title: NMP DAY3 SOX2KD INPUT Rep1

city: Cincinnati

first: Shreyasi

last: Mukherjee

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
For RNA-Seq experiments, raw reads were quality-checked using  FASTQC and adapters were trimmed using cutadapt.
Reads were pseudo-aligned to the hg19 reference index using salmon.
The tximport package was then used for downstream analysis to convert transcript-level counts to gene-level estimates. Differential gene expression analysis was performed using DESeq2 using default parameters
For ChIP-Seq experiments, Reads were aligned to the hg19 genome using bowtie2
Duplicates were marked using Picard and removed using samtools
A consensus set of peaks were called for each TF at each stage using HOMER getDifferentialPeaksReplicates.pl using stage-matched input samples as background and -style factor.
For ATAC-Seq, trimmed paired-end reads were aligned to the hg19 genome using bowtie2 and the parameters -X 2000 -very-sensitive-local
Peaks were called on replicates using Genrich and the parameters j -r -e -v -q 0.1
Genome_build: hg19
Supplementary_files_format_and_content: .bw' files are bigWig files for visualization of ChIP-Seq and ATAC-Seq data
Supplementary_files_format_and_content: .csv' files are TPM matrices from RNA-Seq experiment

source_name: Induced pluripotent stem cells

growth_protocol: iPS72.3 cells were routinely maintained in mTesr. CRISPRi-SOX2 cells were maintained in Essential 8 medium.

extract_protocol:
For RNA-Seq experiments, Total RNA was extracted using the Nucleospin RNA Extraction kit.For ChIP-Seq experiments, after differentiation to the desired stage, cells were dual crosslinked in plate with 1.5mM EGS and 1% formaldehyde. The fixation was then quenched with 125mM glycine. Cells were then washed twice and scraped in ice-cold PBS and resuspended in sonication buffer.For ATAC-Seq experiments, 50,000 cells were collected following differentiation to the desired stage, and lysed in 50ul of ATAC-lysis buffer (10mM Tris-HCl, pH 7.4. 10mM NaCl, 3mM MgCl2, 0.1% NP-40) to obtain a crude nuclei prep
For RNA-Seq experiments, 300ng of total RNA was poly-A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit (Illumina; 20020595). For ChIP-Seq experiments, DNA libraries were prepared using 1-5 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674) according to manufacturer’s instructions. For ATAC-Seq, the eluted DNA was amplified in a reaction with 25ul NEBNext High-Fidelity 2x PCR Mastermix (NEB; M0541L) and custom 25um Nextera PCR Primers (Ad1_noMx universal primer, 0.5um Ad2.x indexing primer). PCR was performed as follows: 1 cycle of 72C for 5min, 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 1min. 5ul of the amplified DNA was then used to perform qPCR to determine the optimal number of additional cycles to prevent amplification saturation of DNA libraries. In all cases, either 4 or 5 additional cycles of PCR was performed at: 98C for 10s, 63C for 30s and 72C for 1 min. Double size selection of amplified libraries (0.5x – left sided, 1.8x – right sided) was performed using AMPure XP beads
ChIP-Seq, RNA-Seq and ATAC-Seq

treatment_protocol: DE differentiation was carried out in RPMI-1640 media supplemented with non-essential amino acids Cells were treated with 100ng/ml Activin A and 2um CHIR99021 for 24hrs. In the next two days, cells were treated with 100ng/ml Activin A and 2um CHIR99021 in RPMI-1640 with increasing concentrations (0.2% on Day 2, 2% on Day 3) of ES-grade FBS . For NMP differentiation, cells were passaged using E8. The following day, media was changed to Essential 6 Medium. 24 hours later, cells were treated with 200ng/ml FGF8b in E6 media. After a further 24 hours, cells were treated with 200ng/ml FGF8b and 3um CHIR99021 in E6 media

tag: developmental stage

value: Day 3 neuromesodermal progenitors

value: 1ug/ml dox at Days 2 and 3

tag: chip antibody


title: neuroblastoma SK-N-BE(2)C xenograft, untreated control, rep3

status: Public on Jul 27 2022

type: SRA

city: Stockholm

first: Ninib

last: Baryawno

address: Tomtebodavägen 18a

department: Department of Women's and Children's health

country: Sweden

institute: Karolinska institutet

description: xenograft sample 12

library_source: transcriptomic

data_processing:
For xenografts, reads were aligned to a combined mm10+hg38 reference using STAR v2.7.9a (2-pass approach).
Raw reads per gene were quantified using htseq-count v0.12.4.
Assembly: Xenograft data: combined hg38+mm10 reference. Transgenic TH-MYCN data: combined hg19+mm10 reference (any reads mapping to human genes other than MYCN were filtered out priior to downstream analyses).
Supplementary files format and content: rawcounts_xenografts.csv: a matrix of read counts per gene per sample (all hg38 + mm10 genes)
Supplementary files format and content: rawcounts_thmycn.csv: a matrix of read counts per gene per sample (all mm10 genes + human MYCN)

molecule: polyA RNA

organism: Homo sapiens

source_name: neuroblastoma xenograft

growth_protocol: SK-N-AS and SK-N-BE(2)C cell lines were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 ug/ml streptomycin, and 100 IU/ml penicillin G (all from Life Technologies/Thermo Fisher Scientific). Female NMRI nu/nu mice (purchased from Scanbur) of four to six weeks of age were injected with 5 million SK-N-AS or SK-N-BE(2)C cells subcutaneously in the flank and monitored daily for tumor growth.

extract_protocol:
Mouse tumor tissue used for RNA sequencing was stored in RNAlater solution (Thermo Fisher, Waltham, MA, USA) at -80 °C. Total RNA from xenograft/tumor tissue was isolated using the RNeasy Mini Kit (Qiagen).
All libraries were generated using the TruSeq Stranded protocol (Illumina). All libraries were sequenced on the NextSeq500 platform. Xenograft samples were sequenced with a 75 bp single-end strategy. TH-MYCN samples were sequenced with a 2x42 bp paired-end strategy.

treatment_protocol: NMRI mice and transgenic TH-MYCN mice were treated with brequinar 50 mg/kg i.p with either one dose (24h and 72h samples) or every third day for a total of 120 days (TH-MYCN relapse samples).

tag: tissue

value: neuroblastoma xenograft

tag: cell line

tag: cell type

value: neuroblastoma

tag: treatment

value: untreated control


title: NMP DAY3 WT INPUT Rep1

country: USA

library_source: genomic

molecule: genomic DNA


title: neuroblastoma SK-N-BE(2)C xenograft, brequinar treated 24h, rep1

description: xenograft sample 13

value: brequinar 24h


title: LiverILC2_1

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

data_processing:
The libraries were sequenced for 60 cycles (single-end reads) on an Illumina HiSeq 1500 instrument.
Reads were mapped to mouse genome assembly version of December 2011 (mm10) by using the Bowtie2 mapping tool with a default setting.
Peaks were called using the MACS2 software with the broad option and those identified in both replicates were used for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph.gz

organism: Mus musculus

growth_protocol: Mice received daily i.p. injections of PBS or rIL-33 (0.5 µg) for 5 days. Then, liver and lung ILC2s (5000-50000 cells) were sorted using flow cytometry ARIA III [gating: Lin− (CD3e−Ly6G−Ly6c−CD11b−CD45R−TER119−TCRb−) CD127+Thy1+ST2+]

extract_protocol:
The nuclei were resuspended in Tagment DNA enzyme buffer supplemented with Tn5 transposase (Illumina, 15027865) to tag and fragment the accessible chromatin. The DNA fragments were purified with a MinElute kit (Qiagen, 28004)
DNA fragments were amplified by 11 - 13 PCR cycles.

treatment_protocol: described in growth protocol

tag: strain

value: BALB/c

tag: genotype

value: wild type

tag: celltype

value: liver ILC2s from PBS-treated mice


title: DE DAY3 SOX17KO INPUT Rep2

value: Day 3 definitive endoderm


title: DE DAY3 SOX17KO INPUT Rep1


title: neuroblastoma SK-N-BE(2)C xenograft, untreated control, rep2

description: xenograft sample 11


title: neuroblastoma SK-N-BE(2)C xenograft, untreated control, rep1

description: xenograft sample 10


title: rest3

data_processing:
Sequencing was performed on the Illumina HiSeq 1500 platform using the TruSeq Rapid SBS Kit (Illumina, FC-402-4002) in the 50-base single-end mode.
The TopHat program (version 1.3.2 with default parameters) was used to align reads to a mouse reference genome (mm10).
Then, gene expression values were calculated as reads per kilobase of exon unit per million mapped reads using the Cufflinks program (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph.gz
Supplementary_files_format_and_content: FPKMCuffDiff.xlsx
Supplementary_files_format_and_content: TagCountCuffDiff.xlsx

molecule: total RNA

source_name: Primary hepatocyte

growth_protocol: Primary hepatocyte were isolated with two step-digestion method (Charni-Natan, M. et al, STAR Protocol 2020). Primary hepatocytes were incubated with or without 10 ng/mL recombinant IL-13 (rIL-13) for 2 h at 37°C and then stimulated with 100 µM cAMP or 100 nM glucagon, with or without 10 ng/ml rIL-13 for 3 h at 37°C. Then, RNA were extracted.

extract_protocol:
Total RNA from 10^6 primary hepatocytes were extracted using the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared using a TruSeq RNA Sample Prep Kit (Illumina, 20020594)

value: Vehicle-treated (unstimulated)


title: PAX6-depleted CEC, rep2

type: RNA

city: Kyoto

first: Koji

last: Kitazawa

state: Kyoto

address: 465 Kajiicho Kamigyoku

department: Ophthalmology

country: Japan

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: CEL files are loaded using oligo R package (version 3.5.3).　Probe set definition is based on pd.hugene.2.0.st R package. Gene level raw expression values are computed using the 'target=core' argument and values are RMA normalized.

source_name: Cornea

label_protocol: Standard Affymetrix protocol.

growth_protocol: All the cells were cultured in CEC medium which consists of Dulbecco’s modified Eagle’s medium and Ham’s F-12 media (1:1 mixture) (Life Technologies) containing B27-supplement (Life Technologies), Rho-kinase (ROCK) inhibitor (10 M) (Nacalai Tesque), epidermal growth factor (10 ng/ml) (Life Technologies), Epigallocatechin gallate (SIGMA) and penicillin-streptomycin (50 IU/ml) (Nakalai Tesque),

extract_protocol: Each sample was resuspended in a Qiagen lysis buffer, and RNA was prepared using the RNeasy Purification kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: PAX6 was depleted with CRISPR/Cas9 in primary human corneal epithelial cells

tag: disease state

value: Normal

value: Cornea

value: corneal epithelial cells


title: WT CEC, rep1

value: WT


title: neuroblastoma SK-N-AS xenograft, brequinar treated 72h, rep2

description: xenograft sample 8

value: SK-N-AS

value: brequinar 72h


title: rest2


title: neuroblastoma SK-N-AS xenograft, brequinar treated 72h, rep3

description: xenograft sample 9


title: neuroblastoma SK-N-AS xenograft, brequinar treated 72h, rep1

description: xenograft sample 7


title: LiverILC2_2


title: D3 DAY3 WT INPUT Rep2


title: WT CEC, rep2


title: neuroblastoma SK-N-AS xenograft, brequinar treated 24h, rep3

description: xenograft sample 6


title: neuroblastoma SK-N-AS xenograft, untreated control, rep2

description: xenograft sample 2


title: neuroblastoma SK-N-AS xenograft, brequinar treated 24h, rep2

description: xenograft sample 5


title: PAX6-depleted CEC, rep1


title: rest1


title: D3 DAY3 WT INPUT Rep1


title: DE DAY1 INPUT Rep2

value: Day 1 mesendoderm


title: neuroblastoma SK-N-AS xenograft, brequinar treated 24h, rep1

description: xenograft sample 4


title: DE DAY2 INPUT Rep2

value: Day 2 endoderm progenitors


title: neuroblastoma SK-N-AS xenograft, untreated control, rep1

description: xenograft sample 1

value: neuroblastoma xenograft


title: DE DAY2 INPUT Rep1


title: GlucarIL13_3

value: Glucagon-treated in the presence of IL-13


title: neuroblastoma SK-N-AS xenograft, untreated control, rep3

description: xenograft sample 3

value: neuroblastoma

value: untreated control


title: DE DAY1 INPUT Rep1


title: GlucarIL13_1


title: Day 18 SBCHIR + Shear, scRNAseq

city: Randwick

first: Jingjing

last: Li

state: New South Wales

address: UNSW, Gate 11 Botany Street

department: Graduate School of Biomedical Engineering

country: Australia

institute: UNSW

description: Dropseq

library_source: transcriptomic single cell

data_processing:
Raw scRNA-Seq data was processed using CellRanger software (version 1.3.0). The BCL files obtained from the Illumina NextSeq platform were processed to Fastq files using the CellRanger mkfastq program. The CellRanger count program was run on individual datasets from different conditions.
Assembly: GRCh38
Supplementary files format and content: Expression matrix table as comma-separated values files

source_name: hESC H9 SOX17mCHERRY/wRUNX1CGFP/w

growth_protocol: The dual fluorescent reporter human embryonic stem cell H9 line (SOX17mCherry/wRUNX1CGFP/W) used in these studies was generated in Professor Elefanty’s lab (Ng et al., 2016). hESC lines were maintained in culture on 6-well plates in TeSR-E8 medium  and plates were pre-coated with GelTrex® growth factor reduced at 1:100 in DPBS overnight. Routine passaging of hESC lines were enzymatic harvested with TrypLE and split 1:4 every 48 hours.

extract_protocol:
Cells were dissociated into single cell suspension using TrypLE Select (Invitrogen) or Collagenases Type I (Worthington) and passed through a 23-gauge needle and 40 µm cell strainer. Six million cells were harvested from differentiation cultures for each experimental condition. Single cells were randomly captured by Drop-seq (Macosko et al., 2015) according to the protocol described by the McCarroll lab, Department of Genetics, Harvard Medical School (version 3.1, www.mccarrolllab.com/dropseq). Between 2100 - 3000 cells were sequenced for each per culture condition.
cDNA amplification profiles of 4 captures from single PCR has 1000 - 1100 bp average size of the cDNA. The cDNA libraries were tagmented, multiplexed and sequenced on Illumina Nextseq 500 using Nextseq 500 High Output v.2 kit (75 cycles, Illumina Cat# FC-404-2005) following Macosko et al. recommendations with the following modifications. The libraries were spiked in with 10% of PhiX Control v3 (Illumina Cat# FC-110-3001) at a final concentration of 1.8 pM; Drop-seq libraries were denatured and were loaded at final concentration of 1.3 pM.

treatment_protocol:
hESC differentiation was induced by stepwise multiple cytokine recipe. APEL medium was supplemented for the first 4 days with 40 ng/ml recombinant human (rh) BMP4 , 50 ng/ml rh VEGF  and 25 ng/ml rh SCF, 10 ng/ml rh ACTIVIN Aand 10 ng/ml rh FGF2 . Cultures included additional CHIR99021 3μM and/or SB431542 4μM at day 2 for the SB/CHIR treatment group. After 4 days, the differentiation medium was changed to APEL medium supplemented with 50 ng/ml rh VEGF, 20 ng/ml BMP4, 10 ng/ml FGF2, 50 ng/ml rh SCF and 30 ng/ml rh IGF2 . At day 9 of differentiation, differentiation medium was replaced with APEL medium including 50 ng/ml rh VEGF, 100 ng/ml rh SCF, 50 ng/ml rh IL-3, 25 ng/ml rh IL-6, 25 ng/ml rh TPO, 25 ng/ml rh FLT3L , 3 U/ml rh EPO, 10 ng/ml FGF2 and 20 ng/ml rh IGF2 . After day 13, IL-3 and EPO were omitted.
Well plates were placed on an orbital shaker housed within a cell culture incubator (37°C, 5% CO2, normoxia) from Day 10 of differentiation for 8 days. The rotational speed of the orbital shaker was increased in a stepwise manner for the first 8 hours (20 rpm every 2 hours until 100 rpm was reached) and kept constant thereafter. The cell culture medium in each well was monitored daily to ensure that culture volume was maintained at 2-4 ml without evaporation. Media were replaced every two days at 1:2 ratio of conditioned medium to fresh medium. The generated suspension cells were harvested at day 18 from cultures and analyzed by flow cytometry and subculture.

value: hESC H9 SOX17mCHERRY/wRUNX1CGFP/w

value: Day18 differentiation

tag: treatment 1

value: SB/CHIR treatment from Day2 to day4

tag: treatment 2

value: orbital shear plate from Day10 to day18


title: Day 18 DMSO+ Shear, scRNAseq

description: Dropseq

value: DMSO (drug vehicle) treatment from day 2to day 4


title: ES INPUT Rep2

value: pluripotent ES cells


title: Day 18 DMSO, scRNAseq

description: Dropseq

value: DMSO (drug vehicle) treatment from day 2 to day 4

value: Static well plate


title: ES INPUT Rep1


title: ThGM cells from PBMCs of donor 3 replicate 1

city: Philadelphia

first: Sankar

last: Addya

state: PA

address: 233 South 10th Street

department: Kimmel Cancer Center

institute: Thomas Jefferson University Hospital

data_processing:
Bases were trimmed from R2 reads per the library kit recommendations (Takara SMARTer Stranded Total RNA-Seq kit v2 Pico input)
Paired-end reads were aligned quantified against GRCm38/GENCODE.M18 reference annotations using RSEM-STAR (RSEM v1.2.31, STAR 2.6.0c) in strand-specific mode with parameters --strand-specific --forward-prob 0
Assembly: GRCm38
Supplementary files format and content: .genes.results files from RSEM-STAR include columns with Ensembl gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: Th cells from healthy donor PBMCs

growth_protocol:
Human samples: Human ThGM, Th1, and GM-CSF+Th1 cells were isolated from peripheral blood of healthy donors using a combination of FACS sorting and cytokine sceretion assay. RNA from human ThGM, Th1, and GM-CSF+Th1 cells were isolated and their transcriptome were analyzed by RNA sequencing. Mouse samples: Mouse naive CD4+ T cells were polarized to ThGM and Th1 cells and RNA from several time points were islated and analyzed using RNA sequencing.
Mouse samples: Mouse naive CD4+ T cells were polarized to ThGM and Th1 cells and RNA from several time points were islated and analyzed using RNA sequencing.

extract_protocol:
Human samples:  ThGM (CD25-CXCR5-CXCR3-CCR4+CCR10+) and Th1 cells (CD25-CXCR5-CXCR3+CCR4-CCR10-) were FACS sorted. GM-CSF+-ThGM and -Th1 cells were enriched based on their GM-CSF expression using GM-CSF secretion assay kit. RNA from human ThGM, Th1, and GM-CSF+Th1 cells were isolated and their transcriptome were analyzed by RNA sequencing.
Mouse samples: Mouse naive CD62LhiCD44-CD25-CD4+) T cells were FACS sorted and culture with T cell depleted splenocytes and  polarized to ThGM and Th1 cells. RNA from 4, 8,16, 24, 48, and 72h  were isolated and analyzed using RNA sequencing.
Takara SMARTer Stranded Total RNA-Seq kit v2 Pico input

treatment_protocol: Human samples were treated with PMA/Ionomycin for 3h for GM-CSF secression assay.

value: ThGM

tag: donor


title: ThGM cells from PBMCs of donor 2 replicate 2


title: Gluca2

value: wild type

value: Glucagon-treated


title: NMP DAY3 SOX2KD C59 Rep3

value: Day 3 neuromesodermal progenitors

value: 1ug/ml dox at Days 2 and 3


title: GlucarIL13_2


title: Gluca3


title: NMP DAY3 SOX2KD C59 Rep2


title: NMP DAY3 SOX2KD C59 Rep1


title: cAMPrIL13_3

value: cAMP-treated in the presence of IL-13


title: Day 18 SBCHIR, scRNAseq

description: Dropseq


title: Gluca1


title: ThGM cells from PBMCs of donor 2 replicate 1


title: ThGM cells from PBMCs of donor 1 replicate 2


title: Th1 cells from PBMCs of donor 3 replicate 2


title: cAMPrIL13_1


title: cAMPrIL13_2


title: ThGM cells from PBMCs of donor 3 replicate 2


title: GM-CSF+Th1 cells from PBMCs of donor 3 replicate 2


title: h1 cells from PBMCs of donor 3 replicate 1


title: Th1 cells from PBMCs of donor 2 replicate 1


title: ThGM cells from PBMCs of donor 1 replicate 1


title: Th1 cells from PBMCs of donor 1 replicate 2


title: NMP DAY3 WT C59 Rep2


title: Th1 cells from PBMCs of donor 2 replicate 2


title: cAMP3

value: cAMP-treated


title: NMP DAY3 WT C59 Rep3


title: Th1 cells from PBMCs of donor 1 replicate 1


title: GM-CSF+Th1 cells from PBMCs of donor 3 replicate 1


title: cAMP2


title: NMP DAY3 WT C59 Rep1


title: GM-CSF+Th1 cells from PBMCs of donor 2 replicate 1


title: cAMP1


title: GM-CSF+Th1 cells from PBMCs of donor 1 replicate 2


title: liver lymph node, 10x, biol rep3

city: Chicago

first: Daria

last: Esterhazy

state: IL

address: 924 E 57th Street

department: Pathology

institute: University of Chicago

description: 10x Genomics

data_processing:
Gene counts were calculated by aligning raw fastq files to the mm10 genome using CellRanger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
Live YFP+ cells were sorted from single cell suspensions of lymph nodes from CD11c-YFP mice
Cells were loaded onto sChromium NextGEM Chip (10x Genomics) for 3’ end library preparation using dual indexes according to manufacturer’s protocol (10x Genomics).

value: lymph node

value: YFP+ cells

tag: age

value: 6-8 weeks


title: GM-CSF+Th1 cells from PBMCs of donor 1 replicate 1


title: GM-CSF+Th1 cells from PBMCs of donor 2 replicate 2


title: NMP DAY3 SOX2 KD WNT Rep3


title: NPA_SMtrt_rep3

city: Pieve Emanuele-Milan

first: Giulia

last: Solda'

address: via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

data_processing:
Bcl files were converted to fastq with bcl2fastq with default parameters
Reads were mapped to the hg38 reference genome and to the UCSC Homo sapiens transcriptome [Illumina’s iGenomes reference annotation, downloaded from University of California, Santa Cruz (UCSC); http://support.illumina.com/sequencing/sequencing_software/igenome.html] with STAR v.2.7.1a
Gene counts were generated with htseq-count v.0.11.2 using the following parameters: -m intersection-nonempty -t exon -s reverse. The raw gene count matrix was generated excluding genes with no counts.
Differential expression analysis between treated and untreated samples (design: replicate + treatment) was evaluated with the Wald χ2 test of significance for the negative binomially distributed counts using the DeSeq2 Bioconductor package, after removing genes with extremely low counts (less than 10 counts overall)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: fibroblasts

growth_protocol: Fibroblasts were cultured in RPMI-1640 medium supplemented with 10% heat- inactivated FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin. The cells were cultured as monolayer in a humidified atmosphere at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells using the EuroGoldTriFast reagent (EuroClone) according to the manufacturer’s instructions. RNA concentration was determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and RNA integrity was assessed on a LabChip GX Touch (PerkinElmer, Waltham, MA, USA). The Illumina TruSeq Stranded mRNA Sample LS Preparation Kit (Illumina, San Diego, CA, USA) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: An aliquot corresponding to 5 µmoles of SM was taken from a stock solution (25 mg/ml in chloroform/methanol 2:1), transferred in a sterile tube, dried under a nitrogen flow and solubilised in 10 ml of heat inactivated FBS supplemented with antibiotics to obtain 500 µM final concentration. After stirring and sonication using ultrasonic bath (1 min, three times) the solution was incubated at 37°C overnight, diluted 1:10 in the culture medium and added to the cells 24 hours after plating.

value: fibroblasts

value: Niemann Pick type A

value: treated with sphingomyelin for 30 days


title: NMP DAY3 SOX2 KD WNT Rep2


title: NPA_SMtrt_rep2


title: NPA_untrt_rep1

value: untreated


title: NMP DAY3 SOX2 KD WNT Rep1


title: NPA_untrt_rep2


title: celiac lymph node, 10x, biol rep3

description: 10x Genomics


title: liver lymph node, 10x, biol rep2

description: 10x Genomics


title: duodenal lymph node, 10x, biol rep3

description: 10x Genomics


title: NMP DAY3 WT WNT Rep3


title: NMP DAY3 WT WNT Rep1


title: NMP DAY3 WT WNT Rep2


title: celiac lymph node, 10x, biol rep2

description: 10x Genomics


title: NPA_SMtrt_rep1


title: NMP SOX2KD ATAC DAY3 Rep2


title: NMP WT ATAC DAY3 Rep2


title: NPA_untrt_rep3


title: NMP WT ATAC DAY3 Rep1


title: NMP SOX2KD ATAC DAY3 Rep1


title: duodenal lymph node, 10x, biol rep2

description: 10x Genomics


title: DE DAY 3 SOX17KO C59 - Late Rep3

value: Day 3 definitive endoderm


title: DE DAY3 - SOX17KO ATAC Rep2


title: DE DAY3 - SOX17KO ATAC Rep1


title: DE DAY 3 SOX17KO C59 - Late Rep1


title: duodenal lymph node, 10x, biol rep1

description: 10x Genomics


title: DE DAY2 - WT ATAC Rep2


title: pancreas migDCs, biol rep4, bulk RNAseq

data_processing:
Raw fastq files were pseudo-aligned to M26 (GRCm39) using Kallisto.
Gene counts were converted to transcripts per million (tpm) by scaling by gene length.
Genes were filtered to remove lowly expressed genes.
Assembly: M26 (GRCm39)

source_name: pancreas tissue

extract_protocol:
Migratory DCs (live CD45+LIN-CD11c+MHCIIhiCD103+CD11b-) were sorted from each tissue directly into Qiagen TCL buffer containing 1% beta-mercaptoethanol.
RNA libraries for RNA-seq were prepared using published protocols (Esterhazy Nature 2019).

value: pancreas tissue

value: migratory dendritic cells


title: DE DAY1 - ATAC Rep1

value: Day 1 mesendoderm


title: DE DAY2 - ATAC Rep1

value: Day 2 endoderm progenitors


title: DE DAY1 - ATAC Rep2


title: DE DAY 3 SOX17KO C59 - Early Rep3


title: DE DAY2 - ATAC Rep2


title: Sham_RNA-seq 4

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
The sequencing reads were trimmed using Trimmomatic
Trimmed high quality reads were then mapped to the mouse genome (mm10) using STAR
Mapped read counts were obtained using featureCounts
Differential expression analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: The *.counts files are the raw counts generated from featureCounts which served as the input for Deseq2.

source_name: Bladder

extract_protocol:
RNA from bladder tissue was extracted using Trizol and DNase digestion was performed. RNA quality was determined using the Agilent Bioanalyzer.
RNA-sequencing libraries were prepared using theNEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with a starting amount of 500ng RNA. Libraries were sequenced in single-end sequence reads on the Illumina HiSeq 2500 platform

value: Bladder

value: Sham


title: Sham_RNA-seq 3


title: DE DAY 3 SOX17KO C59 - Early Rep2


title: pancreas migDCs, biol rep3, bulk RNAseq


title: Sham_RNA-seq 1


title: Sham_RNA-seq 2


title: ES - ATAC Rep2

value: pluripotent ES cells


title: DE DAY3 - WT ATAC Rep1


title: ES - ATAC Rep1


title: liver lymph node, 10x, biol rep1

description: 10x Genomics


title: DE DAY 3 SOX17KO WNT Rep2


title: pancreas migDCs, biol rep2, bulk RNAseq


title: duodenal migDCs, biol rep4, bulk RNAseq

source_name: duodenal tissue

value: duodenal tissue


title: DE DAY 3 SOX17KO C59 - Early Rep1


title: DE DAY 3 SOX17KO C59 - Late Rep2


title: DE DAY 3 SOX17KO WNT Rep3


title: DE DAY 3 SOX17KO WNT Rep1


title: celiac lymph node, 10x, biol rep1

description: 10x Genomics


title: NeMO_RNA-seq 3

value: NeMO


title: pancreas migDCs, biol rep1, bulk RNAseq


title: NeMO_RNA-seq 2


title: NeMO_RNA-seq 1


title: duodenal migDCs, biol rep3, bulk RNAseq


title: NeMO_RNA-seq 4


title: DE DAY 3 WT C59 - Late Rep3

value: Activin/CHIR Day1, Activin/C59 Days 2 and 3


title: duodenal migDCs, biol rep2, bulk RNAseq


title: ChIP_F1_PPARγ_day7

city: Tokyo

first: Yuta

last: Hiraike

address: Hongo 7-3-1, Bunkyo-ku

institute: The University of Tokyo

data_processing:
The sequence data were mapped to mm9 genome using batman aligner – “BatMis” version 3.0.0 with option “-n2 -m1” (using only uniquely mapped and allowing mismatch up to 2).
Peak calling was performed using MACS version 1.4.2 with P values 10^-5
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files showing the peaks of each samples.

source_name: ingSVF-derived adipocytes

growth_protocol: SVF cells were mainteined in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Samples were treated by nuclear extraction buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 minutes and immediately cross-linked with 1% formaldehyde for 7.5 minutes at room temperature. Cross-linking was quenched using 125 mM glycine for 5 minutes. The chromatin was sheared by probe sonicator (Branson) and was spun at 15,000rpm for 5 minutes. Antibodies were added for overnight incubation at 4C. Mix of Protein A and Protein G magnetic beads (Thermo Scientific) were added to samples for 4h at 4C. Subsequent procedures were performed as described previously (Hiraike Y., Waki H. et.al. 2017).
ChIP-seq libraries were prepared using KAPA hyper prep kit (KAPA Biosystems) according to the manufacturer's instructions.

treatment_protocol: At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 μM dexamethosone, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 μM rosiglitazone.

tag: time course


title: HiC_F1_day7

data_processing:
Hi-C data were processed by Hi-C pro pipeline version 2.9.0 considered with restriction fragment information of MboI and mm9 mouse genome with default option. Briefly, this pipeline was able to exclude low - quality mapped pairs.
The valid pairs were used for further analyses.
Genome_build: mm9
Supplementary_files_format_and_content: hic files showing valid pairs of reads.

extract_protocol:
five million cells were crosslinked with 1% formaldehyde following quenching with 0.2 M of glycine. Cells were lysed with Hi-C lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% Igepal CA-630) and the chromatin was digested by MboI (NEB, R0147) restriction enzyme. The both ends of the digested chromatin were filled in and marked with biotin-14-dATP (Life Technologies, 19524-016) by DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210), and ligated by T4 DNA Ligase (NEB, M0202). The DNA was purified by ethanol precipitation and sheared to 300-500 bp using Covaris E220 following size selection by AMPure XP beads (Beckman Coulter, A63882). Then the DNA fragments were enriched by Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602).
After repair of sheared DNA ends, the Illumina indexed adapters were ligated to them. Hi-C libraries were amplified by 8-12 cycles of PCR before high-throughput sequencing.


title: DE DAY 3 WT C59 - Late Rep2


title: ChIP_F1_NFI_day7


title: ChIP_F1_NFI_day0


title: DE DAY 3 WT C59 - Late Rep1


title: DE DAY 3 WT C59 - Early Rep2

value: Activin/C59 at Days 1,2 and 3


title: RNA_F1_day7_rep3

data_processing:
The sequenced data were mapped to mm9 genome and Refseq information derived at UCSC web site (https://genome.ucsc.edu/)
The STAR aligner37 version 2.7.3a was applied to make RNA-seq count data with “FilterMultimapNmax 1”.
The RPKM data for RNA-Seq count were used for further analyses.
Genome_build: mm9
Supplementary_files_format_and_content: txt files showing RPKM value of each samples .

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Techologies) and RNeasy Mini Kit (Qiagen).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.


title: ChIP_F1_PPARγ_day0


title: RNA_129_day7_rep3


title: DE DAY 3 WT C59 - Early Rep1


title: RNA_129_day7_rep1


title: RNA_F1_day7_rep2


title: liver migDCs, biol rep1, bulk RNAseq

source_name: liver tissue

value: liver tissue

value: 6-8 weeks


title: DE DAY 3 WT C59 - Early Rep3


title: RNA_B6_day7_rep2


title: RNA_F1_day7_rep1


title: RNA_B6_day7_rep3


title: DE DAY 3 WT WNT Rep2


title: RNA_B6_day7_rep1


title: RNA_129_day7_rep2


title: DE DAY 3 WT WNT Rep3


title: liver migDCs, biol rep2, bulk RNAseq


title: APP2_miRNA

city: Wuhan

first: Xiong

last: Wang

state: Hubei

address: Jiefang Ave No.1095

department: Department of Laboratory Medicine

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean reads were aligned to the reference genome mm10 using HISAT2
Unmapped reads were used to identify circRNAs using CIRI2. miRBase was used as reference to find known or novel miRNAs with miRDeep2. The mapped reads of mRNA were assembled by Stringtie. Expression levels were estimated by reads based FPKM, and the difference was calculated using R “DEseq” package, and significant difference was defined if p value < 0.05, and log2 (fold change) ≠ 0. The value of log2(fold change) > 1 and p value < 0.05 was considered as significantly dysregulated RNAs.
Genome_build: mm10

source_name: Hippocampus

extract_protocol:
Three male APP/PS1 transgenic mice and three wild type littermates were used for RNA-seq. Total RNA (containing miRNA) was isolated from hippocampus with TRIzol reagent (Thermo Fisher Scientific, CA, USA), according to the manufacturer’s instructions. Total RNA was quantified with Qubit 3.0 Spectrophotometer (Thermo Fisher Scientific, CA, USA). RNA purity was evaluated with NanoDrop 2000 (Thermo Fisher Scientific, CA, USA). RNA integrity was assessed with 1% agarose gels and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).
The sequencing libraries for mRNA and circRNA were generated by TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA).The sequencing libraries for miRNAs were generated by TruSeq small RNA sample Preparation kit (Illumina, CA, USA).
After cluster generation using TruSeq PE Cluster Kit v3-cBot-HS (Illumia, CA, USA), the libraries were sequenced on an Illumina Hiseq 2500 platform.

value: Hippocampus

value: 4 months


title: APP3_miRNA


title: WT4_miRNA

value: WT


title: duodenal migDCs, biol rep1, bulk RNAseq


title: RNA-Seq Sucla2 KO replicate4

city: Indianapolis

first: Brett

middle: Harrison

last: Graham

state: IN

address: 975 West Walnut Street, IB 252C

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

description: Sucla2 KO replicate4

data_processing:
The sequence data were mapped to themouse reference genome mm10 with STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Assembly: mouse reference genome mm10
Supplementary files format and content: excel table includeing raw counts, log2 fold change, p-values and FDR

source_name: Cerebral Cortex

extract_protocol:
Cerebral cortex was removed and flash frozen in liquid nitrogen. Total RNA was isolated using the Quick-RNA Miniprep Plus Kit from Zymo Research (CAT: R1057T).
KAPA mRNA Hyperprep Kit (KK8581) was ued to prepare the RNA-seq libraries.

value: Cerebral Cortex

value: Sucla2-/-, CamKIIa-Cre


title: liver migDCs, biol rep4, bulk RNAseq

value: migratory dendritic cells


title: DE DAY 2 C59 - Late Rep3

value: Activin/CHIR Day1, Activin/C59 Day2


title: RNA-Seq Sucla2 KO replicate3

description: Sucla2 KO replicate3


title: RNA-Seq Sucla2 KO replicate1

description: Sucla2 KO replicate1


title: liver migDCs, biol rep3, bulk RNAseq


title: WT1_miRNA


title: RNA-Seq Sucla2 KO replicate2

description: Sucla2 KO replicate2


title: APP1_miRNA


title: APP3


title: RNA-Seq WT replicate4

description: WT replicate4

value: Sucla2+/+, CamKIIa-Cre


title: DE DAY 2 C59 - Late Rep2

value: Day 2 endoderm progenitors


title: WT2


title: WT2_miRNA


title: RNA-Seq WT replicate2

description: WT replicate2


title: APP2


title: WT1


title: RNA-Seq WT replicate3

description: WT replicate3


title: APP1


title: DE DAY 3 WT WNT Rep1

value: Day 3 definitive endoderm


title: WT4


title: DE DAY 2 C59 - Early Rep3

value: Activin/C59 at Days 1 and 2


title: DE DAY 2 C59 - Early Rep2


title: RNA-Seq WT replicate1

description: WT replicate1


title: WT_OXA1

city: Shanghai

first: Ha

last: Zhu

address: 800 Xiangyin Road

department: Institute of Immunology

institute: Second Military Medical University

description: 1.5´105/ml wild type cells and ZCCHC4 KO cells are seed into 6 well plate, and then treated with 62.5µM OXA for 12h.  Then cells are subjected for RNA-seq.

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute  using Illumina HiSeq platform.
High-quality reads were aligned to the human reference genome (GRCh38/hg38).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).

source_name: HepG2 cells

extract_protocol:
Total RNA was extracted with Trizol reagent.
cDNA library construction and sequencing were performed by  Beijing Genomics Institute using Illumina HiSeq platform.

treatment_protocol: Wild type cells and ZCCHC4 KO cells are seed into 6 well plate, and then treated with 62.5µM OXA for 12h.

value: HepG2 cells

value: wildtype

value: Cells are treated with 62.5uM OXA for 12h


title: WT_OXA2


title: DE DAY 2 C59 - Early Rep1

data_processing:
For RNA-Seq experiments, raw reads were quality-checked using  FASTQC and adapters were trimmed using cutadapt.
Reads were pseudo-aligned to the hg19 reference index using salmon.
The tximport package was then used for downstream analysis to convert transcript-level counts to gene-level estimates. Differential gene expression analysis was performed using DESeq2 using default parameters
For ChIP-Seq experiments, Reads were aligned to the hg19 genome using bowtie2
Duplicates were marked using Picard and removed using samtools
A consensus set of peaks were called for each TF at each stage using HOMER getDifferentialPeaksReplicates.pl using stage-matched input samples as background and -style factor.
For ATAC-Seq, trimmed paired-end reads were aligned to the hg19 genome using bowtie2 and the parameters -X 2000 -very-sensitive-local
Peaks were called on replicates using Genrich and the parameters j -r -e -v -q 0.1
Genome_build: hg19
Supplementary_files_format_and_content: .bw' files are bigWig files for visualization of ChIP-Seq and ATAC-Seq data
Supplementary_files_format_and_content: .csv' files are TPM matrices from RNA-Seq experiment

extract_protocol:
For RNA-Seq experiments, Total RNA was extracted using the Nucleospin RNA Extraction kit.For ChIP-Seq experiments, after differentiation to the desired stage, cells were dual crosslinked in plate with 1.5mM EGS and 1% formaldehyde. The fixation was then quenched with 125mM glycine. Cells were then washed twice and scraped in ice-cold PBS and resuspended in sonication buffer.For ATAC-Seq experiments, 50,000 cells were collected following differentiation to the desired stage, and lysed in 50ul of ATAC-lysis buffer (10mM Tris-HCl, pH 7.4. 10mM NaCl, 3mM MgCl2, 0.1% NP-40) to obtain a crude nuclei prep
For RNA-Seq experiments, 300ng of total RNA was poly-A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit (Illumina; 20020595). For ChIP-Seq experiments, DNA libraries were prepared using 1-5 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674) according to manufacturer’s instructions. For ATAC-Seq, the eluted DNA was amplified in a reaction with 25ul NEBNext High-Fidelity 2x PCR Mastermix (NEB; M0541L) and custom 25um Nextera PCR Primers (Ad1_noMx universal primer, 0.5um Ad2.x indexing primer). PCR was performed as follows: 1 cycle of 72C for 5min, 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 1min. 5ul of the amplified DNA was then used to perform qPCR to determine the optimal number of additional cycles to prevent amplification saturation of DNA libraries. In all cases, either 4 or 5 additional cycles of PCR was performed at: 98C for 10s, 63C for 30s and 72C for 1 min. Double size selection of amplified libraries (0.5x – left sided, 1.8x – right sided) was performed using AMPure XP beads
ChIP-Seq, RNA-Seq and ATAC-Seq


title: ZCCHC4 KO1_OXA2

value: ZCCHC4 knockout


title: ZCCHC4 KO1_OXA1


title: DE DAY 2 WNT Rep3


title: DE DAY 2 WNT Rep2


title: ATAC-Seq Sucla2 KO replicate3

description: Sucla2 KO replicate3

data_processing:
Sequence reads were mapped to the mouse reference genome mm10 using bowtie2.
Duplicated reads, reads mapped to mitochorndrial DNA, and reads with low mapping quality were discarded in further analysis.
macs2 was used to identify peaks.
Reads fallen in the promoter regions and the mouse cortex-specific enhancers regions were quantified with featureCounts
Differential chromatin accessibiltiy analysis was performed using edgeR
Assembly: mouse reference genome mm10
Supplementary files format and content: excel table includeing raw and normalized counts in the dfined regions, log2 fold change, p-values/FDR, target genes.

extract_protocol: Fresh frozen mouse cortex tissues were cut into small pieces. Nuclei were isolated with the Sigma EZ Prep kit. Tn5 from the Illumina Nextera DNA library preparation kit was used for transposition, The nextera libraries were samplified using the Nextera PCR master mix and KAPA biosystems HiFi hotstart ready mix.


title: ATAC-Seq Sucla2 KO replicate2

description: Sucla2 KO replicate2


title: ATAC-Seq Sucla2 KO replicate1

description: Sucla2 KO replicate1


title: DE DAY 2 C59 - Late Rep1


title: DE DAY 2 WNT Rep1


title: leaf sr 24_h_2

city: Baoding

first: mengyang

last: liu

state: Hebei

address: Hebei Agricultural University West Campus, Lianchi District

institute: Hebei Agricultural University

data_processing:
Illumina HiSeqTM 2500
Quality of the RNA-seq reads were evaluated using the FastQC software.
Raw data (raw reads) in the fastq format were processed and cleaned (clean reads). The clean data were mapped to the B. rapa reference genome (v1.5)from the Brassica database (BRAD) (http://brassicadb.org/brad/).
HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and the FPKM (Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) of each gene was calculated based on the length of the gene and read counts mapped to this gene35.
Assembly: B. rapa reference genome was obtained from Ensembl
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Brassica rapa subsp. pekinensis

source_name: leaf

growth_protocol: All seeds were sown in pots in the greenhouse at 26–28 ℃ with 16 h daytime/15 ℃ with 8 h nighttime and 90% humidity. All samples were collected one week after transplanting.

extract_protocol:
Total RNA was extracted using the EASYspinPlus Plant RNA Rapid Extraction Kit provided by Beijing Aidelai Biotechnology Co., Ltd.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: three biological replicates of Chinese cabbage soft rot-resistant mutant sr and WT against Pcc infection at 0, 6, 12, and 24 hpi (24 samples)

value: leaf

value: sr

value: Pcc infection

tag: time

value: 24 hr


title: leaf sr 24_h_3


title: leaf sr 24_h_1


title: DE DAY1 C59 Rep3

source_name: Induced pluripotent stem cells

value: Day 1 mesendoderm


title: ATAC-Seq WT replicate2

description: WT replicate2

value: Cerebral Cortex


title: leaf sr 12_h_1

value: 12 hr


title: leaf sr 6_h_3

value: 6 hr


title: leaf sr 12_h_3


title: Escort Cells scRNA-seq

city: Hangzhou

first: Zhi

last: Dong

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou

institute: Zhejiang University

description: 10x Genomics

data_processing:
Cell Ranger’s raw gene count matrix was analyzed using the Seurat (v4.0.2) R package with standard protocols.
Assembly: BDGP6.32
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
GFP positive cells from C587-GAL4 / yw; UAS-CD8-RFP/+ ovaries were sorted via Fluorescence-activated cell sorting (FACS). The sorted cells were loaded on a Chromium Single cell Controller (10 X Genomics) using the Chromium Single-cell 3’ Library & Gel Bead kit v3 according to manufacturer’s directions.
The raw sequencing data was processed with alignment, barcode assignment and UMI counting by Cell Ranger (version 6.1.1) using the previously published pipeline (61). The reference index for Cell Ranger was built using the Drosophila melanogaster genome (version BDGP6.32) available on the Ensembl genome database.

value: ovary

value: Escort Cells

value: 4-7 days


title: ATAC-Seq WT replicate3

description: WT replicate3

value: Sucla2+/+, CamKIIa-Cre


title: DE DAY1 C59 Rep2


title: leaf sr 6_h_2


title: DE DAY1 C59 Rep1


title: leaf sr 12_h_2


title: DE DAY1 WNT Rep2


title: leaf sr 6_h_1


title: leaf WT 24_h_2

value: WT


title: leaf WT 24_h_3


title: DE DAY1 WNT Rep3


title: leaf sr 0_h_1

value: 0 hr


title: DE DAY1 WNT Rep1


title: leaf sr 0_h_2


title: leaf WT 12_h_3


title: leaf WT 24_h_1


title: leaf WT 12_h_2


title: leaf WT 12_h_1


title: iWAT-Cdo1AKO-1

first: Ying-Ying

last: Guo

address: Dongan Road, Xuhui District

department: School of basic medical sciences

institute: Fudan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routinesfor determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differentialexpressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species.Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts and FPKM values for each Sample

source_name: subcutaneous adipose tissue

extract_protocol:
The RNA wes isolated form iWAT of WT and Cdo1AKO mice by using trizol.
RNA libraries for RNA-seq were prepared using RNA lib NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: subcutaneous adipose tissue

value: tissue

value: High fat diet


title: iWAT-Cdo1AKO-2


title: iWAT-Control-3


title: leaf WT 6_h_3

value: leaf


title: leaf sr 0_h_3

value: sr


title: iWAT-Cdo1AKO-3


title: iWAT-Control-1


title: ES Rep2

value: pluripotent ES cells


title: ES Rep1


title: leaf WT 6_h_1

value: Pcc infection


title: leaf WT 0_h_2


title: leaf WT 6_h_2


title: STR_Pos_S12_FRE1202A227_S30

city: Worcester

first: Ryan

last: Logan

address: 366 Plantation Street

institute: University of Massachusetts Chan Medical School

data_processing:
Quality control was performed by Fastqc
Perform trimming by trimmomatic, align the sequence using Hisat2 with Ensembl reference and read count with Hiseq
In the processed data, genes are filtered to retain those with count per million (CPM) greater than 1 in subgroups formed by sex and brain regions.

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy micro plus kit including the use of DNA elimination columns (Qiagen).
4.5 ul of RNA was used from each sample for cDNA generation using the Takara Smart-Seq HT kit following manufactures instructions, with 15 cycles of cDNA amplification. All samples passed QC with full length cDNA and proceeded to library preparation using Illumina Nextera XT kit with UDI indexes added using 12 PCR cycles. Libraries were assessed using an Agilent High sensitivity NGS kit before library pooling and sequencing. Libraries were sequenced on a NovaSeq 6000 on an S2 100 cycle flow cell, 2x50 bp, for an average of ~30 million reads per sample.

value: Brain

value: Microglia

value: Tamoxifen

tag: Sex

value: Female

tag: brain region

value: Striatum


title: STR_Pos_S11_FRE1202A224_S76

value: Male


title: iWAT-Control-2


title: NMP SOX2KD DAY 3 - BCAT Rep2

first: Shreyasi

last: Mukherjee

institute: Cincinnati Children's Hospital Medical Center

tag: developmental stage

value: Day 3 neuromesodermal progenitors

value: 1ug/ml dox at Days 2 and 3

tag: chip antibody

value: Invitrogen 71-2700


title: STR_Pos_S10_FRE1202A221_S49

tag: tissue


title: leaf WT 0_h_1

value: WT

value: 0 hr


title: transgenic TH-MYCN mouse tumor, relapse after brequinar 120 days, rep3

first: Ninib

last: Baryawno

institute: Karolinska institutet

description: TH-MYCN sample 9

data_processing:
For xenografts, reads were aligned to a combined mm10+hg38 reference using STAR v2.7.9a (2-pass approach).
Raw reads per gene were quantified using htseq-count v0.12.4.
Assembly: Xenograft data: combined hg38+mm10 reference. Transgenic TH-MYCN data: combined hg19+mm10 reference (any reads mapping to human genes other than MYCN were filtered out priior to downstream analyses).
Supplementary files format and content: rawcounts_xenografts.csv: a matrix of read counts per gene per sample (all hg38 + mm10 genes)
Supplementary files format and content: rawcounts_thmycn.csv: a matrix of read counts per gene per sample (all mm10 genes + human MYCN)

source_name: TH-MYCN tumor

extract_protocol:
Mouse tumor tissue used for RNA sequencing was stored in RNAlater solution (Thermo Fisher, Waltham, MA, USA) at -80 °C. Total RNA from xenograft/tumor tissue was isolated using the RNeasy Mini Kit (Qiagen).
All libraries were generated using the TruSeq Stranded protocol (Illumina). All libraries were sequenced on the NextSeq500 platform. Xenograft samples were sequenced with a 75 bp single-end strategy. TH-MYCN samples were sequenced with a 2x42 bp paired-end strategy.

value: TH-MYCN tumor

value: homozygous

value: brequinar 120 days


title: ES Rep3


title: 375KO_set1

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

description:
12M_375KO_set_1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, genome mapping and gene counting were processed through Cell Ranger (v3.0.1; mapped to 10x genomics pre-built reference mm10-1.2.0) and SoupX (v1.5.2; for ambient RNA removal).
Cell Ranger output was then subject to downstream analysis with Seurat (v3.2.1). To maintain data quality, cells with less than 1500 detected genes or greater than 25% of the reads mapping to mitochondrial genes were discarded. 702 potential doublets, which were detected using scDblFinder (v1.4.0), were discarded, resulting in 11697 singlets for downstream analyses.
To control sequencing depth, counts were normalized using sctransform and glmGamPoi (v1.2.0).
Wildtype and miR-375 KO samples were merged using the Seurat integration anchor workflow based on the 3000 most variable genes. Clustering and identification of nearest neighbors relied on 30 principal component analysis (PCA) dimensions. Cells were clustered at a resolution of 0.7, resulting in 17 cell clusters in the dataset.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: small intestine (jejunum)

extract_protocol:
Mouse jejunal crypts from male B6 albino wildtype and miR-375 knockout mice were isolated and resuspended in an ice-cold PBS containing 0.04% (w/v) bovine serum albumin and pelleted at 1000 x g at 4°C for 5 min. The crypts were subsequently digested with 0.3 U/mL Dispase I (MilliporeSigma Burlington, MA; D4818) in HBSS at 37°C for 12 min with gentle agitation. The dispase I activity was stopped by adding fetal bovine serum to a final concentration of 10% (v/v) and DNaseI to a final concentration of 50 μg/mL. The sample was filtered through 40 μm strainer, pelleted at 500 x g at 4°C for 5 min, washed with cold HBSS, filtered again, and then resuspended in an ice-cold PBS containing 0.04% (w/v) bovine serum albumin. Prior to submission, single cell suspensions were triturated by pipetting and evaluated for total viable cell number by using trypan blue staining with a TC20 automated cell counter (Bio-Rad Laboratories, Richmond, CA).
Single-cell RNA sequencing of these samples was performed at the Cornell University Biotechnology Resource Center. Libraries were prepared using the 10X Genomics Chromium preparation kit (3’ v2 chemistry)(10X Genomics, Pleasanton, CA). Briefly, single cell suspension were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: small intestine (jejunum)

value: 12 months

value: miR-375 knockout


title: 375KO_set2

description:
12M_375KO_set_2
10x Genomics


title: NMP WT DAY 3 - BCAT Rep3

city: Cincinnati

address: 3333 Burnet Ave


title: leaf WT 0_h_3

value: leaf

value: Pcc infection


title: transgenic TH-MYCN mouse tumor, relapse after brequinar 120 days, rep2

city: Stockholm

address: Tomtebodavägen 18a

description: TH-MYCN sample 8


title: ATAC-Seq WT replicate1

description: WT replicate1

value: Cerebral Cortex

value: Sucla2+/+, CamKIIa-Cre


title: STR_Pos_S9_FRE1202A218_S19

value: Brain

tag: cell type

value: Microglia

value: Tamoxifen

value: Striatum


title: transgenic TH-MYCN mouse tumor, relapse after brequinar 120 days, rep1

description: TH-MYCN sample 7

tag: treatment


title: NMP WT DAY 3 - BCAT Rep2

value: Day 3 neuromesodermal progenitors

value: Invitrogen 71-2700


title: NMP SOX2KD DAY 3 - BCAT Rep3

value: 1ug/ml dox at Days 2 and 3


title: transgenic TH-MYCN mouse tumor, brequinar treated 72h, rep3

description: TH-MYCN sample 6

value: TH-MYCN tumor

value: brequinar 72h


title: NMP SOX2KD DAY 3 - LEF1


title: STR_Pos_S6_FRE1202A209_S8

value: Female


title: STR_Pos_S7_FRE1202A212_S38

value: Male


title: transgenic TH-MYCN mouse tumor, brequinar treated 72h, rep1

description: TH-MYCN sample 4

value: homozygous


title: transgenic TH-MYCN mouse tumor, vehicle treated control, rep3

description: TH-MYCN sample 3

value: vehicle treated control


title: STR_Pos_S4_FRE1202A203_S27


title: NMP SOX2KD DAY 3 - BCAT Rep1


title: WT-hESC_siRNA control rep2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: WT-hESC_siRNA control

hyb_protocol: Equal amounts RNA labeled with Cy3, ranging from 200 to 300 pmol, were mixed with 20 ug of poly(A) and 20 µg of yeast tRNA (Sigma-Aldrich) in a volume of 9 µL. To this volume, 1 µL of RNA fragmentation buffer was added (RNA fragmentation reagents; Ambion) and after 15 min at 70°C, 1 µL of stop solution. Formamide, 20x SSC, 50x Denhardt's, and 20% SDS were added to a final concentration of 50% formamide, 6x SSC, 5x Denhardt's, and 0.5% SDS. This mix was boiled for 3 min at 95°C and then added to the prehybridized slide. Hybridization took place overnight at 37°C in a hybridization chamber. Arrays were then washed for 5 min at 37°C in 0.5x SSC and 0.1% SDS, twice for 5 min at room temperature (21°C) with 0.5x SSC and 0.1% SDS, three times with 0.5x SSC at room temperature, and 5 min with 0.1x SSC. The slides were then drained with a 2000-rpm spin for 2 min. The slides were stored in darkness until they were scanned.

scan_protocol: Images from Cy3 channel were equilibrated and captured with a GenePix 4000B (Molecular Devices) and spots quantified using GenPix 5.1 software (Molecular Devices).

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

source_name: hESC cell line

label_protocol: Extracted RNA was reverse-transcribed and labeled using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814) according to the manufacturer’s instructions.

growth_protocol: The hESC used in this study are Shef-1 cells (Thomson at al., 1998), obtained from the Department of Biomedical Science, University of Sheffield (UK). All hESC were maintained on Matrigel-coated plates (Corning) using mTeSR1 or NODAL-free mTeSR7 media (Stem Cell Tech).

extract_protocol: RNA was isolated using the RNeasy kit from Qiagen (74104)

value: hESC

tag: silenced


title: STR_Pos_S5_FRE1202A206_S56

tag: genotype


title: STR_Pos_S2_FRE1202A198_S55


title: NMP WT DAY 3 - BCAT Rep1


title: WT-hESC_siRNA control rep1

description: WT-hESC_siRNA control


title: NMP WT DAY3 - LEF1


title: STR_Pos_S8_FRE1202A215_S66


title: transgenic TH-MYCN mouse tumor, vehicle treated control, rep2

description: TH-MYCN sample 2


title: transgenic TH-MYCN mouse tumor, brequinar treated 72h, rep2

description: TH-MYCN sample 5


title: transgenic TH-MYCN mouse tumor, vehicle treated control, rep1

description: TH-MYCN sample 1


title: STR_Pos_S1_FRE1202A195_S26


title: NMP WT DAY3 - TCF7L1

value: Active Motif 61125


title: WT-hESC_siRNA contro lrep3

description: WT-hESC_siRNA control


title: PFC_Pos_S12_FRE1202A226_S20


title: NMP SOX2KD DAY 3 - TCF7L1


title: PFC_Pos_S11_FRE1202A223_S67


title: N/C-MYC-silenced hESC_rep3

description: N/C-MYC-silenced hESC

value: n/c-myc


title: N/C-MYC-silenced hESC_rep1

description: N/C-MYC-silenced hESC


title: NMP WT DAY3 - SOX2


title: DE DAY3 - SOX17KO BRG1

value: Day 3 definitive endoderm


title: TH-MYCN tumor, H3K27Ac, control, rep3

data_processing:
ChIP-seq analysis of TH-MYCN tumor samples were performed by Active Motif. For enhancer analyses, 75 bp reads were mapped to the mouse genome using the BWA algorithm with default settings. Duplicate reads were removed and only uniquely mapped reads with mapping quality >= 25 were used for further analyses. Using in-house software, alignments at 3’ ends were extended in silico to a length of 200 bp which was the average genomic fragment length of the size-selected libraries. Extended alignments were assigned to 32-nt bins across the genome and the number of fragments per bin was determined.
Assembly: mm10
Supplementary files format and content: bigWig files containing histograms of fragment densities in 32-nt bins across the genome.

source_name: TH-MYCN tumor tissue

growth_protocol: Transgenic TH-MYCN mice were kept on the 129X1/SvJ background. Genotypes were determined from ear tissue biopsies using qPCR with specific probes designed for wild-type and the MYCN transgene (Transnetyx, Cordova, TN, USA). Only MYCN homozygous mice (of either sex) were used for in vivo studies.

extract_protocol:
Tissue for ChIP sequencing was snap frozen and stored in liquid nitrogen ChIP experiments and library preparation was performed by Active Motif using the HistonePath workflow. Mouse tumor tissues were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was then isolated by adding lysis buffer followed by tissue disruption with a Dounce homogenizer. Lysates were sonicated and DHA sheared to an average length of 300-500 bp. Genomic DNA (input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. DNA was quantified on a NanoDrop spectrophotometer. 30 μg chromatin was precleared with protein A agarose beads (Invitrogen) and genomic DNA regions of interest isolated using 4 μg of H3K27Ac antibody (Active Motif, cat# 39133). Complexes were washed, eluted with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR reactions were carried out in triplicates on specific genomic regions using SYBR Green Supermix (Bio-Rad).
Illumina sequencing libraries were prepared from ChIP and input DNA by end-polishing, dA-addition and adaptor ligation. After PCR amplification, DNA libraries were sequenced on the NextSeq 500 platform (Illumina), 75 bp reads, single-end.

treatment_protocol: For timepoint sampling of homozygous TH-MYCN tumors subject to single-agent treatment, mice with palpable abdominal tumors received one intraperitoneal dose of either brequinar (50 mg/kg), or vehicle (70% PBS, 30% PEG-400). Mice were then sacrificed and tumors were sampled after 72 hours.

value: TH-MYCN tumor tissue

value: vehicle


title: TH-MYCN tumor, pooled input

value: none (input)


title: PI3Kβ-depleted hESC_rep3

description: PI3Kβ-depleted hESC


title: N/C-MYC-silenced hESC_rep2

description: N/C-MYC-silenced hESC


title: DE DAY3 - WT BRG1


title: WT, rep2

city: Kyoto

first: Koji

last: Kitazawa

address: 465 Kajiicho Kamigyoku

institute: Kyoto Prefectural University of Medicine

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Trimmomatic (version 0.36) was used to remove adapters and filter raw reads <36 bases as well as leading and trailing bases < quality 20.
Assembly: Filtered reads were mapped to hg19 using HISAT2 (v2.1.0).
Supplementary files format and content: Project_20180308_MN_kit_featureCounts.txt

source_name: Corneal epithelial cells

growth_protocol: All the cells were cultured in CEC medium which consists of Dulbecco’s modified Eagle’s medium and Ham’s F-12 media (1:1 mixture) (Life Technologies) containing B27-supplement (Life Technologies), Rho-kinase (ROCK) inhibitor (10 M) (Nacalai Tesque), keratinocyte growth factor (10 ng/ml) (Fujifilm Wako Pure Chemical, Osaka, Japan), Epigallocatechin gallate (SIGMA) and penicillin-streptomycin (50 IU/ml) (Nakalai Tesque),

extract_protocol:
Each sample was resuspended in a Qiagen lysis buffer, and RNA was prepared using the RNeasy Purification kit (Qiagen) following the manufacturer's recommendations.
Sequencing libraries were TruSeq Stranded mRNA Sample Prep Kit (Illumina) following manufacture`s instruction. The initial amount of total RNA was 1000 ng.

treatment_protocol: KLF4 was depleted with CRISPR/Cas9 in primary human corneal epithelial cells

value: cornea

value: Primary corneal epithelial cells

value: Normal

value: WT


title: PI3Kβ-depleted hESC_rep1

description: PI3Kβ-depleted hESC


title: PFC_Pos_S10_FRE1202A220_S39

value: Brain

value: Microglia

value: Tamoxifen


title: PI3Kα-depleted hESC_rep3

description: PI3Kα-depleted hESC


title: WT, rep1


title: TH-MYCN tumor, H3K27Ac, control, rep2


title: PFC_Pos_S7_FRE1202A211_S28

value: Male


title: PFC_Pos_S8_FRE1202A214_S57

value: Female


title: TH-MYCN tumor, H3K27Ac, Brq 72h, rep3

value: homozygous

value: brequinar


title: TH-MYCN tumor, H3K27Ac, Brq 72h, rep2


title: DE DAY3 - WT H3K27AC

value: Active Motif 39133


title: TH-MYCN tumor, H3K27Ac, control, rep1


title: PI3Kα-depleted hESC_rep2

description: PI3Kα-depleted hESC

value: hESC


title: PI3Kβ-depleted hESC_rep2

description: PI3Kβ-depleted hESC


title: PI3Kα-depleted hESC_rep1

description: PI3Kα-depleted hESC


title: DE DAY3 - SOX17KO H3K27AC

value: Day 3 definitive endoderm


title: DE DAY3 - SOX17KO TCF7L2


title: PFC_Pos_S6_FRE1202A208_S74


title: PFC_Pos_S9_FRE1202A217_S9


title: DE DAY3 - SOX17KO LEF1


title: PFC_Pos_S5_FRE1202A205_S47


title: DE DAY3 - SOX17KO TCF7L1

value: Active Motif 61125


title: KLF4-#2, knockout, rep1

value: KLF4 depleted


title: KLF4-#2, knockout, rep2


title: KLF4-#1, knockout, rep2


title: DE DAY3 - SOX17KO TCF7


title: PFC_Pos_S4_FRE1202A202_S17


title: DE DAY3 - SOX17KO BCAT Rep 2

value: Invitrogen 71-2700


title: STR_Pos_S3_FRE1202A200_S73

value: Striatum


title: PFC_Pos_S2_FRE1202A197_S46


title: 3m HOX, scRNAseq

city: Kansas City

first: Sheng

last: Xia

state: MO

address: 2401 Gillham Rd

department: Children's Mercy Research Institute

institute: Children's Mercy Kansas City

description:
single cell RNA
10x Genomics

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
mm10
tsv and mtx files can be opened with Seurat (R package) and analyzed. Cloupe file can be opened with Loupe cell browser to visualize the data.
Supplementary files format and content: RDS

source_name: lung

extract_protocol:
Lungs from the experimental C57BL/6 mice were inflated with enzymes, chopped with a razor blade into fine chunks, put into prewarmed enzyme with DNase for digestion, and placed in a 37 °C incubator and rotated for 15min. Then lungs were passed through a 1mL pipet tip. Place the digestion mix back into the incubator and rotate for another 15min. Stop the digestion with FBS and pass the homogenized digested lysate through a 70um filter (Fisher Scientific, Rockford, IL). After centrifugation, incubate with 1X red cell lysis buffer (Sigma-Aldrich, St. Louis, MO) for 3 minutes. After centrifugation and resuspension with Leibovitz media containing 3% FBS, filter lysate with 70um filter, washing with Leibovitz media.
Fresh lung single cell digests furnished 1X104 cells, which were loaded on a 10x Genomics v3 scRNA chip using 10x Genomics v3 scRNA reagents. Library preps were done, and completed libraries were sequenced on an Illumina NovaSeq 6000 instrument with 25,000 reads/cell targeted. Raw sequencing data was processed through bcl2fastq2 (Illumina, San Diego, CA), resulting in 1 fastq file per library.

value: lung

value: male

value: BPD


title: DE DAY3 - SOX17KO BCAT Rep 1


title: 2f HOX, scRNAseq

description:
single cell RNA
10x Genomics

value: female


title: PFC_Pos_S1_FRE1202A194_S16

value: Brain

value: Microglia


title: DE DAY3 - WT BCAT Rep2


title: HCC1954_S-BM3

city: DALLAS

first: Srinivas

last: Malladi

state: Texas

address: NB7218, DEPARTMENT OF PATHOLOGY, UT SOUTHWESTERN MEDICAL CENTER

department: PATHOLOGY

institute: UT Southwestern Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
The trimmed reads were a whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized count table as a tab delimited text file

source_name: Brain tropic synchronous metastatic cells

growth_protocol: Culutured in R3F

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen). Libraries were prepared with either TruSeq RNA Sample Prep Kit v2 (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 million cells were cultured in 1ml R3F for overnight

tag: cell line source

value: Synchronous met. Cells


title: HCC1954_S-BM4


title: HCC1954_S-BM2


title: HCC1954_S-BM1


title: 4m HOX, scRNAseq

description:
single cell RNA
10x Genomics

tag: disease state


title: TH-MYCN tumor, H3K27Ac, Brq 72h, rep1

value: TH-MYCN tumor tissue


title: HCC1954_M-BM4

source_name: Brain tropic metachronous metastatic cells

value: Metachronous met. Cells


title: MB_Pos_S10_FRE1202A222_S58

value: Tamoxifen

value: Female

value: Midbrain


title: 1f HOX, scRNAseq

description:
single cell RNA
10x Genomics


title: 1m HOX, scRNAseq

description:
single cell RNA
10x Genomics


title: 4m RA, scRNAseq

description:
single cell RNA
10x Genomics

value: ctrl


title: MB_Pos_S11_FRE1202A225_S10

value: Male


title: 2m RA, scRNAseq

description:
single cell RNA
10x Genomics


title: HCC1954_M-BM3


title: MB_Pos_S9_FRE1202A219_S29


title: MB_Pos_S12_FRE1202A228_S40


title: HCC1954_M-BM2


title: 3f RA, scRNAseq

description:
single cell RNA
10x Genomics


title: MB_Pos_S8_FRE1202A216_S75


title: KLF4-#1, knockout, rep1

value: cornea

value: Primary corneal epithelial cells

value: Normal

value: KLF4 depleted


title: 2f RA, scRNAseq

description:
single cell RNA
10x Genomics

value: lung


title: DE DAY3 - TCF7L2 Rep1

value: Day 3 definitive endoderm


title: DE DAY3 - WT BCAT Rep1

value: Invitrogen 71-2700


title: DE DAY3- LEF1 Rep2


title: MB_Pos_S7_FRE1202A213_S48

value: Brain


title: HCC1954_M-BM1


title: 4f HOX, scRNAseq

description:
single cell RNA
10x Genomics

value: female

value: BPD


title: DE DAY3 - LEF1 Rep1


title: 1m RA, scRNAseq

description:
single cell RNA
10x Genomics

value: male


title: 1f RA, scRNAseq

description:
single cell RNA
10x Genomics


title: HCC1954_Lat4

source_name: Brain tropic latent or residual cells

value: Latent cells


title: MB_Pos_S4_FRE1202A204_S37

value: Microglia

value: Tamoxifen


title: DE DAY3 - TCF7L2 Rep2


title: MB_Pos_S6_FRE1202A210_S18

value: Female

value: Midbrain


title: MB_Pos_S5_FRE1202A207_S65

value: Male


title: HCC1954_Lat2


title: DE DAY3 - TCF7 Rep1


title: Th1 72h replicate 2

city: Philadelphia

first: Sankar

last: Addya

address: 233 South 10th Street

institute: Thomas Jefferson University Hospital

data_processing:
Bases were trimmed from R2 reads per the library kit recommendations (Takara SMARTer Stranded Total RNA-Seq kit v2 Pico input)
Paired-end reads were aligned quantified against GRCm38/GENCODE.M18 reference annotations using RSEM-STAR (RSEM v1.2.31, STAR 2.6.0c) in strand-specific mode with parameters --strand-specific --forward-prob 0
Assembly: GRCm38
Supplementary files format and content: .genes.results files from RSEM-STAR include columns with Ensembl gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: CD4+ T cells from spleen of WT mice

extract_protocol:
Human samples:  ThGM (CD25-CXCR5-CXCR3-CCR4+CCR10+) and Th1 cells (CD25-CXCR5-CXCR3+CCR4-CCR10-) were FACS sorted. GM-CSF+-ThGM and -Th1 cells were enriched based on their GM-CSF expression using GM-CSF secretion assay kit. RNA from human ThGM, Th1, and GM-CSF+Th1 cells were isolated and their transcriptome were analyzed by RNA sequencing.
Mouse samples: Mouse naive CD62LhiCD44-CD25-CD4+) T cells were FACS sorted and culture with T cell depleted splenocytes and  polarized to ThGM and Th1 cells. RNA from 4, 8,16, 24, 48, and 72h  were isolated and analyzed using RNA sequencing.
Takara SMARTer Stranded Total RNA-Seq kit v2 Pico input


title: DE DAY3 - TCF7 Rep2


title: HCC1954_Lat3


title: DE DAY3 - TCF7L1 Rep1

value: Active Motif 61125


title: Th1 72h replicate 1


title: MB_Pos_S3_FRE1202A201_S7


title: DE DAY3 - TCF7L1 Rep2


title: Th1 48h replicate 1


title: HCC1954_Lat1


title: DE DAY3 - SOX17 Rep2

value: SOX17 R&D AF1924


title: DE DAY3 - SOX17 Rep1


title: DE DAY2 - BCAT Rep2

value: Day 2 endoderm progenitors


title: MB_Pos_S2_FRE1202A199_S64


title: Th1 16h replicate 2


title: DE DAY2 - BCAT Rep1


title: MB_Pos_S1_FRE1202A196_S36


title: TMDNUD

city: New York

first: Soobeom

last: Lee

state: NY

address: 550 First Avenue, Smilow 1307 New York NY

institute: NYU

data_processing:
Library strategy: MACE-seq
Raw data was preprocessed using Cutadapt5 to eliminate poly-A-tails as well as bad-quality base reads. FastQC was used to assess the quality of sequencing after trimming
Cleaned reads were mapped to a reference genome using Bowtie2.
Quantification of mapped reads to each gene was performed using HT-seq.
ENSEMBL-GTF data was used to provide genomic locations for quantification as well as additional data for annotation (such as gene name, gene description, GO-Terms etc).
APA  usage was analyzed as described in QAPA using SALMON for quantifying 3’UTRs of PolyASite.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: pau_results.tsv contains TPM normalized counts data and proportion of isoforms with different 3'UTRs.

growth_protocol: To achieve this, we generated five independent human Cas9-expressing CD19+ B cell lines, including three BCP-ALL cell lines (Reh, NALM6 and 697) and two mature B-cell neoplasm cell lines (Chronic Lymphocytic Leukemia/CLL: HG3; B Cell Lymphoma/BCL: TMD8). All cell lines were cultured in RPMI-1640 media supplemented with 20% fetal bovine serum, 55 μM β-mercaptoethanol (Gibco # 21985023) and penicillin, streptomycin (Gibco #15140122).

extract_protocol: Massive Analyses of cDNA Ends (MACE-Seq) was performed by GenXPro GmbH in Frankfurt am Main using the MACE-Seq kit according to the manual of the manufacturers. Briefly, cDNA was generated from fragmented RNA with barcoded poly-A primers during reverse transcription. After second- strand synthesis and 5’ adapter integration, a PCR with minimum number of cycles was used to produce a library that was sequenced on an Illumina NextSeq500 machine with 1x 75 bps.

treatment_protocol: All lentiviral transfections were performed in HEK293T cells using Polyethylenimine (PEI) reagent at 4:2:3 ratios of sgRNA or Cas9 construct: pVSVG: pPax2 in OPTI-MEM solution. All retroviral transfections were performed in Platinum-E cells using Polyethylenimine (PEI) reagent with 10 μg transfer plasmid in OPTI-MEM solution. All amphitropic retroviral transfections were performed Polyethylenimine (PEI) reagent at 5:2:5 ratios of MSCV-based construct: pVSVG: pCL-Ampho retrovirus packaging construct (Novus Biologicals, NBP2-29541) in OPTI-MEM solution Viral supernatant was collected 48-hrs post-transfection. Spin infections were performed at room temperature at 1,500g for 90 mins with polybrene reagent (Fisher Scientific). Reh, 697, NALM6, K562, HG3, TMD8 Cas9-expressing cell lines were generated by lentiviral transduction with retroviral Cas9-2A-blast (Addgene, plasmid #73310). Human GM12878 Cas9 lines were generated by lentiviral transduction with Cas9-2A-EGFP (Addgene plasmid #63592). 697 Cas13d-expressing cell line was generated by transduction with lentiviral tet-inducble RfxCas13d (Addgene, plasmid # 138149). Doxycycline (Sigma) treatment was performed at 0.5 μg/mL supplemented every two days in culture.

tag: guide rna

tag: cell line


title: RehROS

source_name: Reh

value: sgROSA

value: Reh


title: Th1 24h replicate 1

tag: donor


title: Th1 16h replicate 1


title: 2022, N2a, siRNA, siFgfr1, totalRNA, Rep4

city: Old Westbury

first: Ying-Tao

last: Zhao

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing:
The FASTQ files of RNA-seq were aligned to the mouse mm10 genome using STAR 2.7.7a by the parameters of “--runThreadN 40 --outFilterMultimapNmax 1 --outFilterMismatchNmax 3 --outFilterScoreMinOverLread 0.25 --outFilterMatchNminOverLread 0.25”. The number of reads aligned to the exon regions of each gene were quantified by a perl script. The DESeq2 was used to perform the principal component analysis. The edgeR was used to compare the gene expression levels. The FDR < 0.05 was used as the cutoff to identify differentially expressed genes. The Gene Ontology enrichment analyses were performed using the DAVID, and the genes expressed in Neuro 2a cells were used as the background genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for the exonic regions of each gene for each Sample
Supplementary files format and content: BigWig bw files of the plus and minus strands for each sample

source_name: Neuro 2a cells

growth_protocol: Neuro 2a cells were purchased from the ATCC (CCL-131). The cells were cultured and maintained in Dulbecco's modified Eagle's medium (DMEM, Thermo Fisher Scientific, USA) and were supplemented with 10% fetal bovine serum (FBS), L-glutamine (2 mM), penicillin (100 U/ml) and streptomycin (100mg/mL). The cells were incubated at 37°C in a humidified atmosphere incubator containing 5% CO2. The cells were sub-cultured in fresh medium after reaching 70-80% confluence (about every 2-3 days).

extract_protocol:
RNA was isolated from Neuro 2a cells, and the total RNA was then extracted using the Trizol reagent (Invitrogen, #15596026) following the manufacturer’s instruction. Isolated rRNA-depleted total RNA.
RNA-seq libraries were prepared according to the manufacturer instructions with the Stranded Total RNA Library Prep Kit (Zymo, #R3003). The libraries were prepared with 1000 ng of total RNAs.

treatment_protocol: The siRNA transfection of Neuro 2a cells was performed using siRNA transfection reagent (Santacruz Biotech, sc-29528) according to the manufacturer’s instructions. The siRNAs used in this study include siRNAs for Hs6st1 (Santacruz Biotech, sc-146089), siRNAs for Fgfr1 (Santacruz Biotech, sc-29317), and control siRNA (Santacruz Biotech, sc-37007). Briefly, for each transfection, Neuro 2a cells were plated for one day and then were incubated with siRNA (60 pmol), the transfection reagent, and the transfection medium for six hours at 37°C incubator. After the incubation, the cells were overlaid with the same volume of fresh growth medium containing 10% FBS and were cultured overnight in 37°C incubator. In the next day, the medium was exchanged to fresh growth medium containing 10% FBS, and the cells were incubated at 37°C, 5% CO2 for an additional 72 hours before harvesting for analysis.

value: Neuro 2a cells

value: neuronal cells

value: Fgfr1 knockdown

value: Fgfr1 siRNAs


title: Th1 8h replicate 1


title: DE DAY2 - LEF1 Rep1


title: DE DAY2- LEF1 Rep2


title: N6ROS


title: ThGM 72h replicate 3

value: ThGM


title: RehNUD


title: TMDROS


title: 2022, N2a, siRNA, siFgfr1, totalRNA, Rep3


title: 697ROS


title: Th1 4h replicate 1


title: 2022, N2a, siRNA, siFgfr1, totalRNA, Rep2


title: N6NUD


title: DE DAY2 - TCF7L2 Rep2


title: 2022, N2a, siRNA, siFgfr1, totalRNA, Rep1


title: ThGM 72h replicate 2


title: DE DAY2 - TCF7L2 Rep1


title: 2022, N2a, siRNA, siHs6st1, totalRNA, Rep3

value: Hs6st1 knockdown

value: Hs6st1 siRNAs


title: DE DAY2 - TCF7L1 Rep2


title: ThGM 72h replicate 1


title: 2022, N2a, siRNA, siHs6st1, totalRNA, Rep1


title: 697NUD


title: 2022, N2a, siRNA, siHs6st1, totalRNA, Rep2


title: ThGM 48h replicate 1


title: DE DAY2 - TCF7L1 Rep1


title: Wang2,scRNAseq

city: Milwaukee

first: Yu-Chieh

last: Wang

state: WI

address: 8701 Watertown Plank Rd.,

department: Dermatology and Cancer

institute: Medical College of Wisconsin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: BARNYARD: GRCh38 + mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: human cerebal organiod transplanted into mouse brain

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up and illumina primers were added for later sequencing.


title: DE DAY2 - TCF7 Rep1

state: OH

data_processing:
For RNA-Seq experiments, raw reads were quality-checked using  FASTQC and adapters were trimmed using cutadapt.
Reads were pseudo-aligned to the hg19 reference index using salmon.
The tximport package was then used for downstream analysis to convert transcript-level counts to gene-level estimates. Differential gene expression analysis was performed using DESeq2 using default parameters
For ChIP-Seq experiments, Reads were aligned to the hg19 genome using bowtie2
Duplicates were marked using Picard and removed using samtools
A consensus set of peaks were called for each TF at each stage using HOMER getDifferentialPeaksReplicates.pl using stage-matched input samples as background and -style factor.
For ATAC-Seq, trimmed paired-end reads were aligned to the hg19 genome using bowtie2 and the parameters -X 2000 -very-sensitive-local
Peaks were called on replicates using Genrich and the parameters j -r -e -v -q 0.1
Genome_build: hg19
Supplementary_files_format_and_content: .bw' files are bigWig files for visualization of ChIP-Seq and ATAC-Seq data
Supplementary_files_format_and_content: .csv' files are TPM matrices from RNA-Seq experiment

source_name: Induced pluripotent stem cells

extract_protocol:
For RNA-Seq experiments, Total RNA was extracted using the Nucleospin RNA Extraction kit.For ChIP-Seq experiments, after differentiation to the desired stage, cells were dual crosslinked in plate with 1.5mM EGS and 1% formaldehyde. The fixation was then quenched with 125mM glycine. Cells were then washed twice and scraped in ice-cold PBS and resuspended in sonication buffer.For ATAC-Seq experiments, 50,000 cells were collected following differentiation to the desired stage, and lysed in 50ul of ATAC-lysis buffer (10mM Tris-HCl, pH 7.4. 10mM NaCl, 3mM MgCl2, 0.1% NP-40) to obtain a crude nuclei prep
For RNA-Seq experiments, 300ng of total RNA was poly-A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit (Illumina; 20020595). For ChIP-Seq experiments, DNA libraries were prepared using 1-5 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674) according to manufacturer’s instructions. For ATAC-Seq, the eluted DNA was amplified in a reaction with 25ul NEBNext High-Fidelity 2x PCR Mastermix (NEB; M0541L) and custom 25um Nextera PCR Primers (Ad1_noMx universal primer, 0.5um Ad2.x indexing primer). PCR was performed as follows: 1 cycle of 72C for 5min, 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 1min. 5ul of the amplified DNA was then used to perform qPCR to determine the optimal number of additional cycles to prevent amplification saturation of DNA libraries. In all cases, either 4 or 5 additional cycles of PCR was performed at: 98C for 10s, 63C for 30s and 72C for 1 min. Double size selection of amplified libraries (0.5x – left sided, 1.8x – right sided) was performed using AMPure XP beads
ChIP-Seq, RNA-Seq and ATAC-Seq


title: DE DAY2 - TCF7 Rep2


title: 2022, N2a, siRNA, ctrl, totalRNA, Rep2

value: WT

value: Control siRNAs


title: Wang3,scRNAseq

description: 10x Genomics

value: human cerebal organiod transplanted into mouse brain


title: 2022, N2a, siRNA, ctrl, totalRNA, Rep3


title: ThGM 24h replicate 1


title: ThGM 16h replicate 1


title: Wang1,scRNAseq

description: 10x Genomics


title: DE DAY2 - SOX17 Rep2


title: 2022, N2a, siRNA, ctrl, totalRNA, Rep1


title: ThGM 16h replicate 2


title: ThGM 16h replicate 3


title: ThGM 4h replicate 1


title: DE DAY1 - BCAT Rep1

value: Day 1 mesendoderm

value: Invitrogen 71-2700


title: DE DAY2 - SOX17 Rep1


title: DE DAY1 - BCAT Rep2


title: ThGM 8h replicate 1


title: DE DAY1- LEF1 Rep2


title: Naïve  CD4+ T cells 0h  replicate 2

value: naive CD4+ T cells


title: HDAC3_control_input

first: Mitchell

last: Lazar

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

description:
HDAC3_Control.bed
HDAC3_NS-dKO.bed

data_processing:
RNA-seq
RNA-sequencing output, including published HDAC3 BAT-KO data (23), was analyzed in tandem using the DIYTranscriptomics course pipeline (61). Briefly, this pipeline uses Kallisto to align and quantify reads, EnemblDB to annotate data, edgeR to normalize read counts, and Limma to determine DEGs. Cut-offs used for these analyses were a CPM of 1 in a minimum of 4 of 31 total samples to identify a transcript as expressed and a log2FC>|0.58| and adjusted p-value <0.05 for all DEGs per mouse line.
ChIP-seq
FASTQ files were aligned to the GRCm38 (mm10) reference genome using bowtie2 v2.4.2 aligner with the following parameters: -N 1. Duplicate reads were removed with samtools rmdup. Then tag directories were made with Homer v4.11.1. HDAC3 peaks in Control and NCoR1/2 dKO were called using Homer from pooled replicates, using HDAC3 KO as background. findPeaks was used with default parameters, which sets the cutoff to 4-fold minimum enrichment over the background.
Assembly: mm10
Supplementary files format and content: RNA-seq: abundance files in Kallisto’s .h5 format
Supplementary files format and content: RNA-seq: gene ID and log2 fold change in CSV format
Supplementary files format and content: ChIP-seq: peak files in bed format

source_name: brown adipose tissue

growth_protocol: all male mice between 11-14 weeks old

extract_protocol:
RNA-seq
RNA was isolated from snap-frozen BAT as previously described (23) using TRIzol-chloroform extraction followed by RNeasy Mini spin columns (Qiagen) and on-column DNase-digestion
Novogene or TruSeq
ChIP-seq
Chromatin immunoprecipitation (ChIP) was done as previously described with minor modifications (23). Total protein for each sonicated sample was quantified by BCA and normalized to 1.5mg of protein for each ChIP prior to incubation with antibody overnight. 5% input was saved prior to antibody incubation and used as input control. Antibodies used were HDAC3 (Genetex GTX109679) and rabbit IgG (CST 2729S) and immunoprecipitated with BSA blocked Protein A agarose beads (Invitrogen 15918014). ChIP DNA was isolated using phenol/chloroform extraction and treated with RNAse A prior to sequencing library preparation.
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) with AMPure XP Beads (Beckman Coulter, Inc. #A63881) was used to amplify and size select ChIP DNA. Agilent High Sensitivity DNA Kit (5007-4626) KAPA Library Quantification Kit (KR0405) were used to quantify libraries and fragment sizes prior to sequencing.
An n=3 was sequenced for NCoR1/2 Control and NCoR1/2 BAT-dKO groups, n=2 for HDAC3 BAT-KO, and n=1 each for input and IgG. The sequencing was done at the Next-Generation Sequencing Core at the University of Pennsylvania on a NextSeq platform (Illumina) at 100SR for a total of 30 million reads per sample.

treatment_protocol: 2 weeks housing at 30C

tag: strain

tag: allele

tag: temperature

value: 14 days 30°C

value: brown adipose tissue


title: HDAC3_BAT-KO_HD3-ChIP_rep2

description:
HDAC3_Control.bed
HDAC3_NS-dKO.bed

value: HDAC3, Ucp1-Cre


title: HDAC3_control_IgG-ChIP

description:
HDAC3_Control.bed
HDAC3_NS-dKO.bed

value: IgG


title: HDAC3_BAT-KO_HD3-ChIP_rep1

description:
HDAC3_Control.bed
HDAC3_NS-dKO.bed


title: NCoR1-2_BAT-dKO_HD3-ChIP_rep3

value: NCoR1, NCoR2, Ucp1-Cre


title: DE DAY1 - LEF1 Rep1

department: Developmental Biology

growth_protocol: iPS72.3 cells were routinely maintained in mTesr. CRISPRi-SOX2 cells were maintained in Essential 8 medium.


title: DE DAY1 - TCF7L2 Rep2


title: NCoR1-2_BAT-dKO_HD3-ChIP_rep2


title: NCoR1_BAT-KO_RNA-seq_rep3

value: NCoR1, Ucp1-Cre


title: NCoR1_BAT-KO_RNA-seq_rep1


title: NCoR1-2_BAT-dKO_HD3-ChIP_rep1


title: DE DAY1 - TCF7L1 Rep2

value: Active Motif 61125


title: NCoR1-2_control_HD3-ChIP_rep2

value: NCoR1, NCoR2


title: DE DAY1 - TCF7L2 Rep1


title: DE DAY1 - TCF7L1 Rep1


title: NCoR1_BAT-KO_RNA-seq_rep2


title: NCoR1-2_control_HD3-ChIP_rep1


title: NCoR1_control_RNA-seq_rep3


title: NCoR1_control_RNA-seq_rep4


title: DE DAY1 - TCF7 Rep1


title: DE DAY1 - TCF7 Rep2


title: Tri6_RC_S7

city: Chicago

first: Rajeshwar

last: Awatramani

state: Illinois

address: 320 E Searle

department: Neurology

institute: Northwestern University

data_processing:
This project was sequenced on the Illumina HiSeq4000 with the production of single-end, 50 bp reads
The quality of reads, in FASTQ format, was evaluated using FastQC
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt
Trimmed reads were aligned to the Mus musculus genome (mm10) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for mm10 obtained from Ensembl
Normalization and differential expression were calculated using DESeq2
Assembly: mm10
Supplementary files format and content: One file with the raw gene counts and another one with the normalized counts using DESeq2 for every gene and every sample

source_name: Transected sciatic nerve from homozygous Shh 1/2/3 enhancer deletion

extract_protocol:
Trizol reagent was added to harvested sciatic nerve and RNA was prepared according to manufacturer’s protocol (Invitrogen cat#15596018). RNA samples were reverse transcribed on Applied Biosystems MiniAmp Thermal Cycler using QuantaBio qScript cDNA Supermix
The Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries of high-quality RNA samples (RIN > 7)

tag: line

value: Homo Shh 1/2/3 enhancer deletion

value: Sciatic nerve


title: NCoR1-2_BAT-dKO_RNA-seq_rep4


title: Naïve  CD4+ T cells 0h  replicate 1


title: NCoR1_control_RNA-seq_rep2


title: Tri5_RC_S5


title: DE DAY1 - SOX17 Rep2

value: SOX17 R&D AF1924


title: DE DAY1 - SOX17 Rep1


title: NCoR1-2_BAT-dKO_RNA-seq_rep2


title: NCoR1-2_BAT-dKO_RNA-seq_rep3


title: NCoR1_control_RNA-seq_rep1


title: H430_RC_S42


title: NCoR1-2_BAT-KO_RNA-seq_rep1


title: ES - BCAT Rep2

value: pluripotent ES cells


title: NCoR1-2_control_RNA-seq_rep3


title: NCoR1-2_control_RNA-seq_rep2


title: ES - LEF1 Rep2


title: NCoR1-2_control_HD3-ChIP_rep3


title: ES - TCF7L2 Rep2


title: P_RC_S3

source_name: Transected sciatic nerve from WT C57BL/6

value: WT


title: ES - BCAT Rep1


title: H306_RC_S44


title: NCoR1-2_control_RNA-seq_rep4


title: NCoR1-2_control_RNA-seq_rep1


title: J_RC_S40


title: O_RC_S1


title: I_RC_S38


title: NCoR2_BAT-KO_RNA-seq_rep4

value: NCoR2, Ucp1-Cre


title: F_RC_S36


title: ES - TCF7L1 Rep2


title: ES - TCF7L2 Rep1


title: H311_RC_S46


title: NCoR2_BAT-KO_RNA-seq_rep3


title: ES - TCF7L1 Rep1


title: NCoR2_BAT-KO_RNA-seq_rep2


title: Amx_liver_rep4

city: San Antonio

first: Xiaoli

last: Sun

state: TX

address: 7703 Floyd Curl Dr

department: Pharmacology

institute: University of Texas Health Science Center at San Antonio

description: mRNA

data_processing:
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments.
To compare differential gene expression between indicated groups, HOMER’s analyzeRepeats with the option rna and the parameters -condenseGenes, -noadj, and -count exons was used on two-three replicates per condition.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include TPM values and differential expressed genes for each Sample.

source_name: Liver

extract_protocol:
RNA was harvested using Quick RNA mini prep kit (Life Technologies). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ldlr-/- mice were fed on Western diet for 11 weeks. Starting at week 3 of the feeding period, mice were orally gavaged 25mg/kg amlexanox or vehicle for 8 weeks until end point.

value: Liver

value: Ldlr-/-

tag: diet

value: Western diet

tag: diet duration

value: 11 weeks

value: Amlexanox

tag: treatment duration

value: 8 weeks


title: ES - TCF7 Rep2

treatment_protocol: DE differentiation was carried out in RPMI-1640 media supplemented with non-essential amino acids Cells were treated with 100ng/ml Activin A and 2um CHIR99021 for 24hrs. In the next two days, cells were treated with 100ng/ml Activin A and 2um CHIR99021 in RPMI-1640 with increasing concentrations (0.2% on Day 2, 2% on Day 3) of ES-grade FBS . For NMP differentiation, cells were passaged using E8. The following day, media was changed to Essential 6 Medium. 24 hours later, cells were treated with 200ng/ml FGF8b in E6 media. After a further 24 hours, cells were treated with 200ng/ml FGF8b and 3um CHIR99021 in E6 media

tag: developmental stage

tag: chip antibody


title: Amx_liver_rep2

description: mRNA

tag: tissue

tag: treatment


title: ES - TCF7 Rep1


title: Amx_liver_rep3

description: mRNA

tag: genotype


title: ES - LEF1 Rep1


title: NCoR2_control_RNA-seq_rep4

value: 14 days 30°C

value: brown adipose tissue


title: NCoR2_BAT-KO_RNA-seq_rep1


title: ES - SOX17 Rep2


title: Amx_liver_rep1

description: mRNA


title: Veh_liver_rep4

description: mRNA

value: Vehicle


title: NCoR2_control_RNA-seq_rep3