldIsoRec4

source_name: Old isochronic recovery


title: 7F_M_354

value: GP


title: RNA-seq_OV organoid, Day 5, GFP negative, replicate 3


title: PLC/PRF/5 cells, PKO, rep3

city: Chongqing

first: Dongmei

last: Gou

state: Chongqing

address: 1 Yixue Yuan Road

institute: Chongqing Medical University

data_processing:
Adapter sequences were trimmed by using cutadapt. The parameter settings used was “ -a AGATCGGAAGAGC -m 35 -n 2”.
The cleaned reads were mapped back to genome using BSMAP software version 2.90 (Xi & Li, 2009). The parameter settings used was “-n 0 -v 0.08 -g 1”. Methylation ratios were extracted from BSMAP output (SAM) using a Python script (methratio.py) which is distributed with the BSMAP package. Only unique mapped reads were used to calculate methylation ratios. Only cytosines in a CpG context with sufficient sequencing depth (greater than or equal to 5x coverage) were retained for further analysis.
Supplementary files format and content: Differentially methylated regions (DMRs) were detected using metilene (Jühling et al., 2016) in de-novo mode among CpG sites with at least 5x coverage. The parameter settings used was “--mincpgs 5 --minMethDiff 0.1 --mtc 1 -X 1 -Y 1 -v 0.7”. Then detected DMR were filtered according to the standard: (1) Q-value must be less than 0.05; (2) methylation level difference must be greater than 0.1; (3) CpG number contained in DMR must be greater than 5; (4) the length of the DMR must be greater than 50bp.

growth_protocol: DMEM, 10% fetal bovine serum, 4mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
About 1µg of genomic DNA mixed with unmethylated lambda DNA was digested by MspI enzyme for 16 hours at 37℃
After digestion, the libraries were constructed as the Illumina Pair-End protocol with some modifications. Briefly, purified digested DNA was subsequently treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair, blunt and phosphorylate ends.
After that, the blunt DNA were 3’ adenylated using Klenow Fragment (3’-5’ exo-) and following with ligation to adaptors synthesized with 5’-methylcytosine instead of cytosine using T4 DNA Ligase.
After each step, the DNA was purified using MinElute PCR Purification Kit (Qiagen). ZYMO EZ DNA Methylation-Gold Kit™ was employed to convert unmethylated cytosine into uracil according to the instructions. Finally, PCR was carried out in a final reaction volume of 50µl consisting of 20µl adapter ligated DNA, 4µl 2.5mM dNTP, 5µl 10×buffer, 0.5µl JumpStart™ Taq DNA Polymerase, 2µl PCR primers and 18.5µl water and the following thermal cycling program was 94°C 1 min, 12cycles of 94 °C 10s, 62°C 30s, 72°C 30 then prolong with 5min at 72°C and products could be hold at 12°C.
Before analysis with Illumina sequencing platform, the size selected library was analyzed by the Bioanalyzer analysis system (Agilent, Santa Clara, USA) and quantified by the real time PCR.

value: Primary Liver Carcinoma/Poliomyelitis Research Foundation/5

value: PCK1 knockdout


title: DNA from blood from OldIsoRec3


title: PLC/PRF/5 cells, PKO, rep2


title: RNA-seq_OV organoid, Day 5, GFP negative, replicate 2


title: PLC/PRF/5 cells, PKO, rep1


title: 7F_M_353


title: RNA-seq_OV organoid, Day 5, GFP negative, replicate 1


title: DNA from blood from OldIsoRec8


title: DNA from blood from OldIsoRec1


title: 7F_M_352


title: PLC/PRF/5 cells, Parental, rep2

value: Parental


title: DNA from blood from OldIso11

source_name: Old isochronic parabiosis


title: DNA from blood from OldIsoRec9


title: PLC/PRF/5 cells, Parental, rep1


title: 7F_M_348


title: RNA-seq_OV organoid, Day 4, GFP positive, replicate 2

value: Day 4


title: RNA-seq_OV organoid, Day 4, GFP positive, replicate 1


title: 7F_M_351


title: 7F_M_377


title: 7F_M_347


title: HeLa, Rh(III), T06

city: Guangzhou

first: chen

last: Xiao-xiao

state: Guangdong

address: Xiaoguwei

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequenced reads were trimmed for adaptor sequence, low-complexity or low-quality sequence were removed by perl script, and the clean reads were mapped to homo sapiens genome (hg38) using HISAT (Version 2.0) software.
StringTie was used for assemble transcripts and map and quanity gene-expression level which esimated by FPKM value
Assembly: ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/dna/
Supplementary files format and content: tab-delimited text file includes count and FPKM values for each Sample

source_name: uterus

growth_protocol: HeLa epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 oC

extract_protocol:
Total RNA was extracted by Trizol reagent and purified using RNeasy mini kit (Qiagen, Germany). The integrity and concentration of RNA was assessed using the RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina manufacturer's protocols.

treatment_protocol: HeLa cells was treated with Rhodium(III)

value: HeLa

value: epithelial cells

value: WT

value: Rhodium(III) 1 uM, 6 h


title: HeLa, Rh(III), T04


title: RNA-seq_OV organoid, Day 4, GFP negative, replicate 3


title: DNA from blood from OldIso9


title: RNA-seq_OV organoid, Day 4, GFP negative, replicate 2


title: 7F_M_346


title: HeLa, control, T03

value: 1%DMSO, 6 h


title: 7F_M_345


title: PLC/PRF/5 cells, Parental, rep3


title: DNA from blood from OldIso7


title: RNA-seq_OV organoid, Day 4, GFP positive, replicate 3


title: HeLa, control, T02


title: 7F_M_350


title: 7F_M_344


title: RNA-seq_OV organoid, Day 3, replicate 3

value: Day 3


title: RNA-seq_OV organoid, Day 4, GFP negative, replicate 1


title: RNA-seq_OV organoid, Day 3, replicate 2


title: 7F_M_343


title: DNA from blood from OldIso10

value: C57BL/6 WT


title: RNA-seq_OV organoid, Day 3, replicate 1


title: 7F_M_342


title: DNA from blood from YoungIsoRec8

source_name: Young isochronic recovery

value: blood


title: 4015-1_Day14_nonBPD

city: Research Triangle Park

first: Douglas

middle: A.

last: Bell

state: NC

address: PO Box 12233

department: Immunity Inflammation and Disease Lab

institute: National Institute of Environmental Health Sciences

data_processing:
75 bp single-end sequencing was performed on NovaSeq 6000 platform using S4 flow cell (Illumina).
Raw sequencing reads in FASTQ files sequenced to 22-150 million reads
Aligned with STAR version 2.6.0c
Gene read counts obtained using featureCounts from the Subread package version 1.5.1 using release 39 of the GENCODE annotation
Assembly: hg38
Supplementary files format and content: counts: 1st column = Gene symbol, 2nd column = Gene read counts

source_name: Peripheral blood

extract_protocol:
Total RNAs were isolated from whole blood cell using PAXgene Blood miRNA Kit (PreAnalytix/Qiagen).
Aliquots of RNA (250 ng) were used to generate poly-adenylated RNA libraries with TruSeq Stranded Total RNA Ribo-Zero Human Gold kit (Illumina). Samples were indexed with NEXTfle-96 RNA-Seq Barcodes (Bioo-scientific, Austin, TX).

value: Peripheral blood

tag: sample id

value: whole blood cells

tag: variable-disease

value: nonBPD

tag: variable-time

tag: variable-o2 treatment

value: yes

tag: variable-o2 level

tag: covariate-ga

tag: covariate-bw

tag: covariate-sex

value: F

tag: covariate-b cell%

tag: covariate


title: 4015-1_Day28_nonBPD

tag: cell type


title: DNA from blood from OldIso8

tag: age (years)


title: DNA from blood from YoungIsoRec7

tag: tissue


title: 7F_M_341

tag: brain region

value: GP

tag: age

tag: strain


title: DNA from blood from YoungIsoRec4

tag: mouse strain

tag: mouseid


title: 4014-1_Day14_nonBPD

tag: sample id

tag: variable-disease


title: RNA-seq_OV organoid, Day 2, replicate 3

tag: cell line

value: Rx-GFP K/I EB5

value: ESC

tag: treatment

value: optic vesicle organoid differentiation

tag: time

value: Day 2


title: 7F_M_340


title: RNA-seq_OV organoid, Day 2, replicate 2


title: 7F_M_339


title: 4014-1_Cord_nonBPD

tag: variable-time

value: CordBlood

tag: variable-o2 treatment

tag: variable-o2 level

tag: covariate-ga

tag: covariate-bw


title: DNA from blood from YoungIsoRec3

tag: age (years)


title: DNA from blood from YoungIsoRec10

tag: tissue


title: 4013-1_Day28_nonBPD

tag: cell type

value: no

tag: covariate-sex

tag: covariate-b cell%

tag: covariate


title: DNA from blood from YoungIsoRec9

tag: mouse strain

tag: mouseid


title: 7F_M_338

tag: brain region

tag: age

tag: strain


title: RNA-seq_OV organoid, Day 2, replicate 1

tag: cell line

tag: treatment

tag: time


title: 4013-1_Cord_nonBPD

tag: sample id

tag: variable-disease

tag: variable-time

tag: variable-o2 treatment

tag: variable-o2 level


title: RNA-seq_OV organoid, Day 1, replicate 2

tag: cell type

value: Day 1


title: 7F_M_337


title: DNA from blood from YoungIso10

source_name: Young isochronic parabiosis

tag: tissue

tag: age (years)


title: DNA from blood from YoungIso9


title: 4013-1_Day14_nonBPD

tag: covariate-ga

tag: covariate-bw

tag: covariate-sex

tag: covariate-b cell%

tag: covariate


title: 4012-1_Day28_nonBPD


title: DNA from blood from YoungIso8

tag: mouse strain

tag: mouseid


title: 4015-1_Cord_nonBPD


title: RNA-seq_OV organoid, Day 1, replicate 1

tag: cell line

tag: treatment


title: 7F_M_336

tag: brain region

tag: age

tag: strain


title: RNA-seq_OV organoid, Day 0, replicate 3

tag: time

value: Day 0


title: 7F_M_335


title: 4012-1_Day14_nonBPD

tag: sample id

tag: variable-disease

tag: variable-time

tag: variable-o2 treatment

tag: variable-o2 level


title: 7F_M_334


title: DNA from blood from YoungIso7

tag: tissue

tag: age (years)


title: RNA-seq_OV organoid, Day 0, replicate 2

tag: cell type


title: DNA from blood from YoungIso6


title: DNA from blood from YoungIso11


title: 4012-1_Cord_nonBPD

tag: covariate-ga

tag: covariate-bw

tag: covariate-sex

tag: covariate-b cell%

tag: covariate


title: RNA-seq_OV organoid, Day 0, replicate 1

tag: cell line

tag: treatment


title: 7F_M_333

tag: brain region

tag: age

tag: strain


title: DNA from liver from OldHetRec6

tag: mouse strain

value: liver

tag: mouseid


title: RNA-seq_OV organoid, Day 1, replicate 3

tag: time


title: 7F_M_332


title: 4011-1_Day28_nonBPD

tag: sample id

tag: variable-disease

tag: variable-time

tag: variable-o2 treatment

tag: variable-o2 level

value: M


title: 4011-1_Cord_nonBPD

tag: tissue

tag: cell type

tag: covariate-ga

tag: covariate-bw


title: RNA_seq_TCF1KO_LSK_P45_DN2_Rep2B_Rep3T

city: Philadelphia

first: Naomi

last: Goldman

state: PA

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
RNA-seq libraries were pair-end sequenced by Illumina NextSeq 550. RNA-seq samples were aligned by STAR_2.5.0a_alpha with parameters ‘--readFilesCommand zcat --outFilterMultimapNmax 1--outSAMtype SAM--alignEndsTypeLocal--outReadsUnmapped Fastx--outFilterMismatchNmax 1--alignMatesGapMax 400000--sjdbGTFfile’, with the GTF file being either the mus musculus GRCm38.91 gtf file for C57BL/6 strain or the mus musculus GRCm38.91 gtf shifted to NOD coordinates for the NOD strain.
HTSeq v0.6.1 facilitated counting RNA-seq reads on Gencode vM11 gene models with parameters ‘-s yes-t exon-m intersection-nonempty’.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with read count

source_name: BM derived CD44+ CD25+ DN2

extract_protocol:
Transduction of Tcf7 KO scid.adh cells was accomplished by addition of retroviral supernatants to culture medium supplemented with polybrene (8mg/ml) and spinfected at 1,750 RPM for 25 minute. 72hrs after transduction, live transduced cells were sorted for downstream experiments. Cells from co-cultures were stained with L/D APCef780, and fluorescent antibodies to B220, CD44, CD45, Thy1.2, Ckit, CD25, and CD11b. Sorting was performed on a BD FACSAria after 7 days to isolate DN1 (CD45+c-KithiCD44hI CD25low) and DN2 cells (CD45+c-KitlowCD44low CD25high). Cells were washed with 1 x PBS (Corning, cat# 21031CV) and lysed with 350 μl RLT Plus buffer (Qiagen) supplemented with 10% 2-mercaptoethanol (Sigma, cat# M6250), vortexed briefly, snap-frozen on dry ice, and stored at -80°C. Subsequently, total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, cat# 74034).
Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+37 bp) was performed on a NextSeq 550 following the manufacturer's protocol.

value: Tcf7eGFP fl/fl Cre+

value: Cultured on OP9-DLL1


title: 4011-1_Day14_nonBPD

value: Peripheral blood

value: whole blood cells

tag: covariate-sex

tag: covariate-b cell%

tag: covariate


title: DNA from liver from OldHetRec5

value: C57BL/6 WT

tag: age (years)


title: 7F_M_329

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: age

tag: strain


title: 7F_M_331


title: 7F_M_330


title: RNA_seq_TCF1KO_LSK_P45_DN2_Rep2B_Rep2T

tag: treatment


title: DNA from liver from OldHetRec2

tag: mouse strain

tag: mouseid


title: DNA from liver from OldHetRec4


title: DNA from liver from OldHetRec1


title: 7F_M_327


title: RNA_seq_TCF1KO_LSK_P45_DN2_Rep2B_Rep1T


title: RNA_seq_TCF1KO_LSK_P45_DN2_Rep1B_Rep1T


title: 4010-2_Day14_nonBPD

tag: sample id

tag: variable-disease

value: nonBPD

tag: variable-time

value: yes

value: F


title: 4010-1_Day28_nonBPD

tag: tissue

tag: variable-o2 treatment

tag: variable-o2 level


title: DNA from liver from OldHet5


title: 7F_M_325

value: GP


title: RNA_seq_TCF1KO_LSK_P45_DN2_Rep1B_Rep2T


title: RNA_seq_TCF1KO_LSK_P45_DN2_Rep1B_Rep3T


title: 4010-2_Cord_nonBPD

tag: cell type

tag: covariate-ga

tag: covariate-bw


title: 7F_M_328


title: RNA_seq_TCF1KO_LSK_P45_DN1_Rep2B_Rep2T

source_name: BM derived CD44+ CD25- DN1


title: 4010-1_Day14_nonBPD

tag: covariate-sex

tag: covariate-b cell%

tag: covariate


title: 7F_M_326

tag: brain region

tag: age


title: DNA from liver from OldHet4

tag: age (years)


title: DNA from liver from OldHet3

tag: mouse strain


title: 4010-2_Day28_nonBPD


title: RNA_seq_TCF1KO_LSK_P45_DN1_Rep2B_Rep3T

tag: strain

tag: treatment


title: DNA from liver from OldHetRec3

tag: mouseid


title: 7F_M_324


title: 4010-1_Cord_nonBPD

tag: sample id

tag: variable-disease

tag: variable-time


title: 4009-1_Day28_nonBPD

tag: tissue

tag: variable-o2 treatment

tag: variable-o2 level


title: RNA_seq_TCF1KO_LSK_P45_DN1_Rep2B_Rep1T


title: 4009-1_Day14_nonBPD

tag: cell type

tag: covariate-ga

tag: covariate-bw


title: DNA from liver from OldHet2


title: DNA from liver from OldHet1


title: 7F_M_323


title: 7F_M_322


title: RNA_seq_TCF1KO_LSK_P45_DN1_Rep1B_Rep3T


title: RNA_seq_TCF1KO_LSK_P45_DN1_Rep1B_Rep2T


title: 7F_M_320


title: 4008-1_Day14_nonBPD

tag: covariate-sex

tag: covariate-b cell%

tag: covariate


title: DNA from liver from OldIsoRec7

tag: age (years)


title: DNA from liver from OldIsoRec5

tag: mouse strain


title: DNA from liver from OldIsoRec6


title: 4007-1_Day14_nonBPD


title: RNA_seq_TCF1KO_LSK_P45_DN1_Rep1B_Rep1T

tag: strain


title: 4009-1_Cord_nonBPD


title: 7F_M_319

tag: brain region

tag: age


title: 7F_M_189


title: RNA_seq_TCF1KO_LSK_L7d_DN2_Rep2B_Rep3T

tag: treatment


title: RNA_seq_TCF1KO_LSK_L7d_DN2_Rep2B_Rep2T


title: RNA_seq_TCF1KO_LSK_L7d_DN2_Rep2B_Rep1T


title: 4007-1_Cord_nonBPD

tag: sample id

tag: variable-disease


title: 4005-1_Day28_BPD

tag: tissue

value: BPD

tag: variable-time


title: 7F_M_188


title: DNA from liver from OldIsoRec3

tag: mouseid


title: DNA from liver from OldIsoRec4


title: RNA_seq_TCF1KO_LSK_L7d_DN2_Rep1B_Rep3T


title: 4005-1_Day14_BPD

tag: cell type

tag: variable-o2 treatment

tag: variable-o2 level


title: DNA from liver from OldIsoRec2


title: RNA_seq_TCF1KO_LSK_L7d_DN2_Rep1B_Rep2T


title: 7F_M_187


title: 4002-1_Day28_nonBPD

tag: covariate-ga

tag: covariate-bw

tag: covariate-sex


title: RNA_seq_TCF1KO_LSK_L7d_DN2_Rep1B_Rep1T


title: 7F_M_318


title: DNA from liver from OldIso6

tag: age (years)


title: 4002-1_Day14_nonBPD

tag: covariate-b cell%

tag: covariate


title: 7F_M_185

tag: brain region

tag: strain


title: RNA_seq_TCF1KO_LSK_L7d_DN1_Rep2B_Rep3T

tag: treatment


title: DNA from liver from OldIso5

tag: mouse strain


title: 7F_M_184

tag: age


title: RNA_seq_TCF1KO_LSK_L7d_DN1_Rep2B_Rep2T


title: DNA from liver from OldIso4

tag: tissue


title: 3019-1_Day14_nonBPD

tag: sample id

tag: variable-disease

tag: variable-time


title: RNA_seq_TCF1KO_LSK_L7d_DN1_Rep2B_Rep1T


title: 4002-1_Cord_nonBPD

tag: cell type

tag: variable-o2 treatment


title: DNA from liver from OldIso3

tag: mouseid


title: RNA_seq_TCF1KO_LSK_L7d_DN1_Rep1B_Rep3T


title: DNA from liver from OldIso2


title: 7F_M_183


title: 3019-1_Cord_nonBPD

tag: variable-o2 level

tag: covariate-ga

tag: covariate-bw


title: 7F_M_186


title: 7F_M_182


title: 3018-1_Cord_nonBPD

tag: covariate-sex

tag: covariate-b cell%


title: RNA_seq_TCF1KO_LSK_L7d_DN1_Rep1B_Rep2T


title: DNA from liver from OldIsoRec1

tag: age (years)


title: DNA from liver from OldIso1


title: 7F_M_179

tag: brain region

tag: strain


title: 3017-1_Day14_BPD

tag: covariate


title: 3018-1_Day28_nonBPD


title: 7F_M_180

tag: age


title: LSD1KO_A485_EpiLC_RNA_2

first: Jiwei

last: Chen

address: 130 DongAn Road

institute: Fudan University

data_processing:
Raw reads were trimmed as described in ChIP-Rx and then aligned to the mm9 genome assembly using STAR v2.7.9a with parameter “--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 --outSJfilterReads Unique”. PCR duplicates were then filtered using Picard Tools v2.25.5 (https://broadinstitute.github.io/picard/). Reads were normalized to total read counts per million (cpm) and visualized as bigwig-formatted coverage tracks using deepTools v3.5.1.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include Count values for each Sample

source_name: Embryonic stem cell

growth_protocol: ESCs were grown in N2B27 based serum free medium containing MEK inhibitor PD0325901 and GSK inhibitor CHIR99021 (2i), and LIF (Sigma).

extract_protocol:
RNA was extracted and purified with Trizol reagent (Life Technologies) following manufacturer’s instructions. RNA was further treated with DnaseI (Sigma) and then purified with RNeasy mini kit (Qiagen).
NEBNext rRNA Depletion Kit (New England BioLabs) and NEBNext Ultra II Directional RNA Kit (New England BioLabs) were used to deplete ribosomal RNA and prepare RNA-seq libraries, respectively.

treatment_protocol: Spontaneous differentiation was performed by culturing naive ESCs for two passages (4 days) in Dulbecco’s modified Eagle’s medium (DMEM, Corning) supplemented with 15% FBS (Sigma), 1×penicillin-streptomycin (Life Technologies), 1×GlutaMAX (Life Technologies), 1×minimum essential medium nonessential amino acids (NEAA, Life Technologies), and 1×β-mercaptoethanol (Life Technologies). EpiLC differentiation was performed following the previously published protocol. Briefly, naive ESCs were seeded on 6-well tissue culture dishes pre-treated with fibronectin (Millipore) and cultured 2 days with EpiLC media containing 1:1 mixed DMEM/F-12 (Life Technologies) and Neurobasal (Life Technologies) base media, 1×N2 (Life Technologies), 1×B27 (Life Technologies), 1×penicillin-streptomycin (Life Technologies), 1×GlutaMAX (Life Technologies), 1×minimum essential medium nonessential amino acids (Life Technologies), 1×β-mercaptoethanol (Life Technologies), 1% KOSR (Life Technologies), 20 ng/ml Activin A (R&D Systems), and 12 ng/ml FGF2 (R&D Systems).Embryoid body (EB) differentiation was performed using the hanging-drop method with adaptation as previously described. Briefly, 6×104 cells/ml naive ESCs in EB differentiation medium were loaded on the lids of 15-cm petri dishes (Fisher) as 28 µL drops and cultured for 6 days.

value: Embryonic stem cell

tag: genotype

tag: treatment

value: EpiLC differentiation, A485


title: 7F_M_178


title: LSD1CI_DMSO_EpiLC_RNA_2

value: EpiLC differentiation, DMSO


title: 7F_M_177


title: RNA_seq_TCF1KO_LSK_L7d_DN1_Rep1B_Rep1T


title: RNA_seq_TCF1KO_LSK_L1d_DN2_Rep2B_Rep1T


title: 3016-1_Day28_nonBPD

tag: tissue

tag: sample id

tag: variable-disease

value: no


title: LSD1KO_DMSO_EpiLC_RNA_2

tag: cell type


title: WT_DMSO_EpiLC_RNA_2

value: WT


title: 3016-1_Cord_nonBPD

tag: variable-time

value: CordBlood

tag: variable-o2 treatment


title: RNA_seq_TCF1KO_LSK_L1d_DN2_Rep1B_Rep1T


title: 7F_M_175


title: LSD1KO_A485_EpiLC_RNA_1


title: 3015-1_Day28_nonBPD

tag: variable-o2 level

tag: covariate-ga


title: 7F_M_174


title: RNA_seq_TCF1KO_LSK_L1d_DN1_Rep2B_Rep3T


title: 7F_M_173


title: RNA_seq_TCF1KO_LSK_L1d_DN1_Rep2B_Rep2T


title: LSD1KO_DMSO_EpiLC_RNA_1


title: 7F_M_172


title: 3015-1_Cord_nonBPD

tag: covariate-bw

tag: covariate-sex


title: LSD1CI_DMSO_EpiLC_RNA_1


title: RNA_seq_TCF1KO_LSK_L1d_DN1_Rep2B_Rep1T


title: RNA_seq_TCF1KO_LSK_L1d_DN2_Rep2B_Rep2T


title: 3013-1_Day28_BPD

tag: covariate-b cell%


title: 3017-1_Cord_BPD

value: M


title: 7F_M_171

tag: brain region


title: WT_DMSO_EpiLC_RNA_1


title: 3013-1_Day14_BPD


title: RNA_seq_TCF1KO_LSK_L1d_DN2_Rep1B_Rep2T

tag: strain

value: Tcf7eGFP fl/fl Cre+


title: 7F_M_176


title: 7F_M_170


title: LSD1CI_DMSO_FBS_RNA_2

value: FBS, DMSO


title: RNA_seq_TCF1KO_LSK_L1d_DN1_Rep1B_Rep2T

value: Cultured on OP9-DLL1


title: 3013-1_Cord_BPD

value: Peripheral blood

value: whole blood cells

tag: covariate


title: 3015-1_Day14_nonBPD

value: nonBPD


title: LSD1KO_A485_FBS_RNA_2

value: FBS, A485


title: RNA_seq_TCF1KO_LSK_L1d_DN1_Rep1B_Rep1T


title: 3012-1_Day28_BPD

value: yes


title: LSD1KO_DMSO_FBS_RNA_2


title: 7F_M_168

value: GP

tag: age


title: RNA_seq_TCF1KO_LSK_HMGd_DN1_Rep2B_Rep2T


title: 3012-1_Day14_BPD

value: BPD


title: WT_DMSO_FBS_RNA_2

value: Embryonic stem cell

tag: genotype


title: RNA_seq_TCF1KO_LSK_HMGd_DN1_Rep2B_Rep1T

tag: treatment


title: 7F_M_167


title: 3012-1_Cord_BPD

tag: tissue


title: 7F_M_166


title: RNA_seq_TCF1KO_LSK_HMGd_DN1_Rep1B_Rep3T


title: RNA_seq_TCF1KO_LSK_L1d_DN1_Rep1B_Rep3T


title: 7F_M_165


title: LSD1KO_A485_FBS_RNA_1


title: LSD1CI_DMSO_FBS_RNA_1


title: 3011-2_Cord_nonBPD

tag: sample id

value: F


title: RNA_seq_TCF1KO_LSK_HMGd_DN1_Rep1B_Rep2T


title: 3011-2_Day28_nonBPD

tag: variable-disease


title: LSD1KO_DMSO_FBS_RNA_1

tag: cell type


title: 7F_M_164


title: RNA_seq_TCF1KO_LSK_HMGd_DN1_Rep1B_Rep1T


title: RNA_seq_TCF1KO_LSK_EV_DN1_Rep2B_Rep3T


title: 3011-1_Day28_nonBPD

tag: variable-time


title: WT_DMSO_FBS_RNA_1


title: 7F_M_169


title: 7F_M_163


title: 3011-1_Day14_nonBPD

tag: variable-o2 treatment


title: 7F_M_162


title: RNA_seq_TCF1KO_LSK_EV_DN1_Rep2B_Rep2T


title: 3010-2_Day28_nonBPD

tag: variable-o2 level


title: RNA_seq_TCF1KO_LSK_EV_DN1_Rep2B_Rep1T


title: 7F_M_161


title: MLL4KOLSD1CI_RNA_3

value: naive ESC


title: MLL4KOLSD1CI_RNA_4


title: MLL4KOLSD1CI_RNA_2


title: 7F_M_160


title: 7F_M_159


title: 3010-2_Cord_nonBPD

value: no

tag: covariate-ga


title: MLL4KOLSD1CI_RNA_1


title: RNA_seq_TCF1KO_LSK_EV_DN1_Rep1B_Rep2T


title: RNA_seq_TCF1KO_LSK_EV_DN1_Rep1B_Rep1T


title: 3010-1_Cord_nonBPD

tag: covariate-bw


title: 3009-3_Day14_nonBPD

tag: covariate-sex


title: 7F_M_157


title: RNA_seq_DN3-KO_HMG-E10_P45_Rep2

source_name: Scid.adh cell line

value: WT TCF-1 RV


title: RNA_seq_DN3-KO_HMG-E10_P45_Rep1


title: 7F_M_156


title: MLL4LSD1DKO_RNA_2


title: 7F_M_158


title: 3010-1_Day28_nonBPD

tag: covariate-b cell%


title: 3010-2_Day14_nonBPD


title: 7F_M_155

tag: brain region


title: MLL4LSD1DKO_RNA_1


title: RNA_seq_DN3-KO_HMG-E10_L7_Rep2

value: DL7 TCF-1 RV


title: MLL4KO_RNA_2


title: RNA_seq_TCF1KO_LSK_EV_DN1_Rep1B_Rep3T

tag: strain


title: 3009-1_Day28_nonBPD

tag: covariate


title: 7F_M_154

tag: age


title: RNA_seq_DN3-KO_HMG-E10_L7_Rep1


title: MLL4KO_RNA_1

tag: genotype


title: 3009-1_Day14_nonBPD


title: MLL4LSD1DKO_RNA_4

tag: treatment


title: 7F_M_153


title: RNA_seq_DN3-KO_HMG-E10_L6_Rep2

value: DL6 TCF-1 RV


title: 3008-1_Day28_nonBPD

tag: tissue

value: M


title: 7F_M_152


title: WT_RNA_11

value: WT


title: RNA_seq_DN3-KO_HMG-E10_L6_Rep1


title: 3009-3_Cord_nonBPD

tag: sample id

value: CordBlood


title: 3008-1_Day14_nonBPD

value: Peripheral blood

tag: variable-disease


title: WT_RNA_10

tag: cell type


title: 7F_M_151


title: 3008-1_Cord_nonBPD

value: whole blood cells

tag: variable-time


title: 7F_M_150


title: 3006-1_Day28_nonBPD

value: nonBPD

tag: variable-o2 treatment


title: 7F_M_149


title: RNA_seq_DN3-KO_HMG-E10_L2_Rep2

value: DL2 TCF-1 RV


title: RNA_seq_DN3-KO_HMG-E10_L2_Rep1


title: RNA_seq_DN3-KO_HMG-E10_L1_Rep2

value: DL1 TCF-1 RV


title: LSD1Res_noDOX_4


title: MLL4LSD1DKO_RNA_3


title: 3004-1_Day28_nonBPD

value: yes

tag: variable-o2 level


title: 7F_M_148

value: GP


title: LSD1Res_DOX_3

value: Embryonic stem cell


title: RNA_seq_DN3-KO_HMG-E10_L1_Rep1


title: 3004-1_Day14_nonBPD

tag: covariate-ga

value: F


title: 3004-1_Cord_nonBPD

tag: covariate-bw


title: 7F_M_147


title: RNA_seq_DN3-KO_HMG-E10_HMG_rep2

value: DHMG TCF-1 RV


title: LSD1Res_DOX_2

value: naive ESC


title: LSD1Res_noDOX_3


title: RNA_seq_DN3-KO_HMG-E10_HMG_rep1


title: 7F_M_146


title: 3003-1_Day28_nonBPD

tag: covariate-sex


title: LSD1Res_noDOX_2


title: 7F_M_145


title: LSD1Res_DOX_4


title: 3003-1_Day14_nonBPD

tag: covariate-b cell%


title: RNA_seq_DN3-KO_HMG-E10_EV_Rep2

value: empty vector RV


title: LSD1Res_DOX_1


title: RNA_seq_DN3-KO_HMG-E10_EV_Rep1


title: 7F_M_144

tag: brain region


title: LSD1Res_noDOX_1


title: primary monocytes, 2 [s2]

data_processing:
Data preprocessing and genomic alignment
Transcript splicing、lncRNA prediction、and Gene quantification
Differential screening analysis and Functional Analysis
CircRNA prediction, Expression analysis and Interaction research
Gene structure optimization and New transcript prediction
Assembly: GRCh37
Supplementary files format and content: table-delimited text files induces raw counts for each sample
Supplementary files format and content: table-delimited text files induces FPKM values for each sample

growth_protocol: THP-1 cells (Cell Bank, Shanghai Institutes for Biological Science, Chinese Academy of Sciences) were cultured in RPMI 1640 medium supplied with  10% (v/v) fetal bovine serum (Gibco), 2 mM L-Glutamine, 1mM sodium pyruvate  and 10 mM HEPES at 37℃in a cell incubator containing 5% CO2. PBMCs were collected by using Ficoll-Paque PLUS (Citiva) according to manufacturer's instructions. CD14+ monocytes were separated from PBMCs via magnetic beads sorting (Miltenyi Biotech), and the purity (>98%) was verified by anti-CD14 antibody  (BD biosciences) through flow cytometry (BD FORTESSA).

treatment_protocol: THP-1 cells or primary monocytes were pretreated with 50 uM Diosmetin or vehicle for 30 minutes, then type I IFN 1000 U/ml was added. PBMCs from patients of SLE were incubated with Diosmetin 50 uM or vehicle for 3 hours. Cells were collected to extract RNA or protein for downstream analysis.

tag: cell line

value: primary CD14+ monocytes

value: monocyte

value: Diosmetin, IFN


title: LSD1KO_DOX_2


title: primary monocytes, 1 [s1]

value: WT

value: IFN


title: 7F_M_142

tag: strain


title: 3002-1_Day14_nonBPD

value: Peripheral blood

tag: covariate


title: LSD1KO_noDOX_2

tag: genotype


title: 3002-1_Cord_nonBPD

value: whole blood cells

value: CordBlood


title: 7F_M_141

tag: age


title: THP-1 cell line, 2 [B_DMSO_IFN]

tag: tissue

tag: treatment


title: THP-1 cell line, 3 [C_Dio]


title: LSD1KO_DOX_1


title: LSD1KO_noDOX_1


title: 3001-1_Cord_nonBPD

tag: sample id

tag: variable-disease

value: nonBPD

value: M


title: 7F_M_139


title: THP-1 cell line, 1 [A_DMSO]

tag: cell type

value: control


title: 2024-1_Day14_nonBPD

tag: variable-time

tag: variable-o2 treatment

value: yes


title: 7F_M_138

value: GP


title: 3003-1_Cord_nonBPD

tag: variable-o2 level

tag: covariate-ga


title: DKOLSD1_noDOX_4

value: Embryonic stem cell


title: 7F_M_137


title: 7F_M_143


title: 2024-1_Cord_nonBPD

tag: covariate-bw

tag: covariate-sex

value: F


title: 3002-1_Day28_nonBPD

tag: covariate-b cell%


title: fermon-05-09_CCGTCC_L003_R1_001

city: Madison

first: Daniel

last: Jackson

state: WI

address: 600 highland Ave

institute: University of Wisconsin-Madison

data_processing:
BioconductorM2 tools
Sequencing reads were aligned to the UCSC hg19 Homo sapiens genome and gene count assigned with RsubreadM3 1.22.3 package
Gene annotation was performed using the org.Hs.eg.dbM4 3.3.0 and annotateM5 1.50.1 packages
The edgeRM6,M7 3.14.0 package was used to scale raw library sizes, estimate gene-wise dispersion using the empirical likelihood empirical Bayes method, and fit quasi-likelihood negative binomial models with covariates for BEC donor and virus strain to assess differential gene expression.
Assembly: hg19
Supplementary files format and content: tab-delimited EXCEL file showing top defentaly expressed genes vs different isolates of EV-D68

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini  kit (Qiagen) with added DNAse digest step. 1.3 ug of total RNA was used for the construction of sequencing libraries.
Illumina® TruSeq® Stranded mRNA Sample Preparation kits (Illumina Inc., San Diego, California, USA). Each library was prepared and standardized according to Illumina Inc. protocol

treatment_protocol: BEC cultures were infected with 1X105 plaque forming unit equivalents (PFUe) per well of purified EV-D68 which was diluted in PneumaCult-ALI maintenance medium without hydrocortisone. The cultures were gently shaken for 15 minutes at room temperature and then incubated at 34℃ for 2 hours.

value: lung

tag: cell line

value: Primary

value: bronchial epithelial cells


title: DKOLSD1_DOX_3

value: naive ESC


title: fermon-04-09-1_AGTTCC_L003_R1_001


title: 7F_M_136

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

tag: brain region

tag: strain


title: fermon-15-03-1_ACTGAT_L005_R1_001

tag: genotype


title: 2023-1_Day14_nonBPD

value: no

tag: covariate


title: 7F_M_140

tag: age


title: 2023-1_Day28_nonBPD

tag: tissue


title: DKOLSD1_noDOX_3

tag: treatment


title: 7F_M_135


title: fermon-03-10-1_ATTCCT_L005_R1_001

value: WT


title: DKOLSD1_DOX_2


title: 7F_M_133


title: 2022-1_Day28_nonBPD

tag: sample id

tag: variable-disease


title: DKOLSD1_noDOX_2

tag: cell type


title: 2022-1_Cord_nonBPD

tag: variable-time

tag: variable-o2 treatment


title: DKOLSD1_DOX_4


title: DKOLSD1_DOX_1


title: 7F_M_132


title: 2021-2_Day28_nonBPD

tag: variable-o2 level

tag: covariate-ga


title: 7F_M_131


title: ctl-1-05-09-1_GCCAAT_L002_R1_001


title: ctl-1-04-09-1_TGACCA_L001_R1_001


title: 2021-2_Day14_nonBPD

tag: covariate-bw

tag: covariate-sex


title: LSD1KO_EB_A485_RNA_2

source_name: Embryoid bodies

value: Embryoid bodies

value: EB differentiation, A485


title: 7F_M_130


title: ctl1-03-10-1_TGACCA_L005_R1_001

tag: cell line


title: 7F_M_129

tag: brain region


title: LSD1KO_EB_DMSO_RNA_2

value: EB differentiation, DMSO


title: 2021-1_Day28_nonBPD

value: Peripheral blood

value: whole blood cells

tag: covariate-b cell%


title: fermon-02-02-1_ATGTCA_L003_R1_001

tag: genotype


title: LSD1KO_EB_A485_RNA_1


title: 7F_M_128

tag: strain


title: 7F_M_134

tag: age


title: ctl-1-15-03-1_TTAGGC_L001_R1_001

tag: tissue


title: 2021-1_Day14_nonBPD

value: nonBPD

tag: covariate


title: LSD1KO_EB_DMSO_RNA_1

tag: treatment


title: ctl-1-02-02-1_ACAGTG_L002_R1_001


title: 7788-15-03-1_GTCCGC_L004_R1_001


title: 2021-2_Cord_nonBPD

tag: sample id

tag: variable-disease

value: CordBlood

value: M


title: 7788-05-09-1_GTGGCC_L004_R1_001

tag: cell type


title: 2023-1_Cord_nonBPD

tag: variable-time

tag: variable-o2 treatment


title: 7F_M_63

value: GP


title: 2021-1_Cord_nonBPD

value: yes

tag: variable-o2 level

tag: covariate-ga


title: WT_EB_DMSO_RNA_2


title: 7F_M_62


title: DKOLSD1_noDOX_1

value: Embryonic stem cell


title: 7788-04-09-1_CGATGT_L005_R1_001

value: lung


title: 2020-1_Day28_nonBPD

tag: covariate-bw

tag: covariate-sex


title: WT_EB_DMSO_RNA_1


title: 2019-1_Day28_nonBPD


title: 7788-03-10-1_GTGAAA_L004_R1_001

tag: cell line

value: Primary


title: 7F_M_61

tag: brain region


title: LSD1KO_A485_RNA_2

tag: genotype


title: 7788-02-02-1_GTTTCG_L004_R1_001

value: bronchial epithelial cells


title: 2019-1_Day14_nonBPD

tag: covariate-b cell%


title: LSD1KO_DMSO_RNA_2

value: naive ESC


title: 7731-15-03-1_TTAGGC_L005_R1_001


title: 2017-1_Day28_BPD

value: BPD

value: F


title: 7F_M_58

tag: age

tag: strain


title: 7F_M_59


title: 7731-05-09_ACTTGA_L002_R1_001

tag: tissue

value: WT


title: 7F_M_57


title: 7731-04-09_CAGATC_L002_R1_001

tag: treatment


title: 2017-1_Cord_BPD

tag: sample id

tag: covariate


title: 7F_M_56


title: 2017-1_Day14_BPD

tag: cell type

tag: variable-disease


title: LSD1KO_DMSO_RNA_1


title: 7F_M_55


title: 2015-1_Day28_nonBPD

tag: variable-time

tag: variable-o2 treatment


title: 7731-03-10-1_TAGCTT_L002_R1_001


title: 2015-1_Day14_nonBPD

tag: variable-o2 level

tag: covariate-ga


title: RCORDKO_EB_RNA_3

value: Embryoid bodies

value: EB differentiation


title: 7731-02-02-1_GATCAG_L002_R1_001


title: RCOR1KO_EB_RNA_4


title: 7F_M_60


title: 7F_M_54


title: 2386-15-03-1_GAGTGG_L004_R1_001


title: 2015-1_Cord_nonBPD

value: Peripheral blood

tag: covariate-bw

tag: covariate-sex


title: 7F_M_53

tag: brain region


title: RCOR1KO_EB_RNA_3

tag: genotype


title: LSD1KO_A485_RNA_1


title: 2386-05-09_CGATGT_L001_R1_001

tag: cell line


title: 2014-1_Day28_BPD

value: whole blood cells

tag: covariate-b cell%


title: WTEB_RNA_7


title: RCORDKO_EB_RNA_4


title: 7F_M_52

tag: age

tag: strain


title: 2386-04-09_ATTCCT_L001_R1_001

tag: tissue

tag: treatment


title: RCOR2KO_EB_RNA_2


title: 7F_M_51


title: 2386-03-10-1_ATCACG_L001_R1_001


title: 2014-1_Day14_BPD

tag: sample id

tag: covariate


title: RCORDKO_EB_RNA_1

tag: cell type


title: 2012-1_Day28_BPD

tag: variable-disease

tag: variable-time


title: 7F_M_49


title: 0541-15-03-1_GGCTAC_L003_R1_001


title: 2014-1_Cord_BPD

tag: variable-o2 treatment

tag: variable-o2 level


title: RCORDKO_EB_RNA_2


title: 2386-02-02-1_ACTGAT_L001_R1_001


title: RCOR1KO_EB_RNA_2


title: 7F_M_50


title: 7F_M_48


title: RCOR1KO_EB_RNA_1


title: 2011-1_Day28_nonBPD

value: nonBPD

value: no

tag: covariate-ga

tag: covariate-bw


title: 7F_M_47

tag: brain region


title: 0541-04-09-1_CTTGTA_L003_R1_001

tag: genotype


title: RCOR2KO_EB_RNA_1


title: 0541-05-09-1_ATCACG_L005_R1_001

tag: cell line


title: 2011-1_Day14_nonBPD

tag: covariate-sex

value: M

tag: covariate-b cell%


title: 0541-03-10-1_CGTACG_L004_R1_001


title: 2011-1_Cord_nonBPD

value: CordBlood


title: 2009-1_Day28_nonBPD


title: RCORDKO_RNA_4


title: WTEB_RNA_6


title: 2008-1_Day14_nonBPD


title: CA-13_3

city: Lishui

first: Ming

middle: Guo

last: Cao

address: No 01, Rd Xueyuan Avenue

institute: Lishui University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: md5
Supplementary files format and content: Differential_expression gene lists

source_name: paracancer tissue derived cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: patient diagnosis

value: oral squamous cell carcinoma

value: paracancer tissue derived cells

tag: donor

value: donor 3


title: 7F_M_44

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

value: GP

tag: age

tag: strain


title: 0541-02-02_AGTCAA_L003_R1_001

tag: tissue

value: lung

value: Primary

value: bronchial epithelial cells

tag: treatment


title: 7F_M_45


title: RCORDKO_RNA_3

tag: cell type

value: Embryonic stem cell

value: naive ESC


title: 2012-1_Day14_BPD

tag: sample id

tag: variable-disease

value: BPD

tag: variable-time

value: yes

tag: covariate


title: RCOR1KO_RNA_4


title: 2006-1_Day28_nonBPD

value: Peripheral blood

tag: variable-o2 treatment

tag: variable-o2 level

tag: covariate-ga

tag: covariate-bw

value: F


title: CA-13_2

tag: genotype

value: WT

value: donor 2


title: RCOR1KO_RNA_3


title: 7F_M_41

tag: brain region


title: 2006-1_Cord_nonBPD

value: whole blood cells

value: nonBPD

value: no

tag: covariate-sex

tag: covariate-b cell%


title: 7F_M_42

tag: age


title: 7F_M_46

tag: strain


title: 7F_M_40


title: 2005-2_Day28_nonBPD

tag: tissue


title: 2005-2_Day14_nonBPD


title: PA-35_3

source_name: cancer tissue derived cells

tag: patient diagnosis

value: oral squamous cell carcinoma

value: cancer tissue derived cells

tag: donor


title: WT_RNA_9

tag: cell type

tag: treatment


title: PA-35_2


title: RCORDKO_RNA_2


title: 7F_M_39

value: GP


title: PA-35_1

value: donor 1


title: 2005-2_Cord_nonBPD

tag: sample id

tag: variable-disease

tag: variable-time

value: CordBlood


title: RCORDKO_RNA_1


title: 7F_M_38


title: 2005-1_Day28_nonBPD

tag: variable-o2 treatment

tag: variable-o2 level

tag: covariate


title: 7F_M_37


title: 7F_M_43


title: RCOR1KO_RNA_2

tag: genotype


title: HBEC3 cells, TET3KO2

city: Grand Rapids

first: Gerd

last: Pfeifer

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Research Institute

data_processing:
Paired-end reads were trimmed using TrimGalore(version 0.5.0) with the following parameters : --length 50, --clip_R1 10, --clip_R2 18, --three_prime_clip_R1 10, and --three_prime_clip_R2 10.
Trimmed reads were aligned to the hg19 using Bismark version 0.19.0
Duplication were removed using the deduplicate_bismark script provided with Bismark
CpG methylation values were called by the bismark_methylation_extractor script provided with Bismark and the following parameters: --no_overlap, --comprehensive, --merge_non_CpG, and --cytosine_report.
Assembly: hg19
Supplementary files format and content: bigWig, methylation coverage with cutoff 3

growth_protocol: keratinocyte SFM medium , Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA was extracted using a Quick-DNA Miniprep Plus kit (Zymo Research, D4070).
The Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024) was used according to the manufacturer’s instructions to perform bisulfite conversion and library preparation.
WGBS

tag: cell line

value: Human Bronchial cells

value: TET3 knockout


title: HBEC3 cells, TET3KO3


title: CA-13_1

value: paracancer tissue derived cells


title: RCOR1KO_RNA_1

value: Embryonic stem cell

value: naive ESC


title: WT_RNA_8


title: 2005-1_Cord_nonBPD

value: Peripheral blood

value: yes

tag: covariate-ga

tag: covariate-bw

tag: covariate-sex


title: 7F_M_35

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: brain region

tag: age

tag: strain


title: HBEC3 cells, TET3KO1


title: 7F_M_36


title: 2004-1_Day28_nonBPD

tag: tissue

value: F

tag: covariate-b cell%


title: 7F_M_33


title: 2004-1_Day14_nonBPD

tag: cell type


title: HBEC3 cells, YAF2 KO2

value: YAF2 knockout


title: HBEC3 cells, YAF2 KO3


title: RCOR2KO_RNA_3

tag: treatment


title: RCOR2KO_RNA_4


title: HBEC3 cells, YAF2 KO1


title: 2003-2_Day28_BPD

tag: sample id

value: whole blood cells

tag: variable-disease

value: BPD

value: M


title: 7F_M_32


title: 2005-1_Day14_nonBPD

value: nonBPD

tag: variable-time

tag: variable-o2 treatment


title: 2003-2_Day14_BPD

tag: variable-o2 level

tag: covariate


title: PBS 1h H9 R3

city: Raleigh

first: Ryan

middle: W

last: Tam

state: North Carolina

address: 840 Main Campus Drive, Building Partners II, Room 3700

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

data_processing:
CLC Workbench 23.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter - Quality limit: 0.05)
Trimmed sequence reads were mapped to ensembl v97 hg38 using CLC genomic benchwork (default settings)
Read count extraction and normalization were performed using CLC genomic benchwork.
Differential expression was performed using CLC genomic benchwork using default settings.
Assembly: hg38
Supplementary files format and content: xlsx files include TPM and RPKM normalized values and raw counts for each sample.

growth_protocol: hMSN-like cells were obtained following previously described protocols [15] and have been described in detail in prior work [51]. Briefly, the feeder-independent H9 and H1 hESCs (WA09 and WA01; WiCell, Madison, WI, USA) were maintained in 6-well tissue culture dishes (Greiner Bio-One, Alphen aan den Rijn, NL) coated with 0.5 µg/mL reduced growth factor Matrigel solution (Corning, Durham, NC, USA) in E8 medium (Stemcell Technologies, Cambridge, MA, USA) and passaged using standard protocols. Cells were grown to ~75–80% confluency prior to differentiation. On days in vitro (DIV) 0 of differentiation, E8 medium was removed, cells were washed with 1X PBS (Gibco, Waltham, MA, USA), and media switched to DMEM-F12/Neurobasal media (2:1) (Gibco) supplemented with N2 (Gibco) and B27 minus Vitamin A (Gibco) (together referred to as N2B27). From DIV 0 to 4, cultures were supplemented with SB431542 (10 µM in 95% EtOH; Selleck Chemicals, Houston, TX, USA), LDN-193189 (100 nM in DMSO; BioVision, Waltham, MA, USA), and dorsomorphin (200 nM; BioVision). Media was changed every day. From DIV 5 to 8, cultures were supplemented with just LDN-193189 and dorsomorphin. Media was changed every day. On DIV 9, cultures were washed with 1X PBS, and media switched to N2B27 supplemented with activin A (25 ng/mL in 4 mM HCl; R&D, Minneapolis, MN, USA). Cells were then lifted using cell scrapers (Greiner Bio-One) since EDTA treatment drastically reduced survivability, pipetted up and down 1 time with a 5 mL serological pipette, and replated with 5.21E5 cells/cm2 onto Matrigel-coated 6-well plates. Half-media was changed the next day and then every other day afterward. On DIV 18, cultures were passaged using 0.5 mM EDTA for 2 min at 37 °C, as we no longer observed issues with survivability with EDTA treatment, and pipetted up and down 10–15 times using P1000 mechanical pipette then replated onto Poly-L-Ornithine (15 µg/mL in water; Sigma, St. Louis, MO, USA) and Laminin (5 µg/mL in PBS; Corning) coated 24-well plates (Greiner Bio-One) at 2.11E5 cells/cm2. Half-media was changed the next day and then every other day afterward. From DIV 20 to 24, media was switched to N2B27 with Vitamin A (Gibco). On day 25 for analysis, BDNF and GDNF (10 ng/mL in 0.1% BSA (w/v); Peprotech) were added to aid neuronal maturation and survival (referred to as Maturation Medium). Cells were lifted, similar to the DIV18 passage, on DIV 30 to 35 and all cells were replated onto Poly-L-Ornithine (2 µg/cm2) and Laminin (1 µg/cm2) coated 24-well plates to maintain neuron attachment. Cells were maintained in a humid incubator at 37 °C with 5% CO2. Striatal interneuron-like cells were obtained following a previously published differentiation protocol [55]. H9 and H1 hESCs were grown to ~80-90% confluency prior to differentiation. On days in vitro (DIV) 0 of differentiation, E8 medium was removed, cells were washed with 1X PBS (Gibco, Waltham, MA, USA), and media switched to DMEM-F12/Neurobasal media (2:1) (Gibco) supplemented with N2 (Gibco) and B27 (Gibco) (together referred to as N2B27). From DIV 0 to 9, cultures were supplemented with SB431542 (10 µM in 95% EtOH; Selleck Chemicals, Houston, TX, USA), LDN-193189 (100 nM in DMSO; BioVision, Waltham, MA, USA), and XAV939 (2 µM in DMSO; R&D, Minneapolis, MN, USA). Media was changed every day. On DIV 9, cells were lifted using cell scrapers (Greiner Bio-One) since EDTA treatment drastically reduced survivability, pipetted up and down 1 time with a 5 mL serological pipette, and replated with 5.21E5 cells/cm2 onto Matrigel-coated 6-well plates. From DIV 10 to 20, cultures were supplemented with SHH (200 ng/mL in 0.1% (w/v) BSA in 1X PBS; R&D, Minneapolis, MN, USA) and Purmorphamine (1 µM in DMSO; Sigma, St. Louis, MO, USA). Half-media was changed every other day afterward. On DIV 20, cultures were passaged using 0.5 mM EDTA for 2 min at 37 °C, as we no longer observed issues with survivability with EDTA treatment, and pipetted up and down 10–15 times using P1000 mechanical pipette then replated onto Poly-L-Ornithine (15 µg/mL in water; Sigma, St. Louis, MO, USA) and Laminin (5 µg/mL in PBS; Corning) coated 24-well plates (Greiner Bio-One) at 2.11E5 cells/cm2. Half-media was changed the next day and then every other day afterward. From DIV 20 to 45, media was supplemented with only BDNF (10 ng/mL in 0.1% BSA (w/v); Peprotech) to aid neuronal maturation and survival. Cells were maintained in a humid incubator at 37 °C with 5% CO2.

extract_protocol:
For RNA extraction, total RNA was extracted as previously described [109]. In brief, hMSN-like cultures were washed 1 time in PBS. Total RNA was isolated using Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s protocol. RNA samples were collected in 2 mL RNAse-free tubes and chilled on ice throughout the procedure. Total RNA was then used for RNA-seq.
RNA libraries for RNA-seq were prepared by Genewiz/Azenta.

treatment_protocol: To perform tonic neurotransmitter preincubations hMSN-like and interneuron-like cells were grown to DIV45, half-media was removed, and new media containing either ascorbic acid (100 µM in water; Sigma, St. Louis, MO, USA), dopamine hydrochloride (10 nM in 100 µM ascorbic acid; Sigma, St. Louis, MO, USA), acetylcholine chloride (750 nM in water; Sigma, St. Louis, MO, USA), or L-glutamic acid (2 µM in water; Sigma, St. Louis, MO, USA) was added and left in the wells to be incubated at 37 °C until the next day. This process was repeated every day for 21 days, then RNA extracted for sequencing. To perform antagonist incubations, hMSN-like cells were grown to DIV45, half-media was removed, replaced with media containing both R(+)-SCH23390 hydrochloride (250 µM; Sigma, St. Louis, MO, USA), S(-)-Sulpiride (250 µM; Sigma, St. Louis, MO, USA) was added and incubated at 37 °C for 60 min. Half media was then removed and media containing either dopamine hydrochloride (1 mM in 100 µM ascorbic acid; Sigma, St. Louis, MO, USA), R(+)-SCH23390 hydrochloride (250 µM; Sigma, St. Louis, MO, USA), S(-)-Sulpiride (250 µM; Sigma, St. Louis, MO, USA), or PBS (1X; Gibco), individually or in combination, was added and incubated at 37 °C for 60 min then extracted RNA for sequencing. Chronic incubation proceeded by removing all culture media, replacing with maturation media, and repeating dopamine, SCH23390, and Sulpiride incubations for 5 days. Chronic time-course doses were time-matched to extract all samples on DIV50. To perform acute incubations, hMSN-like cells were grown to DIV45, half-media was removed, replaced with dopamine hydrochloride (10 nM–1 mM in 100 µM ascorbic acid; Sigma, St. Louis, MO, USA), L-glutamic acid (5 µM in water; Sigma, St. Louis, MO, USA), SKF82958 (1–100 µM; Sigma, St. Louis, MO, USA), quinpirole (1–100 µM; Sigma, St. Louis, MO, USA), or CGS21680 (0.1–10 µM; Sigma, St. Louis, MO, USA), and incubated at 37 C for 60 min prior to harvesting for RNA-seq. Withdrawal incubations were performed by dosing as previously described for chronic dopamine for 5 days, then ceasing dopamine dosage for two weeks. A final dopamine dosage was performed after 2 weeks and RNA extracted. All doses were performed at 37 C for 60 min.

tag: cell line

value: differentiated human embryonic stem cell

value: PBS 1X 1h, RNA Extraction


title: 7F_M_356

city: La Jolla

value: GP


title: 2003-2_Cord_BPD

value: CordBlood

tag: covariate-ga


title: 7F_M_31


title: RCOR2KO_RNA_1

tag: genotype


title: PBS 1h H9 R2


title: 7F_M_34


title: 7F_M_30


title: WT_RNA_6

value: WT


title: 2003-1_Day28_nonBPD

tag: covariate-bw

tag: covariate-sex


title: 7F_M_29

tag: brain region

tag: age


title: LSD1CIEB_RNA_4

value: Embryoid bodies

value: EB differentiation


title: 2003-1_Day14_nonBPD

tag: tissue


title: 7F_M_28

tag: strain


title: PBS 1h H9 R1

tag: cell type


title: 2003-1_Cord_nonBPD

tag: covariate-b cell%


title: WT_RNA_7

value: Embryonic stem cell

tag: treatment


title: LSD1CIEB_RNA_3


title: 7F_M_27


title: WTEB_RNA_5


title: DGA pre Dop H9 R1

value: Acetylcholine 750 nM, Dopamine 10 nM, Glutamate 2 microM 3 weeks, Dopamine 1 mM 1h, RNA Extraction


title: RCOR2KO_RNA_2

value: naive ESC


title: 2002-1_Day28_BPD

value: Peripheral blood

tag: sample id

tag: variable-disease

value: yes


title: 7F_M_26


title: 2002-1_Day14_BPD

tag: variable-time

tag: variable-o2 treatment

value: F


title: LSD1CIEB_RNA_2


title: DGA pre AA H9 R2

value: Acetylcholine 750 nM, Dopamine 10 nM, Glutamate 2 microM 3 weeks, Ascorbic Acid 100 microM 1h, RNA Extraction


title: 7F_M_25


title: 2002-1_Cord_BPD

value: whole blood cells

value: BPD

tag: variable-o2 level

tag: covariate


title: LSD1CIEB_RNA_1


title: DGA pre Dop H9 R3

tag: cell line


title: 1040-1_Cord_nonBPD

value: nonBPD

tag: covariate-ga


title: 1039-1_Day14_nonBPD

tag: covariate-bw


title: 7F_M_23


title: Acetyl pre Dop H9 R3

value: differentiated human embryonic stem cell

value: Acetylcholine 750 nM 3 weeks, Dopamine 1mM 1h, RNA Extraction


title: WTEB_RNA_4

tag: genotype


title: 1039-1_Cord_nonBPD

tag: covariate-sex


title: DGA pre AA H9 R1


title: 7F_M_21

tag: brain region

value: GP

tag: age


title: LSD1KOEB_RNA_1


title: 7F_M_22

tag: strain


title: LSD1KOEB_RNA_2

tag: cell type


title: 1038-1_Day28_nonBPD

tag: tissue

value: M

tag: covariate-b cell%


title: WTEB_RNA_3

value: WT

tag: treatment


title: Acetyl pre Dop H9 R1


title: DGA pre AA H9 R3


title: Acetyl pre AA H9 R3

value: Acetylcholine 750 nM 3 weeks, Ascorbic Acid 100 microM 1h, RNA Extraction


title: 7F_M_20


title: 7F_M_24


title: WTEB_RNA_2

value: Embryoid bodies

value: EB differentiation


title: 7F_M_19


title: Acetyl pre AA H9 R2


title: 1038-1_Day14_nonBPD

tag: sample id

tag: variable-disease


title: 1038-1_Cord_nonBPD

tag: variable-time

value: CordBlood

tag: variable-o2 treatment


title: Acetyl pre Dop H9 R2


title: 7F_M_18


title: Acetyl pre AA H9 R1


title: 1037-1_Day28_BPD

tag: variable-o2 level

tag: covariate


title: LSD1CI_RNA_4

value: Embryonic stem cell

value: naive ESC


title: 7F_M_17


title: Glut pre Dop H9 R3

tag: cell line

value: Glutamate 2 microM 3 weeks, Dopamine 1 mM 1h, RNA Extraction


title: 1037-1_Day14_BPD

value: Peripheral blood

value: yes

tag: covariate-ga

tag: covariate-bw


title: LSD1CI_RNA_3

tag: genotype


title: 7F_M_16

tag: brain region


title: LSD1CI_RNA_2


title: 7F_M_15

tag: age


title: 1036-1_Day28_nonBPD

value: whole blood cells


title: 1037-1_Cord_BPD

value: BPD

tag: covariate-sex


title: 7F_M_14

tag: strain


title: 1036-1_Day14_nonBPD

tag: tissue

tag: cell type

value: nonBPD


title: 7F_M_13


title: WT_RNA_5

tag: treatment


title: Glut pre AA H9 R3

value: differentiated human embryonic stem cell

value: Glutamate 2 microM 3 weeks, Ascorbic Acid 100 microM 1h, RNA Extraction


title: WT_RNA_4


title: WTEB_RNA_1


title: LSD1KO_RNA_6


title: 1033-1_Day28_nonBPD

tag: sample id

value: F

tag: covariate-b cell%


title: Glut pre AA H9 R1


title: 7F_M_11

value: GP


title: 1033-1_Day14_nonBPD

tag: variable-disease

tag: variable-time


title: Glut pre AA H9 R2


title: 1033-1_Cord_nonBPD

tag: variable-o2 treatment

tag: variable-o2 level


title: Dop pre Dop H9 R3

tag: cell line

value: Dopamine 10 nM 3 weeks, Dopamine 1 mM 1h, RNA Extraction


title: 7F_M_10


title: Glut pre Dop H9 R2


title: 7F_M_9


title: LSD1KO_RNA_4


title: Glut pre Dop H9 R1


title: LSD1KO_RNA_5


title: 1031-1_Day28_nonBPD

value: no

tag: covariate-ga

tag: covariate


title: LSD1CI_RNA_1

tag: genotype


title: Dop pre Dop H9 R2


title: Dop pre Dop H9 R1


title: LSD1KO_RNA_3


title: 1031-1_Day14_nonBPD

tag: covariate-bw


title: 1031-1_Cord_nonBPD


title: 7F_M_12

tag: brain region

tag: age


title: Dop pre AA H9 R3

value: Dopamine 10 nM 3 weeks, Ascorbic Acid 100 microM 1h, RNA Extraction


title: LSD1KO_RNA_2


title: Dop pre AA H9 R2


title: DGA pre Dop H9 R2

value: Acetylcholine 750 nM, Dopamine 10 nM, Glutamate 2 microM 3 weeks, Dopamine 1 mM 1h, RNA Extraction


title: 7F_M_8

tag: strain


title: 7F_M_7


title: 1030-2_Day28_nonBPD

tag: tissue

tag: covariate-sex


title: 7F_M_6


title: Dop pre AA H9 R1

tag: cell type

tag: treatment


title: LSD1KO_RNA_1


title: 7F_M_5


title: WT_RNA_2

value: WT


title: 1030-2_Cord_nonBPD

tag: sample id

value: CordBlood

tag: covariate-b cell%


title: AA pre Dop H9 R3

value: Ascorbic Acid 100 microM 3 weeks, Dopamine 1 mM 1h, RNA Extraction


title: 1030-2_Day14_nonBPD

tag: variable-disease

tag: variable-time


title: 7F_M_4


title: AA pre Dop H9 R2


title: 1030-1_Day28_nonBPD

tag: variable-o2 treatment

tag: variable-o2 level


title: 7F_M_3


title: AA pre Dop H9 R1

tag: cell line


title: 1030-1_Day14_nonBPD

tag: covariate-ga

tag: covariate


title: LSD1Res_DOX_input

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” and then aligned to the mouse mm9 and human hg19 genome assemblies using Bowtie v2.4.4 with default parameters . All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.12. The number of spike-in hg19 reads was counted with SAMtools v1.12 and normalization factor alpha = 1e6/hg19_count was calculated. Normalized bigwig was generated with bamCoverage function from deepTools v3.5.1 using scale factors calculated above and reads mapped to the ENCODE blacklist regions were removed using BEDTools v2.30.0 .
Peaks were called using MACS2 v2.2.7.1 with option ‘nomodel’ and peak annotation was performed with R package ChIPseeker v1.28.3.
Assembly: mm9
Supplementary files format and content: bigwig

source_name: Embryonic stem cells

extract_protocol:
ESCs were fixed with 1% formaldehyde (Thermo Fisher) and sheared with E220 focused ultrasonicator (Covaris), respectively. Sheared chromatins were mixed with 20% of lysate from HEK293T cells processed identically as spike-in for normalization. Mixed chromatin were incubated at 4℃ overnight with antibodies. Protein A/G beads (Santa Cruz Biotechnology) were then incubated with the chromatin and antibody mixture for 2 hours at 4℃. Beads were washed, reverse-crosslinked, and DNA were purified with Qiaquick PCR purification kit (Qiagen).
KAPA HyperPrep Kit (Roche) was used to prepare ChIP-Rx libraries.

tag: genotype

value: Embryonic stem cells

tag: chip antibody


title: 7F_M_2

tag: brain region

tag: age


title: 1030-1_Cord_nonBPD

tag: tissue

value: Peripheral blood

tag: covariate-bw


title: WT_RNA_1

tag: cell type

value: Embryonic stem cell

value: naive ESC


title: AA pre AA H9 R2

tag: treatment

value: Ascorbic Acid 100 microM 3 weeks, Ascorbic Acid 100 microM 1h, RNA Extraction


title: 7F_M_1

tag: strain


title: LSD1Res_DOX_HA

value: HA


title: LSD1Res_DOX_P300


title: 1029-2_Day28_nonBPD

tag: sample id

value: whole blood cells

value: nonBPD

value: yes

tag: covariate-sex

value: M

tag: covariate-b cell%


title: AA pre AA H9 R1

value: differentiated human embryonic stem cell


title: 7F_M_0

value: GP


title: LSD1Res_DOX_LSD1


title: 1029-2_Day14_nonBPD

tag: variable-disease

tag: variable-time

tag: variable-o2 treatment


title: WT_RNA_3


title: LSD1Res_noDOX_HA


title: Chronic Dop 24h H9 R3

tag: cell line

value: Dopamine 1 mM 1h for 5 days, remove, 24h RNA Extraction


title: LSD1Res_noDOX_input


title: Testes, XAP5 cKO,D16, rep2

city: Wuhan

first: Weihua

last: Wang

state: Hubei

address: No. 8, Sanjiaohu Rd., Wuhan Economic & Technological Development Zone

institute: Jianghan University

data_processing:
The quality of raw data was evaluated using FastQC (v0.11.2)
Sequencing reads were trimmed for adaptor/low-quality sequence using Trimmomatic (v0.36)
Clean data were aligned to reference genome via software Hisat2 (v2.1.0)
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Differential expression analysis of two conditions/groups was performed using the DESeq2 (v1.12.4)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes counts for XAP5L WT and KO samples
Supplementary files format and content: tab-delimited text file includes counts for XAP5 WT and cKO samples

source_name: testes

extract_protocol:
Total RNA was extracted from the samples using the TRIzol reagent (Invitrogen).
RNA libraries for sequencing were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: testes

value: XAP5 cKO


title: Chronic Dop 24h H9 R2


title: 1029-1_Day28_nonBPD

tag: variable-o2 level

tag: covariate-ga

tag: covariate


title: Testes, XAP5 cKO,D16, rep1

tag: genotype


title: 1029-1_Day14_nonBPD


title: Chronic Dop 24h H9 R1


title: AA pre AA H9 R3


title: LSD1Res_noDOX_P300

tag: chip antibody


title: Testes, WT, D16,  rep3

tag: tissue

value: WT


title: Chronic Dop 1h H9 R3

value: Dopamine 1 mM 1h for 5 days, RNA Extraction


title: 1029-1_Cord_nonBPD

value: CordBlood

tag: covariate-bw


title: LSD1Res_noDOX_LSD1

tag: cell type

value: Embryonic stem cells


title: Testes, WT, D16,  rep2

tag: treatment


title: 1028-1_Day28_nonBPD

value: Peripheral blood


title: Chronic Dop 1h H9 R2


title: DKOLSD1_DOX_input


title: Testes, XAP5 cKO,D16, rep3


title: 1028-1_Day14_nonBPD


title: Testes, WT, D16, rep1


title: Chronic Dop 1h H9 R1


title: Sperm, XAP5L KO, D56, rep3

source_name: sperm

value: sperm

value: XAP5L KO


title: Acute Dop 24h H9 R3

value: Dopamine 1 mM 1h, remove, 24h RNA Extraction


title: DKOLSD1_DOX_LSD1


title: DKOLSD1_DOX_HA

value: HA


title: Sperm, XAP5L KO, D56, rep2


title: 1029-2_Cord_nonBPD

value: whole blood cells

value: nonBPD


title: 1027-1_Day28_nonBPD

value: no

value: M


title: Acute Dop 24h H9 R1

value: differentiated human embryonic stem cell


title: Sperm, XAP5L KO, D56, rep1


title: DKOLSD1_noDOX_input


title: 1027-1_Day14_nonBPD


title: DKOLSD1_noDOX_HA


title: Sperm, WT, D56, rep3


title: Sperm, WT, D56, rep2


title: DKOLSD1_noDOX_LSD1


title: 1026-1_Day28_nonBPD

value: F


title: 1025-1_Day14_nonBPD


title: LSD1KO_EB_input

value: Embryoid bodies


title: Sperm, WT, D56, rep1


title: Acute Dop 1h H9 R2

value: Dopamine 1 mM 1h, RNA Extraction


title: 1028-1_Cord_nonBPD

value: yes


title: Acute Dop 1h H9 R1


title: SKF829 1h H1 R3

value: SKF82958 50 microM 1h, RNA Extraction


title: 1022-1_Cord_nonBPD

value: CordBlood


title: WT_EB_input

value: WT


title: Tff2_scRNAseq, biol rep 1

first: Zhengyu

address: 1130 St Nicolas Ave

institute: CUIMC

description: 10x Genomics

data_processing:
Singe-cell RNA sequencing data were analyzed using the 10X CellRanger software (10x Genomics). Samples were combined using the Cell Ranger aggregate function. Gene-cell matrix was filtered to remove cells with less than 1000 transcripts and/or a high fraction of mitochondrial counts (>20%). The gene-cell matrix was then normalized to count per million of reads (cpm). Normalized single-cell gene expression profiles were transformed to gene expression signature by z-score and used to meta-cell profiles that were used only as input for ARACNe67 to reverse engineer a  regulatory network. Specifically, z-score expression signatures were used to identify for each individual cell the closest 10 cells based on the reciprocal enrichment analysis of the 200 most differentially expressed genes (100 most overexpressed and 100 most downregulated) as implemented in the viperSimilarity function of the VIPER package. A metacell profile  was  then generated for each cell by integrating the raw counts of the 10 closest cells  (KNN approach)  in the viperSimilarity space.  Metacell profiles were normalized and used as input for ARACNe. ARACNe was run with 100 bootstrap iterations using 1824 transcription factors (genes annotated in gene ontology molecular function database, as GO:0003700, “transcription factor activity”, or as GO:0003677, “DNA binding”, and GO:0030528, “transcription regulator activity”, or as GO:00034677 and GO: 0045449, “regulation of transcription”) and 3477 signaling pathway-related genes (annotated in GO biological process database as GO:0007165 “signal transduction” and in GO cellular component database as GO:0005622, “intracellular”, or GO:0005886, “plasma membrane”). ARACNe was able to infer the regulons of  2774  regulatory proteins.
From 922 sequenced cells, 194 cells were removed during our quality control. The gene expression profiles of the 728 high quality cells were normalized to CPM and z-score transformed for VIPER analysis. However, even if all these cells were FACS-sorted for Tff2, only 354 cells showed detectable levels of Tff2 transcripts. To exclude any possible results due to the technical noise that affects single cell sequencing68, we focused our downstream analyses on the subset (354 cells) of Tff2-expressing cells.
Assembly: mm10
Supplementary files format and content: cvs, one file containing all the cells

source_name: pancreas

extract_protocol:
Whole pancreas was digested and CD45-TER119-EpCAM+RFP+ cells were sorted. Briefly, pancreatic tissue was minced into small pieces (1-2 mm in size) and digested in DMEM/F12 medium containing collagenase-V (1 mg/mL), BSA (10mg/mL) and DNase I (2 U/mL) at 37 C° for 20 min. After multiple washes in ice-cold Hank’s balanced salt solution (HBSS) supplemented with 5% FBS, pancreatic tissue was collected and centrifuged at 500g. The pellet was re-suspended in HBSS + FBS and mechanically broken down through a syringe with a 22-gauge needle. After multiple washes, cells were filtered through a 40 μm cell strainer and then into a polystyrene tube with a cell-strainer cap. For cell sorting, cells were stained with EpCAM, TER119, and CD45. DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride) was used to exclude dead cells. All FACS analyses an on LSRII or LSRFortessa instruments. Cell sorting was performed on a BD Influx cell sorter.
Library was prepared according to standard 10x Genomics protocol

value: pancreas

tag: age

value: adult

value: Tff2+ cells

value: Tff2CreERT2; R26-tdTomato

value: Tamoxifen induced


title: SKF829 1h H1 R2


title: Tff2_scRNAseq, biol rep 2

description: 10x Genomics


title: Acute Dop 24h H9 R2

value: Dopamine 1 mM 1h, remove, 24h RNA Extraction


title: WT_EB_H3K27ac


title: LSD1KOEB_scRNA_2

description: 10x Genomics

data_processing:
scRNA-seq reads were aligned and counted by Cell Ranger v7.1.0 with default parameters. Filtering, clustering, and assigning cell type identity to clusters were performed using R package Seurat v4.3.0. Briefly, genes expressed in less than 10 cells and cells in which total UMI < 500 or total expressed genes < 500 were removed. Gene counts were normalized by NormalizeData function. 2,000 highly variable genes were selected in each sample based on a variance stabilizing transformation performed by FindVariableFeatures function. Next, expression matrices were scaled and centered followed by principal component analysis (PCA) for dimensional reduction. PC1 to PC30 were used to construct nearest neighbor graphs in the PCA space (FindNeighbors function) followed by Louvain clustering to identify clusters (resolution = 0.4, FindClusters function). Then, cell clusters were assigned to ESCs, endoderm cells, mesoderm cells and ectoderm cells by their canonical gene markers.
Assembly: mm9
Supplementary files format and content: barcode.tsv, genes.tsv and matrix.mtx to generate genexcells matrix

extract_protocol:
Day 6 EBs were disscoiated by TrypLE and dissociated cells were resuspended in PBS+ 0.04%BSA. The quantity and quality of the cells were accessed by Acridine Orange and Propidium iodide dye on a Cellometer Auto 2000 (Nexcelom).
16,000 cells were loaded on a 10x Chromium Controller based on 10x Chromium Single Cell 3' Library manual (10x Genomics). After cell partitioning and GEM generation, reverse transcription was performed, and cDNA was pooled and cleaned up by beads. cDNA was further amplified and cleaned up by SPRI beads (Beckman). The quality of cDNA was assessed by High Sensitivity D5000 Tapestation (Agilent Technologies) and quantified by Qubit 2.0 DNA HS assay (ThermoFisher). 3’ Gene expression library prep was carried out according to the 10x Chromium Next GEM Single Cell 3' v3.1 manual.


title: Acute Dop 1h H9 R3


title: LSD1KO_EB_H3K4me1


title: 1019-1_Day28_nonBPD

value: Peripheral blood

tag: sample id

value: whole blood cells

value: nonBPD


title: LSD1KOEB_scRNA_1

description: 10x Genomics


title: SKF812 1h H1 R3

value: differentiated human embryonic stem cell

value: SKF81297 50 microM 1h, RNA Extraction


title: 1019-1_Day14_nonBPD

tag: covariate-sex

value: F


title: SKF829 1h H1 R1


title: SKF812 1h H1 R2


title: LSD1KO_DMSO_H3K27ac

value: Embryonic stem cells


title: SKF812 1h H1 R1


title: 1019-1_Cord_nonBPD

value: yes

tag: covariate-b cell%


title: 1022-1_Day14_nonBPD

tag: variable-disease


title: LSD1KO_EB_H3K27ac

value: Embryoid bodies


title: LSD1KO_A485_H3K27ac


title: 1021-1_Day14_nonBPD

tag: variable-time


title: WT_EB_H3K4me1


title: LSD1KO_A485_input


title: LSD1KO_DMSO_input


title: Quin and CGS 1h H1 R2

value: Quinpirole 20 microM 1h, CGS21680 5 microM 1h, RNA Extraction


title: Quin and CGS 1h H1 R3


title: 1018-1_Day28_nonBPD

tag: variable-o2 treatment


title: 1021-1_Cord_nonBPD

value: CordBlood


title: XIAK51.2A_PANCREAS_NOLNMATCH_KPiC_3

city: Oxford

first: Xin

last: Lu

state: Oxfordshire

address: Old Road Campus

department: Ludwig Institute for Cancer Research

institute: University of Oxford

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore version 0.6.4_dev with Cutadapt version 2.9 using Python version 3.8.1
Trimmed sequence reads were mapped to Mus_musculus.GRCm38.dna.primary_assembly.fa and Mus_musculus.GRCm38.84.gtf using both STAR version 2.7.5c and HISAT2 version 2.2.0
Read counts for features were extracted using featureCounts version 2.0.1 from SubRead following alignment by STAR and HISAT2
Assembly: Mus_musculus.GRCm38.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: primary cell line, mouse, KPC;iASPPΔ8/Δ8

growth_protocol: 10% DMEM, 10% FBS, supplemented with glutamine, pencillin and streptomycin, 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
3' mRNA libraries for RNA-seq were prepared using Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD following manufacturer's protocols

value: pancreas

tag: cell line

value: primary

value: PDAC


title: 1018-1_Day14_nonBPD

tag: variable-o2 level


title: XKPC55.2J_PANCREAS_KPC_2

value: KPC


title: 1018-1_Cord_nonBPD

tag: covariate-ga


title: LSD1KO_input_3


title: XKPC55.2C_PANCREAS_KPC_3


title: Quinpirole 1h H1 R3

value: Quinpirole 20 microM 1h, RNA Extraction


title: WTEB_scRNA_1

description: 10x Genomics

value: WT


title: 1017-1_Day28_nonBPD

value: Peripheral blood

value: no

tag: covariate


title: LSD1KO_P300

tag: genotype


title: Quinpirole 1h H1 R2


title: XKPC45.2J_PANCREAS_KPC_1


title: 1016-1_Day14_nonBPD

value: whole blood cells

value: nonBPD


title: 1016-1_Cord_nonBPD


title: XKPC37.7I_PANCREAS_KC_1

value: KC


title: LSD1KO_RCOR2

tag: chip antibody


title: XKPC63.1A_PANCREAS_KPC_3

tag: tissue


title: 1015-1_Day28_nonBPD

tag: covariate-bw

value: M


title: LSD1KO_HDAC2

tag: cell type

value: Embryonic stem cells


title: Quinpirole 1h H1 R1

value: differentiated human embryonic stem cell

tag: treatment


title: XKPC34.8D_PANCREAS_KC_1


title: Chronic Dop 5day and Antag H1 R3

value: SCH23390 250 microM, Sulpiride 250 microM 1h, add Dopamine 1 mM 1h, remove, repeat 5 days, RNA Extraction


title: LSD1KO_HDAC1


title: XKPC19.2G_PANCREAS_KC_2


title: WT_input_4


title: 1015-1_Day14_nonBPD

value: yes


title: Quin and CGS 1h H1 R1

value: Quinpirole 20 microM 1h, CGS21680 5 microM 1h, RNA Extraction


title: XIAK52.1D_PANCREAS_KPiC_1

value: pancreas


title: Chronic Dop 5day and Antag H1 R2


title: Chronic Dop 5day and Antag H1 R1


title: 1015-1_Cord_nonBPD

value: CordBlood


title: WT_P300


title: XIAK51.2A_PANCREAS_LNMATCH_KPiC_3

value: primary

value: PDAC


title: Chronic Dop 5day 2week withdrawal H1 R3

value: Dopamine 1 mM 1h for 5 days, remove, 2 weeks RNA Extraction


title: WT_RCOR2

value: WT