title: BLCA_Trp_278

value: BASQ


title: BLCA_Trp_219

status: Public on Aug 24 2023

type: RNA

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200ul of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45° at 60rpm Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data was RNA normalized, adjusted for labeling batch using ComBat and merged by median probe set values per gene symbol.
probe group file: Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
meta-probeset file: Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit or GeneChip WT Pico kit.

extract_protocol: Total RNA was extracted using the HighPure FFPET kit (Roche)

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: palliative

tag: lundtax rna-subtype

value: UroB

tag: lundtax ihc-subtype

value: Uro

tag: consensus classifier subtype

value: LumP

tag: rm-lymphnode

value: yes

tag: rm-local

value: no

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: BLCA_Trp_215

value: GU

value: StromaRich


title: BLCA_Trp_216

value: LumU


title: BLCA_Trp_218

value: Mes


title: BLCA_Trp_214

value: LumNS


title: BLCA_Trp_204


title: BLCA_Trp_190


title: BLCA_Trp_209


title: BLCA_Trp_211


title: BLCA_Trp_199


title: BLCA_Trp_203

value: UroA


title: BLCA_Trp_186


title: BLCA_Trp_193


title: BLCA_Trp_197


title: BLCA_Trp_185

value: UroC


title: BLCA_Trp_189


title: BLCA_Trp_223


title: BLCA_Trp_184


title: BLCA_Trp_187


title: BLCA_Trp_183


title: BLCA_Trp_177


title: BLCA_Trp_181


title: BLCA_Trp_180


title: BLCA_Trp_175


title: BLCA_Trp_178


title: BLCA_Trp_179


title: BLCA_Trp_172


title: BLCA_Trp_217

value: ScNE


title: BLCA_Trp_174


title: BLCA_Trp_170


title: BLCA_Trp_166


title: BLCA_Trp_171


title: BLCA_Trp_161


title: BLCA_Trp_164


title: BLCA_Trp_159


title: Y4_liver input

status: Public on Aug 08 2023

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

library_source: genomic

data_processing:
library strategy: hMeDIP-seq
Illumina sequencing reads (~31 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with trimgalore/0.6.6 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned to the GRCm38/mm10 genome assembly using bowtie/2-2.4.2 with parameters “--end-to-end --no-mixed --no-discordant --very-sensitive -I 10 -X 700”.
Sam output files were then filtered to keep reads with a minimum mapping quality of 10 using samtools/1.9. sambamba/0.7.1 was used to keep uniquely mapping reads with parameters “-F "[XS] == null and not unmapped and not duplicate"”. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were also removed from the analysis using bedtools/2.30.0.
The bamCoverage function in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. Input reads were subtracted from 5hmC samples using bigWigCompare function.
Peaks were called using macs/2.2.7.1 with parameters “-f BAMPE -g 1.87e9 -B --broad -q 0.001 --broad-cutoff 0.001” using input as control and 5hmC as treatment sample.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using the bamCoverage function in deepTools/3.5/0; Scores represent the coverage on the genome location.

molecule: genomic DNA

organism: Mus musculus

source_name: liver

extract_protocol:
Genomic DNA was isolated from ~25 mg of frozen tissue using the Quick-DNA Miniprep Pus Kit (Zymo Research) following the manufacturer's protocol with an overnight proteinase K digestion. The amount and quality of extracted DNA was assessed by NanoDrop One (Thermo Fisher). The hMeDIP assay was performed using the MagMeDIP-seq Package (Diagenode, C02010040) with an antibody against 5hmC (Diagenode, C15200200-50). 1.2 µg of genomic DNA was sonicated into ~200 bp fragments using the S220 focused ultrasonicator (Covaris). To maximize IP yield, we processed the samples in duplicates and then pool before performing IPure purification. Prior to immunoprecipitation, samples were spiked with hydroxymethylated (Diagenode, C02040018) and unmethylated DNA controls.
Immunoprecipitated and 10% input DNA was used to prepare libraries according to the MagMeDIP-seq Package protocol except libraries were dual indexed using the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (New England Biolabs) followed by PCR amplification. The quantity and quality of individual libraries were verified on a BioAnalyzer DNA 1000 (Agilent) then pooled into equimolar amounts. The quantity of the pooled library was assessed using the NEBNext Library Quant Kit (New England Biolabs) and Qubit HS DNA kit (Thermo Fisher).

treatment_protocol: Old as treated group

tag: strain

tag: Sex

value: male

tag: age

value: 15 weeks

tag: tissue

value: liver

tag: antibody


title: Y2_liver input

value: female

value: 11 weeks


title: BLCA_Trp_152

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

value: palliative

value: Uro


title: Y3_liver input

value: 12 weeks


title: BLCA_Trp_151

tag: clinical tnm staging

tag: chemotherapy type

value: no

value: yes


title: BLCA_Trp_155

tag: lundtax rna-subtype

tag: lundtax ihc-subtype


title: BLCA_Trp_192

value: BASQ

tag: consensus classifier subtype

tag: rm-lymphnode


title: BLCA_Trp_154

value: GU

tag: rm-local

tag: rm-lung


title: BLCA_Trp_133

value: LumP

tag: rm-liver

tag: rm-bone


title: BLCA_Trp_134

tag: rm-other


title: O4_liver input

tag: strain

tag: Sex

value: 81 weeks


title: O3_liver input

tag: age

value: 79 weeks

tag: tissue


title: O1_liver input

value: 86 weeks

tag: antibody


title: Y4_liver_5hmC

value: male


title: O4_liver_5hmC


title: Y1_liver input


title: Y1_liver_5hmC


title: Y2_liver_5hmC


title: O2_liver_5hmC

value: 95 weeks


title: O1_liver_5hmC

value: liver


title: HCT116 cells, WT, Day 7, 400% biol rep 3, whole transcriptome

status: Public on Jul 17 2023

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Rd

department: Pharmacology

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing:
Paired-end demultiplexed fastq files were generated using bcl2fastq2 (Illumina, v2.17), from NovaSeq6000 SP4 reagent’s bcl files. Initial quality control was performed using FastQC v0.11.8 and multiqc v1.7. Fastq files were imported batch wise, trimmed for adapter sequences followed by quality trimming using CLC Genomics Workbench (CLC Bio, v23.0.3). The imported high-quality reads were mapped against gene regions and transcripts annotated by ENSEMBL v99 hg38 using the RNA-Seq Analysis tool v2.7 (CLC Genomics Workbench), only matches to the reverse strand of the genes were accepted (using the strand-specific reverse option). Differential gene expression analysis between the sample groups was done using the Differential Expression for RNA-seq tool v2.8, where the normalization method was set as TMM. Differential expression between the groups was tested using a control group, outliers were downweighed, and filter on average expression for FDR correction was enabled.
Assembly: The imported high-quality reads were mapped against gene regions and transcripts annotated by ENSEMBL v99 hg38 using the RNA-Seq Analysis tool v2.7 (CLC Genomics Workbench), only matches to the reverse strand of the genes were accepted (using the strand-specific reverse option).

source_name: Large intestine; Colon

growth_protocol: HCT116, colorectal cancer, cells were maintained in McCoy's 5A Media supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Trizol whole cell RNA extraction
Roche Kapa RNA HyperPrep Kits with RiboErase (HMR) (Catalog #KK8561) were used to generate the RNA libraries.
UMI adapters synthesized by IDT (Integrated DNA Technology) were used during the ligation process.

value: Large intestine; Colon

tag: cell line

tag: cell type

value: epithelial

tag: genotype

value: WT

tag: disease state

value: Carcinoma; Colorectal


title: HCT116 cells, WT, Day 7, 400% biol rep 2, whole transcriptome


title: E10.5 embryo, Ebf2-GFP enriched

status: Public on Jul 19 2023

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

description: Illumina NovaSeq 6000, Illumina HiSeq 4000

library_source: transcriptomic single cell

data_processing:
Reads from sequencing runs corresponding to a given sample were pooled and aligned using Cell Ranger software (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files containing feature names and cell barcodes and matrix files containing feature counts

source_name: Dorsal upper back

extract_protocol:
Embryos were collected at the specified timepoints and head and limbs were removed. The dorsal upper back portion was minced and digested with either 0.25% trypsin (Fisher) or Collagenase D: 6.1 mg ml−1 (Roche) and Dispase II: 2.4 mg ml−1 (Roche). Samples were placed at 37 °C with constant agitation (200 r.p.m), followed by quenching for 30 min with an equal volume of complete medium (DMEM/10% FBS). Dissociated cells were suspended using a P1000 pipette and filtered through a 100-μm filter. Cells were then pelleted at 400g for 4 min, and red blood cells were lysed in 155 mM NH4Cl, 12 mM NaHCO3 and 0.1 mM EDTA for 4 min. An equal volume of complete medium was added, and the cells were filtered through a 40-μm filter for downstream analyses. Isolated cells were suspended in FACS buffer (HBSS, 3% 0.45 µM filtered FBS; Thermo Fisher). Cells were stained in FACS buffer with antibodies for 1 h at 4 °C in the dark. Cells were washed twice with cold FACS buffer and sorted on a FACS Aria cell sorter (BD Biosciences) with a 100-μm nozzle. All compensation was performed at the time of acquisition in BD FACS DIVA software (8.0.1) using single stained cells and compensation beads. Single cells were flow sorted to isolate live (DAPI(−)) cells and remove debris. We enriched for mesenchymal, DM and brown adipose lineage cells as follows.  (i) E11.5 and E12.5 DM and mesenchymal cells based on cell surface expression of PDGFRa and/or LRIG1 [30% PDGFRa+, LRIG1(-) cells; 25% PDGFRa(-), LRIG1+ cells, 30% PDGFRa+, LRIG1+ cells, 15% PDGFRa(-), LRIG1(-) cells]. (ii) E13.5-E15.5 fibroblasts through selection of PDGFRa+ cells [75% PDGFRa+; 25% PDGFRa(-)]. (iii) E10.5, E14.5, and E15.5 brown adipose lineage cells based on expression of Early B Cell Factor-2 (Ebf2)-GFP [75% Ebf2-GFP+; 25% Ebf2-GFP(-)].
Single cell libraries were prepared  according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics) and sequenced on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000 by the University of Pennsylvania Next Gen Sequencing Core or CHOP Center for Applied Genomics Sequencing Core. Reads were aligned using Cell Ranger software from 10x Genomics.

value: Dorsal upper back

tag: developmental stage


title: O2_liver input

value: female


title: HCT116 cells, WT, Day 7, 400%  biol rep 1, whole transcriptome


title: Y3_liver_5hmC

value: 12 weeks


title: HCT116 cells, WT, Day 3, 50%  biol rep 1, whole transcriptome


title: HCT116 cells, WT, Day 3, 50% biol rep 3, whole transcriptome


title: HCT116 cells, WT, Day 3, 50% biol rep 2, whole transcriptome


title: mouse olfactory bulb, 50 μm-spot, 10x visium [MOB-10x-1]

status: Public on Jul 11 2023

city: shanghai

first: di

last: sun

address: pujian road 160

department: institute of molecular medicine

country: China

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
*library strategy: Spatial transcriptomic sequencing
The H&E image was used to accurately distinguish between tissues and backgrounds, with spots outside the tissue being removed. Spots with fewer than 50 observed genes (UMI > 2) were filtered out. And genes with counts in less than 10 spatial spots were discarded. Mitochondrial and ribosomal genes were also removed.
Giotto suite was used to perform spatial gene expression normalization, plotting, dimensionality reduction, spatial domains detection, and differential gene expression analysis. To incorporate spatial information into clustering, we utilized a hidden Markov random field (HMRF) model integrated with Giotto and allocated each cell to one of k spatial domains based on the accepted beta parameter. Furthermore, Giotto's findScanMarkers function was employed to annotate each spatial domain using identified markers.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: mouse olfactory bulb

extract_protocol:
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Dendrimeric DNA coordinate barcoding arrays capture spatial mRNAs of tissues with high efficiency"
Spatial transcriptomic sequencing by Decoder-seq, details in Methods "Amplification, library construction, and sequencing"

value: mouse olfactory bulb


title: T98G d9 HLA-DR+rep1

status: Public on Jul 07 2023

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

institute: Lund University

description:
T98G_29
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt

data_processing:
bcl2fastq2 v2.20 was used to convert BCL files generated by Illumina NextSeq to standard FASTQ file formats
Alignment to GRCm38.p5 was done using STAR v2.5.3a (Dobin A, Bioinformatics, 2013) with default settings except for the following ones: --sjdbOverhang 74 --quantMode GeneCounts.
The resulting gene counts were further processed and normalised using DESeq2 R package v1.20 (Love M, Genome Biology, 2014).
Assembly: hg38
Supplementary files format and content: count tables (.txt) and metadata tables (.txt)

growth_protocol: Cells were maintained in Dulbecco´s Eagle Modified (DMEM) RPMI-1640, Ham´s Nutrient F10 Mixture (F10) and Ham´s Nutrient F12 Mixture (F12) growth medium supplemented with 10% (v/v) FBS, Glutamax and Penicillin/Streptomycin solution (100U/ml penicillin, 100mg/ml streptomycin). All cells were cultured in humid environment at 37°C and 5% CO2. Human embryonic fibroblasts (HEF) were grown on plates coated with 0.1% gelatine and maintained in Dulbecco´s Eagles Modified growth medium supplemented with 10% FBS, Glutamax and 1% penicillin/streptomycin.

extract_protocol:
To profile reprogramming-induced transcriptomic changes in human cancer cell lines and human embryonic fibroblasts (HEF), total RNA from 3,000–5,000 FACS-sorted cells was extracted using TRIzol Reagent (ThermoFischer Scientific) following the manufacturer’s protocol. cDNA was transcribed with SMARTSeq v4 Ultra low input RNA kit (TakaraBio), amplified with 8 PCR cycles and purified with AMPure XP beads. The cDNA was quantified using High sensitivity DNA kit (Agilent) on Bioanalyzer 2100 (Agilent).
Sequencing library was prepared using Nextera XT DNA library preparation kit (Illumina) according to the manufacturer´s instructions. Briefly, cDNA was enzymatically tagmented, followed by indexing via 12 cycles of PCR. The library was normalized with beads, pooled and sequenced on Illumina NextSeq 500 platform (75bp paired-end).

treatment_protocol: Cells were sorted by FACS.

tag: tumor type

value: glioblastoma

tag: transduction

value: The cells were transduced with SFFV-hPIB-EGFP lentiviral particles to induce reprogramming (4h to overnight).

tag: time point

value: Cells were collected 9 days after viral transduction

tag: sorted cells

value: HLA-DR+

tag: agent


title: T98G d9 HLA-DR+rep3

description:
T98G_31
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: T98G d3 CD45+HLA-DR+ rep2

description:
T98G_13
counts.Time.Course.txt
counts.VPA.txt

value: Cells were collected 3 days after viral transduction


title: T98G d3 CD45+HLA-DR+ rep1

description:
T98G_12
counts.Time.Course.txt
counts.VPA.txt


title: U2OS, no treatment, rep3, batch2

status: Public on Jun 22 2023

city: Shanghai

first: Qinying

last: Ye

address: Haike Road #230

institute: ShanghaiTech University

data_processing:
Trim galore was used to remove adaptor sequences of ATAC-seq data.
Cleaned data were then aligned to human genome (hg39) with bowtie2 (--very-sensitive -X 2000).
Samtools was used for removing duplicated and mitochondrial reads in aligned bam files.
Peak calling was performed with Genrich.
Assembly: hg39
Supplementary files format and content: bigwig

source_name: Bone

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% P/S with 5% CO2 at 37℃

extract_protocol:
ATAC-seq libraries were generated from approximately 100,000 cell nuclei with the TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme TD501)
ATAC-seq was performed as described previously with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501). Briefly, 50,000 cells were collected at 500×g for 5 min and resuspended in 50μl cold ATAC-seq lysis buffer and incubated on ice for 10min. Following centrifugation at 500×g at 4°C for 5 min, cells were pelleted and resuspended in 50μl transposition mix and then incubated at 37°C. The reaction was purified with VAHTS DNA Clean Beads and PCR amplified for 15 cycles. Purified ATAC-seq libraries were sequenced on the NovaSeq platform.

treatment_protocol: treat with 1.5ug/ml Adriamycin or 100 uM Etopside 4h

value: Bone

value: Epithelial

tag: treatment

value: no treatment

tag: batch


title: U2OS, treat with Etopside, rep3, batch2

value: treat with Etopside


title: U2OS, treat with Etopside , rep4, batch2


title: O3_liver_5hmC

tag: strain

value: 79 weeks

value: liver


title: HCT116 cells, WT, Day 5, 250%  biol rep 1, whole transcriptome

value: Large intestine; Colon

value: epithelial

value: WT


title: U2OS, no treatment, rep4, batch2


title: HCT116 cells, WT, Day 5, 250% biol rep 3, whole transcriptome

value: Carcinoma; Colorectal


title: Breast tissue Emseq Replicate 1

status: Public on Jun 19 2023

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

data_processing:
illumina adapter sequence was trimmed trim_galore
reads were mapped to human genome using bowtie2
C to T transition was extracted using samtools mpileup
regional methylation was calculated using custom scripts based on the C to T transition rate
SNP was identified using gatk
Assembly: hg38
Supplementary files format and content: custom format with regional methylation level
Library strategy: EM-seq

source_name: Breast

extract_protocol:
genomic DNA isolated from the GM12878 cell line by Coriell Institute
RIMSseq with or without exome Target enrichment

value: Breast


title: T98G d9 HLA-DR+rep2

description:
T98G_30
counts.Cell.Lines.txt
counts.Time.Course.txt
counts.VPA.txt


title: HCT116 cells, WT, Day 5, 250% biol rep 2, whole transcriptome


title: T98G d3 CD45+HLA-DR+ rep3

description:
T98G_14
counts.Time.Course.txt
counts.VPA.txt


title: NA12878 RIMSseq WGS

data_processing:
illumina adapter sequence was trimmed trim_galore
reads were mapped to human genome using bowtie2
C to T transition was extracted using samtools mpileup
regional methylation was calculated using custom scripts based on the C to T transition rate
SNP was identified using gatk
Assembly: hg38
Supplementary files format and content: custom format with regional methylation level
Library strategy: WGS

value: lymphoblastoid


title: T98G d3 CD45+HLA-DR+ rep4

description:
T98G_15
counts.Time.Course.txt
counts.VPA.txt

value: glioblastoma


title: NR2F2 KD HMVEC-L 2

status: Public on May 31 2023

city: Bethesda

first: Gabriela

middle: A

last: Ferreyra

state: MD

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

description: HMVEC-L  NR2F2 KD  Gene expression data

hyb_protocol: Fragmented labeled cRNA (65 ug per sample) were hybridized for 16 hr at 45C on PrimeView Human Gene  Expression  Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400 following manufacturer protocols.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw data were normalized using RMA in Transcriptome Analysis Console (TAC) 4.0 and presented as log transformed signal intensity. The probe set results were all within bounds.

label: Biotin

source_name: HMVEC-L

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNAusing genechip 3' IVT express kit (Affymetrix) following manufacturer protocol

growth_protocol: Human lung microvascular endothelial cells (LMVECs; Lonza, Walkersville, MD) were grown in endothelial cell growth medium (EGM-2 or EGM-2MV; Lonza.Twenty-four hours prior to transfection, cells were seeded onto 35 mm plates.

extract_protocol: 48 hours after tranfection total RNA was isolated  using the RNeasy Mini Kit (Qiagen) following manufacturer protocols and  quality was evaluated using RNA 6000 Nano LabChip

treatment_protocol: Cells were transiently transfected with 10 nM of control siRNA or siRNA against NR2F2 using Dharmafect 1 (Dharmacon).

tag: gender

value: female


title: NR2F2 KD HMVEC-L 5

description: HMVEC-L  NR2F2 KD  Gene expression data


title: NR2F2 KD HCAEC 5

description:
GAF191010_COUPTF2 _ #5
HCAEC  NR2F2 KD  Gene expression data

source_name: HCAEC

growth_protocol: Normal human coronary artery endothelial cells (CAECs; Lonza, Walkersville, MD) were grown in endothelial cell growth medium (EGM-2 ; Lonza).Twenty-four hours prior to transfection, cells were seeded onto 35 mm plates.

treatment_protocol: Cells were transiently transfected with 10 nM of control siRNA, siRNA against NR2F2 or siRNA against BMPR2 or DKK1 using Dharmafect 1 (Dharmacon).


title: Control for HMVEC-L 2

description: HMVEC-L  KD control Gene expression data


title: Control for HMVEC-L 1


title: NR2F2 KD HMVEC-L 4

description: HMVEC-L  NR2F2 KD  Gene expression data


title: Control for HMVEC-L 3


title: NR2F2 KD HCAEC 2

description:
GAF191010_COUPTF2 _ #2
HCAEC  NR2F2 KD  Gene expression data


title: Control for HMVEC-L 4


title: NR2F2 KD HMVEC-L 1

description: HMVEC-L  NR2F2 KD  Gene expression data


title: Control for HMVEC-L 5


title: NR2F2 KD HCAEC 1

description:
GAF191010_COUPTF2 _ #1
HCAEC  NR2F2 KD  Gene expression data


title: Breast tissue Emseq Replicate 2


title: NR2F2 KD HMVEC-L 3

description: HMVEC-L  NR2F2 KD  Gene expression data


title: Input limb

status: Public on May 25 2023

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Assembly: mm10

source_name: AR and H3K4me2 ChIP-seq from limb and bulbocavernosus muscles.

extract_protocol: P2618 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from --- ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + --- cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: age

value: 9 weeks


title: NR2F2 KD HCAEC 3

description:
GAF191010_COUPTF2 _ #3
HCAEC  NR2F2 KD  Gene expression data


title: NR2F2 KD EA.hy926 4

description:
GAF171108_COUPTF2_KD_4
EA.hy926 NR2F2 KD  Gene expression data

source_name: EA.hy926 cells

growth_protocol: Human EA.hy926 cells (ATCC, Manassas, VA) were grown in DMEM supplemented with 10% heat-inactivated FBS (Life Technologies, Grand Island, NY). Twenty-four hours prior to transfection, cells were seeded onto 35 mm plates.

treatment_protocol: Cells were transiently transfected with 10 nM of an siRNA control (Dharmacon, Lafayette, CO) or siRNA against NR2F2 (Life Technologies) using lipofectamine RNAiMAX (Life Technologies).

value: somatic cell hybrid


title: Control for HCAEC 4

description:
GAF191010_Control_#4
HCAEC control Gene expression data


title: Control for HCAEC 3

description:
GAF191010_Control_#3
HCAEC control Gene expression data


title: NR2F2 KD HCAEC 4

description:
GAF191010_COUPTF2 _ #4
HCAEC  NR2F2 KD  Gene expression data


title: Control for EA.hy926 4

description:
GAF171108_COUPTF_Ctrl_4
EA.hy926 KD control Gene expression data


title: NR2F2 KD EA.hy926 1

description:
GAF171108_COUPTF2_KD_1
EA.hy926 NR2F2 KD  Gene expression data


title: NR2F2 KD EA.hy926 2

description:
GAF171108_COUPTF2_KD_2
EA.hy926 NR2F2 KD  Gene expression data


title: Control for EA.hy926 3

description:
GAF171108_COUPTF_Ctrl_3
EA.hy926 KD control Gene expression data


title: Control for EA.hy926 1

description:
GAF171108_COUPTF_Ctrl_1
EA.hy926 KD control Gene expression data


title: AR limb


title: H3K4me2 limb


title: NR2F2 KD EA.hy926 3

description:
GAF171108_COUPTF2_KD_3
EA.hy926 NR2F2 KD  Gene expression data


title: Control for HCAEC 1

description:
GAF191010_Control_#1
HCAEC control Gene expression data


title: Control for HCAEC 2

description:
GAF191010_Control_#2
HCAEC control Gene expression data


title: AR-KO-1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
We aligned these reads to the mm10 build of the mouse genome using Homer
The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR
Assembly: mm10

molecule: polyA RNA

source_name: RNA isolated from muscle tissues from Wild type mice and from mice in which AR (Androgen receptor) or GR (glucocorticoid recptor) are selectively ablated in mature skeletal muscle myofibers.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA-Seq libraries were generated from 700ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: tissue

value: gastrocnemius muscles

value: ARskm-/y


title: AR-KO-4


title: WT-4 (AR control)

value: Control


title: AR-KO-2


title: Jurkat-5F9_HiC_Rep1

status: Public on May 01 2023

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

data_processing:
Raw reads were processed using the HiC-Pro 3.0 pipeline with default parameters.
Results were converted to Juicer (.hic) format for further processing and visualization.
Assembly: Hg38 + NL4-3
Supplementary files format and content: .hic, contact matricies at default resolutions for each sample

source_name: Blood

growth_protocol: Jurkat T cells were grown in R10 (RPMI + 10% FBS) at high viability, passaged 1:10 twice weekly.

extract_protocol:
DNA bound to antibody-beads was isolated using a DNA clean and concentrator kit (Zymo Biosciences).
Biotin bound DNA was selecte using streptavadin beads, which were treated with TDE1 (Illumina) to generate a library.

treatment_protocol: Cells were fixed in 2% EM grade PFA for 10 minutes at room temperature with shaking, quenced with 2M glycine to a final concentration of 0.125M, lysed in HiC lysis buffer on ice for 30 minutes, washed twice with HiC lysis buffer, resuspended in an SDS containing buffer. Remaining nuclei were treate with MboI restriction digest over night, followed by ligation at room temperature. Nuclei were then sheered in a Covaris S220 militube. Sheared samples were clarified by centrifugation, precleared with protein A beads, incubated with the antibody overnight, and then collected with additional protein A beads.

value: Blood

value: Jurkat Cm6

value: CD4 T cell lymphoma

tag: antibody


title: WT-2 (AR control)


title: WT-3 (AR control)


title: Control for HCAEC 5

description:
GAF191010_Control_#5
HCAEC control Gene expression data


title: AR-KO-3


title: WT-1 (AR control)


title: Jurkat-1G2_HiC_Rep1

tag: cell line


title: Jurkat-1D7_HiC_Rep1

tag: cell type


title: Jurkat-1D7_HiC_Rep2


title: Jurkat-uninfected_HiC_Rep2


title: Jurkat-uninfected_HiC_Rep1


title: Control for EA.hy926 2

description:
GAF171108_COUPTF_Ctrl_2
EA.hy926 KD control Gene expression data


title: Jurkat-1D7_H3K27AcHiChiP_Rep1

value: Abcam, ab4734


title: Jurkat-8B10_H3K27AcHiChiP_Rep2

value: Abcam, ab4732


title: Jurkat-1G2_H3K27AcHiChiP_Rep1

value: Abcam, ab4729


title: Jurkat-1D7_H3K27AcHiChiP_Rep2

value: Abcam, ab4735


title: Jurkat-8B10_H3K27AcHiChiP_Rep1

value: Abcam, ab4731


title: Jurkat-uninfected_H3K27AcHiChiP_Rep1

value: Abcam, ab4733


title: Hi-C_U2OS, treat with Adriamycin , rep1

status: Public on Jan 11 2023

data_processing:
Sequenced reads were trimmed for adaptor sequence
using Hicexplorer to create cool file
Assembly: hg38
Supplementary files format and content: cool

extract_protocol: Hi-C experiments was perfomed according to Hi-C 2.0

treatment_protocol: treat with 1.5ug/ml Adriamycin 4h

value: Bone

value: Epithelial

tag: genotype

value: WT

value: treat with Adriamycin


title: Hi-C_U2OS, treat with Adriamycin, rep2


title: Hi-C_U2OS, no treatment, rep2

value: no treatment


title: Hi-C_U2OS, no treatment, rep1


title: RNA-seq_U2OS, treat with Etopside , rep2

data_processing:
The reference genomes (Homo sapiens GRCh38) and the annotation file were downloaded from ENSEMBL database
HISAT2 v2.1.0 was used for building the genome index, and clean data was then aligned to the reference genome.
The read count for each gene in each sample was counted by Subread v2.0.0 featureCounts function.
Differentially expressed genes were identified using DESeq2 v1.30.1. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files include counts values for each sample

extract_protocol:
Total RNA was extracted using Trizol (Vazyme)
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: treat with 1.5 ug/ml Adriamycin or 100 uM Etopside 4h

value: treat with Etopside


title: RNA-seq_U2OS, no treatment, rep2


title: RNA-seq_U2OS, treat with Adriamycin , rep1


title: RNA-seq_U2OS, treat with Etopside, rep1


title: RNA-seq_U2OS, treat with Adriamycin, rep2


title: U2OS, treat with Etopside , rep2


title: RNA-seq_U2OS, no treatment, rep1


title: U2OS, treat with Etopside, rep1


title: U2OS, no treatment, rep2


title: U2OS, treat with Adriamycin , rep1


title: Dialout_2kG_2PMDox2_6

status: Public on Nov 01 2022

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

institute: Stanford University

description:
Illumina Nextseq 500, Illumina NovaSeq 6000
Dialout library to link CBCs to guides

data_processing:
Fastq files were de-multiplexed by index primer
Demultiplexed fastq files for the same sample, with the same index, and from the same sequencing run were concatenated
1) Note, for each scRNAseq library, there were four 10xGenomics index primers for each library, designated SAMPLEID_a _b _c & _d.
1) All scRNAseq libraries, except "scRNAseq_2kG_2PMDox1_6", were sequenced on a 2nd NovaSeq run, and fastq files from those runs are designated "_NS2_"
1) Fastq files were uploaded to the 10X genomics server to run CellRanger (which maps reads to the human genome, assigns reads to the distinct CellBarcodes (CBCs) for each droplet, and counts reads in each droplet for all transcripts in the human genome.
1) CellRanger distinguishes droplets with true cells from droplets with debris or ambient RNA, and generates a matrix of genes by CBCs (the filtered feature barcode matrix), which was used for downstream analysis.
2) Dialout libraries linking CBCs to guides were sequenced to saturation (~40x coverage) using either Illumina NextSeq (files w/o ".2") or Novaseq (files with ".2" in the name).
2) Dialout read 1 covers the 10x Genomics barcode/CBC and UMI. Read 2 covers 24 invariant bases of U6 promoter sequence before reading into the guide protospacer sequence
For the Supplementary file: _Dialout_guides_per_CBC.txt, 1) dialout reads with fewer than 4 exact duplicate were removed to reduce noise from PCR chimeras, 2) for each cell barcode x guide combination, the number of distinct Unique Molecular Identifiers (UMIs) was counted. The guide with the highest number of UMIs, plus 2nd, 3rd and 4th place guides were recorded.
For the Supplementary file: _aggregated.2kG.library.mtx.gene_x_cell.RDS.gz. Matrix files for each sample were merged, and assigned column names:  TARGETGENE:GUIDESEQUENCE:CBC-SAMPLNAME & rows as SYMBOL:ENSEMBLID, and then subset to only those CBCs called as singlets (in the calls.csv files for each sample, and also, across all samples, in _Dialout_guides_per_CBC.txt).
For the Supplementary files: _ALL_{log2fcs,Pvalues}_dup4_s4n3.99x.txt, we applied edgeR to the RDS genes x singlets table (with sample ID/10X lane number as a covariate), to detect differentially expressed genes for singlet cells with guides to each target (up to 15 guides) versus singlet cells with non-targeting or safe targeting guides. Individual edgeR results tables for each contrast were then aggregated to give genes x perturbation tables of log2 fold changes & p.values, respectively.
For the remaining supplemental files: To identify sets of genes that are co-expressed across single cells in a dataset, we applied consensus non-negative matrix factorization (NMF) (Kotliar, D. et al. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq. Elife 8, (2019).) to the Genes x Singlet cells counts matrix. NMF decomposes an input cell x gene read count matrix (X) into (i) a cell x components matrix (W) and (ii) a component x gene matrix (H), such that X = W • H. The cell x component matrix W represents the contribution of each component to the cell’s transcriptional profile, and the component x gene matrix H encodes information about gene expression programs, e.g. housekeeping and cell cycle pathways. Consensus NMF performs this analysis 100 times, to identify components that are stable regardless of starting conditions. Based on several metrics, we chose 60 for the number of components (K).
Supplementary file: 2kG.library.usages.k_60.dt_0_2.consensus.txt, is the consensus Cell x Components matrix, from cNMF.
Supplementary file: 2kG.library.spectra.k_60.dt_0_2.consensus.txt, is the consensus Components x Genes matrix, from cNMF.
Supplementary file: 2kG.library.gene_spectra_score.k_60.dt_0_2.txt, is a variant of the Components x Genes matrix that identifies genes that are most representative of each component as those that have a high specificity z-score (zero if that gene has the same weight across all components, and high if that gene is weighted strongly only for one component). We refer to genes with high specificity scores for a component as a "program".
Supplementary file: 2kG.library_MAST_DEtopics.txt, is a Perturbation x Program matrix measuring the association of cells with guides to a given target with specific programs, using Model-based Analysis of Single Cell Transcriptomics Package (MAST, Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015)). to compare the expression of each program in cells carrying gRNAs targeting a given gene vs cells carrying control gRNAs (safe-targeting and negative control guides), including 10X lane as a covariate to account for batch effects. Values are MAST scores.
Supplementary fil: Table.S2.X.AllMASTStatisticalTestResults.txt, is a second table of MAST outputs for Perturbation effects on programs, including log2 fold changes (of Program gene expression with each perturbation), p. values and FDRs (either across all 60 programs, or across all 60x2357perturbations (experiment wide FDR)). Program IDs are given as K for the analysis (always 60) underscore Program # (e.g. 60_15 is Program 15).
Assembly: hg19
Supplementary files format and content: Matrix files (.mtx). Filtered feature barcode matrices with rows=genes and columns=cell barcodes, and values=read counts, for all high quality cells called by CellRanger. Includes all reads from each sample (both Novaseq runs). To read, in R, do: library(Matrix);mymatrix=readMM("filename")
Supplementary files format and content: Barcodes files (barcodes.tsv). The list of cell barcodes (CBCs) for high quality cells. Use for column names of the extracted matrix file.
Supplementary files format and content: Features files (features.tsv). Tab delimited table of gene names (symbols & ENSEMBL gene numbers) quantified by CellRanger. User for row names of the extracted matrix file. Features should be the same for all sample matrices.
Supplementary files format and content: Singlet calls files (calls.tsv). Tab delimited table, with header row, with columns: CBC_10x (cell barcode, in the same order as barcodes.tsv), Guide (guide protospacer sequence), Genec(gene/target of top guide), UMI_count (# of UMIs for guide with most UMIs), Good_singlet (1 if cell is a singlet, as defined by having >=4 UMIs for the top guide and <=4x fewer than this for the next most frequent guide), Multiplet (1 if singlet, 2, 3 or 4 for doublet, triplet or quadruplet, 0 if no guide was assigned to the cell (e.g. 3 or fewer UMIs for the top guide, including entries for CBCs w/ no guides detected).
_Dialout_guides_per_CBC.txt, is tab delimited text recording dialout guide reads for each CellRanger-called cell CBC. Reads that were duplicated less than 4 times were removed from the analysis, to reduce the influence of PCR chimeras generated in Dialout library construction, after which counts of distinct UMIs associated with each guide detected for each CBC were made. Column IDs: gene_symbol=Target ID/gene symbol for top guide, X10x_cbc (10x Barcode for droplets called as containing cells, with an extension indicating lane: 1 to 6 for 11AMDox samples 1 to 6, 7 to 13 for 2PMDox1 samples 1 to 7, and 14 to 20 for 2PMDox2 samples 1 to 7),  guides_per_cbc= number of guide reads detected for that CBC, umis_per_cbc=total distinct UMIs in guide reads per CBC, max_umi_ct=the number of distinct UMIs for the guide with the most UMIs, guide_w_max=sequence of that guide, X2nd_place_umi_ct, X3rd_place, X4th_place= UMI counts for guides with the 2nd, 3rd or 4th most UMIs. CBCs with 4 or more UMIs for the top guide and less than or equal to 1/4 of this for the next most frequent guide were considered to be singlets (1 cell & 1 guide/droplet) for further analysis.
_aggregated.2kG.library.mtx.gene_x_cell.RDS.gz. RDS format genes x cell matrix (genes=rows, CBCs=columns) for all cells called as singlets (>=4 UMIs for top guide & <=1/4 this for 2nd to top guide). Column names are formatted as   TARGETGENE:GUIDESEQUENCE:CBC-SAMPLNAME & rows as SYMBOL:ENSEMBLID. To access, gunzip, then, in R, do: readRDS("_aggregated.2kG.library.mtx.gene_x_cell.RDS")
_ALL_log2fcs_dup4_s4n3.99x.txt (tab delimited). Differential expression log2 fold changes for all cells with guides to a given target versus all cells with non-targeting or safe targeting guides (by edgeR, using lane number as a covariate)
_ALL_Pvalues_dup4_s4n3.99x.txt (tab delimited). Differential expression raw p.values for all cells with guides to a given target versus all cells with non-targeting or safe targeting guides (by edgeR, using lane number as a covariate)
2kG.library.usages.k_60.dt_0_2.consensus.txt, is the consensus Cell x Components matrix, from consensus non-negative matrix factorization (cNMF, see data processing steps, below)..
2kG.library.spectra.k_60.dt_0_2.consensus.txt, is the consensus Components x Genes matrix, from cNMF.
2kG.library.gene_spectra_score.k_60.dt_0_2.txt, is a variant of the Components x Genes matrix that identifies genes that are most representative of each component as those that have a high specificity z-score (zero if that gene has the same weight across all components, and high if that gene is weighted strongly only for one component). We refer to the set of genes with high specificity scores for a component as a "program".
2kG.library_MAST_DEtopics.txt, is a Program x Perturbation matrix measuring the association of cells with a given perturbation (guides to a given target) with specific programs, using Model-based Analysis of Single Cell Transcriptomics Package (MAST, Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015)). MAST was used to compare the expression of each program in cells carrying gRNAs targeting a given gene vs cells carrying control gRNAs (# safe-targeting and negative control guides), including 10X lane as a covariate to account for batch effects. Values are MAST scores.
Table.S2.X.AllMASTStatisticalTestResults.txt, is a second table of MAST outputs for Perturbation effects on programs, including log2 fold changes (of Program gene expression with each perturbation), p. values and FDRs (either across all 60 programs, or across all 60x2357 perturbations (experiment wide FDR)). Program IDs are given as K for the analysis (always 60) underscore Program # (e.g. 60_15 is Program 15).

source_name: Vascular

growth_protocol: Telomerase-immortalized human aortic endothelial cells (TeloHAEC) were purchased from ATCC, and grown in Lifeline VEGF endothelial cell media with 1x Penn/Strep. TeloHAEC were plated at a density of 0.5-1.0 x 10^6 cells per 10cm plate and split before reaching 4 x 10^6/plate (3 to 4 days).

extract_protocol:
Cells were "superloaded" at 150,000 cells per 10X Chromium controller lane, on 20 lanes (for a total of 3 million cells), and scRNA-seq and dialout libraries prepared as described below.
1) scRNA-seq libraries were prepared using 3’ scRNA-seq V3 kits (10X Genomics), according to manufacturer instructions. Note that the 10x Indexes were a mix of 4 oligos for each library (each starting with a different base to avoid sequencing biases). Thus each scRNAseq library has 4 fastq files (denoted _a, b, c & d).
2) From the initial amplified cDNA, we used a two stage PCR protocol to generate “dialout” libraries, for each lane. Because the CROP-seq vector expresses a PolII polyadenylated transcript that ends just downstream of the guide sequence, the dialout libraries identify the sgRNA sequences associated with each droplet. In several cases multiple libraries were made for a sample. Libraries without ".2" in their name (e.g. Dialout_2kg_11AMDox_4_ATTACTCG) were sequenced on an Illumina NextSeq machine. Others, e.g. "Dialout_2kg_11AMDox_6.2_CGCTCATT" were sequenced on an Illumina Novaseq machine, together with scRNA-seq libraries.

treatment_protocol:
1) To create the TeloHAEC CRISPRi line, cells were transduced with lentiviral vectors containing 1) dox-inducible (tetracycline operator controlled) dCas9-KRAB-BFP (CRISPRi machinery, which targets epigenetic repressors to efficiently silence enhancers or promoters58–60) and 2) rtTA (tetracycline activator) with a hygromycin marker. After hygromycin selection (250ug/ml for 4 days), cells were treated with 1 ug/ml doxycycline (dox, a stable tetracycline analogue) for 3 days before FACS sorting for the top 15% of BFP positive cells, and after a period in culture without dox, treated again with dox and re-sorted.
2) For Perturb-seq CRISPRi TeloHAEC were transduced with a Lentivirus library carrying guide RNAs against the promoters of 2885 genes (15 guides per target + 1000 control guides, for 36,880 total guides),  in a CROP-opti-blast backbone, selected for blasticidin resistance (15ug/ml) for 3 to 4 days, and then treated for 5 days with 2ug/ml doxycycline to induce the CRISPRi machinery.

value: Vascular

value: CRISPRi TeloHAEC

value: Endothelial

value: Transduced with 36880-guide Perturb-seq library

tag: batch &_sample_number

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 6


title: Dialout_2kG_2PMDox2_7

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 7


title: Jurkat-5F9_H3K27AcHiChiP_Rep1

value: Blood

value: Jurkat Cm6

value: CD4 T cell lymphoma

value: Abcam, ab4730


title: Dialout_2kG_2PMDox2_2

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 2


title: Dialout_2kG_2PMDox2_3

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 3


title: Dialout_2kG_2PMDox2_1

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 1


title: Dialout_2kG_2PMDox1_7

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 7


title: Dialout_2kG_2PMDox2_5

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 5


title: Dialout_2kG_2PMDox2_4

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 4


title: Dialout_2kG_2PMDox1_5

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 5


title: Dialout_2kG_2PMDox1_6

value: Vascular

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 6


title: Dialout_2kG_2PMDox1_1

value: CRISPRi TeloHAEC

value: Endothelial

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 1


title: Dialout_2kG_2PMDox1_3

value: Transduced with 36880-guide Perturb-seq library

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 3


title: Dialout_2kG_2PMDox1_4

description: Dialout library to link CBCs to guides

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 4


title: Dialout_2kG_11AMDox_5

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 5


title: Dialout_2kG_2PMDox1_2

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 2


title: Dialout_2kG_11AMDox_6

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 6


title: Dialout_2kG_11AMDox_3

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 3


title: U2OS, no treatment, rep1

value: Bone

value: Epithelial

value: WT

value: no treatment


title: Dialout_2kG_11AMDox_2

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 2


title: U2OS, treat with Adriamycin, rep2

value: treat with Adriamycin


title: Dialout_2kG_11AMDox_1

value: Vascular

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 1


title: scRNAseq_2kG_2PMDox2_6

description: 3' mRNA scRNAseq

value: CRISPRi TeloHAEC

value: Endothelial

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 6


title: scRNAseq_2kG_2PMDox2_7

description: 3' mRNA scRNAseq

value: Transduced with 36880-guide Perturb-seq library

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 7


title: scRNAseq_2kG_2PMDox2_4

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 4


title: scRNAseq_2kG_2PMDox2_5

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 5


title: scRNAseq_2kG_2PMDox2_2

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 2


title: scRNAseq_2kG_2PMDox2_3

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 3


title: scRNAseq_2kG_2PMDox2_1

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #3, 2nd set of lanes for cells collected at 2 PM (base name "2PMDox2"):Lane number 1


title: Dialout_2kG_11AMDox_4

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 4


title: scRNAseq_2kG_2PMDox1_7

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 7


title: scRNAseq_2kG_2PMDox1_1

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 1


title: scRNAseq_2kG_2PMDox1_2

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 2


title: scRNAseq_2kG_2PMDox1_3

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 3


title: CCOs differentiation, day 21

status: Public on Oct 10 2022

city: Singapore

first: Boon Seng

last: SOH

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: A*STAR

description: single cell RNA-Seq

data_processing:
Primary analysis of scRNA-Seq data to generate gene by cell count matrix was performed by using CSI NGS Portal (https://csibioinfo.nus.edu.sg/csingsportal) with Cell Ranger pipeline (10x Genomics).
Downstream analysis including cell filtering, data normalization and clustering analysis were carried out using R library Seurat v3.2.1.
The cells were filtered based on their number of gene features and percentage of mitochondrial genes. The threshold used for gene features is between 2000 to 7500, and less than 10% mitochondrial gene expression. Genes to be used in analysis were expressed in at least 10 cells.
LogNormalize function was used to normalize gene expression within each cell, by dividing the counts of each gene by the total counts in the cell, followed by a scale factor multiplication of 10,000 and then a natural log-transform of the result.
Variable genes were identified using the FindVariableFeatures function and used to perform a principal component (PC) analysis using RunPCA. Within all the PCs, top 20 PCs were used to do Uniform Manifold Approximation and Projection (UMAP) analysis.
Clustering was carried out using the FindClusters function. Gene expression differences between the various cell clusters was carried out using FindAllMarkers function, filtering out genes expressed in less than 25% of cells in the compared clusters, and selecting genes with differential expression levels above 25%.
Finally, clusters were identified by going through the list of differentially expressed genes and comparing the highly expressed genes with published literature.
Genome_build: hg19
Supplementary_files_format_and_content: CCO_Project_merged_UMI_counts.txt containing counts, CCO_Project_clusters_and_markers.xlsx containing table of top 100 differentially upregulated genes between clusters identified from the single cell RNA sequencing data across the three timepoints of organoids.

source_name: H7 cell line

growth_protocol: Cells were grown in cardio-sphere growth medium (CGM) and RPMI-1640 Medium (1x) (Hyclone) supplemented with B27

extract_protocol:
Organoids of various ages (Day 8, Day 14, and Day 21) were dissociated using TrypLE (ThermoFisher, 12604013). Organoids were washed once with 1xPBS and then incubated in TrypLE solution at 37 °C for 10 to 15 mins. Subsequently, organoids were dissociated into single cells by gentle pipetting using wide-bore tips. Cell solutions were then diluted with 1xPBS and passed through 40um strainer (Falcon, 352340) to remove any undissociated cell clumps. Cells were then centrifuged down to remove TrypLE and washed once with 1xPBS (300 × g for 5 min at 4 °C). Pellets were eventually re-suspended in 1xPBS and stored on ice.
Cell viability and concentration were checked using an automated cell counter (BioRad). Cell stocks were diluted to around 1000 cells/uL with 1xPBS before downstream steps. Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 was used to construct the library.  For all library preparation, recovery of 6000 cells was aimed. Briefly, cells together with Gel Bead-in-Emulsions (GEM)-reverse transcription reagents, and GEM beads were loaded to the 10xChip, in which individual cells are captured, lysed, reverse transcribed and barcoded. Subsequently, barcoded cDNA was amplified and used for library construction. Libraries which passed the quality control were then sent out for sequencing.
10x Genomics single-cell RNA Library preparation and sequencing

value: Organoid

tag: time


title: scRNAseq_2kG_11AMDox_6

description: 3' mRNA scRNAseq

value: Vascular

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 6


title: scRNAseq_2kG_11AMDox_3

description: 3' mRNA scRNAseq

value: CRISPRi TeloHAEC

value: Endothelial

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 3


title: scRNAseq_2kG_11AMDox_4

description: 3' mRNA scRNAseq

value: Transduced with 36880-guide Perturb-seq library


title: scRNAseq_2kG_2PMDox1_5

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 5


title: scRNAseq_2kG_11AMDox_2

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 2


title: scRNAseq_2kG_11AMDox_5

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 5


title: scRNAseq_2kG_11AMDox_1

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #1, for cells collected at 11 AM (base name "11AMDox"):Lane number 1


title: CCOs differentiation, day 8

description: single cell RNA-Seq


title: CCOs differentiation, day 14

description: single cell RNA-Seq


title: 211130-GW18-Post-HPC

status: Public on Oct 07 2022

city: Los Angeles

first: Chongyuan

last: Luo

address: 695 Charles E Young Dr S

department: Human Genetics

institute: UCLA

data_processing:
Sequencing reads were first demultiplexed by matching the first 8 base pairs of R1 reads to the predefined well barcodes (https://github.com/luogenomics/demultiplexing). Demultiplexed reads were trimmed to remove sequencing adaptors using Cutadapt 1.18 with the following parameters in paired-end mode: -f fastq -q 20 -m 50 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. 18 bp and 10 bp were further trimmed from the 5’- and 3’- end of R1 reads, respectively. 10 bp were trimmed from both 5’- and 3’- ends of R2 reads. sn-m3C-seq reads were mapped to hg38 reference genome using a modified Taurus-MH package (https://github.com/luogenomics/Taurus-MH) (18). Briefly, each read end (R1 or R2) is mapped separately using Bismark with Bowtie1 with read1 as complementary (always G to A converted) and read2 (always C to T converted) as original strand. After the first alignment, unmapped reads are retained and split into 3 pieces by 40bp, 42bp, and 40bp resulting in six subreads (read1 and read2). The subreads derived from unmapped reads were mapped separately using Bismark Bowtie1. All aligned reads are merged into BAM using Picard SortSam tool with query names sorted. For each fragment, the outermost aligned reads are chosen for the chromatin conformation map generation. The chromatin contacts with both ends mapped to the same positions were considered duplicates and removed for further analysis. Duplicates reads were removed from BAM files using Picard MarkDuplicates tool before the generation of allc files using Allcools bam-to-allc tool (https://lhqing.github.io/ALLCools/).
Assembly: hg38
Supplementary files format and content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines). contact files are tab delimited files of contacts, columns in these files are: 1 - chromosome of first sequence, 2 - position of first sequence, 3 - chromosome of second sequence, 4 - position of second sequence, 5 strand of the first sequence , 6 strand of the second sequence .
Library strategy: sn-m3C-seq

source_name: hippocampus

extract_protocol: For pre-natal brain samples, sn-m3C-seq was performed without the labeling of neuronal nuclei using anti-NeuN antibody, whereas post-natal samples were labeled by anti-NeuN antibody during the nuclei isolation procedure. For sn-m3C-seq performed without labeling, frozen powder of brain tissue was resuspended in 10 mL of DPBS with 2% formaldehyde and incubated at room temperature for 10 mins with slow rotation. The crosslinking reaction was quenched with 1.17 mL of 2M Glycine for 5 mins at room temperature. Crosslinked tissue sample was pellet by centrifugation with 2,000 x g for 10 mins at 4°C. The same centrifugation condition was used to pellet nuclei throughout the sn-m3C-seq procedure. The pellet was resuspended in 3mL of NIBT (10mM Tris-HCl pH=8.0, 0.25M Sucrose, 5mM MgCl2, 25mM KCl, 1mM DTT, 0.1% Triton X-100 and 1:100 Protease Inhibitor Cocktail (Sigma #P8340). The resuspended tissue sample was dounced with a dounce homogenizer (Sigma #D9063) for 40 times with a loose pestle and 40 times with a tight pestle. The lysate was mixed with 2 mL of 50% Iodixanol (prepared by mixing OptiPrep™ Density Gradient Medium (Sigma #D1556) with diluent (120 mM Tris-Cl pH=8.0, 150 mM KCl and 30mM MgCl2) with a volume  ratio of 5:1). The lysate was gently layered on top of 25% Iodixanol cushion and centrifuged at 10,000 x g for 20 min at 4°C using a swing rotor. The nuclei pellet was resuspended in 1mL of cold DPBS followed by the quantification of nuclei using a Biorad TC20 Automated Cell Counter (Biorad #1450102). In situ 3C reaction was performed using Arima Genomics Arima-HiC+ Kit. Each in situ 3C reaction uses 300K to 450K nuclei. Nuclei aliquots were pellet and resuspended in 20 µl H2O mixed with 24 µl Conditioning Solution and incubated at 62°C for 10 min. After the incubation, 20 µl of Stop Solution 2 was added to the reaction and incubated at 37°C for 15 min. A restriction digestion mix containing 7 µl of 10X NEB CutSmart Buffer (NEB #B7204), 4.5 µl of NlaIII (NEB #R0125), 4.5 µl of MboI (NEB #R0147) and 12 µl of 1X NEB CutSmart Buffer was added to the reaction followed by incubation at 37°C for 1 hr. The restriction digestion reaction was stopped by incubation at 65°C for 20 mins. A ligation mix containing 70 µl of Buffer C and 12 µl of Enzyme C was added and was followed by incubation at room temperature for 15 min. The reaction was then placed at 4°C overnight. Prior to fluorescent-activated nuclei sorting (FANS), 900 µl of cold DPBS supplemented with 100 µl of Ultrapure BSA (50 mg/mL, Invitrogen #AM2618) was added to the in situ 3C reaction. To fluorescently stain nuclei, 1 µl of 1 mg/mL Hoechst 33342 was added prior to sorting. FANS was performed at UCLA Broad Stem Cell Research Center Flow Cytometry core using BD FACSAria sorters. Single nuclei were sorted into 384 well plates containing 1 µl M-Digestion Buffer containing proteinase K and ~0.05 pg Lambda DNA isolated from dcm+ E.Coli (Promega #D1501).

value: hippocampus

tag: developmental stage/age

tag: donor

tag: Sex

value: male


title: 220705-UA18-22-HPC


title: 210830-GW18-Post-HPC


title: 211130-UCSF2020-005-HPC


title: 220314-GW23-HPC


title: 210830-GW18-Ant-HPC


title: 211130-UA19-27-HPC

value: 7 months


title: scRNAseq_2kG_2PMDox1_4

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 4


title: 211130-GW18-Ant-HPC


title: scRNAseq_2kG_2PMDox1_6

description: 3' mRNA scRNAseq

value: 10x droplet generator batch #2, 1st set of lanes for cells collected at 2 PM (base name "2PMDox1"):Lane number 6


title: 211130-GW20-HPC

value: female


title: 211130-UA19-22-HPC

value: 4 months


title: 210830-GW20-HPC


title: 211130-UMB6096-HPC

value: 28 yo


title: 211130-UMB4267-HPC


title: 210830-UMB6096-HPC


title: 211029-UA19-27-HPC


title: 211029-UMB5551-HPC

value: 54 yo


title: 210528-UMB5621-PFC

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex

value: 37 yo


title: 210528-UMB5577-PFC

value: 21 yo


title: 210830-UMB4267-HPC


title: 211029-UA19-22-HPC


title: 220223-UCSF2020-005-PFC


title: 210316-UA19-22-PFC


title: 210316-UMB4267-PFC


title: 210505-UMB6096-PFC


title: 210505-UMB5577-PFC


title: 210316-GW20a-PFC


title: 210224-GW23-PFC


title: 210224-UMB5577-PFC


title: 210224-GW20b-PFC


title: 210224-GW20a-PFC


title: 210224-GW18-PFC


title: 191219-7mo-PFC


title: BAL03

status: Public on Sep 30 2022

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

data_processing:
Sequenced reads were processed using the 10X Genomics Cell Ranger V3.1.0 pipeline and aligned to the GRCh38-1.2.0 transcriptome
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: matrix table of unique molecular index (UMI) counts per gene per sample (filtered for cells over background, or  raw matrix)

source_name: BAL fluid

extract_protocol:
Samples were filtered through 40μm filters, rinsed with HBSS, and then centrifuged at 1400 rpm for 10min at 4C. After removing supernatant, pellet was treated with PharmLyse to lyse red blood cells if necessary and resuspended in HBSS.
5x10^5 cells were taken for scRNA-seq and processed using the 10x Genomics Chromium with Single Cell 3’ v2 chemistry

treatment_protocol: a therapeutic bronchoscope was wedged in the right middle lobe where 120 mL of 0.9% saline were instilled and aspirated. Adequate sample return was considered to be 60 mL. If less than 60 mL was returned, additional aliquots of 60 mL of 0.9% saline were instilled until at least 60 mL of sample was obtained. The sample was immediately placed on ice until processing.

tag: disease state

value: healthy (body mass index (BMI)<30 Kg/m2, no history of lung disease or malignancy)

value: BAL fluid

tag: protocol

value: single-cell RNA-seq


title: BAL04


title: 210111-UMB1863-PFC

value: 30 yo


title: BAL02


title: BAL01


title: 210830-UA19-27-HPC


title: 210316-UA18-22-PFC


title: Intestinal epithelium, Irradiated

status: Public on Sep 09 2022

city: Portland

first: Melissa

last: Wong

state: OR

address: 2720 S Moody Ave, Mailcode KCRB

institute: Oregon Health & Science Universtiy

description:
Bmi1-GFP (www.jax.org/strain/017351)
10x Genomics

data_processing:
Cellranger 3.1.0 (10X Genomics) was used for base call file processing, sample demultiplexing, unique molecular identifier (UMI) collapsing, and alignment. We aligned our FASTQ files to an mm10 genome that included the eGFP reporter sequence.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Intestinal epithelial cells

extract_protocol:
Adult intestinal tissues were isolated and prepared as previously described (PMC5404029). Briefly, adult mice were euthanized, intestinal tissues rapidly isolated, luminal contents flushed with ice-cold PBS and tissues fixed by incubation with 4% PFA in PBS for 1hr at room temperature or further prepped for subsequent epithelial cell dissociation for Flow cytometry or FACS (PMC6008251). Developmental tissue samples were isolated and prepared similar to previous reports (PMC5376969). Dams were euthanized and embryos quickly isolated and genotyped as described above. For E12.5 embryos, the whole embryo was fixed in 2% EM-grade PFA in PBS (Electron Microscopy Sciences) for 1hr at room temperature or intestines were isolated by dissection under wholemount microscope (Leica microsystems) for dissociation and subsequent flow cytometry or FACS. For E14.5 and later samples, the small intestine was isolated by dissection under wholemount microscope and fixed in 2% EM-grade PFA as above or dissociated.
Developmental and adult epithelial cells were FACS-isolated and used for downstream processing. Single cell RNA-sequencing was performed using the Chromium Single Cell 3’ GEM, Library, and Gel Bead Kit (10X Genomics) and the Chromium Single Cell B Chip Kit (10X Genomics) according to the 10X Chromium version 3 protocol (CG000183). In short, FACS-isolated cell populations suspended in PBS were loaded into 10X chromium microfluidic chips and single cells were encapsulated into Gel Bead-in-Emulsion by the Chromium controller (10X Genomics). RNA from individual cells were barcoded and libraries prepped according to the 10X chromium version 3 chemistry using the C1000 Touch thermal cycler (Bio-Rad). Quality of prepped cDNA and resultant libraries were assessed with the Agilent 2100 Bioanalyzer. Sequencing was performed on the HiSeq 2500 sequencer (Illumina) by the OHSU Massively-Parallel Sequencing Shared Resource core.

value: Intestinal epithelial cells

tag: developmental stage

value: Adult


title: Intestinal epithelium, Adult


title: Intestinal epithelium, Embryo day 17.5

value: Embryo day 17.5


title: main cohort, spleen, RML6, term wpi, rep 3

status: Public on Sep 01 2022

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital of Zurich

data_processing:
Quality control of reads was performed using FastQC. Low-quality ends were clipped (5’: 3 bases; 3’: 10 bases).
Trimmed reads were aligned to the reference genome and transcriptome (FASTA and GTF files, respectively, downloaded from the UCSC mm10) with STAR version 2.3.0e_r291 with default settings.
Differentially expressed genes were identified based |log2FC| > 0 and FDR < 0.05 using the R package edgeR[36] from Bioconductor (version 3.0). Only genes with at least 10 counts in at least 50% of the samples in one of the groups were considered in the analysis. Differentially expressed genes (DEGs) were defined as genes changing with |log2FC| > 0.5 and FDR < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2-fold ratios, p-Values, FDR as well as normalized counts and FPKM values for each sample

source_name: spleen

extract_protocol:
RNA was extracted from snap frozen areas using the RNeasy Plus Universal Kit (QIAGEN), following manufacturer’s instructions. Quantity and quality of RNA were analyzed with Qubit 1.0 Fluorometer (Life Technologies) and Bioanalyzer 2100 (Agilent Technologies), respectively.
The TruSeq RNA Sample Prep kit v2 (Illumina) was employed for library preparation. In brief, 1 μg of total RNA per sample was poly A enriched, reverse transcribed into double-stranded cDNA and then ligated with TruSeq adapters. PCR was performed to selectively enrich for fragments containing TruSeq adapters at both termini. Quantity and quality of enriched libraries were analyzed using Qubit (1.0) Fluorometer and Caliper GX LabChip GX (Caliper Life Sciences). The resulting product is a smear with a mean fragment size of approximately 260 bp. Libraries were then normalized to 10 nM in Tris-Cl 10 mM, pH 8.5, with 0.1% (vol/vol) Tween 20. Cluster generation was performed with the TruSeq PE Cluster kit v4-cBot-HS (Illumina), using 2 pM of pooled normalized libraries on the cBOT. Sequencing was performed on Illumina HiSeq 4000 paired-end at 2 × 126 bp using the TruSeq SBS kit v4-HS (Illumina).

value: spleen

tag: treatment


title: Intestinal epithelium, Embryo day 12.5

value: Embryo day 12.5


title: main cohort, spleen, RML6, term wpi, rep 2


title: main cohort, spleen, NBH, term wpi, rep 3

value: NBH


title: main cohort, spleen, RML6, 20 wpi, rep 2


title: main cohort, spleen, NBH, term wpi, rep 1


title: main cohort, spleen, RML6, 20 wpi, rep 3


title: main cohort, spleen, NBH, 20 wpi, rep 2


title: main cohort, spleen, RML6, 20 wpi, rep 1


title: main cohort, spleen, NBH, term wpi, rep 2


title: main cohort, spleen, NBH, 18 wpi, rep 3


title: main cohort, spleen, NBH, 18 wpi, rep 2


title: main cohort, spleen, RML6, 18 wpi, rep 1


title: main cohort, spleen, RML6, 18 wpi, rep 3


title: main cohort, spleen, RML6, 16 wpi, rep 2


title: main cohort, spleen, RML6, 16 wpi, rep 3


title: main cohort, spleen, NBH, 16 wpi, rep 3


title: main cohort, spleen, RML6, 16 wpi, rep 1


title: main cohort, spleen, NBH, 16 wpi, rep 2


title: main cohort, spleen, RML6, 18 wpi, rep 2


title: main cohort, spleen, RML6, 14 wpi, rep 3


title: main cohort, spleen, RML6, 14 wpi, rep 2


title: main cohort, spleen, RML6, term wpi, rep 1


title: main cohort, spleen, RML6, 14 wpi, rep 1


title: main cohort, spleen, NBH, 20 wpi, rep 3


title: main cohort, spleen, NBH, 14 wpi, rep 2


title: main cohort, spleen, NBH, 14 wpi, rep 3


title: main cohort, spleen, RML6, 12 wpi, rep 3


title: main cohort, spleen, NBH, 20 wpi, rep 1


title: main cohort, spleen, RML6, 12 wpi, rep 2


title: main cohort, spleen, RML6, 8 wpi, rep 2


title: main cohort, spleen, NBH, 12 wpi, rep 2


title: main cohort, spleen, NBH, 18 wpi, rep 1


title: main cohort, spleen, NBH, 14 wpi, rep 1


title: main cohort, spleen, NBH, 12 wpi, rep 3


title: main cohort, spleen, RML6, 8 wpi, rep 3


title: main cohort, spleen, RML6, 12 wpi, rep 1


title: main cohort, spleen, NBH, 8 wpi, rep 1


title: main cohort, spleen, NBH, 8 wpi, rep 2


title: main cohort, spleen, NBH, 8 wpi, rep 3


title: main cohort, spleen, NBH, 12 wpi, rep 1


title: main cohort, spleen, RML6, 4 wpi, rep 3


title: main cohort, spleen, RML6, 8 wpi, rep 1


title: main cohort, spleen, RML6, 4 wpi, rep 2


title: main cohort, spleen, NBH, 16 wpi, rep 1


title: main cohort, spleen, RML6, 4 wpi, rep 1


title: main cohort, spleen, NBH, 4 wpi, rep 3


title: main cohort, spleen, NBH, 4 wpi, rep 2


title: validation cohort, muscle, RML6, term wpi, rep 6

source_name: skeletal muscle

value: skeletal muscle


title: main cohort, spleen, NBH, 4 wpi, rep 1


title: validation cohort, muscle, RML6, term wpi, rep 5


title: main cohort, muscle, RML6, term wpi, rep 3


title: main cohort, muscle, RML6, term wpi, rep 2


title: main cohort, muscle, RML6, term wpi, rep 1


title: validation cohort, muscle, NBH, term wpi, rep 6


title: validation cohort, muscle, NBH, term wpi, rep 5


title: main cohort, muscle, NBH, term wpi, rep 3


title: main cohort, muscle, NBH, term wpi, rep 2


title: validation cohort, muscle, NBH, term wpi, rep 4


title: validation cohort, muscle, RML6, 20 wpi, rep 6


title: validation cohort, muscle, RML6, 20 wpi, rep 5


title: main cohort, muscle, RML6, 20 wpi, rep 3


title: validation cohort, muscle, NBH, 20 wpi, rep 4


title: main cohort, muscle, RML6, 20 wpi, rep 1


title: validation cohort, muscle, RML6, 20 wpi, rep 4


title: validation cohort, muscle, NBH, 20 wpi, rep 5


title: main cohort, muscle, RML6, 20 wpi, rep 2


title: main cohort, muscle, NBH, 20 wpi, rep 2


title: main cohort, muscle, RML6, 18 wpi, rep 2


title: main cohort, muscle, RML6, 18 wpi, rep 1


title: main cohort, muscle, NBH, 18 wpi, rep 2


title: main cohort, muscle, NBH, 18 wpi, rep 3


title: main cohort, muscle, NBH, 18 wpi, rep 1


title: validation cohort, muscle, RML6, 16 wpi, rep 5


title: validation cohort, muscle, RML6, 16 wpi, rep 6


title: validation cohort, muscle, RML6, 16 wpi, rep 4


title: main cohort, muscle, RML6, 16 wpi, rep 3


title: main cohort, muscle, RML6, 16 wpi, rep 2


title: main cohort, muscle, RML6, 16 wpi, rep 1


title: main cohort, muscle, NBH, term wpi, rep 1


title: validation cohort, muscle, NBH, 20 wpi, rep 6


title: main cohort, muscle, NBH, 20 wpi, rep 3


title: validation cohort, muscle, NBH, 16 wpi, rep 4


title: main cohort, muscle, NBH, 16 wpi, rep 3


title: main cohort, muscle, NBH, 20 wpi, rep 1


title: main cohort, muscle, RML6, 14 wpi, rep 2


title: main cohort, muscle, NBH, 16 wpi, rep 2


title: main cohort, muscle, RML6, 14 wpi, rep 1


title: main cohort, muscle, RML6, 18 wpi, rep 3


title: validation cohort, muscle, NBH, 16 wpi, rep 6


title: main cohort, muscle, NBH, 16 wpi, rep 1


title: validation cohort, muscle, RML6, 12 wpi, rep 6


title: validation cohort, muscle, NBH, 16 wpi, rep 5


title: validation cohort, muscle, RML6, 12 wpi, rep 5


title: validation cohort, muscle, RML6, 12 wpi, rep 4


title: main cohort, muscle, NBH, 14 wpi, rep 3


title: main cohort, muscle, NBH, 14 wpi, rep 2


title: main cohort, muscle, RML6, 14 wpi, rep 3


title: main cohort, muscle, RML6, 12 wpi, rep 2


title: main cohort, muscle, RML6, 12 wpi, rep 3


title: validation cohort, muscle, NBH, 12 wpi, rep 5


title: validation cohort, muscle, NBH, 12 wpi, rep 4


title: main cohort, muscle, RML6, 12 wpi, rep 1


title: validation cohort, muscle, NBH, 12 wpi, rep 6


title: main cohort, muscle, NBH, 14 wpi, rep 1


title: main cohort, muscle, NBH, 12 wpi, rep 3


title: main cohort, muscle, NBH, 12 wpi, rep 2


title: main cohort, muscle, NBH, 12 wpi, rep 1


title: validation cohort, muscle, RML6, 8 wpi, rep 6


title: main cohort, muscle, RML6, 8 wpi, rep 4


title: validation cohort, muscle, RML6, 8 wpi, rep 5


title: main cohort, muscle, RML6, 8 wpi, rep 3


title: main cohort, muscle, RML6, 8 wpi, rep 2


title: main cohort, muscle, NBH, 8 wpi, rep 3


title: main cohort, muscle, RML6, 8 wpi, rep 1


title: validation cohort, muscle, NBH, 8 wpi, rep 5


title: validation cohort, muscle, NBH, 8 wpi, rep 4


title: main cohort, muscle, RML6, 4 wpi, rep 3


title: main cohort, muscle, RML6, 4 wpi, rep 2


title: validation cohort, muscle, NBH, 8 wpi, rep 6


title: main cohort, muscle, NBH, 8 wpi, rep 2


title: main cohort, muscle, NBH, 4 wpi, rep 1


title: main cohort, blood, RML6, term wpi, rep 3

source_name: peripheral, whole blood

value: peripheral, whole blood


title: main cohort, muscle, NBH, 4 wpi, rep 3


title: main cohort, muscle, NBH, 8 wpi, rep 1


title: main cohort, blood, RML6, term wpi, rep 2


title: main cohort, blood, RML6, term wpi, rep 1


title: main cohort, blood, NBH, term wpi, rep 2


title: main cohort, blood, NBH, term wpi, rep 3


title: main cohort, blood, RML6, 20 wpi, rep 3


title: main cohort, blood, NBH, term wpi, rep 1


title: main cohort, blood, RML6, 20 wpi, rep 2


title: main cohort, blood, NBH, 20 wpi, rep 3


title: main cohort, blood, NBH, 20 wpi, rep 2


title: main cohort, blood, RML6, 20 wpi, rep 1


title: main cohort, blood, NBH, 20 wpi, rep 1


title: main cohort, blood, RML6, 18 wpi, rep 2


title: main cohort, blood, NBH, 18 wpi, rep 3


title: main cohort, blood, RML6, 18 wpi, rep 1


title: main cohort, muscle, RML6, 4 wpi, rep 1


title: main cohort, blood, NBH, 18 wpi, rep 2


title: main cohort, blood, NBH, 18 wpi, rep 1


title: main cohort, blood, RML6, 16 wpi, rep 3


title: main cohort, blood, NBH, 16 wpi, rep 1


title: main cohort, blood, RML6, 16 wpi, rep 1


title: main cohort, muscle, NBH, 4 wpi, rep 2


title: main cohort, blood, RML6, 14 wpi, rep 2


title: main cohort, blood, RML6, 14 wpi, rep 3


title: main cohort, blood, NBH, 14 wpi, rep 3


title: main cohort, blood, RML6, 14 wpi, rep 1


title: main cohort, blood, NBH, 14 wpi, rep 2


title: main cohort, blood, RML6, 12 wpi, rep 1


title: main cohort, blood, RML6, 12 wpi, rep 6


title: main cohort, blood, RML6, 12 wpi, rep 3


title: main cohort, blood, NBH, 12 wpi, rep 1


title: main cohort, blood, RML6, 18 wpi, rep 3


title: main cohort, blood, RML6, 8 wpi, rep 3


title: main cohort, blood, NBH, 8 wpi, rep 3


title: main cohort, blood, RML6, 8 wpi, rep 1


title: main cohort, blood, NBH, 8 wpi, rep 2


title: main cohort, blood, RML6, 8 wpi, rep 2


title: main cohort, blood, NBH, 8 wpi, rep 1


title: main cohort, blood, RML6, 4 wpi, rep 2


title: main cohort, blood, RML6, 4 wpi, rep 3


title: main cohort, blood, NBH, 16 wpi, rep 2


title: main cohort, blood, RML6, 16 wpi, rep 2


title: main cohort, blood, NBH, 16 wpi, rep 3


title: main cohort, blood, NBH, 4 wpi, rep 2


title: main cohort, blood, NBH, 4 wpi, rep 1


title: Jmjd3 - KO [H3K27me3 CUT&Tag]

status: Public on Aug 04 2022

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

data_processing:
Library strategy: CUT&Tag
Nextera adapters were trimmed from sequenced reads with Cutadapt 2.6 (Python 3.7.4).
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.3.4.1 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Trimmed sequences were aligned to spike-in DNA (Amp - pBluescript II SK(+)) using Bowtie2 version 2.3.4.1 with the following parameters: --very-sensitive .
Duplicates, non-uniquely aligned reads were filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads.
Spike-in normalized genome coverage was calculated using bamCoverage v3.3.2 (Deeptools v3.3.2).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Spike-in normalized bigwigs.

source_name: Satellite Stem cells

extract_protocol:
Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were then sorted by fluorescence activated cell sorting. FACS sorted cells were collected in microfuge tubes. Cells were permeabilized with digitonin and the genomic DNA was cleaved and tagged by pA-Tn5 after incubation with histone H3 lysine 27 trimethyl primary antibody.
Library was prepared using i5 and i7 universal primers and NEBNext High-fidelity 2x PCR Master mix. Before following the thermal cycling conditions recommended by the manufacturer, the samples were incubated at 72°C for gap filling.

treatment_protocol: Cardiotoxin Injections into the tibialis anterior and gastrocnemius muscle of hind limb.

tag: strain

value: Jmjd3 KO

value: Cardiotoxin injury

value: Tibialis Anterior and Gastrocnemius muscles

value: Satellite Stem cells

tag: development stage


title: main cohort, blood, NBH, 14 wpi, rep 1


title: Utx - KO [H3K27me3 CUT&Tag]

value: Utx KO


title: Tdt Control [H3K27me3 CUT&Tag]

value: Tdt Control


title: Tdt Control [H3K4me3 CUT&Tag]

extract_protocol:
Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were then sorted by fluorescence activated cell sorting. FACS sorted cells were collected in microfuge tubes. Cells were permeabilized with digitonin and the genomic DNA was cleaved and tagged by pA-Tn5 after incubation with histone H3 lysine 4 trimethyl primary antibody.
Library was prepared using i5 and i7 universal primers and NEBNext High-fidelity 2x PCR Master mix. Before following the thermal cycling conditions recommended by the manufacturer, the samples were incubated at 72°C for gap filling.


title: Utx - KO [H3K4me3 CUT&Tag]


title: U-lab [CUT&Tag]

extract_protocol:
Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were then sorted by fluorescence activated cell sorting. FACS sorted cells were collected in microfuge tubes. Cells were permeabilized with digitonin and the genomic DNA was cleaved and tagged by pA-Tn5 after incubation with UTX and JMJD3 lab generated and commercial primary antibodies.
Library was prepared using i5 and i7 universal primers and NEBNext High-fidelity 2x PCR Master mix. Before following the thermal cycling conditions recommended by the manufacturer, the samples were incubated at 72°C for gap filling.

value: Tdt.Ctrl/ Pax7 gCre/gCre TdT Fl/Fl

value: UTX (lab generated)


title: J-lab [CUT&Tag]

value: JMJD3 (lab generated)


title: Utx Ko rep-2 [RNA-seq]

data_processing:
Sequencing adapters were trimmed using Cutadapt v2.6.
Transcript quantification with Salmon v1.1.0.
Differential expression with DEseq2 v1.28.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Table containing differentially expressed genes.
Supplementary_files_format_and_content: Quantified transcripts for all samples.

extract_protocol: Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were further collected in microfuge tubes by fluorescence activated cell sorting.


title: Utx Ko rep-1 [RNA-seq]


title: Jmjd3 - KO [H3K4me3 CUT&Tag]


title: main cohort, blood, NBH, 12 wpi, rep 2


title: main cohort, blood, RML6, 4 wpi, rep 1


title: Tdt Control rep-2 [RNA-seq]


title: main cohort, blood, NBH, 4 wpi, rep 3


title: Tdt Control IgG [H3K4me3 CUT&Tag]

value: IgG-His


title: Jmjd3 Ko rep-2 [RNA-seq]

value: Adult


title: Jmjd3 Ko rep-1 [RNA-seq]


title: Jmjd3-Ko [scRNA-seq]

description: Single-cell RNA-Seq

data_processing:
Performed on 10X Cell Ranger pipeline.
cellranger mkfastq  v2.1.1
cellranger count v2.1.1
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tar archives include barcodes.tsv, features.tsv, and matrix.mtx files; single-cell gene expression matrix.


title: Tdt.Control [scRNA-seq]

description: Single-cell RNA-Seq


title: PD1hiTim3+ TIL RNAseq 3

city: Pittsburgh

first: B. Rhodes

last: Ford

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh

description:
TPM_TIL_LN_VVova.csv
TIL_PD1hiTim3_rep3

data_processing:
trimmed high quality reads were aligned to genome using HISAT2
Transcripts per Million (TPMs) calculated using Subread
Differentially expressed genes (DEG) determined using DEseq2 with cutoffs of 2 fold and padj<0.05
Genome_build: mm10 ensembl
Supplementary_files_format_and_content: Transcripts per Million (TPM) file, normalized counts

source_name: B16 melanoma tumor

growth_protocol: Mice were injected intradermally with 2.5 × 105 B16 melanoma cells. Mice were sacrificed and dLN and TIL harvested on day 14, when tumors were typically 8-10 mm in diameter.

extract_protocol:
CD8 T cells were isolated from tumors by surgical excision followed by flow sorting. cDNA was prepared from ~1,000 cells using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Libraries were prepared using the Nextera XT DNA Library Preparation kit. Libraries were denatured and diluted using the NextSeq 500 protocol Revision D.Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500.

treatment_protocol: In immunotherapy experiments, when tumors were palpable (typically day 5), mice began anti-PD-1, anti-4-1BB, or isotype control therapy. Mice were treated with 200 μg of anti-PD-1, 200 μg of anti-4-1BB, or equivalent isotype control intraperitoneally three times per week for the duration of the experiment.

value: CD8+ T cell

value: B16 melanoma

tag: timepoint

value: Day 14 post-tumor

tag: sorting scheme


title: PD1hiTim3+ TIL RNAseq 2

description:
TPM_TIL_LN_VVova.csv
TIL_PD1hiTim3_rep2


title: ECM10_slide

status: Public on Jul 06 2022

city: New York

first: Jana

last: Biermann

state: New York

address: 622 W168th Street

institute: Columbia University

description:
Single-nuclei RNA sequencing, SlideSeqV2
ECM10_slide

data_processing:
We used the Slide-seq tools pipeline (Stickels et al., 2021) to process our Slide-seq data, and loaded the data into Seurat. For MBM05_rep3_slide and MBM11_rep3_slide, due to their lower quality compared to other samples, we filtered out cells with fewer than 20 unique genes. For all other samples, we imposed no further quality control thresholds.
Assembly: GRCh38
Supplementary files format and content: raw counts and spatial coordinates
Supplementary files format and content: csv file of individual gene expression count matrix for each sample
Supplementary files format and content: csv file of SlideSeqV2 bead coordinates and barcodes for each sample

source_name: Melanoma subcutaneous metastasis

extract_protocol:
RNA from 10 uM frozen tumor sections was extracted and spatially indexed as described in Stickels et al. (Nature Biotechnology, 2021). Briefly, sections were cut and then mounted on a "puck". RNA was hybridized for 15 min in 6x SCC and then reveres transcribed using Maxima RT.  Tissue was then digested and cleared using clearing buffer and proteinase K and unbound capture oligos were removed using EXO-I treatment. 2nd strand synthesis was then performed using sn-SMRT oligos and Klenow Enzyme and the libraries were amplified using PCR with Truseq and SMART PCR primers.
Libraries after PCR amplification were tagmented and indexed using Nextera XT kit and Nextera N70x oligos. After SPRI cleanup libraries were quantified using D5000 tapestation and perpared for sequencing.
single-nuclei RNAseq; SlideSeqV2

tag: metastatic site

value: ECM

tag: patient id

tag: mutation status

value: BRAF/NRAS WT

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq

value: no


title: Tdt Control - IgG [H3K27me3 CUT&Tag]

tag: genotype

value: Cardiotoxin injury

tag: tissue

tag: cell type

tag: antibody


title: ECM08_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
ECM08_slide

value: BRAF V600E


title: ECM01_rep2_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
ECM01_rep2_slide


title: MBM13_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM13_slide

source_name: Melanoma brain metastasis

value: MBM


title: PD1hiTim3+ TIL RNAseq 1

description:
TPM_TIL_LN_VVova.csv
TIL_PD1hiTim3_rep1

tag: disease state


title: MBM11_rep3_slid

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM11_rep3_slid


title: ECM01_rep1_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
ECM01_rep1_slide


title: MBM18_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM18_slide

value: BRAF WT


title: main cohort, blood, RML6, 12 wpi, rep 2

value: peripheral, whole blood


title: IgG-TF [CUT&Tag]

value: Tdt.Ctrl/ Pax7 gCre/gCre TdT Fl/Fl

value: Tibialis Anterior and Gastrocnemius muscles

value: Satellite Stem cells

value: IgG-TF


title: ECM06_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
ECM06_slide

value: BRAF WT, JAK  P429S


title: MBM11_rep1_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM11_rep1_slide


title: MBM08_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM08_slide


title: Tdt Control rep-1 [RNA-seq]

value: Tdt Control

value: Adult


title: MBM07_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM07_slide

value: BRAF WT/NRAS WT


title: MBM06_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM06_slide

value: NRAS Q61R


title: MBM05_rep2_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM05_rep2_slide


title: MBM05_rep1_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM05_rep1_slide


title: D7_hiPSC1_NT_2

status: Public on Jun 14 2022

first: Zachary

last: Batz

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Reads passing the Illumina chastity filter were demultiplexed then trimmed to remove low quality bases and adapters using Trimmomatic v0.36.
Reads were aligned to the human transcriptome (GRCH38.p13, Ensembl 98) and quantified to the transcript-level using Kallisto v0.45.0.
Transcript counts were summarized to the gene level using tximport 1.14.2 with the lengthScaledTPM option and TMM normalized using edgeR v3.28.1.
Genes with at least 1 count per million reads (CPM) in both replicates of at least one group (e.g., both D4 HiPSC3 samples) were retained for downstream analysis.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Kallisto abundance files are raw abundance tsv outputs from Kallisto for each sample
Supplementary_files_format_and_content: Adundance measurements are summarized gene and transcript abundance data for all samples

source_name: Retinal Organoid

extract_protocol:
Total RNAs were extracted from retinal organoid samples using RNAeasy Plus Mini kit (Qiagen, Germantown, MD).
Quality of isolated RNAs was assessed using Bioanalyszer RNA 6000 nano assays and only high-quality RNAs (RNA integration number (RIN) > 8) were used for construction of mRNA sequencing library. 100ng of total RNA were used to construct the strand-specific libraries using TruSeq RNA Sample Prep Kit-v2 (Illumina, San Diego, CA).

value: Retinal Organoid

tag: time

value: Control

tag: source line


title: D7_hiPSC3_NAM_2

tag: treatment

value: Nicotinamide


title: D7_hiPSC1_NAM_2


title: D7_hiPSC3_NT_2


title: D7_hiPSC3_NAM_1


title: ChIP_CTCF_E105_PT_rep1

status: Public on Jun 20 2022

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

institute: University of Geneva

description: ChIP

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
TruSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Normalization was done by subsampling filtered reads with samtools view to the lowest number of reads among samples of one species, which is 42317564 for mouse and 22886295 for chicken.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: bigwig: normalized coverage track, when multiple biological replicates were done, the average was done
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2

source_name: posterior trunk

extract_protocol:
ChIP-seq experiments were performed as described in (Rodríguez-Carballo et al 2017).
ChIP-seq libraries were prepared as described in (Rodríguez-Carballo et al 2017).

treatment_protocol: dissection: see Amândio et al., 2021

tag: developmental stage

tag: strain

value: WT

tag: chip antibody

value: CTCF Active motif #61311


title: D7_hiPSC1_NAM_1


title: MBM11_rep2_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM11_rep2_slide

value: MBM

value: snRNA-seq

value: no


title: D4_hiPSC1_NAM_2


title: D7_hiPSC3_NT_1


title: D4_hiPSC1_NAM_1


title: D4_hiPSC3_NT_1


title: D4_hiPSC3_NAM_2


title: D4_hiPSC3_NAM_1


title: D4_hiPSC1_NT_2


title: D4_hiPSC1_NT_1


title: MBM05_rep3_slide

description:
Single-nuclei RNA sequencing, SlideSeqV2
MBM05_rep3_slide


title: SOXC_Prx1Cre_E15.5

status: Public on Jun 08 2022

city: Philadelphia

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

institute: The Children's Hospital of Philadelphia Research Institute

data_processing:
Alignment, demultiplexing, barcode assignment and UMI quantification: Cell Ranger (10X Genomics)
Clustering and gene expression analysis: Seurat v3
Pseudotime analysis: Monocle 3
RNA velocity: velocyto.py and velocyto.R
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files as Matrix (.mtx) format and gene expression analysis from Seurat as Excel Spreadsheet (.xlsx)
Table 1.xlsx: Table containing markers for clusters after integration of the control samples
Table 2.xlsx: Table containing markers for mesenchymal control clusters
Table 3.xlsx: Table containing differentially expressed genes between control and SOXC-mutant mesenchymal clusters

source_name: Calvarium

extract_protocol:
Cranial tissues were digested in LiberaseTM to obtain single cell suspensions
Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) for E15.5 samples, and Chromium Single Cell 3’ v3 Reagent Kit (10X Genomics) for all the other samples. Libraries were sequenced using a NovaSeq sequencer.

tag: age

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl Prx1Cre

value: Cranial bones


title: SOXC_Prx1Cre_E13.5

value: Cranial mesenchyme


title: SOXC_WT_E17.5

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl


title: PT_7 LNM ST

status: Public on Apr 30 2022

city: Beijing

first: Zhihua

last: Liu

state: Beijing

address: State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China

data_processing:
Raw sequencing data for each sample were converted to matrices of expression using Space Ranger (version spaceranger-1.2.0, 10X Genomics).
integrate single cell RNA-seq and spatial transcriptomes with Seurat (version 4.0.4)
Genome_build: GRCh38 human reference genome (official Space Ranger version)
Supplementary_files_format_and_content: Raw counts of  cell barcodes and features were provided in ST_raw_feature_bc_matrix.zip.
Supplementary_files_format_and_content: A json file that scaling factor that converts pixel positions in the original.
Supplementary_files_format_and_content: This png file is downsampled versions of the original, full-resolution image of FFPE samples
Supplementary_files_format_and_content: This csv text file contains a table with rows that correspond to spots.

source_name: human breast cancer

extract_protocol:
Fresh frozen lymph node metastasis samples slide gene expression were detected by 10X Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard Illumina protocols

value: human breast cancer

value: 10X Visium

tag: donor

tag: site

value: Lymph node metastasis

tag: pathological type

value: Invasive ductal carcinoma


title: PT_8 LNM ST

department: State Key Laboratory of Molecular Oncology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College


title: PT_6 LNM ST


title: SOXC_WT_E15.5


title: PT_3 LNM ST


title: Retina_nonoperated_rep2

status: Public on Apr 09 2022

first: Xinyi

last: Su

address: 61 Biopolis Drive

institute: IMCB

data_processing:
Sequenced paired-end reads were trimmed and mapped to hg19 reference genome using HISAT2.
Read counts per gene estimated using htseq-count
Read count normalisation and differential expresssion analysis performed using DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: comma delimited text file containing read counts per gene.

organism: Oryctolagus cuniculus

source_name: Retina

extract_protocol:
Retina and Retinal Pigment Epithelium were lyzed with RLT buffer (Qiagen, cat. no. 79216), extracted and purified with Rneasy Mini Kit (Qiagen, cat no. 74106) following manufacturer's recommended protocol.
Illumina sequencing libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, cat.  no. E7765)

treatment_protocol: Vitreous substitution using multiblock thermogelling polymer (PMID: 30962587)

value: Retina

tag: Sex

value: Male

value: 4 to 6 months

value: non-operated


title: Retina_nonoperated_rep3


title: Retina_nonoperated_rep1


title: Retina_2month_rep3

value: vitreous substitution


title: Retina_1month_rep3


title: Retina_1month_rep2


title: Retina_2month_rep1


title: D4_hiPSC3_NT_2

value: Retinal Organoid

value: Control


title: Retina_2month_rep2